Population structure and linkage disequilibrium of ICRISAT foxtail millet (Setaria italica (L.) P. Beauv.) core collection

M. Vetriventhan; H.D. Upadhyaya; C.R. Anandakumar; S. Senthilvel; R.K. Varshney; H.K. Parzies

doi:10.1007/s10681-013-1044-6

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Population structure and linkage disequilibrium of ICRISAT foxtail millet (Setaria italica (L.) P. Beauv.) core collection

Journal article

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Population structure and linkage disequilibrium of ICRISAT foxtail millet (Setaria italica (L.) P. Beauv.) core collection

M. Vetriventhan, H.D. Upadhyaya, C.R. Anandakumar, S. Senthilvel, R.K. Varshney and H.K. Parzies

Euphytica, Vol.196(3), pp.423-435

2014

DOI: https://doi.org/10.1007/s10681-013-1044-6

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Abstract

Use of diverse germplasm is a key factor which allows high level of resolution due to extensive recombination in the history. Therefore, population used in association mapping should posses as many phenotypes as possible. One of the methods to obtain most of the phenotypes is to construct the core collection. The ICRISAT foxtail millet core collection consisting of 155 accessions was genotyped using 72 simple sequence repeat (SSR) markers to investigate the genetic diversity, population structure and linkage disequilibrium (LD). A high degree of molecular diversity among the accessions was found, with an average of 16.69 alleles per locus. STRUCTURE analyses classify the accessions into four subpopulations (SP) based on SSR allelic diversity. The Neighbor joining clustering and the principal coordinate analysis were in accordance with the racial classification. The distribution of molecular genetic variation among and within the four SP and three races showed high degree of variability within each group, and low level of genetic distance (GD) among the groups. LD decay of <40 cM of GD in foxtail millet core collection was observed, which suggests that it could be possible to achieve resolution down to the 40 cM level. From this investigation, it is evident that the foxtail millet core collection developed at ICRISAT is very diverse and could be a valuable resource for trait association mapping, crop breeding and germplasm management.

Details

Title: Population structure and linkage disequilibrium of ICRISAT foxtail millet (Setaria italica (L.) P. Beauv.) core collection
Authors/Creators: M. Vetriventhan (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
H.D. Upadhyaya (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
C.R. Anandakumar (Author/Creator) - Tamil Nadu Agricultural University
S. Senthilvel (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
R.K. Varshney (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
H.K. Parzies (Author/Creator) - University of Hohenheim
Publication Details: Euphytica, Vol.196(3), pp.423-435
Publisher: Kluwer Academic Publishers
Identifiers: 991005542591507891
Copyright: © 2013 Springer Science+Business Media Dordrecht
Murdoch Affiliation: Murdoch University
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 3 Agriculture, Environment & Ecology; 3.4 Crop Science; 3.4.96 QTL
Web Of Science research areas: Agronomy; Horticulture; Plant Sciences
ESI research areas: Plant & Animal Science