title: Exploring potential of pearl millet germplasm association panel for association mapping of drought tolerance traits.
abstract: 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.
authors.affiliation: Institute of Biological, Environmental and Biological Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, United Kingdom.
authors.forename: Deepmala
authors.initials: D
authors.lastname: Sehgal
authors.affiliation: Institute of Biological, Environmental and Biological Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, United Kingdom.
authors.forename: Leif
authors.initials: L
authors.lastname: Skot
authors.affiliation: 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.
authors.forename: Richa
authors.initials: R
authors.lastname: Singh
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Andhra Pradesh, India.
authors.forename: Rakesh Kumar
authors.initials: RK
authors.lastname: Srivastava
authors.affiliation: 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.
authors.forename: Sankar Prasad
authors.initials: SP
authors.lastname: Das
authors.affiliation: 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.
authors.forename: Jyoti
authors.initials: J
authors.lastname: Taunk
authors.affiliation: Institute of Biological, Environmental and Biological Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, United Kingdom; Central Soil Salinity Research Institute (CSSRI), Karnal, India.
authors.forename: Parbodh C
authors.initials: PC
authors.lastname: Sharma
authors.affiliation: Institute of Biological, Environmental and Biological Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, United Kingdom; National Research Centre for Orchids, Darjeeling Campus, Darjeeling, India.
authors.forename: Ram
authors.initials: R
authors.lastname: Pal
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Andhra Pradesh, India.
authors.forename: Bhasker
authors.initials: B
authors.lastname: Raj
authors.affiliation: ICRISAT Sahelian Center, BP 12404, Niamey, Niger.
authors.forename: Charles T
authors.initials: CT
authors.lastname: Hash
authors.affiliation: Institute of Biological, Environmental and Biological Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, United Kingdom.
authors.forename: Rattan S
authors.initials: RS
authors.lastname: Yadav
mesh_terms: D000103:Acetyl-CoA Carboxylase / Q000235:genetics / Q000378:metabolism; D000220:Adaptation, Biological / Q000235:genetics; D000349:Africa; D001208:Asia; D061146:Chlorophyll Binding Proteins / Q000235:genetics / Q000378:metabolism; D002874:Chromosome Mapping; D055864:Droughts; D018506:Gene Expression Regulation, Plant; D008040:Genetic Linkage; D005819:Genetic Markers; D014644:Genetic Variation; D018745:Genome, Plant; D005838:Genotype; D031782:Pennisetum / Q000235:genetics*; D010641:Phenotype; D000069600:Plant Breeding; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D000068098:Seed Bank
chemical_list: D061146:Chlorophyll Binding Proteins; D005819:Genetic Markers; D010940:Plant Proteins; D000103:Acetyl-CoA Carboxylase