onr:"swepub:oai:slubar.slu.se:120044"
Search: onr:"swepub:oai:slubar.slu.se:120044" > Finger millet RNA-s...
- 1 of 1
- Previous record
- Next record
- To hitlist
Finger millet RNA-seq reveals differential gene expression associated with tolerance to aluminum toxicity and provides novel genomic resources
-
- Brhanie Mesfin, Haftom (author)
- Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för växtförädling,Department of Plant Breeding,Aksum University,Addis Ababa University
-
- Ortiz Rios, Rodomiro Octavio (author)
- Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för växtförädling,Department of Plant Breeding
-
- Hammenhag, Cecilia (author)
- Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för växtförädling,Department of Plant Breeding
- show more...
- show less...
- (creator_code:org_t)
- 2022-12-09
- 2022
- English.
- In: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 13
- Journal article (peer-reviewed)
Abstract
Subject headings
Close
- Eleusine coracana, finger millet, is a multipurpose crop cultivated in arid and semi-arid regions of Africa and Asia. RNA sequencing (RNA-seq) was used in this study to obtain valuable genomic resources and identify genes differentially expressed between Al-tolerant and Al-susceptible genotypes. Two groups of finger millet genotypes were used: Al-tolerant (215836, 215845, and 229722) and Al-susceptible (212462, 215804 and 238323). The analysis of the RNA-seq data resulted in 198,546 unigenes, 56.5% of which were annotated with significant hits in one or more of the following six databases: NR (48.8%), GO (29.7%), KEGG (45%), PlantTFDB (19.0%), Uniprot (49.2%), and NT (46.2%). It is noteworthy that only 220 unigenes in the NR database had significant hits against finger millet sequences suggesting that finger millet’s genomic resources are scarce. The gene expression analysis revealed that 322 genes were significantly differentially expressed between the Al-tolerant and Alsusceptible genotypes, of which 40.7% were upregulated while 59.3% were downregulated in Al-tolerant genotypes. Among the significant DEGs, 54.7% were annotated in the GO database with the top hits being ATP binding (GO:0005524) and DNA binding (GO:0003677) in the molecular function, DNA integration (GO:0015074) and cell redox homeostasis in the biological process, as well as cellular anatomical entity and intracellular component in the cellular component GO classes. Several of the annotated DEGs were significantly enriched for their corresponding GO terms. The KEGG pathway analysis resulted in 60 DEGs that were annotated with different pathway classes, of which carbohydrate metabolism and signal transduction were the most prominent. The homologs of a number of significant DEGs have been previously reported as being associated with Al or other abiotic stress responses in various crops, including carboxypeptidase SOL1, HMA3, AP2, bZIP, C3H, and WRKY TF genes. A more detailed investigation of these and other DEGs will enable genomic-led breeding for Al tolerance in finger millet RNA-seq data analysis also yielded 119,073 SNP markers, the majority of which had PIC values above 0.3, indicating that they are highly informative. Additionally, 3,553 single-copy SSR markers were identified, of which trinucleotide SSRs were the most prevalent. These genomic resources contribute substantially to the enrichment of genomic databases for finger millet, and facilitate future research on this crop.
Subject headings
- LANTBRUKSVETENSKAPER -- Lantbruksvetenskap, skogsbruk och fiske -- Jordbruksvetenskap (hsv//swe)
- AGRICULTURAL SCIENCES -- Agriculture, Forestry and Fisheries -- Agricultural Science (hsv//eng)
- LANTBRUKSVETENSKAPER -- Bioteknologi med applikationer på växter och djur -- Genetik och förädling inom lantbruksvetenskap (hsv//swe)
- AGRICULTURAL SCIENCES -- Agricultural Biotechnology -- Genetics and Breeding in Agricultural Sciences (hsv//eng)
Publication and Content Type
- ref (subject category)
- art (subject category)
Find in a library
- Frontiers in Plant Science (Search for host publication in LIBRIS)
To the university's database
- 1 of 1
- Previous record
- Next record
- To hitlist
Find more in SwePub
- By the author/editor
- Brhanie Mesfin, ...
- Ortiz Rios, Rodo ...
- Hammenhag, Cecil ...
- Abreha, Kibrom B ...
- Ramesh, Vetukuri
- Dida, Mulatu Gel ...
- About the subject
-
- AGRICULTURAL SCIENCES
- AGRICULTURAL SCI ...
- and Agriculture Fore ...
- and Agricultural Sci ...
-
- AGRICULTURAL SCIENCES
- AGRICULTURAL SCI ...
- and Agricultural Bio ...
- and Genetics and Bre ...
- Articles in the publication
- Frontiers in Pla ...
- By the university
- Swedish University of Agricultural Sciences
Search outside SwePub
- Extend your search to:
- Google Book Search
- Google Scholar
Kungliga biblioteket hanterar dina personuppgifter i enlighet med EU:s dataskyddsförordning (2018), GDPR. Läs mer om hur det funkar här.
Så här hanterar KB dina uppgifter vid användning av denna tjänst.
- Copyright © LIBRIS - National Library Systems
- LIBRIS.kb.se
