Dissection Of QTL Alleles For Salt Tolerance Based On Linkage And Linkage Disequilibrium Mapping In Japonica Rice

Soil salinity is a major abiotic stress that limits rice production worldwide, understanding the genetic mechanisms controlling rice salt tolerance, identification of QTLs and their carriers related to salt tolerance can subsequently be integrated into rice breeding programs, and developing salt tolerance rice varieties is the most efficient approach to resolve the salinity problem. Linkage mapping and association mapping are two important methods to analyse the genetic basis of complex traits, which are significantly complementary understanding to the accuracy and width of QTL mapping. Recently, many studies have been reported by linkage mapping for salt tolerance-related traits. However, most of the studies used indica rice as tested material, and focused on salt tolerance at the seedling stage, and different developmental stages of rice salt tolerance were obviously specific. Therefore, QTL analysis of salt tolerance in japonica rice at different developmental stages is important for dissecting genetic mechanisms controlling rice salt tolerance and improving rice salt tolerance.In this study, a BC2F2:3 population derived from Dongnong425(a salt-sensitive and widely cultivated variety) as the recurrent parent and Changbai10(a salt-tolerant variety) as the donor parent, and a panel of 341 japonica rice accessions from different geographical origins were used as tested materials, QTL analysis of salt tolerance in janonica rice was carried out based on linkage and linkage disequilibrium mapping at the the germination and early seedling stage, the seedling stage, and during the field growth. Phenotypic effects of each allele of the stable QTLs were compared, and favorable alleles were mined, which will provide useful information to improve salt tolerance in rice by marker-assisted selection(MAS) and accelerate the innovation for rice salt-tolerant germplasms. The main results were as follows:(1) The statistical analyses of salt tolerance-related traits relative germination rate(RGR), relative seedling height(RSH), relative root number(RRN) and relative root length(RRL) at the germination and early seedling stage, score of salt toxicity of leaves(SST), survival days of seedlings(SDS), shoot Na+ concentration(SNC), shoot K+ concentration(SKC), shoot Na+/K+ radio(SNK), root Na+ concentration(RNC), root K+ concentration(RKC) and root Na+/K+ radio(RNK) at the seedling stage, relative panicle length(RPL), relative effective panicles(REP), relative spikelet number per panicle(RSN), relative spikelet fertility(RSF), relative 1000- grain weight(RGW) and relative grain yield per plant(RGY) during the field growth showed that the range of variation in natural population is larger than BC2F2:3 population for each trait. All the parameters in two populations exhibited a normal distribution and showed the genetic characteristics of quantitative traits.(2) The correlation analyses showed that the significance of correlation was nearly identical in the two populations. The salt tolerance-related traits was significantly positively correlated with each other at the germination and early seedling stage, indicating that these indicators showed a strong collaboratively response to salt stress. At the seedling stage, SDS was significantly negatively correlated with SST, SNC and SNK, and no significantly correlated with RNC, RKC and RNK, indicating that the salt toxicity of leaves resulted from over-accumulation of Na+ in shoots. RNC was significantly positively correlated with RKC, but SNC was significantly negatively correlated with SKC, indicating that the processes of Na+ and K+ uptake in rice were considered to occur in parallel and competition occurred when Na+ and K+ in the roots were transported to the shoots; During the field growth, REP, RSN and RGY were significantly positively correlated with each other, indicating that these indicators showed a strong collaboratively response to salt stress.(3) A genetic linkage map with 137 SSR markers was constructed for the BC2F2:3 population, covering 12 chromosomes and spanning 1742.4 cM of the rice genome with an average interval of 12.72 cM between the adjacent markers. The QTL analysis of salt tolerance-related traits using the inclusive composite interval mapping method(ICIM) was conducted at different developmental stages. A total of 11 QTLs were identified at the germination and early seedling stage, including 3 for RGR, 3 for RSH, 3 for RRN and 2 for RRL, which distributed over chromosomes 1, 3, 4, 5, 7 and 8; A total of 17 QTLs were identified at the seedling stage, including 2 for SDS, 2 for SST, 4 for SNC, 3 for SKC, 2 for SNK, 3 for RNC, 1 for RKC and no QTL was detected for RNK, which distributed over chromosomes 1, 2, 3, 5, 6, 7, 9, 11 and 12; A total of 19 QTLs were identified during the field growth, including 5 for RPL, 2 for REP, 3 for RSN, 3 for RSF, 3 for RGW and 3 for RGY, which distributed over chromosomes 1, 2, 3, 4, 5, 6, 7, 8 and 11.(4) Genetic diversity, population structrue, kinship and linkage disequilibrium were analyzed by 160 SSR markers for the natural population. A total of 872 alleles ranging from 2 to 9 per locus were identified from all collections; Population structure analysis identified three main subpopulations for the accessions that corresponded to major geographic origins; The majority of the pairs of japonica rice accessions(57.4%) had zero estimated kinship values, while 40.9% kinship estimates ranged from 0 to 0.2, indicating that most accessions in the panel have no or very weak kinship; Of the SSR pairs in these accessions, 40.05% marker pairs showed significant LD(P<0.01). The LD level for linked markers is significantly higher than that for unlinked markers, and LD level was elevated when the panel was classified into subpopulations. The LD decayed to the background at approximately 20-50 cM within the total panel and each subpopulation.(5) The association mapping between salt tolerance-related traits and SSR markers was performed using both the general linear model(GLM, Q) and the mixed linear model(MLM, Q+K) functions in the TASSEL 3.0 software at the germination and early seedling stage, the seedling stage, and during the field growth in two consecutive years. A total of 22 significant marker-trait associations(P≤0.01) involving 18 markers were identified at the the germination and early seedling stage, including 5 for RGR, 5 for RSH, 5 for RRN and 7 for RRL; A total of 38 significant marker-trait associations(P≤0.01) involving 26 markers were identified at the seedling stage, including 5 for SDS, 4 for SST, 6 for SNC, 5 for SKC, 6 for SNK, 5 for RNC, 4 for RKC and 3 for RNK; A total of 54 significant marker-trait associations(P≤0.01) involving 38 markers were identified during the field growth, including 8 for RPL, 6 for REP, 7 for RSN, 5 for RSF, 6 for RGW and 11 for RGY. The results identified by association mapping in this study were compared with the QTLs identified by linkage mapping in the present and previous studies. Ultimately, 14, 19, and 22 SSR markers identified in this study were found to coincide the salt tolerance-related QTLs identified by linkage mapping.(6) Phenotypic values of alleles of 14, 14 and 22 stably detected and clearly affected salt tolerance loci by linkage and linkage disequilibrium mapping were compared, and 32, 39 and 67 favorable alleles were identified at the germination and early seedling stage, at the seedling stage, and during the field growth, respectively.(7) The number of favorable alleles was investigated in 341 japonica rice accessions based on the favorable alleles related to salt tolerance at the germination and early seedling stage, the seedling stage, and during the field growth, respectively. In addition, based on the favorable alleles that could be pyramided into an individual plant and the expected phenotypic effects(apart from possible epistatic effects), predictions for salt tolerance parental combinations at the germination and early seedling stage, at the seedling stage, during the field growth and for the whole plant growth duration, respectively, were proposed. Therefore, the favorable alleles and carries materials were useful for breeding programs in rice based on marker-assisted selection and salt-tolerant germplasm innovation.