粳稻分蘖数全基因组关联分析及候选基因的挖掘

【目的】利用全基因组关联分析(genome-wide association study,GWAS)检测与粳稻分蘖数显著相关的SNP位点,筛选影响分蘖数的候选基因,为分子辅助育种提高产量提供理论基础。【方法】利用295份来自世界各地的粳稻品种,于2018和2019年分蘖盛期调查水稻分蘖数,结合高通量重测序获得的788 396个高质量多态性SNP,利用TASSEL 5.0软件的MLM模型进行全基因组关联分析,对GEC软件计算的有效独立SNP数目进行阈值确定,判定SNP标记与目标性状关联的显著性。根据2年检测到的峰值SNP和水稻每条染色体LD衰减距离,确定2年共定位分蘖数主效QTL,并进一步提取QTL区间内所有基因外显子区非同义突变SNP和启动子区SNP进行单倍型分析,结合基因注释筛选影响粳稻分蘖数候选基因。【结果】295份粳稻品种的分蘖数在2018和2019年总趋势基本一致,并且均具有较大的表型分布。通过全基因组关联分析,在P<5.46×10-6阈值条件下,从第8、9和10染色体上共鉴定3个与粳稻分蘖数相关的QTL(qTiller8、qTiller9和qTiller10),其中,在...

Genome-Wide Association Study and Candidate Gene Mining of Tillering Number in Japonica Rice

【Objective】Genome-wide association study (GWAS) was used to detect SNP loci that were significantly related to tillering number in japonica rice, and to screen candidate genes affecting tillering number 【Method】This study used 295 japonica rice varieties from around the world, in 2018 and 2019 survey from the tillering stage of rice tillering number, the combination of high throughput sequencing weight gain high quality 788396 polymorphism, SNP, using TASSEL 5.0 software genome-wide association analysis of MLM model, using the GEC software to calculate the number of effective independent SNPS for the determination of threshold value, determine the significance of SNP markers associated with target traits. Based on the peak SNP detected in two years and the LD attenuation distance of each chromosome in rice, the major QTLs for co-localization of biennial number were determined, and the non-synonymous SNPs and promoter regions of all gene exon regions in the QTL interval were further extracted. SNPs were subjected to haplotype analysis, and then combined with gene annotation to screen candidate genes affecting japonica rice tillering number. 【Result】 The tillering number of 295 japonica rice varieties were basically the same in 2018 and 2019, and they all had a large phenotypic distribution. Under the threshold of P < 5.46 × 10^-6, three QTLs (qTiller8, qTiller9 and qTiller10) related to tillering number of Japonica rice were identified on chromosomes 8, 9 and 10 by genome-wide association analysis. qTiller9 jointly detected that the contribution rate of phenotype in 2018 and 2019 was 11.86% and 10.61%, respectively. qtiller8 and qtiller10 were only detected in 2018, and the contribution rate of phenotype was 10.61% The rates were 9.36% and 9.10%, respectively. Haplotype analysis of all 15 genes in qTiller9 interval showed that there were 6 genes in qTiller9 interval (LOC_Os09g25090, LOC_Os09g25100, LOC_Os09g25150, LOC_Os09g25190, LOC_Os09g25200 and LOC_Os09g25220). LOC_Os09g25090 was divided into two haplotypes by promoter SNP, and the tillering number of hap2 (TAA) was significantly higher than that of hap1 (AGG). LOC_Os09g25100 was divided into two haplotypes by non-synonymy mutation SNP, and hap2 (GAGA) had a significantly higher tillering number than hap1 (AGCC). LOC_Os09g25150 was divided into two haplotypes by non-synonymy mutation SNP, and the tillering number of hap2 (ATG) was significantly higher than that of hap1 (GCC). LOC_Os09g25190 was divided into two haplotypes by promoter SNP and the tillering number of hap2 (GCATCGCATCGACGCCGA) was significantly higher than that of hap1 (ATGCTGATGAAGTCATCC). LOC_Os09g25200 was divided into two haplotypes by non-synonymic mutant SNP and the tillering number of hap2 (TAG) was significantly higher than that of hap1 (AGA). LOC_Os09g25220 was divided into two haplotypes by non-synonymic mutant SNP, and the tillering number of hap1 (GG) was significantly higher than that of hap2 (AA).Combined with gene annotation, it was found that LOC_Os09g25090 and LOC_Os09g25100 both predicted the encoding of calcineurin dependent protein kinases and were Ca²⁺ sensors necessary for abscisic acid (ABA) expression. Previous studies have shown that ABA can affect both tillering number and branch number of Arabidopsis. Therefore, LOC_Os09g25090 and LOC_Os09g25100 are candidate genes affecting the tillering number in japonica rice. 【Conclusion】LOC_Os09g25090 and LOC_Os09g25100 were screened as candidate genes affecting the tiller number of japonica rice.