Genome-wide assessment of genetic diversity and association mapping for salt tolerance traits in okra (Abelmoschus esculentus L. Moench) using genotyping-by-sequencing

Abstract

Okra is a vegetable that is widely grown worldwide. However, there are few reports on genetic diversity analysis and genome-wide association studies (GWASs) based on large-scale molecular markers in okra. In this study, 353,001 SNP markers were developed based on a genotyping by sequencing (GBS) strategy to analyze the population structure, genetic diversity and GWAS of 180 okra germplasms from all over the world. Both phylogenetic tree and population structure analyses classified all accessions into three categories, and the classification of most accessions in the two methods were the same. Some okra accessions from warm and cool areas were classified into one category, and some from hot areas were classified into one category. The Shannon‒Wiener index (I), Nei's genetic diversity index (Hei), minor allele frequency (MAF) and polymorphic information content (PIC) of the 180 okra accessions were 0.5071, 0.3366, 0.2580 and 0.2691, respectively. The B subgroup had the highest level of genetic diversity. A total of 180 okra seedlings were treated with 120 mM (T1) and 200 mM (T2) NaCl solutions, and salt tolerance-related traits were analyzed by GWAS. Seventy-seven SNP loci were identified to be associated with four salt tolerance traits. c3341.graph_c0 was aligned in multiple SNP loci, which may be an important unigene regulating the salt tolerance of okra seedlings. To our knowledge, this was the first study to use large-scale SNP markers to carry out population genetic analysis and GWAS in okra.