Sequence-tagged site-based diagnostic markers linked to a novel anthracnose resistance gene RCt1 in chili pepper (Capsicum annuum L.)
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Anthracnose, caused by Colletotrichum spp. is the most devastating disease of chili (Capsicum annuum) in the tropical and subtropical regions of the world. The present study aimed at molecular mapping and development of markers linked to a new gene for anthracnose resistance in the chili cultivar ‘Punjab Lal’. Phenotypic evaluation of F1, F2, and BC1F1 populations derived from a cross between ‘Punjab Lal’ and susceptible cultivar ‘Arka Lohit’ against a virulent isolate of C. truncatum revealed that anthracnose resistance in Punjab Lal is governed by a monogenic-dominant gene designated as RCt1. Forty-four (28 ISSRs and 16 AFLPs) out of 201 markers exhibited parental polymorphism and were used in bulk segregant analysis. Three ISSRs (ISSR411493, ISSR581485, and ISSR1121857) and one AFLP marker (E-ACA/M-CTG516) showed precise polymorphism between resistant and susceptible bulks, and were used for genotyping F2 and BC1 populations. The four putative fragments were converted into sequence-tagged site (STS) markers and southern blotting confirmed their association with the resistance locus. Molecular mapping revealed that the STS markers CtR-431 and CtR-594 were closely linked to the RCt1 locus in coupling at distances of 1.8 and 2.3 cM, respectively. Furthermore, both of these markers showed the presence of resistance-linked allele in seven genotypes including the highly resistant C. chinnese ‘PBC932’ and C. baccatum ‘PBC80’ while negatively validated in 32 susceptible genotypes. Therefore, CtR431 and CtR-594 could be recommended as efficient diagnostic markers to facilitate the introgression of RCt1 locus into susceptible chili variants towards the development of high-yielding anthracnose resistance genotypes in C. annuum background.
KeywordsCapsicum Anthracnose Colletotrichum truncatum Resistance locus ISSR AFLP STS marker
The study is funded by a research grant (FT/YS/LS-171/2013) from the Science and Engineering Research Board (SERB), Dept. Of Science and Technology (DST), Government of India. RM is grateful to SERB, DST, India for the financial support in the form of Young Scientist Fellowship. We also thank DST-FIST, Govt. of India, for the research infrastructure facilities provided to Centre of Biotechnology, Siksha O Anusandhan University.
RM and RKJ conceived and supervised the project. RM collected samples, isolated DNA, and performed molecular marker analysis and detection of linked markers. ER and JNM cloned the STS fragments and performed marker validation. RM and RKJ interpreted the data and prepared the manuscript. All authors read and approved the final manuscript.
Compliance with ethical standards
Conflict of interest
The authors have declared that there is no conflict of interest.
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