Mining Excellent Aluminum Tolerance And Cold Tolerance Genes In Rice Using Microcore Germplasm-Whole Genome Association Analysis

The Ding's Core Germplasms?150?with rich genetic background is very imported for Abiotic stress in rice?aluminum toxicity and cold?.In my study,the core germplasms were simplify sequenced in the whole genome to analyze their structural and genetic relationship.The whole genome association analysis?GWAS??mixed linear model?for stress resistance of core germplasm population was carried out by combining Al-tolerant phenotype data?relative root length?and cold-tolerant phenotype data?dead seedling rate?,respectively.To find and validate the excellent stress resistance genes in rice core germplasm.The results are summarized as follows:?1?SLAF-seq was used to mark the high-density SNP loci and the results showed that the population was divided into 2-4 subgroups.Base on genome-wide association analysis,153SNPs significantly associated with Al tolerance were identified and 25 Al tolerance-related QTLs were unevenly distributed on 12 chromosomes of rice.Five of them were co-located with previous studies.The candidate genes in the QTL region of the SNPs with high significance?qALT3.2,qALT3.3,qALT3.4,qALT3.5,qALT1.2,qALT1.5,qALT2.3,qALT3.6,qALT3.7,qALT4.1,qALT6.1,and qALT9.1?were further detected by RT-PCR,gene annotation,amino acid sequence analysis and multiple screening of expression profiles.Finally,two new genes related to aluminum tolerance were identified?Os03g0437200 and Os01g0304100?.The functional validation of these two genes needs further study.?2?Based on SLAF-seq marker sequencing,the high-density SNP Library was constructed to genome-wide association analysis of cold tolerance in rice seedlings.26 SNPs loci and 213 SNPs related to cold tolerance were detected,and 22 QTLs were located,of which3 were co-located with previous studies.SNP₂6297784 had a high correlation with cold tolerance(9.88x10^-10),which was located on the cold tolerance QTL2.Six candidate genes?Os01g0617900,Os01g0618200,Os01g0618400,Os01g0618800,Os01g0618800,Os01g0618900 and Os01g0620100?were screened by bioinformatics analysis.The Os01g0620100 gene sequence has significant discontinuous variation,and there is a high degree of linkage imbalance in the interval.The results of gene annotation,expression profile analysis and 3D protein structure prediction indicated that the gene might be involved in cold tolerance regulation in rice.?3?The genetic diversity and genotyping of five cold-tolerant genes?OsLEA4,AP37,OsLEA5,ZFP245 and OsiSAP8?were analyzed using 60 materials with complete sequencing data,and predict the optimal haplotypes associated with cold-tolerance.The results of the optimal haplotype combination in this study provide a theoretical reference for future variety breeding.The results of this study provide a research basis for exploring the excellent resistance genes in excellent rice germplasm resources in China,and provide a theoretical basis for further studying the genetic structure of rice germplasm resources to understand the origin and differentiation of rice crop,and broaden the scope of selection for breeders.