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Population structure and association mapping of yield contributing agronomic traits in foxtail millet

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Association analyses accounting for population structure and relative kinship identified eight SSR markers ( p < 0.01) showing significant association ( R 2 = 18 %) with nine agronomic traits in foxtail millet.

Abstract

Association mapping is an efficient tool for identifying genes regulating complex traits. Although association mapping using genomic simple sequence repeat (SSR) markers has been successfully demonstrated in many agronomically important crops, very few reports are available on marker-trait association analysis in foxtail millet. In the present study, 184 foxtail millet accessions from diverse geographical locations were genotyped using 50 SSR markers representing the nine chromosomes of foxtail millet. The genetic diversity within these accessions was examined using a genetic distance-based and a general model-based clustering method. The model-based analysis using 50 SSR markers identified an underlying population structure comprising five sub-populations which corresponded well with distance-based groupings. The phenotyping of plants was carried out in the field for three consecutive years for 20 yield contributing agronomic traits. The linkage disequilibrium analysis considering population structure and relative kinship identified eight SSR markers (p < 0.01) on different chromosomes showing significant association (R 2 = 18 %) with nine agronomic traits. Four of these markers were associated with multiple traits. The integration of genetic and physical map information of eight SSR markers with their functional annotation revealed strong association of two markers encoding for phospholipid acyltransferase and ubiquitin carboxyl-terminal hydrolase located on the same chromosome (5) with flag leaf width and grain yield, respectively. Our findings on association mapping is the first report on Indian foxtail millet germplasm and this could be effectively applied in foxtail millet breeding to further uncover marker-trait associations with a large number of markers.

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Acknowledgments

Thanks are due to the Director, National Institute of Plant Genome Research (NIPGR), New Delhi, India for providing facilities. This work area was supported by the core grant of NIPGR. Dr. Sarika Gupta and Mr. Mehanathan Muthamilarasan acknowledge the award of DST-Young Scientist and Junior Research Fellowship from the Dept. of Science and Technology (DST) and University Grants Commission, New Delhi, respectively. We are also thankful to the National Bureau of Plant Genetic Resources, New Delhi/Hyderabad/Akola, India for providing the seed materials.

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  1. National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, JNU Campus, New Delhi, 110 067, India

    Sarika Gupta, Kajal Kumari, Mehanathan Muthamilarasan, Swarup Kumar Parida & Manoj Prasad

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  1. Sarika Gupta
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  2. Kajal Kumari
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  3. Mehanathan Muthamilarasan
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  4. Swarup Kumar Parida
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  5. Manoj Prasad
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Correspondence to Manoj Prasad.

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Communicated by A. Dhingra.

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Gupta, S., Kumari, K., Muthamilarasan, M. et al. Population structure and association mapping of yield contributing agronomic traits in foxtail millet. Plant Cell Rep 33, 881–893 (2014). https://doi.org/10.1007/s00299-014-1564-0

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