Screening for resistance and genetic population structure associated with Phytophthora capsici-pepper root and crown rot

Pepper, Capsicum spp. (Solanaceae) is one of the vegetable crops with significant and multiple roles in human diet, as a vegetable, spice, food colorant and ornamental purposes worldwide. Pepper root and crown rot (RCR), and or Phytophthora-blight caused by Phytophthora capsici (Oomycetes) is one of the most destructive diseases of Capsicum species globally. To this aim, we screened 37 pepper-accessions for resistance to RCR, P. capsici and characterized their population-genetic-diversity using 21 Inter-Simple-Sequence-Repeats-(ISSR) primer-pairs, and 27 morphological-attributes. Of which, five accessions; including three-ornamental; 11BlockyP-YToran, 19OrnP-PBI, 23CherryP-Orsh, and two-longs; 32OrnP-China, 37ChilP-Paleo were resistant to RCR with the least-infection-rates, RCR <10%. To estimate the genetic-distance, based on morphological-attributes, we used simple-matching, Jaccard and Dice-similarity-coefficient-(SC), following clustering by UPGMA, and also Cophenetic-coefficient and correlation between similarity-matrices. Similarity-coefficient among genotypes was 0.26–0.93, revealed significant differences among five distinct pepper groups, predominantly in size, color, and shape of leaf and fruit. Genetic-similarity was determined by simple-matching-coefficient-(SSM), and dendrogram was constructed by clustering-analysis with un-weighted-pair-groups using arithmetic-averages-(UPGMA), showed the presence of high genetic-variability among the peppers, and assembled the peppers into five distinct genetic groups. According to ISSR analysis, the highest-resolving-power, (Rp) (≥0.77), and heterozygosity-values, Hv (≥0.26) was recorded accordingly. 19 out of 21-primers produced polymorphism, of which MBP-7, MBP -14 and MBP-18 primers (0.499) had the best performance in genetic-diversity of the related pepper population, respectively. The ISSR-assay generated 188-bands, of which 185-bands were polymorphic. Polymorphism-mean-percentage-(P%) varied from 78% to 100% with a mean of 98.5%, and an average of 9.9 bands per primer. Average polymorphism-information-content-(PIC) was 0.449, and matrix-index 4.29. Association between genotypic-phenotypic-traits-(r-0.346**), phenotypic-RCR-resistance-(r = 0.197**), and RCR-resistance-ISSR (r-0.029**) was significant, respectively. There was also a high correlation between RCR resistance and some morphological-attributes, such as node anthocyanin-pigment and its intensity (r = 0.251**), node-woolly (r = 0.255**), fruit-shape (r = 0.273**), exocarp-wavy in fruit-base-(r = 0.208**), and hollow-depth-(r = 0.358**). The genetic markers revealed much genetic variation that can be used both in genotyping and in selecting appropriate breeding strategies against P. capsici, given the documented correlations between disease resistance and certain morphological and genotyping traits.