1.
Munthe, Christian, 1962
(author)
Precaution and Ethics: Handling risks, uncertainties and knowledge gaps in the regulation of new biotechnologies
2017
Book (other academic/artistic) abstract
This volume outlines and analyses ethical issues actualized by applying a precautionary approach to the regulation of new biotechnologies. It presents a novel way of categorizing and comparing biotechnologies from a precautionary standpoint. Based on this, it addresses underlying philosophical problems regarding the ethical assessment of decision-making under uncertainty and ignorance, and discusses how risks and possible benefits of such technologies should be balanced from an ethical standpoint. It argues on conceptual and ethical grounds for a technology neutral regulation as well as for a regulation that not only checks new technologies but also requires old, inferior ones to be phased out. It demonstrates how difficult ethical issues regarding the extent and ambition of precautionary policies need to be handled by such a regulation, and presents an overarching framework for doing so.
2.
Sandin, Per, et al.
(author)
Technology neutrality and regulation of agricultural biotechnology
2018
In: Professionals in food chains: ethics, rules and responsibility. EurSafe 2018, Vienna, Austria 13 – 16 June 2018 / edited by: Svenja Springer, Herwig Grimm. - Wageningen, Netherlands : Wageningen Academic Publishers. - 9789086863211
Conference paper (peer-reviewed) abstract
Agricultural biotechnology, in particular genetically modified organisms (GMOs), is subject to regulation in many areas of the world, not least in the European Union (EU). A number of authors have argued that those regulatory processes are unfair, costly, and slow and that regulation therefore should move in the direction of increased ‘technology neutrality’. The issue is becoming more pressing, especially since new biotechnologies such as CRISPR increasingly blur the regulatory distinction between GMOs and non-GMOs. This paper offers a definition of technology neutrality, uses the EU GMO regulation as a starting point for exploring technology neutrality, and presents distinctions between variants of the call for technology neutral GMO regulation in the EU.
3.
Guschanski, Katerina, et al.
(author)
The evolution of duplicate gene expression in mammalian organs
2017
In: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 27:9, s. 1461-1474
Journal article (peer-reviewed) abstract
Gene duplications generate genomic raw material that allows the emergence of novel functions, likely facilitating adaptive evolutionary innovations. However, global assessments of the functional and evolutionary relevance of duplicate genes in mammals were until recently limited by the lack of appropriate comparative data. Here, we report a large-scale study of the expression evolution of DNA-based functional gene duplicates in three major mammalian lineages (placental mammals, marsupials, egg-laying monotremes) and birds, on the basis of RNA sequencing (RNA-seq) data from nine species and eight organs. We observe dynamic changes in tissue expression preference of paralogs with different duplication ages, suggesting differential contribution of paralogs to specific organ functions during vertebrate evolution. Specifically, we show that paralogs that emerged in the common ancestor of bony vertebrates are enriched for genes with brain-specific expression and provide evidence for differential forces underlying the preferential emergence of young testis-and liver-specific expressed genes. Further analyses uncovered that the overall spatial expression profiles of gene families tend to be conserved, with several exceptions of pronounced tissue specificity shifts among lineage-specific gene family expansions. Finally, we trace new lineage-specific genes that may have contributed to the specific biology of mammalian organs, including the little-studied placenta. Overall, our study provides novel and taxonomically broad evidence for the differential contribution of duplicate genes to tissue-specific transcriptomes and for their importance for the phenotypic evolution of vertebrates.
4.
Seroussi, Eyal, et al.
(author)
Identification of the Long-Sought Leptin in Chicken and Duck : Expression Pattern of the Highly GC-Rich Avian leptin Fits an Autocrine/Paracrine Rather Than Endocrine Function
2016
In: Endocrinology. - : The Endocrine Society. - 0013-7227 .- 1945-7170. ; 157:2, s. 737-751
Journal article (peer-reviewed) abstract
More than 20 years after characterization of the key regulator of mammalian energy balance, leptin, we identified the leptin (LEP) genes of chicken (Gallus gallus) and duck (Anas platyrhynchos). The extreme guanine-cytosine content (similar to 70%), the location in a genomic region with low-complexity repetitive and palindromic sequence elements, the relatively low sequence conservation, and low level of expression have hampered the identification of these genes until now. In vitro-expressed chicken and duck leptins specifically activated signaling through the chicken leptin receptor in cell culture. In situ hybridization demonstrated expression of LEP mRNA in granular and Purkinje cells of the cerebellum, anterior pituitary, and in embryonic limb buds, somites, and branchial arches, suggesting roles in adult brain control of energy balance and during embryonic development. The expression patterns of LEP and the leptin receptor (LEPR) were explored in chicken, duck, and quail (Coturnix japonica) using RNA-sequencing experiments available in the Short Read Archive and by quantitative RT-PCR. In adipose tissue, LEP and LEPR were scarcely transcribed, and the expression level was not correlated to adiposity. Our identification of the leptin genes in chicken and duck genomes resolves a long lasting controversy regarding the existence of leptin genes in these species. This identification was confirmed by sequence and structural similarity, conserved exon-intron boundaries, detection in numerous genomic, and transcriptomic datasets and characterization by PCR, quantitative RT-PCR, in situ hybridization, and bioassays. Our results point to an autocrine/paracrine mode of action for bird leptin instead of being a circulating hormone as in mammals.
5.
6.
Ahmadi Afzadi, Masoud
(author)
Genetic variation in resistance to fungal storage diseases in apple : inoculation-based screening, transcriptomics and biochemistry
2015
Doctoral thesis (other academic/artistic) abstract
Apple is one of the economically and culturally most important fruit crops and has many health-related benefits. Apple production is, however, sensitive to several fungal diseases including blue mold, caused by Penicillium expansum. Problems are more pronounced in organic production or in countries where postharvest application of fungicides is prohibited. To limit or overcome this problem, many studies have been focused on investigations of the mechanism of resistance/tolerance. No major gene(s) have as yet been identified, but quantitatively inherited traits, some of which are related to fruit texture and content of chemical compounds, have been shown to affect the ability of cultivars to withstand storage diseases. In the present thesis, inter-cultivar variation in terms of resistance to fungal storage diseases was investigated at two locations, i.e. Balsgård in Sweden and Njøs in Norway. The association of harvest date, fruit firmness and softening with lesion decay was investigated on large sets of cultivars. The contribution of four fruit texture-related genes (Md-ACO1, Md-ACS1, Md-Exp7 and Md-PG1) in explaining the fruit texture characteristics was examined. Fruit content of chemical compounds with a potential impact on disease resistance was also investigated, and finally the regulation of apple genes upon fungal infection was studied in order to identify candidate genes responsible for disease resistance. Inoculation-based screening indicated large variation across the investigated cultivars in terms of blue mold and bitter rot susceptibility. Harvest date and softening rate of fruits during storage had a large impact on resistance to fungal diseases, thus cultivars with moderate to firm fruits that soften comparatively little during storage could withstand the fungal infection comparatively well. Softening rate is, in its turn, closely associated with harvest date whereas four fruit texture-related genes had lower predictive power than expected. Quantifying the chemical compounds in the fruit samples revealed that some of these compounds, especially flavonols and procyanidin B2, could contribute to resistance against blue mold, whereas contents of malic acids or total titratable acidity had considerably less impact. Differential expression of FLS, LDOX, and CHS genes involved in biosynthesis of flavonoids and PGIP, TT10, WAK1 and CTL1 genes related to cell wall structure indicate the importance of fruit characteristics and biochemical compounds in the resistance mechanism.
7.
Andersson, Mariette, et al.
(author)
Genome editing in potato via CRISPR-Cas9 ribonucleoprotein delivery
2018
In: Physiologia Plantarum. - : Wiley. - 0031-9317 .- 1399-3054. ; 164, s. 378-384
Journal article (peer-reviewed) abstract
Clustered regularly interspaced short palindromic repeats and CRISPR-associated protein-9 (CRISPR-Cas9) can be used as an efficient tool for genome editing in potato (Solanum tuberosum). From both a scientific and a regulatory perspective, it is beneficial if integration of DNA in the potato genome is avoided. We have implemented a DNA-free genome editing method, using delivery of CRISPR-Cas9 ribonucleoproteins (RNPs) to potato protoplasts, by targeting the gene encoding a granule bound starch synthase (GBSS, EC 2.4.1.242). The RNP method was directly implemented using previously developed protoplast isolation, transfection and regeneration protocols without further adjustments. Cas9 protein was preassembled with RNA produced either synthetically or by in vitro transcription. RNP with synthetically produced RNA (cr-RNP) induced mutations, i.e. indels, at a frequency of up to 9%, with all mutated lines being transgene-free. A mutagenesis frequency of 25% of all regenerated shoots was found when using RNP with in vitro transcriptionally produced RNA (IVT-RNP). However, more than 80% of the shoots with confirmed mutations had unintended inserts in the cut site, which was in the same range as when using DNA delivery. The inserts originated both from DNA template remnants from the in vitro transcription, and from chromosomal potato DNA. In 2-3% of the regenerated shoots from the RNP-experiments, mutations were induced in all four alleles resulting in a complete knockout of the GBSS enzyme function.
8.
Burra, Dharani
(author)
Defence related molecular signalling in Potato : new perspectives from “- Omics”
2016
Doctoral thesis (other academic/artistic) abstract
Potato production is hampered by several pathogens and is subjected to intense chemical based disease control, use of which also has undesirable consequences. Resistance breeding programs have also shown limited success. Hence, there is a need to develop durable disease resistance. Omics-techniques enable new layers of knowledge regarding molecules and their interactions mediating defence, which can contribute to identification of durable resistance sources. A novel network-based approach was used to improve the existing annotation of gene probes on the genome based microarray. Approximately 8000 unannotated probes received a new annotation. This improved annotation was used to assess genome wide changes in transcripts and proteins in response to treatments with resistance inducers, β- amino butyric acid (BABA) and Phosphite based salt (Phi). Five thousand transcripts were significantly regulated 48 hours after 10mM BABA treatment while one was regulated with 1mM BABA. In coherence, 10 mM BABA but not 1 mM induced protection to the hemibiotroph Phytophthora infestans. No transcript was significantly regulated 48 hours after Phi treatment. Time course analysis revealed that Phi exerts a transient effect, as significant transcriptomic changes were observed only 3, 6 and 11 hours after treatment. In contrast, plants showed resistance to P. infestans even at 120 hours after Phi treatment. Phi and BABA dependent “Induced state” is not restricted to transcripts related to plant defence, as transcripts related to abiotic stress and primary metabolism were altered, while biotic stress and cell wall related proteins also increased in abundance. Furthermore, an in vitro based blackleg disease screening assay was developed to investigate Potato – Dickeya solani interactions. We show that salicylic (SA) and COI1 are necessary for defence in shoots and tubers to this necrotroph. We also screened a crossing population and identified “potential” D. solani susceptibility genes related to transcriptional regulation. We also show that while SA is necessary to restrict lesion development and pathogen growth in response to the necrotroph Alternaria solani, COI1 affects pathogen growth only. Transcriptomic analysis indicated that rapid defence response to A. solani involves biotic, abiotic and oxidative stress related transcripts regulated by SA and COI1. We identified a citrate binding protein, which is also induced by resistance inducers, as an SA-repressed susceptibility factor to A. solani. Finally, proteomics of PAMP triggered immunity revealed upregulation of oxidative stress proteins while proteins related to oxidative stress tolerance, GTP binding activity were specifically upregulated in effector triggered immunity interactions.
9.
10.
Calleja-Rodriguez, Ainhoa
(author)
Quantitative Genetics and Genomic Selection of Scots pine
2019
Doctoral thesis (other academic/artistic) abstract
The final objective of tree improvement programs is to increase the frequency of favourable alleles in a population, for the traits of interest within the breeding programs. To achieve this, it is crucial to decompose the phenotypic variance accurately into its genetic and environmental components in order to obtain a precise estimation of genetic parameters and to increase genetic gains. The overall aim of this thesis was to increase the accuracy of genetic parameter estimation by incorporating new quantitative genetics models to the analysis of multiple traits in multiple trials of Scots pine, and to develop a genomic selection protocol to accelerate genetic gain. Factor analysis was incorporated to multivariate multi-environment analyses and it allowed to evaluate up to 19 traits simultaneously. As a result, precise patterns of genotype-by-environment interactions (G E) were observed for tree vitality and height; moreover, it was possible to detect the main driver of the G E: differences in temperature sum among sites. Traditional quantitative trait loci (QTL) analysis of phenotypic data was compared with the detection of QTL with estimated breeding values (EBV) for the first time in a three generation pedigree and, as outcome, it was noticed that if a QTL was associated to a EBV and to a phenotypic trait, the proportion of variance explained by the QTLEBV was higher than the QTL-phenotype. Additionally, several QTL were detected across several ages, which may make them suitable as candidates for early selection. Genomic selection (GS) could aid to reduce the breeding cycle by shortening the periods of progeny field testing, and consequently increasing genetic gains per year. Genomic predictions, including additive and non-additive effects through different prediction models were compared with traditional pedigree-based models; it was seen an overestimation of genetic parameters for pedigree-based models, even larger when nonadditive effects could not be discerned from additive and residual effects. Prediction accuracies and abilities of the genomic models were sufficient to achieve higher selection efficiencies and responses per year varying between 50-90% by shortening 50% the breeding cycle. For the selection of the top 50 individuals, higher gains were estimated if non-additive effects are incorporated to the models (7 – 117%).
11.
Dida, Mulatu Geleta, et al.
(author)
Genetic Diversity within a Global Panel of Durum Wheat (Triticum durum) Landraces and Modern Germplasm Reveals the History of Alleles Exchange
2017
In: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 8
Journal article (peer-reviewed) abstract
Durum wheat is the 10th most important crop in the world, and its use traces back to the origin of agriculture. Unfortunately, in the last century only part of the genetic diversity available for this species has been captured in modern varieties through breeding. Here, the population structure and genetic diversity shared among elites and landraces collected from 32 countries was investigated. A total of 370 entries were genotyped with Axiom 35K array to identify 8,173 segregating single nucleotide polymorphisms (SNPs). Of these, 500 were selected as highly informative with a PIC value above 0.32 and used to test population structure via DAPC, STRUCTURE, and neighbor joining tree. A total of 10 sub-populations could be identified, six constituted by modern germplasm and four by landraces of different geographical origin. Interestingly, genomic comparison among groups indicated that Middle East and Ethiopia had the lowest level of allelic diversity, while breeding programs and landraces collected outside these regions were the richest in rare alleles. Further, phylogenetic analysis among landraces indicated that Ethiopia might represent a second center of origin of durum wheat, rather than a second domestication site as previously believed. Together, the analyses carried here provide a global picture of the available genetic diversity for this crop and shall guide its targeted use by breeders.
12.
Dida, Mulatu Geleta, et al.
(author)
Molecular and Genomic Tools Provide Insights on Crop Domestication and Evolution
2016
In: Advances in Agronomy. - : Elsevier. - 0065-2113 .- 2213-6789. ; 135, s. 181-223
Research review (peer-reviewed) abstract
Rapid progress in genomic research and the development of genome-wide molecular markers for various crops significantly improved our knowledge on plant domestication and evolution. Molecular markers and other genomic tools have been used to understand the evolutionary changes that converted wild plants into domesticated crops, and the identification of loci behind domestication syndrome traits will have significant importance in the fast-track domestication of new plants. The application of genomics- assisted selection in plant breeding programs has significantly contributed to efficient plant breeding for desirable traits. Genomic tools also facilitated the efficient identification of progenitors of crops as well as centers of domestication. Multiple genomic regions with signature of selection during plant domestication have been found in various crops. Extensive analyses of plant genomes revealed that genes underlying domestication syndrome traits show a significant loss of diversity, for example, up to 95% of genetic diversity in wild relatives has been lost during domestication process in extreme cases. Genomic research revealed repeated occurrence of polyploidization during plant evolution and various interesting events that occurred following polyploidization such as gene loss and silencing. The loss of most replicated genes through time and nonrandom retention of some duplicated genes that serve as signatures of polyploidy are among interesting changes in polyploid plant genomes. Further insights into the advances in our knowledge on plant domestication and evolution made through the use of DNA markers and genomic tools is provided in this paper.
13.
Dubey, Mukesh
(author)
Relationship of downy mildew resistance with yield related traits helpful for achieving reliable selection criteria in opium poppy (Papaver somniferum L.)
2015
In: Indian Journal Of Genetics And Plant Breeding. - : The Indian Society of Genetics and Plant Breeding. - 0019-5200 .- 0975-6906. ; 75, s. 396-399
Journal article (peer-reviewed) abstract
Present study aims to understand the nature and degree of relationships between different morphometric and yield influencing traits using correlation and path coefficient analysis in medicinally important plant opium poppy. Genotypic and phenotypic correlation coefficients analysis showed significant negative correlation between downy mildew disease severity Index (DSI) and seed and straw yield. Furthermore, path analysis showed direct and positive effect of capsule diameter and number of capsule/plant to straw yield. In contrast, DSI had highest direct and negative contribution to straw yield. These results support effectiveness of selections for high seed and straw yield together with downey mildew-resistance in development of effective selection criteria for crop improvement.
14.
15.
16.
17.
Eriksson, Dennis, et al.
(author)
Measuring the impact of plant breeding on sub-Saharan African staple crops
2018
In: Outlook On Agriculture. - : SAGE Publications. - 0030-7270 .- 2043-6866. ; 47, s. 163-180
Research review (peer-reviewed) abstract
Many countries in sub-Saharan Africa (SSA) are facing huge challenges regarding food insecurity, low agricultural output, and agriculturally incurred environmental degradation. A sustainable and increased crop productivity and diversity is essential to achieve food security in a socially, economically, and environmentally sustainable way. Plant breeding is an important factor contributing to the increased crop productivity and diversity, giving farmers access to genetically improved cultivars that yield more, have better resistance to biotic and abiotic stresses, and meet consumer expectations. To motivate and encourage further investments, it is important to measure the actual impact of breeding. This review considers available research on the impact of breeding through yield gain and of food security, focusing on 10 important staple crops in SSA. The overall impression is that breeding produces a very high return on investment. Such investments remain centerpieces for meeting the challenges in this region. The discussion focuses on the most important future breeding priorities for each crop, the actors involved, and the importance of mechanisms for dissemination and farmer adoption, and concludes with some policy recommendations.
18.
Eriksson, Dennis, et al.
(author)
Overview and Breeding Strategies of Table Potato Production in Sweden and the Fennoscandian Region
2016
In: Potato Research. - : Springer Science and Business Media LLC. - 0014-3065 .- 1871-4528. ; 59, s. 279-294
Journal article (peer-reviewed) abstract
Recent reductions in the public commitment to potato breeding in Sweden, Norway and Finland call for an evaluation of the current situation regarding the commercial basis for, and structure of, potato breeding in these countries. We here review the extent of cultivation, processing and consumption of table potato in Sweden, as well as provide an overview of the potato breeding tools and programmes in the three countries. We then discuss various strategies to provide long-term stability and increase the impact of public potato breeding, based on the similar overall conditions for potato cultivation across the Fennoscandian region. The conclusions are twofold; first, an increased long-term funding of the public potato breeding programmes is necessary to maintain a minimum level of material, and second, a coordination of the breeding activities in the Fennoscandian region would be of great benefit to all involved stakeholders and allow an enhancement of the current national breeding programmes. In addition, we propose a minimum first field year population size for potato breeding.
19.
Eriksson, Dennis
(author)
Regulatory hurdles for genome editing: process- vs. product-based approaches in different regulatory contexts
2016
In: Plant Cell Reports. - : Springer Science and Business Media LLC. - 0721-7714 .- 1432-203X. ; 35, s. 1493-1506
Journal article (peer-reviewed) abstract
Novel plant genome editing techniques call for an updated legislation regulating the use of plants produced by genetic engineering or genome editing, especially in the European Union. Established more than 25 years ago and based on a clear distinction between transgenic and conventionally bred plants, the current EU Directives fail to accommodate the new continuum between genetic engineering and conventional breeding. Despite the fact that the Directive 2001/18/EC contains both process- and product-related terms, it is commonly interpreted as a strictly process-based legislation. In view of several new emerging techniques which are closer to the conventional breeding than common genetic engineering, we argue that it should be actually interpreted more in relation to the resulting product. A legal guidance on how to define plants produced by exploring novel genome editing techniques in relation to the decade-old legislation is urgently needed, as private companies and public researchers are waiting impatiently with products and projects in the pipeline. We here outline the process in the EU to develop a legislation that properly matches the scientific progress. As the process is facing several hurdles, we also compare with existing frameworks in other countries and discuss ideas for an alternative regulatory system.
20.
Hennigs, Lars
(author)
FLOWERING LOCUS T Triggers Early and Fertile Flowering in Glasshouse Cassava (Manihot esculenta Crantz)
2017
In: Plants. - : MDPI AG. - 2223-7747. ; 6
Journal article (peer-reviewed) abstract
Accelerated breeding of plant species has the potential to help challenge environmental and biochemical cues to support global crop security. We demonstrate the over-expression of Arabidopsis FLOWERING LOCUS T in Agrobacterium-mediated transformed cassava (Manihot esculenta Crantz; cultivar 60444) to trigger early flowering in glasshouse-grown plants. An event seldom seen in a glasshouse environment, precocious flowering and mature inflorescence were obtained within 4–5 months from planting of stem cuttings. Manual pollination using pistillate and staminate flowers from clonal propagants gave rise to viable seeds that germinated into morphologically typical progeny. This strategy comes at a time when accelerated crop breeding is of increasing importance to complement progressive genome editing techniques.
21.
Ivarson, Emelie
(author)
Development of Lepidium campestre into a new oil and catch crop
2016
Doctoral thesis (other academic/artistic) abstract
A growing world population and dwindling fossil oil reserves demand an increase in the world plant oil production. The possibility to increase the area of cultivated land is limited due to the shortage of arable land. Also, the possibility for increasing the oil content in the limited number of cultivated oil crops is restricted. New, high-yielding oil crops, which can be grown in areas where no other oil crops can grow and have less environmental impact, need to be developed. It is preferable that such new oil crops would allow us to tailor-make the oil composition in planta for food, fuel or industrial applications. In Sweden, the main oil crop cultivated is winter rapeseed, which, due to weak winter hardiness, only can be grown in southern Sweden. Developing a new winter-hardy oilseed crop would extend the plant oil production in Sweden and other cold climate regions. Lepidium campestre is a wild Brassica species. It is very winter hardy, high-yielding, has an upright stature and synchronous flowering. Moreover, it is biennial, and thus being suitable as a catch crop. However, it needs to be domesticated first so that it possesses all important agronomic traits necessary for being a successful agricultural crop. The aim of this thesis was to improve some properties of L. campestre by genetic engineering with focus on: the seed oil content, pod shatter, seed oil composition and wax ester production in the seed oil. In order to enable genetic engineering of this wild species, a well-functioning regeneration and transformation protocol was first developed, which has greatly facilitated the subsequent genetic improvements of the target traits of the species. Through RNAi-down-regulation of the FAD2 and FAE1 genes, transgenic lines with oxidative stable oil high in oleic acid were generated, indicating the potential of the species for being used for food oil purposes. Moreover, transgenic lines with increased seed oil content were developed by expressing either the AtWRI1 or AtHb2 or BvHb2 gene. Transgenic lines with pod shatter resistance were produced by RNAi down-regulation of the IND gene. Wax esters were produced in this species by expression of the jojoba wax synthesis genes, showing the potential of the species as a new platform for industrial oil production. These transgenic lines are valuable materials for further breeding of this species.
22.
Ivarson, Emelie, et al.
(author)
Effects of overexpression of WRI1 and hemoglobin genes on the seed oil content of Lepidium campestre
2017
In: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 7
Journal article (peer-reviewed) abstract
The wild species field cress (Lepidium campestre), belonging to the Brassicaceae family, has potential to be developed into a novel oilseed- and catch crop, however, the species needs to be further improved regarding some important agronomic traits. One of them is its low oil content which needs to be increased. As far as we know there is no study aiming at increasing the oil content that has been reported in this species. In order to investigate the possibility to increase the seed oil content in field cress, we have tried to introduce the Arabidopsis WRINKLED1 (AtWRI1) or hemoglobin (Hb) genes from either Arabidopsis thaliana (AtHb2) or Beta vulgaris (BvHb2) into field cress with the seed specific expression. The hypothesis was that the oil content would be increased by overexpressing these target genes. The results showed that the oil content was indeed increased by up to 29.9, 20.2, and 25.9% in the transgenic lines expressing AtWRI1, AtHb2, and BvHb2, respectively. The seed oil composition of the transgenic lines did not significantly deviate from the seed oil composition of the wild type plants. Our results indicate that genetic modification can be used in this wild species for its fast domestication into a future economically viable oilseed and catch crop.
23.
Jin, Yunkai, et al.
(author)
New Energy Crops for Biofuel Production
2015
In: Handbook of clean energy systems. - Chichester, UK : John Wiley & Sons, Ltd. - 9781118388587 ; , s. 49-62
Book chapter (peer-reviewed)
24.
Mehrabi, Sara, 1982-, et al.
(author)
The constitutive expression and induction of three β-1,3-glucanases by bird cherry-oat aphid in relation to aphid resistance in 15 barley breeding lines
2016
In: Arthropod-Plant Interactions. - : Springer Science and Business Media LLC. - 1872-8855 .- 1872-8847. ; 10:2, s. 101-111
Journal article (peer-reviewed) abstract
In this study, 15 closely related barley genotypes were analyzed for the abundance of three β-1,3-glucanase transcripts immediately before and during infestation by the bird cherry-oat aphid (Rhopalosiphum padi L.). The barley lines are doubled haploid lines in backcross (BC) generations BC1 and BC2 from a cross between cultivar Lina and a wild barley accession. Previously, they have been characterized as susceptible (S) or resistant (R) to R. padi based on their ability to support nymphal growth. Here we also tested whether resistance was manifested as reduced aphid settling on the plants. Indeed, aphid numbers were lower on R than on S lines in all cases where there were significant differences between R and S lines. The choice of β-1,3-glucanase sequences is based on earlier results comparing two S and two R genotypes, suggesting that at least two of the three studied sequences are susceptibility factors. The comparisons of transcript abundance in plants with aphids showed for two of the β-1,3-glucanase sequences that there were several cases where an S genotype had significantly higher abundance than an R genotype, and in no case did an R line have significantly higher abundance than an S line. Thus, there was some support for the idea that β-1,3-glucanase sequences are susceptibility factors in the interaction between barley and R. padi.
25.
Nemesio Gorriz, Miguel
(author)
Molecular responses against Heterobasidion annosum s.l. in Picea abies
2015
Doctoral thesis (other academic/artistic) abstract
Norway spruce [Picea abies (L.) Karst.] is a main tree species in European forests and is important both ecologically and economically. The root rot fungus Heterobasidion annosum sensu lato (s.l.) is the main P. abies pathogen. Including resistance in breeding programs would help mitigating the impact of the pathogen but knowledge regarding defense mechanisms in P. abies needs a better understanding. The work within this thesis intended to expand the existing knowledge on P. abies resistance mechanisms focusing on hormone signaling, flavonoid biosynthesis and its transcriptional regulation. I found that jasmonic acid is the major hormone controlling defense signaling pathways in P. abies. Furthermore, we validated a candidate gene, PaLAR3, as a resistance marker for H. annosum s.l. in P. abies. PaLAR3 encodes an enzyme responsible for the synthesis of (+) catechin, which showed a fungistatic effect on H. parviporum. Analysis of genetic diversity revealed two allelic lineages of PaLAR3 that showed significant differences in fungal resistance and (+) catechin content that were explained by dissimilarities in inducibility. We studied the role of PaNAC03, a transcription factor that is associated with H. annosum s.l. infection. PaNAC03 not only showed repression of multiple genes including PaLAR3, but bound only to the promoter of one of the PaLAR3 allelic lineages explaining at least partly the differences in allelic expression that were observed. Finally, we identified a full repertoire of members of a MYB/bHLH/WDR transcription factor complex in Norway spruce, which showed differences in protein interactions and expression patterns, and also in ability to control the expression of genes in the flavonoid biosynthetic pathway including PaLAR3.
26.
Nybom, Hilde, et al.
(author)
Analysis of the genetic diversity and structure across a wide range of germplasm reveals prominent gene flow in apple at the European level
2016
In: BMC Plant Biology. - : Springer Science and Business Media LLC. - 1471-2229. ; 16
Journal article (peer-reviewed) abstract
Background: The amount and structure of genetic diversity in dessert apple germplasm conserved at a European level is mostly unknown, since all diversity studies conducted in Europe until now have been performed on regional or national collections. Here, we applied a common set of 16 SSR markers to genotype more than 2,400 accessions across 14 collections representing three broad European geographic regions (North + East, West and South) with the aim to analyze the extent, distribution and structure of variation in the apple genetic resources in Europe.Results: A Bayesian model-based clustering approach showed that diversity was organized in three groups, although these were only moderately differentiated (F-ST = 0.031). A nested Bayesian clustering approach allowed identification of subgroups which revealed internal patterns of substructure within the groups, allowing a finer delineation of the variation into eight subgroups (F-ST = 0.044). The first level of stratification revealed an asymmetric division of the germplasm among the three groups, and a clear association was found with the geographical regions of origin of the cultivars. The substructure revealed clear partitioning of genetic groups among countries, but also interesting associations between subgroups and breeding purposes of recent cultivars or particular usage such as cider production. Additional parentage analyses allowed us to identify both putative parents of more than 40 old and/or local cultivars giving interesting insights in the pedigree of some emblematic cultivars.Conclusions: The variation found at group and subgroup levels may reflect a combination of historical processes of migration/selection and adaptive factors to diverse agricultural environments that, together with genetic drift, have resulted in extensive genetic variation but limited population structure. The European dessert apple germplasm represents an important source of genetic diversity with a strong historical and patrimonial value. The present work thus constitutes a decisive step in the field of conservation genetics. Moreover, the obtained data can be used for defining a European apple core collection useful for further identification of genomic regions associated with commercially important horticultural traits in apple through genome-wide association studies.
27.
Nybom, Hilde, et al.
(author)
Nordiska äpplen – projekt NordApp
2015
In: LTV-fakultetens faktablad.
Other publication (pop. science, debate, etc.) abstract
Frukt av många olika slag odlas över hela världen, och utgör en viktig del av den totala livsmedelsförsörjningen. I varmare länder är mångfalden stor – former och färger bildar en förförande palett om man besöker en fruktmarknad, liksom doft och smak hos de frukter man väljer att bekanta sig närmare med. I de nordiska länderna sätter klimatet dessvärre stopp för merparten av dessa frukter – men vi har lyckligtvis några, främst kärn- och stenfrukter inom familjen Rosaceae. Äpple har sålunda odlats i de nordiska länderna sedan början av medeltiden, och detta är numera vår i särklass viktigaste frukt, såväl kulturellt som ekonomiskt. Vissa utländska äpplesorter fungerar ganska bra i odling även på våra breddgrader men för merparten blir den korta vegetationsperioden och de stränga vintrarna övermäktiga hinder. Offentligt finansierade växtförädlingsprogram har därför bedrivits i Finland, Norge och Sverige för att ta fram klimatanpassade sorter. På senare tid har ökad omsorg om miljö och hälsa aktualiserat ytterligare ett förädlingsmål: resistens mot olika skadegörare.
28.
Nybom, Hilde, et al.
(author)
Resistens mot grönmögel hos äpple
2015
In: LTV-fakultetens faktablad.
Other publication (pop. science, debate, etc.) abstract
Äpple är gott och nyttigt, och allt fler konsumenter frågar efter svensk frukt i affärerna. Men tillgången är inte så stor eftersom svenska odlare endast producerar 20% av de äpplen vi äter i Sverige. Resten importeras från utlandet, där klimatet är gynnsammare, arbetskostnaderna lägre och tillgången på tillåtna växtskyddsmedel större. Konsumenterna är kanske beredda att betala lite extra för svensk frukt men man förväntar sig då att kvaliteten ska vara på topp: vackra, friska och välsmakande frukter!
29.
Ortiz Rios, Rodomiro Octavio
(author)
Advances in Host Plant and Rhizobium Genomics to Enhance Symbiotic Nitrogen Fixation in Grain Legumes
2015
In: Advances in Agronomy. - : Elsevier. - 0065-2113 .- 2213-6789. ; 129, s. 1-116
Research review (peer-reviewed) abstract
Legumes form symbiotic relationship with root-nodule, rhizobia. The nitrogen (N2) fixed by legumes is a renewable source and of great importance to agriculture. Symbiotic nitrogen fixation (SNF) is constrained by multiple stresses and alleviating them would improve SNF contribution to agroecosystems. Genetic differences in adaptation tolerance to various stresses are known in both host plant and rhizobium. The discovery and use of promiscuous germplasm in soybean led to the release of high-yielding cultivars in Africa. High N2-fixing soybean cultivars are commercially grown in Australia and some countries in Africa and South America and those of pea in Russia. SNF is a complex trait, governed by multigenes with varying effects. Few major quantitative trait loci (QTL) and candidate genes underlying QTL are reported in grain and model legumes. Nodulating genes in model legumes are cloned and orthologs determined in grain legumes. Single nucleotide polymorphism (SNP) markers from nodulation genes are available in common bean and soybean. Genomes of chickpea, pigeonpea, and soybean; and genomes of several rhizobium species are decoded. Expression studies revealed few genes associated with SNF in model and grain legumes. Advances in host plant and rhizobium genomics are helping identify DNA markers to aid breeding of legume cultivars with high symbiotic efficiency. A paradigm shift is needed by breeding programs to simultaneously improve host plant and rhizobium to harness the strength of positive symbiotic interactions in cultivar development. Computation models based on metabolic reconstruction pathways are providing greater insights to explore genotype–phenotype relationships in SNF. Models to simulate the response of N2 fixation to a range of environmental variables and crop growth are assisting researchers to quantify SNF for efficient and sustainable agricultural production systems. Such knowledge helps identifying bottlenecks in specific legume–rhizobia systems that could be overcome by legume breeding to enhance SNF. This review discusses the recent developments to improve SNF and productivity of grain legumes.
30.
Ortiz Rios, Rodomiro Octavio
(author)
Application of genomics assisted breeding for generation of climate resilient crops: progress and prospects
2015
In: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 6
Journal article (peer-reviewed) abstract
Climate change affects agricultural productivity worldwide. Increased prices of food commodities are the initial indication of drastic edible yield loss, which is expected to increase further due to global warming. This situation has compelled plant scientists to develop climate change-resilient crops,which can withstand broad-spectrums tresses such as drought, heat, cold, salinity, flood, submergence and pests, thus helping to deliver increased productivity. Genomics appears to be a promising tool for deciphering the stress responsiveness of crop species with adaptation traits or in wild relatives toward identifying underlying genes, alleles or quantitative trait loci. Molecular breeding approaches have proven helpful in enhancing the stress adaptation of crop plants, and recent advances in high-throughput sequencing and phenotyping platforms have transformed molecula rbreeding to genomics-assisted breeding (GAB). In view of this, the present review elaborates the progress and prospects of GAB for improving climate change resilience in crops, which is likely to play an ever increasing role in the effort to ensure global food security.
31.
32.
Ortiz Rios, Rodomiro Octavio
(author)
Assessing and Exploiting Functional Diversity in Germplasm Pools to Enhance Abiotic Stress Adaptation and Yield in Cereals and Food Legumes
2017
In: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 8
Research review (peer-reviewed) abstract
There is a need to accelerate crop improvement by introducing alleles conferring host plant resistance, abiotic stress adaptation, and high yield potential. Elite cultivars, landraces and wild relatives harbor useful genetic variation that needs to be more easily utilized in plant breeding. We review genome-wide approaches for assessing and identifying alleles associated with desirable agronomic traits in diverse germplasm pools of cereals and legumes. Major quantitative trait loci and single nucleotide polymorphisms (SNPs) associated with desirable agronomic traits have been deployed to enhance crop productivity and resilience. These include alleles associated with variation conferring enhanced photoperiod and flowering traits. Genetic variants in the florigen pathway can provide both environmental flexibility and improved yields. SNPs associated with length of growing season and tolerance to abiotic stresses (precipitation, high temperature) are valuable resources for accelerating breeding for drought-prone environments. Both genomic selection and genome editing can also harness allelic diversity and increase productivity by improving multiple traits, including phenology, plant architecture, yield potential and adaptation to abiotic stresses. Discovering rare alleles and useful haplotypes also provides opportunities to enhance abiotic stress adaptation, while epigenetic variation has potential to enhance abiotic stress adaptation and productivity in crops. By reviewing current knowledge on specific traits and their genetic basis, we highlight recent developments in the understanding of crop functional diversity and identify potential candidate genes for future use. The storage and integration of genetic, genomic and phenotypic information will play an important role in ensuring broad and rapid application of novel genetic discoveries by the plant breeding community. Exploiting alleles for yield-related traits would allow improvement of selection efficiency and overall genetic gain of multigenic traits. An integrated approach involving multiple stakeholders specializing in management and utilization of genetic resources, crop breeding, molecular biology and genomics, agronomy, stress tolerance, and reproductive/seed biology will help to address the global challenge of ensuring food security in the face of growing resource demands and climate change induced stresses.
33.
Ortiz Rios, Rodomiro Octavio
(author)
Breeding schemes for the implementation of genomic selection in wheat (Triticum spp.)
2016
In: Plant Science. - : Elsevier BV. - 0168-9452 .- 1873-2259. ; 242, s. 23-36
Journal article (peer-reviewed) abstract
In the last decade the breeding technology referred to as ‘genomic selection’ (GS) has been implemented in a variety of species, with particular success in animal breeding. Recent research shows the potential of GS to reshape wheat breeding. Many authors have concluded that the estimated genetic gain per year applying GS is several times that of conventional breeding. GS is, however, a new technology for wheat breeding and many programs worldwide are still struggling to identify the best strategy for its implementation. This article provides practical guidelines on the key considerations when implementing GS. A review of the existing GS literature for a range of species is provided and used to prime breeder-oriented considerations on the practical applications of GS. Furthermore, this article discusses potential breeding schemes for GS, genotyping considerations, and methods for effective training population design. The components of selection intensity, progress toward inbreeding in half- or full-sibs recurrent schemes, and the generation of selection are also presented.
34.
Ortiz Rios, Rodomiro Octavio
(author)
Diversifying Food Systems in the Pursuit of Sustainable Food Production and Healthy Diets
2017
In: Trends in Plant Science. - : Elsevier BV. - 1360-1385 .- 1878-4372. ; 22, s. 842-856
Research review (peer-reviewed) abstract
Increasing demand for nutritious, safe, and healthy food because of a growing population, and the pledge to maintain biodiversity and other resources, pose a major challenge to agriculture that is already threatened by a changing climate. Diverse and healthy diets, largely based on plant-derived food, may reduce diet-related illnesses. Investments in plant sciences will be necessary to design diverse cropping systems balancing productivity, sustainability, and nutritional quality. Cultivar diversity and nutritional quality are crucial. We call for better cooperation between food and medical scientists, food sector industries, breeders, and farmers to develop diversified and nutritious cultivars that reduce soil degradation and dependence on external inputs, such as fertilizers and pesticides, and to increase adaptation to climate change and resistance to emerging pests.
35.
Ortiz Rios, Rodomiro Octavio
(author)
Editorial: Plant Phenotyping and Phenomics for Plant Breeding
2017
In: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 8
Journal article (peer-reviewed) abstract
A major challenge for food production in the coming decades is to meet the food demands of a growing population (Beddington, 2010). The difficulty of expanding agricultural land, along with the effect of climate change and the increase in world population are the current societal changes that make necessary to accelerate research to improve yield-potential and adaptation to stressful environments (Lobos et al., 2014; Camargo and Lobos). Increasing yields will require implementing novel approaches in gene discovery and plant breeding that will significantly increase both production per unit of land area and resource use efficiency (Parry and Hawkesford, 2010; Tanger et al., 2017). A critical component for accelerating the development of new and improved cultivars is the rapid and precise phenotypic assessment of thousands of breeding lines, clones or populations over time (Fu, 2015) and under diverse environments. The only reasonable way to satisfy all these demands is through acquisition of high-dimensional phenotypic data (high-throughput phenotyping) or “phenomics” (Houle et al., 2010). This approach may predict complex characters that are relevant for plant selection (forward phenomics), and will also provide explanations as to why given genotypes stands out in a specific environment (reverse phenomics) (Camargo and Lobos).
36.
Ortiz Rios, Rodomiro Octavio
(author)
Exploiting Phenylpropanoid Derivatives to Enhance the Nutraceutical Values of Cereals and Legumes
2016
In: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 7
Research review (peer-reviewed) abstract
Phenylpropanoids are a diverse chemical class with immense health benefits that are biosynthesized from the aromatic amino acid L-phenylalanine. This article reviews the progress for accessing variation in phenylpropanoids in germplasm collections, the genetic and molecular basis of phenylpropanoid biosynthesis, and the development of cultivars dense in seed-phenylpropanoids. Progress is also reviewed on high-throughput assays, factors that influence phenylpropanoids, the site of phenylpropanoids accumulation in seed, Genotype × Environment interactions, and on consumer attitudes for the acceptance of staple foods rich in phenylpropanoids. A paradigm shift was noted in barley, maize, rice, sorghum, soybean, and wheat, wherein cultivars rich in phenylpropanoids are grown in Europe and North and Central America. Studies have highlighted some biological constraints that need to be addressed for development of high-yielding cultivars that are rich in phenylpropanoids. Genomics-assisted breeding is expected to facilitate rapid introgression into improved genetic backgrounds by minimizing linkage drag. More research is needed to systematically characterize germplasm pools for assessing variation to support crop genetic enhancement, and assess consumer attitudes to foods rich in phenylpropanoids.
37.
Ortiz Rios, Rodomiro Octavio
(author)
Genomic Selection : State of the Art
2017
In: Genetic Improvement of Tropical Crops. - Cham : Springer International Publishing. - 9783319598178 ; , s. 19-54
Book chapter (peer-reviewed)
38.
Ortiz Rios, Rodomiro Octavio
(author)
Genoproteomics-assisted improvement of Andrographis paniculata: toward a promising molecular and conventional breeding platform for autogamous plants affecting the pharmaceutical industry
2017
In: Critical Reviews in Biotechnology. - : Informa UK Limited. - 0738-8551 .- 1549-7801. ; 37, s. 803-816
Research review (peer-reviewed) abstract
Andrographis paniculata (Burm. f.) Wall. ex Nees. (AP) is a hermaphroditic, self-compatible, and habitual inbreeding plant. Its main bioactive component is andrographolide, which is capable of inducing autophagic cell death in some human cancer cells and helps fight HIV/AIDS. Increasing the andrographolide content by investigating the genetic mechanisms controlling its biosynthesis in order to improve and develop high-yielding cultivars are the main breeding targets for AP. However, there might exist some limitations or barriers for crossability within AP accessions. Recently, this problem was addressed in AP by using a combination of crossbreeding and biotechnology- aided genetic methods. This review emphasizes that development of a breeding platform in a hard-to-breed plant, such as AP, requires the involvement of a broad range of methods from classical genetics to molecular breeding. To this end, a phenological stage (for example, flowering and stigma development) can be simplified to a quantitative morphological trait (for example, bud or stigma length) to be used as an index to express the highest level of receptivity in order to manage outcrossing. The outcomes of the basic crossability research can be then employed in diallel mating and crossbreeding. This review explains how genomic data could produce useful information regarding genetic distance and its influence on the crossability of AP accessions. Our review indicates that co-dominant DNA markers, such as microsatellites, are also capable of resolving the evolutionary pathway and cryptic features of plant populations and such information can be used to select the best breeding strategy. This review also highlights the importance of proteomic analysis as a breeding tool. In this regard, protein diversification, as well as the impact of normal and stress- responsive proteins on morphometric and physiological behaviors, could be used in breeding programs. These findings have immense potential for improving plant production and, therefore, can be regarded as prospective breeding platforms for medicinal plants that have an autogamous mode of reproduction. Finally, this review suggests that novel site-directed genome editing approaches such as TALENs (Transcription Activator-Like Effector Nucleases) and CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein-9 nuclease) systems together with other new plant breeding technologies (NPBT) should simultaneously be taken into consideration for improvement of pharmaceutical plants.
39.
Ortiz Rios, Rodomiro Octavio
(author)
Global agricultural intensification during climate change: a role for genomics
2016
In: Plant Biotechnology Journal. - : Wiley. - 1467-7644 .- 1467-7652. ; 14, s. 1095-1098
Research review (peer-reviewed) abstract
Agriculture is now facing the ‘perfect storm’ of climate change, increasing costs of fertilizer and rising food demands from a larger and wealthier human population. These factors point to a global food deficit unless the efficiency and resilience of crop production is increased. The intensification of agriculture has focused on improving production under optimized conditions, with significant agronomic inputs. Furthermore, the intensive cultivation of a limited number of crops has drastically narrowed the number of plant species humans rely on. A new agricultural paradigm is required, reducing dependence on high inputs and increasing crop diversity, yield stability and environmental resilience. Genomics offers unprecedented opportunities to increase crop yield, quality and stability of production through advanced breeding strategies, enhancing the resilience of major crops to climate variability, and increasing the productivity and range of minor crops to diversify the food supply. Here we review the state of the art of genomic-assisted breeding for the most important staples that feed the world, and how to use and adapt such genomic tools to accelerate development of both major and minor crops with desired traits that enhance adaptation to, or mitigate the effects of climate change
40.
Ortiz Rios, Rodomiro Octavio
(author)
Haploids: Constraints and opportunities in plant breeding
2015
In: Biotechnology Advances. - : Elsevier BV. - 0734-9750 .- 1873-1899. ; 33, s. 812-829
Research review (peer-reviewed) abstract
The discovery of haploids in higher plants led to the use of doubled haploid (DH) technology in plant breeding. This article provides the state of the art on DH technology including the induction and identification of haploids, what factors influence haploid induction, molecular basis of microspore embryogenesis, the genetics underpinnings of haploid induction and its use in plant breeding, particularly to fix traits and unlock genetic variation. Both in vitro and in vivo methods have been used to induce haploids that are thereafter chromosome doubled to produce DH. Various heritable factors contribute to the successful induction of haploids, whose genetics is that of a quantitative trait. Genomic regions associated with in vitro and in vivo DH production were noted in various crops with the aid of DNA markers. It seems that F2 plants are the most suitable for the induction of DH lines than F1 plants. Identifying putative haploids is a key issue in haploid breeding. DH technology in Brassicas and cereals, such as barley, maize, rice, rye andwheat, has been improved and used routinely in cultivar development, while in other food staples such as pulses and root crops the technology has not reached to the stage leading to its application in plant breeding. The centromere-mediated haploid induction system has been used in Arabidopsis, but not yet in crops. Most food staples are derived from genomic resources-rich crops, including those with sequenced reference genomes. The integration of genomic resourceswith DH technology provides new opportunities for the improving selection methods, maximizing selection gains and accelerate cultivar development. Marker-aided breeding and DH technology have been used to improve host plant resistance in barley, rice, and wheat. Multinational seed companies are using DH technology in large-scale production of inbred lines for further development of hybrid cultivars, particularly in maize. The public sector provides support to national programs or small-medium private seed for the exploitation of DH technology in plant breeding.
41.
Ortiz Rios, Rodomiro Octavio
(author)
Integration of Next-generation Sequencing Technologies with Comparative Genomics in Cereals
2016
In: Plant Genomics. - : InTech. - 9789535124566 ; , s. 29-44
Book chapter (peer-reviewed) abstract
Cereals are the major sources of calories worldwide. Their production should be high to achieve food security, despite the projected increase in global population. Genomics research may enhance cereal productivity. Genomics immensely benefits from robust next-generation sequencing (NGS) techniques, which produce vast amounts of sequence data in a time and cost-efficient way. Research has demonstrated that gene sequences among closely related species that share common ancestry have remained well conserved over millions of years of evolution. Comparative genomics allows for comparison of genome sequences across different species, with the implication that genomes with large sizes can be investigated using closely related species with smaller genomes. This offers prospects of studying genes in a single species and, in turn, gaining information on their functions in other related species. Comparative genomics is expected to provide invaluable information on the control of gene function in complex cereal genomes, and also in designing molecular markers across related species. This chapter discusses advances in sequencing technologies, their application in cereal genomics and their potential contribution to the understanding of the relationships between the different cereal genomes and their phenotypes.
42.
Ortiz Rios, Rodomiro Octavio
(author)
Microsatellite-Aided Screening for Fertility Restorer Genes (Rf) Facilitates Hybrid Improvement
2016
In: Rice Science. - : Elsevier BV. - 1672-6308. ; 23, s. 160-164
Journal article (peer-reviewed) abstract
DNA markers enabled to determine the chromosomal locations of the two Rf genes (Rf3 and Rf4) in the wild abortive-cytoplasmic male sterility (WA-CMS) system. Four simple sequence repeats (SSR or microsatellites) RM171, RM258, RM315 and RM443 were used to detect the allelic status with respect to the fertility restoring genes (Rf3 and Rf4) in 300 rice cultivars and breeding lines. Furthermore, 45 lines selected using SSR markers were mated with a CMS line (IR58025A) to analyze their restoring ability. The results revealed that 90 lines had Rf3, 65 lines had Rf4 and 45 lines had Rf3 and Rf4 alleles out of 300 lines screened. Offspring of all test lines except HHZ 8-SAL9DT1-Y1, HHZ 5-SAL9-Y3-1 and IDSA 77 exhibited high pollen and spikelet fertility (> 80%), thus confirming they bear Rf alleles. the hybrid offspring of ARH12-6-1-1-B-3-1, IR32307-10-3-2-1 and Sahel329 had the highest pollen and spikelet fertility, (95.1–97, 4%, and 97.1–98.3%, 97.1-96.1% respectively).
43.
Ortiz Rios, Rodomiro Octavio
(author)
Plant Breeding in the Omics Era
2015
Book (peer-reviewed) abstract
The field of plant breeding has grown rapidly in the last decade with breakthrough research in genetics and genomics, inbred development, population improvement, hybrids, clones, self-pollinated crops, polyploidy, transgenic breeding and more. This book discusses the latest developments in all these areas but explores the next generation of needs and discoveries including omics beyond genomics, cultivar seeds and intellectual and property rights. This book is a leading-edge publication of the latest results and forecasts important areas of future needs and applications.
44.
Ortiz Rios, Rodomiro Octavio
(author)
Using Biotechnology-Led Approaches to Uplift Cereal and Food Legume Yields in Dryland Environments
2018
In: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 9
Research review (peer-reviewed) abstract
Drought and heat in dryland agriculture challenge the enhancement of crop productivity and threaten global food security. This review is centered on harnessing genetic variation through biotechnology-led approaches to select for increased productivity and stress tolerance that will enhance crop adaptation in dryland environments. Peer-reviewed literature, mostly from the last decade and involving experiments with at least two seasons' data, form the basis of this review. It begins by highlighting the adverse impact of the increasing intensity and duration of drought and heat stress due to global warming on crop productivity and its impact on food and nutritional security in dryland environments. This is followed by (1) an overview of the physiological and molecular basis of plant adaptation to elevated CO2 (eCO(2)), drought, and heat stress; (2) the critical role of high-throughput phenotyping platforms to study phenomes and genomes to increase breeding efficiency; (3) opportunities to enhance stress tolerance and productivity in food crops (cereals and grain legumes) by deploying biotechnology-led approaches [pyramiding quantitative trait loci (QTL), genomic selection, marker-assisted recurrent selection, epigenetic variation, genome editing, and transgene) and inducing flowering independent of environmental clues to match the length of growing season; (4) opportunities to increase productivity in C-3 crops by harnessing novel variations (genes and network) in crops' (C-3, C-4) germplasm pools associated with increased photosynthesis; and (5) the adoption, impact, risk assessment, and enabling policy environments to scale up the adoption of seed-technology to enhance food and nutritional security. This synthesis of technological innovations and insights in seed-based technology offers crop genetic enhancers further opportunities to increase crop productivity in dryland environments.
45.
46.
Snell, Per
(author)
Dissecting the gene regulatory networks behind carbon allocation in plants : ex situ studies on combinatorial and subdomains effects of seed transcription factors
2019
Doctoral thesis (other academic/artistic) abstract
Plants store excess energy and metabolites derived from photosynthesis in a variety of storage compounds with starch, protein and triacyglycerol (oil, TAG) being the most common. As humans, we are completely dependent on these compounds either directly as food or indirectly, as materials for large number of goods or feed for animals. With an increased interest in sustainable production systems and the need to feed and clothe a growing population in a changing environment, the need for a better understanding of how plants allocate carbon for storage is increasingly important.One key transcription factor involved in the accumulation of TAG into seeds is WRINKLED1 (WRI1). Using a transient gene expression system together with promoter-reporter gene constructs in Nicotiana benthamiana leaves, it was found that WRI1 is negatively regulating its own expression. This was further investigated by domain swapping between WRI1 homologs from diverse plant species to reveal that this mechanism was intrinsic to the tandem DNA binding AP2-domains of WRI1. Fluorescent electrophoretic mobility shift assay (fEMSA) was employed using purified WRI1 showing that WRI1 is unable to directly interact with its own upstream region.During seed development, non-endospermic seeds accumulate large amounts of oil in the embryo during later stages of embryo development. This is known to be regulated by several master regulators commonly called the LAFL-network (LEAFY COTYLEDON1 (LEC1), ABSCISSIC ACID INSENSITIVE3 (ABI3), FUSCA3 (FUS3) and LEC2). Using transient expression in N. benthamiana leaves it was discovered that LEC1 significantly influences the transactivation ability of LEC2 and especially ABI3. Not only is LEC1 modulating the ability of ABI3 to induce NbWRI1 expression, but also a large set of key genes involved in embryo morphogenesis. This suggests that LEC1 and ABI3 tightly collaborate to drive the embryo development from middle to late stage and the transition between morphogenesis to the acquisition of storage compounds. With the purpose of investigating the differences in carbon partitioning between oat (Avena sativa) which is unique among the cereals in storing significant amount of oil in the endosperm with wheat (Triticum aestivum) that has basically no endosperm oil AsWRI1 was transformed into wheat. The resulting transformant lines showed a significantly altered seed phenotype with increased oil accumulation, disrupted endosperm development and reduced sink strength.
47.
Weston, David J., et al.
(author)
The Sphagnome Project : enabling ecological and evolutionary insights through a genus-level sequencing project
2018
In: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 217:1, s. 16-25
Journal article (other academic/artistic) abstract
Considerable progress has been made in ecological and evolutionary genetics with studies demonstrating how genes underlying plant and microbial traits can influence adaptation and even 'extend' to influence community structure and ecosystem level processes. Progress in this area is limited to model systems with deep genetic and genomic resources that often have negligible ecological impact or interest. Thus, important linkages between genetic adaptations and their consequences at organismal and ecological scales are often lacking. Here we introduce the Sphagnome Project, which incorporates genomics into a long-running history of Sphagnum research that has documented unparalleled contributions to peatland ecology, carbon sequestration, biogeochemistry, microbiome research, niche construction, and ecosystem engineering. The Sphagnome Project encompasses a genus-level sequencing effort that represents a new type of model system driven not only by genetic tractability, but by ecologically relevant questions and hypotheses.
48.
Zhu, Tianqing
(author)
Regulation of embryo development in Norway spruce by WOX transcription factors
2015
Doctoral thesis (other academic/artistic) abstract
In seed plants, the apical-basal axis of the plant body is established during early embryogenesis. Major regulatory genes of the apical-basal axis formation belong to the WUSCHEL-RELATED HOMEOBOX (WOX) gene family of transcription factors. The spatiotemporal expression pattern and the molecular role of the WOX genes has mainly been studied in the angiosperm model plant Arabidopsis (Arabidopsis thaliana). Similar information in conifers is limited. The aim of my thesis has been to characterize WOX genes in Norway spruce (Picea abies) and to elucidate the function of WOX genes expressed during embryo development. We cloned 11 WOX homologs from Norway spruce and examined their phylogenetic relationship to WOX genes from other species. The phylogenetic analyses showed that the major diversification within the WOX gene family took place before the gymnosperm-angiosperm split. PaWOX8/9, PaWOX2 and PaWOX3, which are expressed in embryos, were selected for further studies. PaWOX8/9 and PaWOX2 are highly expressed in early and late embryos, and PaWOX3 is highly expressed in mature embryos. Functional studies were performed in RNAi lines where the genes were down-regulated. Embryos in PaWOX8/9 RNAi lines showed a disturbed apical-basal patterning caused by abnormal orientation of the cell division plane at the basal part of the embryonal mass. In PaWOX2 RNAi lines, vacuolated cells differentiated on the surface of the embryonal mass and the embryos failed to form a proper protoderm. Down-regulation of PaWOX3 disturbed lateral margin outgrowth in cotyledons and needles. Taken together, our results indicate that WOX8/9, WOX2 and WOX3 exert evolutionarily conserved functions during embryo development. We can therefore conclude that the regulatory networks of embryo development are at least partly conserved between angiosperms and gymnosperms.
49.
Chawade, Aakash
(author)
What is cost-efficient phenotyping? Optimizing costs for different scenarios
2019
In: Plant Science. - : Elsevier BV. - 0168-9452 .- 1873-2259. ; 282, s. 14-22
Journal article (peer-reviewed) abstract
Progress in remote sensing and robotic technologies decreases the hardware costs of phenotyping. Here, we first review cost-effective imaging devices and environmental sensors, and present a trade-off between investment and manpower costs. We then discuss the structure of costs in various real-world scenarios. Hand-held low-cost sensors are suitable for quick and infrequent plant diagnostic measurements. In experiments for genetic or agronomic analyses, (i) major costs arise from plant handling and manpower; (ii) the total costs per plant/microplot are similar in robotized platform or field experiments with drones, hand-held or robotized ground vehicles; (iii) the cost of vehicles carrying sensors represents only 5-26% of the total costs. These conclusions depend on the context, in particular for labor cost, the quantitative demand of phenotyping and the number of days available for phenotypic measurements due to climatic constraints. Data analysis represents 10-20% of total cost if pipelines have already been developed. A trade-off exists between the initial high cost of pipeline development and labor cost of manual operations. Overall, depending on the context and objsectives, "cost-effective" phenotyping may involve either low investment ("affordable phenotyping"), or initial high investments in sensors, vehicles and pipelines that result in higher quality and lower operational costs.
50.
Eriksson, Dennis
(author)
Opt out from GMOs in the European Union
2018
In: Encyclopedia of food and agricultural ethics. - Dordrecht : Springer Netherlands. - 9789402411782
Book chapter (other academic/artistic)
