Mapping and Identification a Salt-Tolerant QTL in a Salt-Resistant Rice Landrace, Haidao86

Salinity is a key abiotic constraint on crop production worldwide. To minimize the effect of salinity on rice production, crop improvement strategies based on molecular marker techniques and genetic engineering are being used to develop salt-tolerant rice varieties. The development of such varieties, however, is hindered by limited parental resources. In this study, Haidao 86 (HD86) was observed to exhibit strong salt tolerance during its entire growth period, suggesting that it is a good donor for breeding salt-tolerant rice varieties. To dissect the molecular characteristics underlying the salt tolerance of HD86, we performed quantitative trait locus (QTL) analysis at the seed germination stage of an F2 segregating population derived from crossing HD86 with Nipponbare under 2% NaCl treatment (EC of 32.90 dS/m). One salt-tolerant QTL, qST1, was identified on the long arm of chromosome 1 between the markers CHR1-30M and CHR1-36M, corresponding to a genetic distance of 17.9 cM, and explained about 9.27% of the phenotypic variance. Using 1500 plants of the HD86 BC4F2 introgression lines in the Nipponbare genetic background with heterozygous segments between markers CHR1-30M and CHR1-36M, the exact location of qST1 was narrowed down to a 900 kb region. Combined with a bulk segregant analysis using two extreme phenotype pools of F2, eleven candidates were predicted among the mapped qST1 region. Quantitative RT-PCR analyses revealed that eleven candidates were differentially expressed in response to salt stress at the germination stage in HD86 compared with Nipponbare, suggesting the possible role of these genes in regulating salt tolerance in HD86.