Genetics and molecular mapping of a novel purple blotch-resistant gene ApR1 in onion (Allium cepa L.) using STS and SSR markers

Abstract

Purple blotch (PB), caused by Alternaria porri (Ellis) Cifferi is the most devastating foliar disease of onion worldwide. However, no attempt has been made so far to detect or map a PB-resistant locus in the onion genome. The present investigation was performed to study the inheritance and develop molecular markers linked to PB resistance by using F1, F2, and BC1 populations developed from a cross between the PB-resistant onion cultivar ‘Arka Kalyan’ and the susceptible parent ‘Agrifound Rose’. Disease evaluation with a virulent isolate of A. porri revealed that the F1 was resistant while 498 F2 plants segregated in a 3:1 resistant (R) to susceptible (S) phenotypic ratio and 128 BC1 lines segregated in 1R:1S ratio, suggesting that the PB resistance is controlled by a single dominant gene designated as ApR1. Out of 288 ISSRs and SSRs primer sets, 59 distinguished the two parental lines and were used in bulk segregant analysis to link them with the presumed ApR1 gene. Seven markers viz. 3 ISSRs (AcISSR471257, AcISSR681600, and AcISSR1031416) and four SSRs (AcSSR7, AcSSR22, AcSSR31, and AcSSR33) showed specific polymorphism between resistant and susceptible bulks and were used for genotyping F2 and BC1 mapping populations. The three ISSR fragments were converted into sequence-tagged markers, and southern blotting confirmed their association with the resistant locus and the single-copy status. Molecular mapping revealed that the SSR marker AcSSR7 and STS marker ApR-450 were closely linked to the ApR1 locus in coupling at distances of 1.3 and 1.1 cM, respectively. Further, both of these markers could not be amplified in 23 susceptible onion genotypes with different genetic backgrounds. This is the first report of identification of markers linked to PB-resistant locus in onion. Hence, SSR marker AcSSR7 and STS marker ApR-450 identified in this study could be recommended for facilitating the introgression of ApR1 into susceptible onion variants for the development of high yielding PB-resistant genotypes.