Integrating marker assisted background analysis with foreground selection for identification of superior bacterial blight resistant recombinants in Basmati rice

Basmati rice is highly susceptible to bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae. Transfer of BB resistance genes from non-Basmati sources to Basmati through cross-hybridization requires strict monitoring for recovery of the desirable Basmati quality traits in the recombinants, which show complex inheritance pattern. We integrated background analysis using mapped microsatellite markers with foreground selection to identify superior lines that combine useful genes from a non-Basmati BB resistance donor line IRBB55 with grain and cooking quality characteristics of the popular Basmati rice variety 'Pusa Basmati 1' (PB 1) employing backcross pedigree strategy. Foreground selection using linked markers ensured presence of two genes, xa13 and Xa21 for BB resistance from IRBB55, and the recurrent parent PB I allele for the waxy locus giving intermediate amylose content and maintainer allele at fertility restorer locus in the BC1F5 recombinants. Background analysis enabled selection of recombinants with recurrent parent genome to the extent of 86.3% along with the quality traits. The extent of introgression of non-Basmati donor chromosome segments in the superior selections was estimated to be < 7 8 Mb and < 6.7 Mb in the xa13 and Xa21 linked genomic regions, respectively. Association mapping identified three quantitative trait loci, one each for 1000-grain weight, fertile grains/panicle and cooked kernel length. The backcross-pedigree breeding strategy facilitated recovery of additional desirable characteristics from the donor in some of the selections. The elite selection Pusa 1460-01-32-6-7-67 with maximum genomic background and quality characteristics of the recurrent Basmati parent gave resistance reaction against BB, similar to that of the non-Basmati resistant check variety and recorded an yield advantage of 11.9% over the best check in the multiplication agronomic trial in the Basmati growing region of India. This line, which has been released as a new variety in the name of 'Improved Pusa Basmati 1' for commercial cultivation in India, is an example of successful application of marker assisted selection to variety development.