Developing an enriched wheat 2A chromosome map and mapping of Adult plant stripe rust resistance gene
Diploid A genome wheat species harbor immense genetic variability which has been targeted and proven useful in wheat crop improvement. Further, the development and deployment of sequence based markers in wheat using survey sequences from next generation sequencing has opened avenues for comparative analysis, gene transfer and marker assisted selection (MAS) using high throughput cost effective genotyping techniques. Chromosome 2A of wheat is known to harbor several economically important genes. The present study aimed at in silico identification of genes corresponding to full length cDNAs and mining of SSRs and ISBPs from 2A draft sequence assembly of Chinese Spring for marker development. In totality, 1029 primer pairs (478 gene based, 501 SSRs and 50 ISBPs) were used to screen for polymorphism in diploid A genome species i.e., T. monococcum and T. boeoticum that identified 221 polymorphic loci. Out of these, 119 markers were mapped in T. monococcum X T. boeoticum RIL population. The enriched 2A genetic map constituted 161 mapped markers with final map length of 549.6 cM. Further, the utility of this enriched genetic map was demonstrated towards the fine mapping of adult plant resistance (APR) QTL, QYrtm.pau-2A against stripe rust. Using composite interval mapping, a QTL was detected between G45 and G54 markers explaining 19% of phenotypic variance. The primer sequences of the two genic markers were used to find the scaffold of 343 kb from IWGSC WGA V0.4 data. Thirty five simple sequence repeat markers were designed from the scaffold sequence which are being used for the fine mapping of QYrtm.pau-2A.