Abstract
BackgroundPearl millet [Pennisetum glaucum (L.) R. Br.] is a widely cultivated drought- and high-temperature tolerant C4 cereal grown under dryland, rainfed and irrigated conditions in drought-prone regions of the tropics and sub-tropics of Africa, South Asia and the Americas. It is considered an orphan crop with relatively few genomic and genetic resources. This study was undertaken to increase the EST-based microsatellite marker and genetic resources for this crop to facilitate marker-assisted breeding.ResultsNewly developed EST-SSR markers (99), along with previously mapped EST-SSR (17), genomic SSR (53) and STS (2) markers, were used to construct linkage maps of four F7 recombinant inbred populations (RIP) based on crosses ICMB 841-P3 × 863B-P2 (RIP A), H 77/833-2 × PRLT 2/89-33 (RIP B), 81B-P6 × ICMP 451-P8 (RIP C) and PT 732B-P2 × P1449-2-P1 (RIP D). Mapped loci numbers were greatest for RIP A (104), followed by RIP B (78), RIP C (64) and RIP D (59). Total map lengths (Haldane) were 615 cM, 690 cM, 428 cM and 276 cM, respectively. A total of 176 loci detected by 171 primer pairs were mapped among the four crosses. A consensus map of 174 loci (899 cM) detected by 169 primer pairs was constructed using MergeMap to integrate the individual linkage maps. Locus order in the consensus map was well conserved for nearly all linkage groups. Eighty-nine EST-SSR marker loci from this consensus map had significant BLAST hits (top hits with e-value ≤ 1E-10) on the genome sequences of rice, foxtail millet, sorghum, maize and Brachypodium with 35, 88, 58, 48 and 38 loci, respectively.ConclusionThe consensus map developed in the present study contains the largest set of mapped SSRs reported to date for pearl millet, and represents a major consolidation of existing pearl millet genetic mapping information. This study increased numbers of mapped pearl millet SSR markers by >50%, filling important gaps in previously published SSR-based linkage maps for this species and will greatly facilitate SSR-based QTL mapping and applied marker-assisted selection programs.
Highlights
IntroductionQuantitative trait loci (QTLs) for disease resistance [6,7,8,9,10], drought tolerance [11,12,13], components of drought adaptation [14], flowering time, grain and stover yield [15], and ruminant nutritional quality of straw [16,17] have been mapped, and effective markerassisted selection for several of these traits has been demonstrated [18,19]
The raw Expressed sequence tag (EST) were cleaned of rRNA, vector, ligator and poor quality sequences, which resulted in a reduction in the average number of reads to 99 K per halfplate run, but an increase in the average read length to 224 bp
The remaining 32,124 contigs were either formed from sequence reads from a single genotype, or were formed from sequence reads from the two genotypes but were monomorphic with regard to putative Single nucleotide polymorphism (SNP) when checked in silico
Summary
Quantitative trait loci (QTLs) for disease resistance [6,7,8,9,10], drought tolerance [11,12,13], components of drought adaptation [14], flowering time, grain and stover yield [15], and ruminant nutritional quality of straw [16,17] have been mapped, and effective markerassisted selection for several of these traits has been demonstrated [18,19] These tools have already been applied for marker-assisted backcross improvement of downy mildew resistance of elite hybrid parental lines, which culminated in the 2005 release in India of pearl millet hybrid “HHB 67 Improved”, which was the first public-bred product of DNA-marker-assisted selection to be released for cultivation in that country [19,20]
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