玉米穗轴粗全基因组关联分析

Genome-wide association study of ear cob diameter in maize

玉米穗轴粗是一个影响玉米产量和穗轴产量的重要性状,其遗传机制的解析可以对高产育种提供指导。本研究以309份玉米自交系为材料,利用测序基因型分型技术对其进行基因型鉴定。采用FarmCPU(fixed and random model circulating probability unification)、MLMM(multiple loci mixed linear model)和CMLM(compressed mixed linear model)方法,对2017年和2019年河南原阳、河南郸城、河南虞城、海南三亚以及最佳线性无偏估计值环境的穗轴粗,进行全基因组关联分析,共鉴定12个与穗轴粗显著关联的SNP(single nucleotide polymorphisms)(P<8.60E-07)。其中,S4_29277313利用FarmCPU和MLMM方法在2017年原阳均检测到。S1_29006330、S2_170889116、S2_2046026464和S4_83821463的表型变异解释率介于10.23%~14.17%,为主效SNP。而且,S1_29006330位于已定位的穗轴粗QTL(quantitative trait loci)区间内。共挖掘17个候选基因,其中WAKL14(wall-associated receptor kinase-like 14)、转录因子ZIM35(zinc-finger protein expressed in inflorescence meristem 35)、HMGA(HMG-Y-related protein A)、组蛋白-赖氨酸N甲基转移酶ATX4(Arabidopsis trithorax 4)和XTH32(xyloglucan endotransglucosylase/hydrolase protein 32),可能是影响穗轴粗的重要基因。挖掘的4个穗轴粗主效SNP和5个候选基因可以为分子标记辅助育种、精细定位和基因克隆提供信息。

Maize ear cob diameter is an important trait impacting the yield of grain and cob,and the analysis of its genetic mechanism will provide a guidance for high-yield breeding.In this study,the genotypes of 309 inbred lines were identified by genotyping-by-sequencing technology.FarmCPU(fixed and random model circulating probability unification),MLMM(multiple loci mixed linear model),and CMLM(compressed mixed linear model)were used to identify significant single nucleotide polymorphisms(SNP)for ear cob diameter of Yuanyang of Henan province,Dancheng of Henan province,Yucheng of Henan province,Sanya of Hainan province in 2017 and 2019,and best linear unbiased estimate environment.A total of 12 significant SNP for ear cob diameter were detected at P<8.60E-07.S4_29277313 was detected from Yuanyang in 2017 using FarmCPU and MLMM.The phenotypic variance explained of S1_29006330,S2_170889116,S2_2046026464,and S4_83821463 ranged from 10.23%to 14.17%,and were considered major-effect SNP.In addition,S1_29006330 was mapped in the interval of known QTL for ear cob diameter.A total of 17 candidate genes were identified.Among them,WAKL14(wall-associated receptor kinase-like 14),transcription factor ZIM35(zinc-finger protein expressed in inflorescence meristem 35),HMGA(HMG-Y-related protein A),histone-lysine N-methyltransferase ATX4(Arabidopsis trithorax 4),and XTH32(xyloglucan endotransglucosylase/hydrolase protein 32)might be important genes for ear cob diameter.The identification of four major-effect SNP and five candidate genes can provide an information for molecular marker-assisted breeding,fine mapping,and gene cloning.