Development of EST resources in pearl millet and their use in development and mapping of EST-SSRs in four RIL populations
Rajaram, V.
Development of EST resources in pearl millet and their use in development and mapping of EST-SSRs in four RIL populations - 2010 - 1 page
Elite pearl millet inbreds ICMB 841-P3 and 863B-P2 (RIL population parents differing for drought and salinity tolerance, downy mildew and blast resistance, and stover and grain quality) were drought stressed at boot-leaf stage using a standard dry-down protocol. Total RNA extracted separately from stressed root and leaf tissues of each inbred was used for cDNA synthesis. 454-sequencing of cDNAs yielded raw EST sequences that were cleaned and assembled using the PLANTTA pipeline. A total of 112,864 unigenes were obtained from the four cDNA samples. A total of 5,800 SNPs from 2,146 contigs were identified between the two parents. Similarly, 499 sequences containing class I SSRs were identified from the unigenes and from these 236 non-redundant EST-SSR primer pairs were designed. PCR products from 139 amplifying EST-SSR primer pairs and parental DNA of crosses ICMB 841-P3 x 863B-P2, H 77/833-2 x PRLT 2/89-33, 81B-P6 x ICMP 451-P8 and PT 732B-P2 x P1449-2-P1 were screened for polymorphism. >50 new EST-SSR markers were mapped for each mapping population and a consensus map developed. These four EST-SSR skeleton-mapped RIL populations have been phenotyped for grain Fe and Zn concentration, salinity tolerance, canopy conductance, downy mildew reaction, rust reaction, and/or blast reaction, and QTLs with closely flanking EST-SSR markers were detected for each of these traits. This study increases the number of mapped pearl millet SSRs by >40%, filling gaps in the earlier linkage maps, and will facilitate SSR-based marker-assisted foreground selection in parts of the pearl millet genome where this was not previously possible.
English
Development of EST resources in pearl millet and their use in development and mapping of EST-SSRs in four RIL populations - 2010 - 1 page
Elite pearl millet inbreds ICMB 841-P3 and 863B-P2 (RIL population parents differing for drought and salinity tolerance, downy mildew and blast resistance, and stover and grain quality) were drought stressed at boot-leaf stage using a standard dry-down protocol. Total RNA extracted separately from stressed root and leaf tissues of each inbred was used for cDNA synthesis. 454-sequencing of cDNAs yielded raw EST sequences that were cleaned and assembled using the PLANTTA pipeline. A total of 112,864 unigenes were obtained from the four cDNA samples. A total of 5,800 SNPs from 2,146 contigs were identified between the two parents. Similarly, 499 sequences containing class I SSRs were identified from the unigenes and from these 236 non-redundant EST-SSR primer pairs were designed. PCR products from 139 amplifying EST-SSR primer pairs and parental DNA of crosses ICMB 841-P3 x 863B-P2, H 77/833-2 x PRLT 2/89-33, 81B-P6 x ICMP 451-P8 and PT 732B-P2 x P1449-2-P1 were screened for polymorphism. >50 new EST-SSR markers were mapped for each mapping population and a consensus map developed. These four EST-SSR skeleton-mapped RIL populations have been phenotyped for grain Fe and Zn concentration, salinity tolerance, canopy conductance, downy mildew reaction, rust reaction, and/or blast reaction, and QTLs with closely flanking EST-SSR markers were detected for each of these traits. This study increases the number of mapped pearl millet SSRs by >40%, filling gaps in the earlier linkage maps, and will facilitate SSR-based marker-assisted foreground selection in parts of the pearl millet genome where this was not previously possible.
English