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Novel GBS-Based SNP Markers for Finger Millet and Their Use in Genetic Diversity Analyses

Brhane, Haftom and Brhanie Mesfin, Haftom and Haileselassie, Teklehaimanot and Tesfaye, Kassahun and Ortiz Rios, Rodomiro Octavio and Hammenhag, Cecilia and Abreha, Kibrom Berhe and Geleta, Mulatu Dida (2022). Novel GBS-Based SNP Markers for Finger Millet and Their Use in Genetic Diversity Analyses. Frontiers in Genetics. 13 , 848627
[Research article]

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Abstract

Eleusine coracana (L.) Gaertn., commonly known as finger millet, is a multipurpose crop used for food and feed. Genomic tools are required for the characterization of crop gene pools and their genomics-led breeding. High-throughput sequencing-based characterization of finger millet germplasm representing diverse agro-ecologies was considered an effective method for determining its genetic diversity, thereby suggesting potential candidates for breeding. In this study, the genotyping-by-sequencing (GBS) method was used to simultaneously identify novel single nucleotide polymorphism (SNP) markers and genotype 288 finger millet accessions collected from Ethiopia and Zimbabwe. The accessions were characterized at individual and group levels using 5,226 bi-allelic SNPs, with a minimum allele frequency (MAF) of above 0.05, distributed across 2,500 scaffolds of the finger millet reference genome. The polymorphism information content (PIC) of the SNPs was 0.23 on average, and a quarter of them have PIC values over 0.32, making them highly informative. The grouping of the 288 accessions into seven populations based on geographic proximity and the potential for germplasm exchange revealed a narrow range of observed heterozygosity (Ho; 0.09-0.11) and expected heterozygosity (He) that ranged over twofold, from 0.11 to 0.26. Alleles unique to the different groups were also identified, which merit further investigation for their potential association with desirable traits. The analysis of molecular variance (AMOVA) revealed a highly significant genetic differentiation among groups of accessions classified based on the geographic region, country of origin, days to flowering, panicle type, and Al tolerance (p < 0.01). The high genetic differentiation between Ethiopian and Zimbabwean accessions was evident in the AMOVA, cluster, principal coordinate, and population structure analyses. The level of genetic diversity of finger millet accessions varies moderately among locations within Ethiopia, with accessions from the northern region having the lowest level. In the neighbor-joining cluster analysis, most of the improved cultivars included in this study were closely clustered, probably because they were developed using genetically less diverse germplasm and/or selected for similar traits, such as grain yield. The recombination of alleles via crossbreeding genetically distinct accessions from different regions of the two countries can potentially lead to the development of superior cultivars.

Authors/Creators:Brhane, Haftom and Brhanie Mesfin, Haftom and Haileselassie, Teklehaimanot and Tesfaye, Kassahun and Ortiz Rios, Rodomiro Octavio and Hammenhag, Cecilia and Abreha, Kibrom Berhe and Geleta, Mulatu Dida
Title:Novel GBS-Based SNP Markers for Finger Millet and Their Use in Genetic Diversity Analyses
Series Name/Journal:Frontiers in Genetics
Year of publishing :2022
Volume:13
Article number:848627
Number of Pages:17
ISSN:1664-8021
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 401 Agricultural, Forestry and Fisheries > Agricultural Science
(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 404 Agricultural Biotechnology > Genetics and Breeding
(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 404 Agricultural Biotechnology > Plant Biotechnology
Keywords:finger millet, gene diversity, genotyping-by-sequencing, single nucleotide polymorphism, tetraploid
URN:NBN:urn:nbn:se:slu:epsilon-p-116779
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-116779
Additional ID:
Type of IDID
DOI10.3389/fgene.2022.848627
Web of Science (WoS)000795053700001
ID Code:28469
Faculty:LTV - Fakulteten för landskapsarkitektur, trädgårds- och växtproduktionsvetenskap
Department:(LTJ, LTV) > Department of Plant Breeding (from 130101)
Deposited By: SLUpub Connector
Deposited On:18 Aug 2022 14:27
Metadata Last Modified:18 Aug 2022 14:31

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