玉米茎秆营养品质性状全基因组关联分析及候选基因筛选

doi:10.12190/j.issn.2096-1197.2023.05.01

摘要/Abstract

摘要：

【目的】从分子水平对玉米茎秆主要营养品质性状进行遗传解析，为玉米茎秆主要营养品质性状的遗传改良提供理论依据。【方法】以381份不同类型玉米自交系作为关联群体，2016年、2017年在河南省鹤壁市农业科学院试验园区进行随机区组种植，于玉米抽雄期、灌浆期和成熟期调查茎秆营养品质性状酸性洗涤纤维（ADF）、中性洗涤纤维（NDF）和消化率（IVDMD）。利用Maize SNP50 基因芯片获得高质量的461 053个SNP用于全基因组关联分析。【结果】利用广义线性模型（GLM）分析，在玉米10条染色体上两年共检测出不同生育时期茎秆营养品质性状392个显著相关的SNP（P<1.08×10^-7），表型变异解释率为9.69%~17.34%，发现2次以上独立关联到的SNP有97个，共获得77个与茎秆营养品质性状关联的候选基因；利用混合线性模型（MLM）分析，两年共检测出257个显著相关的SNP（P<2.17×10^-6），表型变异解释率为9.82%~20.20%，发现2次以上独立关联到的SNP有17个，共获得82个候选基因，与GLM模型候选基因重合的有10个。GLM和MLM两种模型共鉴定出159个候选关联基因，有43个候选基因被2次以上重复检测到；其中，Zm00001d021261 在多个位点发现31次与不同年份ADF、NDF和IVDMD相关联，该基因编码产物为ATP结合蛋白和叶绿体传感器激酶，在成熟期叶片中表达量最高；Zm00001d021255在两个位点发现10次与茎秆营养品质性状相关联，该基因编码产物为富半胱氨酸受体样蛋白激酶25，只在发育节间和雌穗中表达，可进一步深入研究验证。【结论】采用GLM和MLM两种模型可以快速、有效地关联到玉米茎秆营养品质相关性状显著性位点，通过重复性显著位点筛选出HC-SNP，进而挖掘出关联基因富集区域。

关键词: 玉米, 茎秆, 酸性洗涤纤维, 中性洗涤纤维, 消化率, 全基因组关联分析

Abstract:

【Objective】Conduct genetic analysis of the main nutritional quality traits of maize stems at the molecular level，to provide theoretical basis for genetic improvement of the main nutritional quality traits of maize stems.【Methods】The study used 381 different types of maize inbred lines as associated populations and planted randomly in the experimental field of the Hebi Academy of Agricultural Sciences in Henan Province in 2016 and 2017. The nutritional quality traits acid washing fiber（ADF），neutral washing fiber（NDF），and digestibility（IVDMD） were investigated during the heading，filling，and maturity stages. Using the Maize SNP50 gene chip，461 053 high-quality SNPs were obtained for genome-wide association analysis.【Results】Using the generalized linear model（GLM） analysis，a total of 392 significantly correlated stem nutritional quality traits SNPs（P<1.08×10^-7） were detected on 10 chromosomes of maize during different growth stages of the two years，with phenotypic variation interpretation rates of 9.69% -17.34%. 97 SNPs were found to be independently associated more than twice，resulting in a total of 77 candidate genes associated with stem nutritional quality traits. Using the mixed linear model（MLM）analysis，a total of 257 significantly correlated SNPs were detected over the two years（P<2.17×10^-6），with phenotypic variation interpretation rates of 9.82% -20.20%. 17 SNPs were found to be independently associated more than twice，resulting in a total of 82 candidate genes. Among them，10 overlap with GLM model candidate genes. A total of 159 candidate association genes were identified by GLM and MLM，among which 43 candidate genes were detected twice or more. Zm00001d021261 was found to be associated with ADF，NDF，and IVDMD in different years 31 times at multiple loci. This gene encoded ATP binding protein and chloroplast sensor kinase，had the highest expression in leaves at maturity stage. Zm00001d021255 was found to be associated with stem nutritional quality traits 10 times at two loci. This gene encoded cysteine rich receptor like protein kinase 25，which was only expressed in developmental internodes and female panicles，can be further studied and validated.【Conclusion】Using GLM and MLM models could quickly and effectively associate significant loci related to maize stem nutrient quality. HC-SNP could be screened through repetitive significant loci，and then associated gene enrichment regions could be excavated.

Key words: Maize, Stem, Acid washing fiber, Neutral washing fiber, Digestibility, Genome-wide association analysis

中图分类号:

S513

王帮太, 杨美丽, 郭华, 王静, 王志红, 鹿红卫, 程建梅, 秦贵文, 陈甲法. 玉米茎秆营养品质性状全基因组关联分析及候选基因筛选[J]. 北方农业学报, 2023, 51(5): 1-22.

WANG Bangtai, YANG Meili, GUO Hua, WANG Jing, WANG Zhihong, LU Hongwei, CHENG Jianmei, QIN Guiwen, CHEN Jiafa. Genome-wide association analysis for maize stem nutritional quality traits and candidate gene selection[J]. Journal of Northern Agriculture, 2023, 51(5): 1-22.

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