QTL Mapping and Expression Analysis of Candidate Genes for Salt and Drought Tolerance in Corchorus capsularis Seedlings

Jute is an essential fibrous crop worldwide. However, salt- and drought-induced stresses affect its production. The complex inheritance for such traits makes Quantitative Trait Loci (QTL) detection cumbersome when using the approach to understand and improve the plant’s tolerance to these stresses. There is a need to identify the underlying mechanistic events under these stress conditions at the seedling stage. Therefore, this study uses genetic and transcriptomic approaches to identify the markers, QTL and candidate genes related to salt and drought tolerance in jute. We also analyzed some phenotypes, including dry root weight (DRW), dry shoot weight (DSW), root fresh weight (RFW), root length (RL), relative water content (RWC), shoot fresh weight (SFW) and Shoot length (SL). One hundred (100) recombinant inbred lines (RILs) of the white Jute and the parents were evaluated under control, salt and drought conditions. Analysis of variance indicates significant differences (p < 0.01) among the RILs, and the estimates of broad-sense heritability of the RILs ranges from 50.0 to 98.5%. Two QTL for RL and SL under drought (qRLD-1–1 and qSLD-1–1, respectively) were found in the same position and associated with the flanking markers Marker5166 and Marker7753. Moreover, qRWCS-1–1 for the relative water content under salt treatment had the highest Phenotypic Variation Explained (PVE, 24.63%) with the flanking markers Marker19007 and Marker28120. Our results suggest that these genes regulate the two stresses at the seedling stage in Corchorus capsularis and function in different pathways. However, further study is needed to validate this. Higher additive effects were observed in sodium chloride (NaCl)-induced stress which suggest that salt stress selection would be more effective and useful at the seedling stage. The relative expression analysis of the candidate genes and the phenotypes of the samples reveal that CCACVL1_12635 and CCACVL1_15402, and CCACVL1_23216 genes are the salt and drought tolerance candidate genes, respectively, and function in the cystatin and potassium ion transporter 1 (KT1) pathways.