| 1. |
- Crooks, Lucy, et al.
(author)
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An Improved Method for Estimating Chromosomal Line Origin in QTL Analysis of Crosses Between Outbred Lines
- 2011
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In: G3. - : Oxford University Press (OUP). - 2160-1836. ; 1, s. 57-64
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Journal article (peer-reviewed)abstract
- Estimating the line origin of chromosomal sections from marker genotypes is a vital step in quantitative trait loci analyses of outbred line crosses. The original, and most commonly used, algorithm can only handle moderate numbers of partially informative markers. The advent of high-density genotyping with SNP chips motivates a new method because the generic sets of markers on SNP chips typically result in long stretches of partially informative markers. We validated a new method for inferring line origin, triM (tracing inheritance with Markov models), with simulated data. A realistic pattern of marker information was achieved by replicating the linkage disequilibrium from an existing chicken intercross. There were approximately 1500 SNP markers and 800 F-2 individuals. The performance of triM was compared to GridQTL, which uses a variant of the original algorithm but modified for larger datasets. triM estimated the line origin with an average error of 2%, was 10% more accurate than GridQTL, considerably faster, and better at inferring positions of recombination. GridQTL could not analyze all simulated replicates and did not estimate line origin for around a third of individuals at many positions. The study shows that triM has computational benefits and improved estimation over available algorithms and is valuable for analyzing the large datasets that will be standard in future.
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| 2. |
- Reslow, Fredrik, et al.
(author)
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Modeling genotype × environment interaction for single and multi-trait genomic prediction in potato (Solanum tuberosum L.)
- 2023
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In: G3. - : Oxford University Press (OUP). - 2160-1836. ; 13
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Journal article (peer-reviewed)abstract
- In this study, we extend research on genomic prediction (GP) to polysomic polyploid plant species with the main objective to investigate single-trait (ST) and multitrait (MT) multienvironment (ME) models using field trial data from 3 locations in Sweden [Helgegården (HEL), Mosslunda (MOS), Umeå (UM)] over 2 years (2020, 2021) of 253 potato cultivars and breeding clones for 5 tuber weight traits and 2 tuber flesh quality characteristics. This research investigated the GP of 4 genome-based prediction models with genotype × environment interactions (GEs): (1) ST reaction norm model (M1), (2) ST model considering covariances between environments (M2), (3) ST M2 extended to include a random vector that utilizes the environmental covariances (M3), and (4) MT model with GE (M4). Several prediction problems were analyzed for each of the GP accuracy of the 4 models. Results of the prediction of traits in HEL, the high yield potential testing site in 2021, show that the best-predicted traits were tuber flesh starch (%), weight of tuber above 60 or below 40 mm in size, and the total tuber weight. In terms of GP, accuracy model M4 gave the best prediction accuracy in 3 traits, namely tuber weight of 40–50 or above 60 mm in size, and total tuber weight, and very similar in the starch trait. For MOS in 2021, the best predictive traits were starch, weight of tubers above 60, 50–60, or below 40 mm in size, and the total tuber weight. MT model M4 was the best GP model based on its accuracy when some cultivars are observed in some traits. For the GP accuracy of traits in UM in 2021, the best predictive traits were the weight of tubers above 60, 50–60, or below 40 mm in size, and the best model was MT M4, followed by models ST M3 and M2.
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| 3. |
- Berlin Kolm, Sofia, et al.
(author)
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Polymorphism and divergence of two willow species, Salix viminalis L. and Salix schwerinii E. Wolf
- 2011
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In: G3. - : Oxford University Press (OUP). - 2160-1836. ; 1:5, s. 387-400
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Journal article (peer-reviewed)abstract
- We investigated species divergence, present and past gene flow, levels of nucleotide polymorphism, and linkage disequilibrium in two willows from the plant genus Salix. Salix belongs together with Populus to the Salicaceae family; however, most population genetic studies of Salicaceae have been performed in Populus, the model genus in forest biology. Here we present a study on two closely related willow species Salix viminalis and S. schwerinii, in which we have resequenced 33 and 32 nuclear gene segments representing parts of 18 nuclear loci in 24 individuals for each species. We used coalescent simulations and estimated the split time to around 600,000 years ago and found that there is currently limited gene flow between the species. Mean intronic nucleotide diversity across gene segments was slightly higher in S. schwerinii (πi = 0.00849) than in S. viminalis (πi = 0.00655). Compared with other angiosperm trees, the two willows harbor intermediate levels of silent polymorphisms. The decay of linkage disequilibrium was slower in S. viminalis compared with S. schwerinii, and we speculate that this is due to different demographic histories as S. viminalis has been partly domesticated in Europe.
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| 4. |
- Johnsson, Martin, et al.
(author)
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Genetics of tibia bone properties of crossbred commercial laying hens in different housing systems
- 2023
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In: G3. - : Oxford University Press. - 2160-1836. ; 13:2
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Journal article (peer-reviewed)abstract
- Osteoporosis and bone fractures are a severe problem for the welfare of laying hens, with genetics and environment, such as housing system, each making substantial contributions to bone strength. In this work, we performed genetic analyses of bone strength, bone mineral density, and bone composition, as well as body weight, in 860 commercial crossbred laying hens from 2 different companies, kept in either furnished cages or floor pens. We compared bone traits between housing systems and crossbreds and performed a genome-wide association study of bone properties and body weight. As expected, the 2 housing systems produced a large difference in bone strength, with layers housed in floor pens having stronger bones. These differences were accompanied by differences in bone geometry, mineralization, and chemical composition. Genome scans either combining or independently analyzing the 2 housing systems revealed no genome-wide significant loci for bone breaking strength. We detected 3 loci for body weight that were shared between the housing systems on chromosomes 4, 6, and 27 (either genome-wide significant or suggestive) and these coincide with associations for bone length. In summary, we found substantial differences in bone strength, content, and composition between hens kept in floor pens and furnished cages that could be attributed to greater physical activity in pen housing. We found little evidence for large-effect loci for bone strength in commercial crossbred hens, consistent with a highly polygenic architecture for bone strength in the production environment. The lack of consistent genetic associations between housing systems in combination with the differences in bone phenotypes could be due to gene-by-environment interactions with housing system or a lack of power to detect shared associations for bone strength.
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| 5. |
- Larsson, Hanna, et al.
(author)
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Distribution of Long-Range Linkage Disequilibrium and Tajima's D Values in Scandinavian Populations of Norway Spruce (Picea abies)
- 2013
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In: G3. - : Oxford University Press (OUP). - 2160-1836. ; 3:5, s. 795-806
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Journal article (peer-reviewed)abstract
- The site frequency spectrum of mutations (SFS) and linkage disequilibrium (LD) are the two major sources of information in population genetics studies. In this study we focus on the levels of LD and the SFS and on the effect of sample size on summary statistics in 10 Scandinavian populations of Norway spruce. We found that previous estimates of a low level of LD were highly influenced by both sampling strategy and the fact that data from multiple loci were analyzed jointly. Estimates of LD were in fact heterogeneous across loci and increased within individual populations compared with the estimate from the total data. The variation in levels of LD among populations most likely reflects different demographic histories, although we were unable to detect population structure by using standard approaches. As in previous studies, we also found that the SFS-based test Tajima's D was highly sensitive to sample size, revealing that care should be taken to draw strong conclusions from this test when sample size is small. In conclusion, the results from this study are in line with recent studies in other conifers that have revealed a more complex and variable pattern of LD than earlier studies suggested and with studies in trees and humans that suggest that Tajima's D is sensitive to sample size. This has large consequences for the design of future association and population genetic studies in Norway spruce.
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| 6. |
- Li, Jingyi, et al.
(author)
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The crest phenotype in domestic chicken is caused by a 197 bp duplication in the intron of HOXC10
- 2021
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In: G3. - : Oxford University Press. - 2160-1836. ; 11:2
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Journal article (peer-reviewed)abstract
- The Crest mutation in chicken shows incomplete dominance and causes a spectacular phenotype in which the small feathers normally present on the head are replaced by much larger feathers normally present only in dorsal skin. Using whole-genome sequencing, we show that the crest phenotype is caused by a 197 bp duplication of an evolutionarily conserved sequence located in the intron of HOXC10 on chromosome 33. A diagnostic test showed that the duplication was present in all 54 crested chickens representing eight breeds and absent from all 433 non-crested chickens representing 214 populations. The mutation causes ectopic expression of at least five closely linked HOXC genes, including HOXC10, in cranial skin of crested chickens. The result is consistent with the interpretation that the crest feathers are caused by an altered body region identity. The upregulated HOXC gene expression is expanded to skull tissue of Polish chickens showing a large crest often associated with cerebral hernia, but not in Silkie chickens characterized by a small crest, both homozygous for the duplication. Thus, the 197 bp duplication is required for the development of a large crest and susceptibility to cerebral hernia because only crested chicken show this malformation. However, this mutation is not sufficient to cause herniation because this malformation is not present in breeds with a small crest, like Silkie chickens.
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| 7. |
- Selga, Catja, et al.
(author)
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The power of genomic estimated breeding values for selection when using a finite population size in genetic improvement of tetraploid potato
- 2022
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In: G3. - : Oxford University Press (OUP). - 2160-1836. ; 12
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Journal article (peer-reviewed)abstract
- Potato breeding relies heavily on visual phenotypic scoring for clonal selection. Obtaining robust phenotypic data can be labor intensive and expensive, especially in the early cycles of a potato breeding program where the number of genotypes is very large. We have investigated the power of genomic estimated breeding values (GEBVs) for selection from a limited population size in potato breeding. We collected genotypic data from 669 tetraploid potato clones from all cycles of a potato breeding program, as well as phenotypic data for eight important breeding traits. The genotypes were partitioned into a training and a test population distinguished by cycle of selection in the breeding program. GEBVs for seven traits were predicted for individuals from the first stage of the breeding program (T1) which had not undergone any selection, or individuals selected at least once in the field (T2). An additional approach in which GEBVs were predicted within and across full-sib families from unselected material (T1) was tested for four breeding traits. GEBVs were obtained by using a Bayesian Ridge Regression model estimating single marker effects and phenotypic data from individuals at later stages of selection of the breeding program. Our results suggest that, for most traits included in this study, information from individuals from later stages of selection cannot be utilized to make selections based on GEBVs in earlier clonal generations. Predictions of GEBVs across full-sib families yielded similarly low prediction accuracies as across generations. The most promising approach for selection using GEBVs was found to be making predictions within full-sib families.
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| 8. |
- Morell Miranda, Pedro, et al.
(author)
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Demographic reconstruction of the Western sheep expansion from whole-genome sequences
- 2023
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In: G3. - : Oxford University Press. - 2160-1836. ; 13:11
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Journal article (peer-reviewed)abstract
- As one of the earliest livestock, sheep (Ovis aries) were domesticated in the Fertile Crescent about 12,000–10,000 years ago and have a nearly worldwide distribution today. Most of our knowledge about the timing of their expansions stems from archaeological data but it is unclear how the genetic diversity of modern sheep fits with these dates. We used whole-genome sequencing data of 63 domestic breeds and their wild relatives, the Asiatic mouflon (O. gmelini, previously known as O. orientalis), to explore the demographic history of sheep. On the global scale, our analysis revealed geographic structuring among breeds with unidirectional recent gene flow from domestics into Asiatic mouflons. We then selected 4 representative breeds from Spain, Morocco, the United Kingdom, and Iran to build a comprehensive demographic model of the Western sheep expansion. We inferred a single domestication event around 11,000 years ago. The subsequent westward expansion is dated to approximately 7,000 years ago, later than the original Neolithic expansion of sheep and slightly predating the Secondary Product Revolution associated with wooly sheep. We see some signals of recent gene flow from an ancestral population into Southern European breeds which could reflect admixture with feral European mouflon. Furthermore, our results indicate that many breeds experienced a reduction of their effective population size during the last centuries, probably associated with modern breed development. Our study provides insights into the complex demographic history of Western Eurasian sheep, highlighting interactions between breeds and their wild counterparts.
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| 9. |
- Brandt, Monika, et al.
(author)
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Imputation-Based Fine-Mapping Suggests That Most QTL in an Outbred Chicken Advanced Intercross Body Weight Line Are Due to Multiple, Linked Loci
- 2017
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In: G3. - : Oxford University Press (OUP). - 2160-1836. ; 7:1, s. 119-128
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Journal article (peer-reviewed)abstract
- The Virginia chicken lines have been divergently selected for juvenile body weight for more than 50 generations. Today, the high- and low-weight lines show a >12-fold difference for the selected trait, 56-d body weight. These lines provide unique opportunities to study the genetic architecture of long-term, single-trait selection. Previously, several quantitative trait loci (QTL) contributing to weight differences between the lines were mapped in an F2-cross between them, and these were later replicated and fine-mapped in a nine-generation advanced intercross of them. Here, we explore the possibility to further increase the fine-mapping resolution of these QTL via a pedigree-based imputation strategy that aims to better capture the genetic diversity in the divergently selected, but outbred, founder lines. The founders of the intercross were high-density genotyped, and then pedigree-based imputation was used to assign genotypes throughout the pedigree. Imputation increased the marker density 20-fold in the selected QTL, providing 6911 markers for the subsequent analysis. Both single-marker association and multi-marker backward-elimination analyses were used to explore regions associated with 56-d body weight. The approach revealed several statistically and population structure independent associations and increased the mapping resolution. Further, most QTL were also found to contain multiple independent associations to markers that were not fixed in the founder populations, implying a complex underlying architecture due to the combined effects of multiple, linked loci perhaps located on independent haplotypes that still segregate in the selected lines.
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| 10. |
- Crooks, Lucy, et al.
(author)
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Identification of Null Alleles and Deletions from SNP Genotypes for an Intercross Between Domestic and Wild Chickens
- 2013
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In: G3. - : Oxford University Press (OUP). - 2160-1836. ; 3:8, s. 1253-1260
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Journal article (peer-reviewed)abstract
- We analyzed genotypes from similar to 10K single-nucleotide polymorphisms (SNPs) in two families of an F-2 intercross between Red Junglefowl and White Leghorn chickens. Possible null alleles were found by patterns of incompatible and missing genotypes. We estimated that 2.6% of SNPs had null alleles compared with 2.3% with genotyping errors and that 40% of SNPs in which a parent and offspring were genotyped as different homozygotes had null alleles. Putative deletions were identified by null alleles at adjacent markers. We found two candidate deletions that were supported by fluorescence intensity data from a 60K SNP chip. One of the candidate deletions was from the Red Junglefowl, and one was present in both the Red Junglefowl and White Leghorn. Both candidate deletions spanned protein-coding regions and were close to a previously detected quantitative trait locus affecting body weight in this population. This study demonstrates that the similar to 50K SNP genotyping arrays now available for several agricultural species can be used to identify null alleles and deletions in data from large families. We suggest that our approach could be a useful complement to linkage analysis in experimental crosses.
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