Characterization of a Bangladeshi rice landrace Horkuch as a suitable donor for salinity tolerance traits for development of new salt tolerant rice cultivars

Abstract

Bangladesh is a low-lying developing country adversely affected by climate change with its coastal area under constant threat of hazards like floods, cyclones, high temperature, sea level rise, salinity intrusion, etc. The rice landrace Horkuch (Oryza sativa) is adapted to the saline conditions in the southern coast of Bangladesh and maintains efficient photosynthesis and detoxification under salt stress, but is low yielding. Therefore, this study was aimed to find the QTLs responsible for the salinity tolerance of Horkuch. A cross was made from salt tolerant Horkuch and high yielding but sensitive IR29. A set of the F2:3 population containing 200 individuals was genotyped using DArTseq™ for discovering over 4000 polymorphic SNP markers. 200 F3 progenies were phenotyped under salt stress at seedling stage and 100 selected high and low tails from the seedling stage screening were phenotyped at reproductive stage. A linkage map was generated from the polymorphic SNPs identified. The total length of linkage map was 2257 cM, with each chromosome varying from 128.8 cM to 241 cM. Average distance between adjacent markers on each chromosome was 8.11 cM. Linkage map construction was followed by identification of multiple novel QTLs. QTLs for root length, total chlorophyll, potassium content and sodium content at seedling stage as well as spikelet fertility, days to flowering, thousand grain weight, plant height and yield, all under stress, were identified at the reproductive stage. A robust QTL associated with total chlorophyll was detected at position 157.47 cM on chromosome 7, with a LOD score of 5.44. It explained 14.25% of the total phenotypic variance. The donor of the allele was Horkuch, the salt tolerant parent. Six QTLs were also detected for root length, of which three were major and three were putative QTLs. Two QTLs were identified for stomatal conductance on chromosome 4 and 5, showing a large effect on stomatal conductance explaining 13.1% and 20.5% of the total phenotypic variance, respectively. A robust QTL associated with primary branching was detected at position 114.36 cM on chromosome 1, with a LOD score of 7.08. It explained 37.2% of the total phenotypic variance. Two QTLs for yield were mapped on chromosomes 1 and 10. The one on chromosome 1 had a LOD score of 3.78 and explained 11.83% of the total phenotypic variance. Selected plants from the population, containing several QTLs from both seedling and reproductive stage were identified. The population was further advanced up to the F5 generation. Presence of QTLs was confirmed by molecular and phenotypic validation at both developmental stages at the F5 generation. QTLs for total chlorophyll, stomatal conductance, root length and third leaf length were confirmed by using SSR markers. Plants with a combination of several QTLs were identified at F5 that also showed tolerance to salinity at seedling stage and had better yield properties under salt stress at the reproductive stage. These plants can therefore be used as donors for introgression and pyramiding of multiple tolerance loci into commercial genotypes to develop salt tolerant variety with high yields. Seedling and reproductive QTLs have never been combined and tested before to produce more tolerance, which is unique to this study. Markers linked to the important QTLs have also been identified and can be used to introgress multiple QTLs into elite varieties using marker assisted backcrossing.