两种密度条件下玉米雄穗分枝数全基因组关联分析

Genome-wide Association Analysis of Tassel Branch Number under High and Low Plant Densities in Maize(Zea mays L.)

玉米雄穗分枝数是产量的重要影响因子之一。为剖析高、低两种密度条件下雄穗分枝数的遗传基础,以248份优良玉米自交系构成的自然群体为研究材料,2014年和2015年分别在高、低两种密度条件(105 000株/公顷, 75 000株/公顷)进行雄穗分枝数的表型鉴定。利用R软件中的‘lme4’程序包对雄穗分枝数的最优线性无偏估计值(BLUP)进行计算,结合分布于全基因组的10 684个单核苷酸多态性(SNPs)标记进行全基因组关联分析。结果表明,随着种植密度的增加,雄穗分枝数有减少的趋势,且两种密度条件下遗传力均较高。同时,两种密度条件下共检测到26个与其显著关联的SNP位点,分布于玉米1号、2号、3号、5号、6号、7号、8号、9号、10号染色体。其中,低密条件下检测到12个SNP位点,高密条件下检测到14个SNP位点,5个SNP位点在两种密度条件下均被检测到,6个SNP位点在高密条件下单个位点解释的表型变异大于10%。除此之外,并确定了4个候选基因,编码产物分别为含CHASE结构域的组氨酸激酶(Histidine kinase)蛋白,富含亮氨酸重复序列(leucine rich repeat, LRR)的蛋白,含有ZF-HD结构域的蛋白和磷酸果糖激酶。采用全基因组关联分析,挖掘在两种密度条件下均检测到的与雄穗分枝数显著相关的一致性可靠标记位点以及在高密条件下特异表达且单个位点解释的表型变异均大于10%的SNP位点,并鉴定相关候选基因,为不同密度条件玉米雄穗性状相关基因的克隆提供关键的理论依据。

Tassel branch number of mai ze is one of the particularly important traits affecting yield. In order to uncover the genetic architecture of tassel branch number under high and low plant densities, the natural population of 248 elite maize inbred lines was used as research material. The phenotypic identification of tassel branch number was conducted in 2014 and 2015 under high and low densities（105 000 plants/hm2, 75 000 plants/hm2）.The best linear unbiased predictions（BLUPs） of the tassel branch number of each line were calculated by using＇lme4＇ pro-gram packages of R software. Combined with 10 684 single nucleotide polymorphisms（SNPs） markers distributed across the genome, the BLUP values of each line were used as phenotype values for GWAS analysis.The results i ndicated that there was a tendency of decreasing for tassel branch number with the increasing of planting densities. Moreover, the heritability under two densities was relatively high. Meanwhile, a total of 26 SNP loci which were significantly associated with tassel number were detected on 1, 2, 3, 5, 6, 7, 8, 9 and 10 chromosome. In them, 12 SNP loci were identified under low plant density, and 14 SNP loci were found under high plant density. 5 SNP loci were identified simultaneously under both planting densities, and the phenotypic variation explained by single locus of 6 SNP loci under high density was greater than 10%. Furthermore, 4 candidate genes were identified, encoding CHASE domain containing histidine kinase protein, leucine rich repeat（LRR） protein, ZF-HD homebox protein and 6-phosphofruckinase, respectively. GWAS was used to detect the consistent and reliable marker loci which were significantly correlated with the number of tassel branch and the SNP loci expressed at high density and the phenotypic variation explained by single locus was greater than 10%,and identify relevant candidate genes, which could provide theoretical reference for the cloning of tassel-related genes under different plant densities in maize.