Integration of gene-based markers in a pearl millet genetic map for identification of candidate genes underlying drought tolerance quantitative trait loci

Abstract

Background: Identification of genes underlying drought tolerance (DT) quantitative trait loci (QTLs) will facilitate understanding of molecular mechanisms of drought tolerance, and also will accelerate genetic improvement of pearl millet through marker-assisted selection. We report a map based on genes with assigned functional roles in plant adaptation to drought and other abiotic stresses and demonstrate its use in identifying candidate genes underlying a major DT-QTL.

Results: Seventy five single nucleotide polymorphism (SNP) and conserved intron spanning primer (CISP) markers were developed from available expressed sequence tags (ESTs) using four genotypes, H 77/833-2, PRLT 2/89-33, ICMR 01029 and ICMR 01004, representing parents of two mapping populations. A total of 228 SNPs were obtained from 30.5 kb sequenced region resulting in a SNP frequency of 1/134 bp. The positions of major pearl millet linkage group (LG) 2 DT-QTLs (reported from crosses H 77/833-2 × PRLT 2/89-33 and 841B × 863B) were added to the present consensus function map which identified 18 genes, coding for PSI reaction center subunit III, PHYC, actin, alanine glyoxylate aminotransferase, uridylate kinase, acyl-CoA oxidase, dipeptidyl peptidase IV, MADS-box, serine/threonine protein kinase, ubiquitin conjugating enzyme, zinc finger C- × 8-C × 5-C × 3-H type, Hd3, acetyl CoA carboxylase, chlorophyll a/b binding protein, photolyase, protein phosphatase1 regulatory subunit SDS22 and two hypothetical proteins, co-mapping in this DT-QTL interval. Many of these candidate genes were found to have significant association with QTLs of grain yield, flowering time and leaf rolling under drought stress conditions.

Conclusions: We have exploited available pearl millet EST sequences to generate a mapped resource of seventy five new gene-based markers for pearl millet and demonstrated its use in identifying candidate genes underlying a major DT-QTL in this species. The reported gene-based markers represent an important resource for identification of candidate genes for other mapped abiotic stress QTLs in pearl millet. They also provide a resource for initiating association studies using candidate genes and also for comparing the structure and function of distantly related plant genomes such as other Poaceae members.

Figure 1

Pearl millet consensus function map based on gene-based SNPs, CISPs and EST-SSRs. Distances are given in Haldane cM on the left side of each linkage bar. Candidate genes integrated as SNP and CISP markers are shown as underlined. Major QTLs of drought tolerance added onto the consensus map from Yadav et al. [4,5] and Bidinger et al. [9] are indicated as hatched boxes on the right side of LG2. Six SNP markers, Xibmsp60, Xibmsp34, Xibmsp14, Xibmsp24, Xibmsp11 and Xibmsp31, showed complete linkage on LG2. Similarly, on LG3 three pairs of SNP loci Xibmsp46 and Xibmsp33, Xibmsp35 and Xibmsp30, and Xibmsp41 and Xibmsp28 showed complete linkage. On LG5, the SNP markers Xibmsp13 and Xibmsp16 were completely linked. Complete linkage between gene-based SNPs and framework markers was observed on LG3 (Xibmsp1 and Xipes0166), LG4 (Xibmsp32, Xibmsp10 and Xicmp3029), LG5 (Xicmp3027 and Xibmsp49, and Xpsmp2078 and Xibmsp47) and LG6 (Xibmsp8 and Xipes0176). In agreement with the previous studies [6], genomic SSR marker Xpsmp2086 showed weak linkage and/or aberrant behaviour i.e. tripled the length of LG4 when incorporated based on its expected position (shown as dashed line in Figure 1). Four CISP markers, Xibmcp5, Xibmcp6, Xibmcp7 and Xibmcp12, and two SNP markers Xibmsp20 and Xibmsp56 remained ungrouped.