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

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 using GBS sequencing, 250 stabilized F7:8 recombinant inbred lines (RILs) mapping population of Indian mustard was developed from a cross CS 614-1-1-100-13 and CS 56 (parents) and evaluated them under control, and irrigated water salinity of EC 12 dSm-1 for two Rabi seasons for 18 traits. Most of traits were shown normal distribution curve, indicating population suitable for QTLs identification. Genotyping-by-sequencing (GBS) of the population was performed and total 2506 SNPs sorted 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 (qDTFsB07.1), days to maturity (qDTMsB08.1), number of primary branches per plant (qPBPcA05.1, and qPBPsA07.1), main shoot length (qMSLsB05.1, and qMSLcB05.1), seeds per siliqua (qSPScA09.1), yield per plant (qYPsB06.1), transpiration rate (qTRsA01.1), Na+ concentration of stem (qNCSsA01.1), K+ concentration of stem (qKCSsB03.1), and K+ concentration of root (qKCRsB01.1) 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).