PMID- 25970600 OWN - NLM STAT- MEDLINE DCOM- 20160414 LR - 20240326 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 10 IP - 5 DP - 2015 TI - Exploring potential of pearl millet germplasm association panel for association mapping of drought tolerance traits. PG - e0122165 LID - 10.1371/journal.pone.0122165 [doi] LID - e0122165 AB - A pearl millet inbred germplasm association panel (PMiGAP) comprising 250 inbred lines, representative of cultivated germplasm from Africa and Asia, elite improved open-pollinated cultivars, hybrid parental inbreds and inbred mapping population parents, was recently established. This study presents the first report of genetic diversity in PMiGAP and its exploitation for association mapping of drought tolerance traits. For diversity and genetic structure analysis, PMiGAP was genotyped with 37 SSR and CISP markers representing all seven linkage groups. For association analysis, it was phenotyped for yield and yield components and morpho-physiological traits under both well-watered and drought conditions, and genotyped with SNPs and InDels from seventeen genes underlying a major validated drought tolerance (DT) QTL. The average gene diversity in PMiGAP was 0.54. The STRUCTURE analysis revealed six subpopulations within PMiGAP. Significant associations were obtained for 22 SNPs and 3 InDels from 13 genes under different treatments. Seven SNPs associations from 5 genes were common under irrigated and one of the drought stress treatments. Most significantly, an important SNP in putative acetyl CoA carboxylase gene showed constitutive association with grain yield, grain harvest index and panicle yield under all treatments. An InDel in putative chlorophyll a/b binding protein gene was significantly associated with both stay-green and grain yield traits under drought stress. This can be used as a functional marker for selecting high yielding genotypes with 'stay green' phenotype under drought stress. The present study identified useful marker-trait associations of important agronomics traits under irrigated and drought stress conditions with genes underlying a major validated DT-QTL in pearl millet. Results suggest that PMiGAP is a useful panel for association mapping. Expression patterns of genes also shed light on some physiological mechanisms underlying pearl millet drought tolerance. FAU - Sehgal, Deepmala AU - Sehgal D AD - Institute of Biological, Environmental and Biological Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, United Kingdom. FAU - Skot, Leif AU - Skot L AD - Institute of Biological, Environmental and Biological Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, United Kingdom. FAU - Singh, Richa AU - Singh R AD - Institute of Biological, Environmental and Biological Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, United Kingdom; Chaudhary Charan Singh Haryana Agricultural University (CCSHAU), Department of Molecular Biology and Biotechnology, Hisar, Haryana, India. FAU - Srivastava, Rakesh Kumar AU - Srivastava RK AD - International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Andhra Pradesh, India. FAU - Das, Sankar Prasad AU - Das SP AD - Institute of Biological, Environmental and Biological Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, United Kingdom; ICAR Research Complex for NEH Region, Tripura Centre, Lembucherra, India. FAU - Taunk, Jyoti AU - Taunk J AD - Institute of Biological, Environmental and Biological Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, United Kingdom; Chaudhary Charan Singh Haryana Agricultural University (CCSHAU), Department of Molecular Biology and Biotechnology, Hisar, Haryana, India. FAU - Sharma, Parbodh C AU - Sharma PC AD - Institute of Biological, Environmental and Biological Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, United Kingdom; Central Soil Salinity Research Institute (CSSRI), Karnal, India. FAU - Pal, Ram AU - Pal R AD - Institute of Biological, Environmental and Biological Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, United Kingdom; National Research Centre for Orchids, Darjeeling Campus, Darjeeling, India. FAU - Raj, Bhasker AU - Raj B AD - International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Andhra Pradesh, India. FAU - Hash, Charles T AU - Hash CT AD - ICRISAT Sahelian Center, BP 12404, Niamey, Niger. FAU - Yadav, Rattan S AU - Yadav RS AD - Institute of Biological, Environmental and Biological Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, United Kingdom. LA - eng GR - BB/F004133/1/Biotechnology and Biological Sciences Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20150513 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Chlorophyll Binding Proteins) RN - 0 (Genetic Markers) RN - 0 (Plant Proteins) RN - EC 6.4.1.2 (Acetyl-CoA Carboxylase) SB - IM MH - Acetyl-CoA Carboxylase/genetics/metabolism MH - Adaptation, Biological/genetics MH - Africa MH - Asia MH - Chlorophyll Binding Proteins/genetics/metabolism MH - Chromosome Mapping MH - Droughts MH - *Gene Expression Regulation, Plant MH - Genetic Linkage MH - Genetic Markers MH - Genetic Variation MH - *Genome, Plant MH - Genotype MH - Pennisetum/*genetics MH - Phenotype MH - Plant Breeding MH - Plant Proteins/*genetics/metabolism MH - Polymorphism, Single Nucleotide MH - *Quantitative Trait Loci MH - Seed Bank PMC - PMC4430295 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2015/05/15 06:00 MHDA- 2016/04/15 06:00 PMCR- 2015/05/13 CRDT- 2015/05/14 06:00 PHST- 2014/11/10 00:00 [received] PHST- 2015/02/07 00:00 [accepted] PHST- 2015/05/14 06:00 [entrez] PHST- 2015/05/15 06:00 [pubmed] PHST- 2016/04/15 06:00 [medline] PHST- 2015/05/13 00:00 [pmc-release] AID - PONE-D-14-46905 [pii] AID - 10.1371/journal.pone.0122165 [doi] PST - epublish SO - PLoS One. 2015 May 13;10(5):e0122165. doi: 10.1371/journal.pone.0122165. eCollection 2015.