Bulk segregant analysis for blast resistance in F2 population derived from two contrasting rice genotypes of north eastern hill region
Loading...
Date
2018
Authors
Journal Title
Journal ISSN
Volume Title
Publisher
College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University, Imphal
Abstract
Rice blast caused by fungus Magnaporthe grisea is one of the most devastating diseases worldwide. Use of resistant cultivar is the most effective way to control this disease. The identification of markers linked to blast resistance is very important as they can be used in marker assisted selection to develop new resistant cultivars. Bulk Segregant Analysis (BSA) is a method that works with selected individuals which hastens the process by reducing the number of required assays, providing rapid and simple alternative for identification of markers linked to a trait and gene mapping. The present study used this technique to select extreme phenotypes in a bi-parental population (F2) derived from two contrasting rice genotype LR5, also known as Lal Jangali (a local landrace of rice resistant to blast) and LR26 (Manipuri black rice traditionally known as Chakhao, susceptible to blast). Disease assessment for blast on progenies and parental genotype was carried out under natural disease occurrence. F2 progenies showing extreme phenotype were selected and subjected to genotyping with the polymorphic markers (including SSRs and SNPs and some previously reported blast markers) obtained from polymorphism survey on the parental genotype in order to identify markers linked to blast resistance. Association of the markers with phenotypic trait in the selected progenies was identified by statistical analysis. Chi square test for goodness of fit revealed that RM1337 (p-value=0.003, 0.002), RM7102 (p-value=0.002, 0.001), snpOS0310 (p-value=0.02, 0.007), snpOS0316 (p-value=0.001, 0) and snpOS0318 (p-value=0.002, 0.001) showed association with tolerance and susceptibility against leaf blast, whereas RM247 (p-value=0.025, 0.016) and snpOS0316 (p-value=0.0.05, 0.004) showed association with these two groups for neck blast. Except for snpOS0310 which is on chromosome 6, all other markers are present on chromosome 12. RM1337 and RM7102 co-localize with already reported Pi20t gene, suggesting its role in resistance to local pathotypes. Regression for blast resistance was also evaluated to estimate the relationship between the marker genotype and blast severity. Population structure analysis was also performed on the selected group of progenies to determine the ancestry, which revealed that the progenies showing resistance to both leaf and neck blast carried maximum percentage of ancestry from the resistant parent LR5 and those susceptible to blast carried more of LR26 ancestry. Larger population and more polymorphic markers can be used to further fine map the segment of chromosome 12 identified in this study.