基于QTL定位和RNA-seq分析挖掘玉米茎粗候选基因

Identification of Candidate Genes Associating with Stem Diameter in Maize(Zea mays L.)Based on Integrating QTL Mapping and RNA-seq

茎粗是影响玉米株型的一个重要性状,为解析玉米茎粗的遗传基础,本研究以茎粗存在显著差异的自交系郑58和D863F及其构建的241个RILs家系为材料,在2个环境及最佳线性无偏预测值(BLUP,best linear unbiased prediction)下进行QTL定位。2个环境及BLUP值下共检测到6个与玉米茎粗有关的QTL,分布于玉米的第3、6和10染色体上,单个QTL解释的表型变异为4.30%~10.73%。对2个亲本茎秆RNA-Seq结果进行分析,QTL定位区间共检测到106个差异表达基因(DEGs,differentially expressed genes),其中49基因个上调,57个基因下调。GO功能富集分析表明,差异表达基因主要富集在分子功能中,涉及催化活性、转移酶活性、苹果酸脱氢酶活性和离子结合等。KEGG富集分析表明,差异表达基因主要参与到次生代谢产物的生物合成,丙氨酸、天冬氨酸和谷氨酸代谢,类苯基丙酸合成代谢等过程。将QTL定位与转录组测序相结合,筛选出12个可能调控茎粗发育的候选基因。这些QTL位点和候选基因可用于进一步的精细定位和功能分析,为开展玉米理想株型分子育种奠定了基础。

Stem diameter is an important trait that affects the plant architecture in maize(Zea mays L.).In order to study the genetic mechanism of stem diameter in maize,a recombinant inbred line(RIL)population(241 lines)derived from Zheng58 and D863F was used to determine the stem diameter at two environmental conditions,followed by QTL mapping using the best linear unbiased prediction values(BLUP). A total of 6 QTL for stem diameter were detected on chromosome 3,6 and 10,each of which contributes to the phenotypic variance ranging from 4.30% to 10.73%. By transcriptome analysis,106(D863F/Zheng58)differentially expressed genes(DEGs)were identified in the physical intervals of the QTL. Forty-nine genes were up-regulated and 57genes were down-regulated. GO functional enrichment analysis showed that most of the DEGs were enriched in molecular functions,including catalytic activity,transferase activity,malate dehydrogenase activity,ion binding and so on. KEGG enrichment analysis showed that the DEGs were mainly concentrated in biosynthesis of secondary metabolites,alanine,aspartate and glutamate metabolism,and phenylpropanoid biosynthesis. Twelve candidate genes were identified by integrating analysis of QTL mapping and RNA sequencing. These results enabled future fine mapping and functional analysis of these QTL and their candidate genes,which might provide a reference in marker-assisted maize breeding for ideal architecture.