Genome-Wide Assessment of Population Structure and Genetic Diversity of the Global Finger Millet Germplasm Panel Conserved at the ICRISAT Genebank

Backiyalakshmi, C and Vetriventhan, M and Deshpande, S P and Babu, C and Allan, V and Naresh, D and Gupta, R and Azevedo, V C R (2021) Genome-Wide Assessment of Population Structure and Genetic Diversity of the Global Finger Millet Germplasm Panel Conserved at the ICRISAT Genebank. Frontiers in Plant Science (TSI), 12. pp. 1-12. ISSN 1664-462X

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Abstract

Finger millet [Eleusine coracana (L.) Gaertn.] is an important climate-resilient nutrient-dense crop grown as a staple food grain in Asia and Africa. Utilizing the full potential of the crop mainly depends on an in-depth exploration of the vast diversity in its germplasm. In this study, the global finger millet germplasm diversity panel of 314 accessions was genotyped, using the DArTseq approach to assess genetic diversity and population structure. We obtained 33,884 high-quality single nucleotide polymorphism (SNP) markers on 306 accessions after filtering. Finger millet germplasm showed considerable genetic diversity, and the mean polymorphic information content, gene diversity, and Shannon Index were 0.110, 0.114, and 0.194, respectively. The average genetic distance of the entire set was 0.301 (range 0.040 – 0.450). The accessions of the race elongata (0.326) showed the highest average genetic distance, and the least was in the race plana (0.275); and higher genetic divergence was observed between elongata and vulgaris (0.320), while the least was between compacta and plana (0.281). An average, landrace accessions had higher gene diversity (0.144) and genetic distance (0.299) than the breeding lines (0.117 and 0.267, respectively). A similar average gene diversity was observed in the accessions of Asia (0.132) and Africa (0.129), but Asia had slightly higher genetic distance (0.286) than African accessions (0.276), and the distance between these two regions was 0.327. This was also confirmed by a model-based STRUCTURE analysis, genetic distance-based clustering, and principal coordinate analysis, which revealed two major populations representing Asia and Africa. Analysis of molecular variance suggests that the significant population differentiation was mainly due to within individuals between regions or between populations while races had a negligible impact on population structure. Finger millet diversity is structured based on a geographical region of origin, while the racial structure made negligible contribution to population structure. The information generated from this study can provide greater insights into the population structure and genetic diversity within and among regions and races, and an understanding of genomic-assisted finger millet improvement.

Item Type:	Article
Divisions:	Genebank RP-Dryland Cereals
CRP:	CGIAR Research Program on Grain Legumes and Dryland Cereals (GLDC)
Uncontrolled Keywords:	finger millet, germplasm, genetic diversity, population structure, DArTseq, Analysis of molecular variance (AMOVA)
Subjects:	Mandate crops > Millets > Finger Millet Others > Germplasm
Depositing User:	Mr Nagaraju T
Date Deposited:	12 Jul 2024 09:11
Last Modified:	12 Jul 2024 09:11
URI:	http://oar.icrisat.org/id/eprint/12769
Official URL:	https://www.frontiersin.org/journals/plant-science...
Projects:	Genomics-Assisted Breeding for High Yielding and Climate-Resilient Finger Millet (ragi) Varieties/Hybrids and Promotion of Best Suitable Cultivars for Food and Nutritional Security in the Karnataka State of India
Funders:	Department of Agriculture, Government of Karnataka, CGIAR genebank platform, Crop Trust
Acknowledgement:	The authors are grateful to Mr. Ramesh Reddy, Mr. Shanku Reddy, Mr. Raju Jadhav, and Mr. Manish Reddy for their help in field trials and also acknowledge Intertek India Private Limited for their help in genomics work.
Links:	Google Scholar

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