Mapping QTLs For Tolerance To Hypoxia And Chlorate Stress Using Recombinant Inbred Lines In Rice

Rice is one of the most important food crops in the world,and more than half of the world population feeds on rice.There are two subspecies of indica rice and japonica rice in Asian cultivated rice.Indica-japonica hybrid F₁ has significant heterosis,and the derived offspring population is prone to segregation of traits,which contains great genetic diversity.Constructing genetic population derived from indica-japonica cross to carry out QTL mapping studies on the genetic basis of agronomic traits are of great significance for breeding rice varieties with excellent traits.Direct seeding rice production can relieve a large amount of labor and is a low-cost cultivation technique.In direct seeding production,submergence and hypoxia are always one of the key environmental factors that hazard directly seed germination.When the rice seed germination stage is under submergence stress,the seed coleoptile will quickly extend in a short time to reach the water surface to contact with oxygen and adapt to submergence stress.Therefore,the length of the coleoptile under submergence conditions can be used as an evaluation index for the tolerance of rice to hypoxia.In this study,272 F₁₆lines of Recombinant Inbred Line（RIL）derived from the parents of indica Luohui 9 and japonica RPY were used as materials.The length of the coleoptile was investgated after the germination of rice seeds was submerged for 5days as the trait evaluation index for hypoxia tolerance.2 QTLs were located on chromosome 1（10.86-12.77c M）and chromosome 3（63.53-64.66c M）using this set of high-density Bin genetic linkage map constructed by RIL,using complete interval mapping method,taking LOD value greater than or equal to 3,with contribution rates of 7.1%and 8.8%,respectively.The submergence tolerance of rice is mainly controlled by genetic factors.The sub1 is a gene cluster for controlling the submergence tolerance.Plants containing its allele sub1A-1 can have stronger tolerance to submergence.The bioinformatics were used to analyze the alleles distribution of sub1 in the 533 germplasm databases from Huazhong Agriculture University,3K RGP rice database,and the RIL population.The results showed that sub1B had 17 haplotypes in 533 germplasm database materials of Huanong,mainly typeⅠ（mainly Japonica）and typeⅡ（mainly Indica）.Sub1C has14 haplotypes in the population,the main haplotypes are typeⅠand typeⅡ,typeⅠis the main haplotype of Japonica,typeⅡis the main haplotype of Indica.There are 124 SNP mutation sites and 31 Indel mutation sites in the sub1B gene in the RIL population,and 78 SNP mutation sites and 35 Indel mutation sites in the sub1C gene in the RIL population.The results paved a way to apply the useful allelic variations or haplotypes of sub1 gene in rice submergence tolerance breeding programs.Potassium chlorate tolerance is one of the reliable indicators for indica-japonica classification in rice,and understanding the genetic basis of rice chlorate tolerance will contribute to reveal the evolutionary mechanism of indica-japonica differentiation.In this study,QTLs related to chlorate tolerance at rice seedling stage were located using the recombinant inbred line population derived from indica-japonica hybridization,and A QTL related to root length of rice seedlings under chlorate stress was located on chromosome 4 between 103.38c M and 106.72c M,with the contribution rate of 9.5%.