Abstract
The present study deals with genome wide identification of single-nucleotide polymorphism (SNP) markers related to powdery mildew (PM) resistance in two pepper varieties. Capsicum baccatum (PRH1- a PM resistant line) and Capsicum annuum (Saengryeg- a PM susceptible line), were resequenced to develop SNP markers. A total of 6,213,009 and 6,840,889 SNPs for PRH1 and Saengryeg respectively have been discovered. Among the SNPs, majority were classified as homozygous type SNPs, particularly in the resistant line. Moreover, the SNPs were differentially distributed among the chromosomes in both the resistant and susceptible lines. In total, 4,887,031 polymorphic SNP loci were identified between the two lines and 306,871 high-resolution melting (HRM) marker primer sets were designed. In order to understand the SNPs associated with the vital genes involved in diseases resistance and stress associated processes, chromosome-wise gene ontology analysis was performed. The results revealed the occurrence that SNPs related to diseases resistance genes were predominantly distributed in chromosome 4. In addition, 6281 SNPs associated with 46 resistance genes were identified. Among the lines, PRH1 consisted of maximum number of polymorphic SNPs related to NBS-LRR genes. The SNP markers were validated using HRM assay in 45 F4 populations and correlated with the phenotypic disease index.
Highlights
Opportunities for transcriptome assembly, functional annotation of genes, and identification of molecular markers[14,15]
The occurrence of mere levels of variations or polymorphism acts as a vital challenge during molecular marker discovery
In order to address these difficulties, generation sequencing (NGS) strategies have been widely applied in genomics based on breeding of important agricultural and horticultural crops
Summary
Opportunities for transcriptome assembly, functional annotation of genes, and identification of molecular markers[14,15]. New software tools in NGS technology enable the cost effective identification, confirmation, and evaluation of genetic markers on a large scale. Kim et al.[29] sequenced and assembled the pepper genome CM334) at a genomic size of 3.48 Gb. CM334) at a genomic size of 3.48 Gb This reference genome will provide the opportunity to improve quality, cultivation, and disease resistance in Capsicum species. The aim of this research is to discover SNP variants for future marker-assisted breeding studies related to PM resistance using Capsicum annuum cv. In the present study resequencing of two pepper varieties, Capsicum baccatum (PRH1- PM resistant line) and Capsicum annuum (Saengryeg - PM susceptible line), using the HiSeq. 4000 Illumina platform and the genome wide identification of SNPs have been implemented
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