Development of SCAR marker associated with downy mildew disease resistance in pearl millet (Pennisetum glaucum L.)

Pearl Millet is an important crop coarse grain cereal crop in the semi arid tropics which is extremely susceptible to oomycete plant pathogen Sclerospora graminicola causing downy mildew (DM) disease. The aim of the current study is to breed resistance against downy mildew disease into high yielding cultivars of pearl millet. Hence, in the present work a sequence characterized amplified region (SCAR) marker was developed as a molecular screening tool to identify DM resistance source and presented here. Of the 27 inter simple sequence repeats (ISSR) decamer primers used to identify polymorphism amongst pearl millet genotypes ICMR-01007 (P1) and ICMR-01004 (P2) and their populations (F1 and F2), only one primer pair ISSR-22 produced polymorphic bands on ICMR-01004 producing 1.4 kb size. The PCR amplification of 1.4 kb band was found tightly linked to the resistant line of ICMR-01004 and also in F2 segregation population was in the ratio 3:1. This band was cloned, sequenced and candidate SCAR primer (SCAR ISSR 863 ) was designed. Segregant analysis of their F2 progeny revealed that the SCAR ISSR 863 marker was linked to downy mildew resistance linkage group (χ(2) 3:1 = 0.86, P = 0.22) with a genetic distance of 0.72 cM. This SCAR marker was further validated using diverse pearl millet lines of India and Africa. Results indicated that the SCAR ISSR 863 band was amplified in all the seven resistant lines and were absent in five susceptible lines. The confirmation of the ISSR-derived SCAR marker in different genetic backgrounds of pearl millet lines suggests that this marker can be exploited for DM resistance screening in pearl millet breeding programs.