High density linkage mapping and QTL analysis of salt tolerance-related traits using ddRAD sequencing in Indian mustard [Brassica juncea (L.) Czern & Coss]

KeyMessage: We identified QTLs for salinity tolerance in Indian mustard, paving the way for salt-tolerant mustard genotypes, enhancing crop resilience in saline environments. Soil salinity is a major abiotic stress that reduced the growth and productivity of numerous crops, including Indian mustard. Natural genetic variations in salt tolerance (ST) were observed but no QTL mapping has been done for ST related traits in Indian mustard. In this study, to identify QTLs for ST traits, 250 stabilized F7:8 recombinant inbred lines (RILs) mapping population of Indian mustard was developed from a cross CS 614–1-1–100-13 × CS 56 and evaluated them under control, and irrigated water salinity of ECiw 12 dSm−1 for two Rabi seasons 2020–21, and 2021–22 for 18 traits. Most of traits were shown normal distribution curve, indicating population suitable for QTLs identification. Genotyping-by-sequencing (GBS) using ddRAD sequencing of the population was performed and total 2506 SNPs sorted from total 2594,666 variants after discarding markers as no progeny polymorphism and not passing chi square test which cover 1127.85 cM distance on linkage map. A total of 47 QTLs associated with ST traits were identified using composite interval mapping (CIM). Out of 47 QTLs, 12 QTLs were major QTL such as: for days to 50% flowering (qDFsB07.1), days to maturity (qDMsB08.1), number of primary branches per plant (qPBRcA05.1, and qPBRsA07.1), main shoot length (qMSLsB05.1, and qMSLcB05.1), seeds per siliqua (qSPScA09.1), yield per plant (qYPPsB06.1), transpiration rate (qEsA01.1), Na+ concentration of stem (qSNasA01.1), K+ concentration of stem (qSKsB03.1), and K+ concentration of root (qRKsB01.1) was identified with SNPs. This novel research findings will facilitate QTLs/genes mapping that can be used to identify candidate gene and transfer this with marker assistant selection (MAS). [Display omitted] •ddRAD sequencing was performed and total 2506 SNPs sorted which cover 1127.85 cM distance on linkage map.•A total of 12 major QTLs associated with ST traits were identified using composite interval mapping (CIM).•Identified two QTLs for controlling MSL under both environment on same chromosome and overlapping QTLs for transpiration rate and iWUE.