Identification and characterisation of quantitative trait loci linked with tolenrance to saline-alkaline stress at germination stage in indica rice (oryza sativa L.)

Abstract

As the direct seeding of rice is getting popular, the farmers have shifted from traditional transplantation method to direct seeding method. The problem with this method however is the direct exposure of seeds to abiotic stresses that affect crop establishment. Studies have not been conducted so far to improve the germination tolerance in saline-alkaline conditions. Therefore, the present study was conducted to perform the genomic analysis of tolerance to saline-alkaline stress at germination stage in rice. Parental varieties Pokkali and Pak Basmati were selected out of six rice varieties on the basis of their performance in saline-alkaline conditions. A mapping population (F2:3) was constructed using Pokkali as tolerant and Pak Basmati as sensitive parent. Germination parameters such as final germination percentage (FGP), germination value (GV), germination energy (GE), germination velocity (GVe), speed of germination (SG), peak value (PV), germination capacity (GC), germination index (GI) and mean germination time (MGT) while growth parameters like germination vigour index (GVI), shoot length (SL), root length (RL) and total dry biomass (DBM) were recorded. Parental varieties were optimised for salinealkaline stress limits. Phenotyping of F3 progenies was conducted with the salinealkaline limits (pH8/15 dS.m-1) optimised in parental varieties. Correlation studies show that germination and growth parameters are positively correlated. It was also found that growth parameters were affected more than germination parameters. The genotypic data of 129 F2 plants for 84 polymorphic markers was used to construct molecular linkage map, with an average interval size of 7.63cM with four gaps of ≤ 40cM and the total length of 3435.5cM. Quantitative Trait Loci (QTL) Cartographer was used for genomic analysis using three mapping techniques i.e. simple interval mapping (SIM), composite interval mapping (CIM) and multiple interval mapping (MIM). Thirty-three QTLs (17 major and 16 minor) were identified using SIM. Forty QTLs (14 major and 26 minor) were identified by CIM. Sixty QTLs were identified using MIM technique. The parental varieties used in this study are potential candidates for abiotic stress studies. These findings would be beneficial in rice breeding programs to develop tolerant cultivars for the saline-alkaline environment through marker assisted selection.