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.

Deciphering Genomic Regions for High Grain Iron and Zinc Content Using Association Mapping in Pearl Millet

“…The value obtained for average gene diversity (0.35) also indicates moderate diversity in the present lines chosen for study. This value is less than that of reported in earlier studies (Nepolean et al, 2012; Tara et al, 2013; Sehgal et al, 2015). Though the highest value of gene diversity (0.73) obtained here is similar to that reported by Mariac et al (2006) (0.75) who characterized wild pearl millet genotypes for diversity studies, the average value in present study is lesser than that recorded by them (0.49 in cultivated and 0.67 in wild lines).…”

The Challenges and Opportunities Associated with Biofortification of Pearl Millet (Pennisetum glaucum) with Elevated Levels of Grain Iron and Zinc

“…A wide variety of pearl millet germplasm collections exist on a global scale, including the Pearl Millet inbred Germplasm Association Panel (PMiGAP) developed at International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India. The PMiGAP has been drawn from a core collection of 1000 pearl millet accessions, landraces and cultivars grown across three continents (Sehgal et al, 2015). ICRISAT has also developed other collections including the Iniari germplasm, which uses landraces from West Africa, which have superior grain filling abilities under terminal drought stress, larger seeds, thicker panicles, and broader leaves (Ito et al, 1999).…”

Genomic Tools in Pearl Millet Breeding for Drought Tolerance: Status and Prospects

“…A germplasm based population [pearl millet inbred germplasm association panel (PMiGAP)] has been developed in pearl millet to capture wider genetic variations of traits (Sehgal et al, 2015). A structure analysis on this systematically developed association panel from ICRISAT global collection revealed six subpopulations corresponding predominantly to pedigree or similar agronomic traits (Sehgal et al, 2015).…”

“…A structure analysis on this systematically developed association panel from ICRISAT global collection revealed six subpopulations corresponding predominantly to pedigree or similar agronomic traits (Sehgal et al, 2015). This result evidenced the importance of including different morphological forms in a molecular study for genome-wide marker discovery, QTL detection, or estimate of genomic based breeding value.…”