中国农业科学 ›› 2019, Vol. 52 ›› Issue (11): 1839-1857.doi: 10.3864/j.issn.0578-1752.2019.11.001

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

玉米叶绿素含量的全基因组关联分析

史大坤1,姚天茏1,刘楠楠2,邓敏3,段海洋1,王路林1,万炯1,高炯浩1,谢惠玲1,汤继华1,张雪海1()   

  1. 1 河南农业大学农学院/省部共建小麦玉米作物学国家重点实验室,郑州 450002
    2 福建农林大学海峡联合研究院,福州 350002
    3 湖南农业大学农学院/湖南省玉米工程技术研究中心,长沙 410128
  • 收稿日期:2019-01-21 接受日期:2019-02-28 出版日期:2019-06-01 发布日期:2019-06-11
  • 通讯作者: 张雪海
  • 作者简介:史大坤,E-mail:912320091@qq.com。|姚天茏,E-mail:yaotianlong0629@qq.com。
  • 基金资助:
    河南省科技攻关项目(182102110349);省部共建小麦玉米作物学国家重点实验室自主设置课题(39990080);河南农业大学博士科研启动金(30500563);2019年度河南农业大学科技创新基金(KJCX2019A01)

Genome-Wide Association Study of Chlorophyll Content in Maize

SHI DaKun1,YAO TianLong1,LIU NanNan2,DENG Min3,DUAN HaiYang1,WANG LuLin1,WAN Jiong1,GAO JiongHao1,XIE HuiLing1,TANG JiHua1,ZHANG XueHai1()   

  1. 1 College of Agronomy, Henan Agricultural University/National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002
    2 Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002
    3 College of Agronomy, Hunan Agricultural University/Maize Engineering Research Center of Hunan Province, Changsha 410128
  • Received:2019-01-21 Accepted:2019-02-28 Online:2019-06-01 Published:2019-06-11
  • Contact: XueHai ZHANG

摘要:

目的 叶绿素含量与作物产量呈正相关。通过提高叶绿素含量来提高作物产量是作物育种的方向之一。因此,利用全基因组关联分析(genome-wide association study, GWAS)解析玉米叶绿素含量的遗传基础,可为玉米高光效理想株型设计育种提供理论指导。方法 以538份玉米自交系构成的关联群体为研究对象,在5个环境下,通过对其授粉后5 d的棒三叶(穗位叶、穗上叶、穗下叶)叶绿素含量进行测定,并借助覆盖玉米全基因组的558 629个单核苷酸多态性标记(SNPs),利用3种模型(Q、K和Q+K)对叶绿素含量进行全基因组关联分析,随后选择最优模型的GWAS结果并结合eQTL(expression quantitative trait loci)分析对叶绿素含量的自然变异进行解析。结果 5个环境下,棒三叶叶绿素含量均遵从正态分布且叶绿素含量间呈正相关;方差分析表明棒三叶叶绿素含量的环境效应、基因型效应、基因型与环境互作效应均达到了极显著水平;此外,穗上叶、穗位叶和穗下叶叶绿素含量的遗传力分别为0.66、0.66和0.67。比较3种模型发现K模型对假阳性(I型错误)控制最好,在此模型下共检测到29个与棒三叶叶绿素含量显著关联的SNP(P≤3.99×10-6),涉及到18个位点,共有76个候选基因落在这18个位点内,其中85.5%(65/76)的候选基因具有eQTL,11.8%(9/76)的候选基因与对应表型显著相关(P<0.05),说明这9个基因可能是通过表达量变化来调控表型变异。在这76个基因中,60个候选基因有功能注释,功能涉及到能量代谢、物质输送代谢途径和生物合成调节等过程。此外还发现2个可以在不同环境或不同叶片共定位的位点,其中,共定位位点内的基因GRMZM2G074759编码一种与AAE3高度相似的酰基活化酶,该基因通过提高α-酮戊二酸(ALA)和草酰乙酸含量进而影响氨基酸生物合成,提高籽粒赖氨酸含量,改善玉米品质。此外,ALA的合成会促使叶绿素含量升高,进而提高作物产量,推测该基因为最可能的候选基因。结论 K模型对假阳性的控制效果最好,基于K模型,共检测到18个玉米叶绿素含量显著关联位点,发现多个参与叶绿素合成途径相关基因。

关键词: 玉米, 叶绿素含量, 全基因组关联分析, 高光合效率

Abstract:

【Objective】 Chlorophyll content was positively correlated with crop yield, improving crop yield by increasing chlorophyll content has become an important breeding goal in maize. Thus, elucidating the genetic basis of chlorophyll content using genome-wide association study (GWAS) can provide theoretical support for ideotype-based maize breeding with high photosynthetic efficiency. 【Method】 The association mapping panel (AMP) used in this study was consisted of 538 maize inbred lines, chlorophyll content of maize three leaves (above the uppermost ear leaf, uppermost ear leaf and below the uppermost ear leaf ) of the AMP was investigated at 5 days after pollination at five locations, then a GWAS with three models (Q, K, Q+K) were carried out using 558 629 single nucleotide polymorphisms (SNPs). The combination of optimal GWAS model with expression quantitative trait loci (eQTL) analysis, natural variation of chlorophyll content was further explored. 【Result】 All traits measured at the five locations exhibited an approximately normal distribution and positive correlations between paired traits were also observed. Analysis of variance indicated that significant variations were observed across environment, genotype and the genotype × environment interaction. In addition, the heritability of chlorophyll content was 0.66, 0.66, and 0.67 for above the uppermost ear leaf, uppermost ear leaf and below the uppermost ear leaf, respectively. When test with the optimal GWAS model, K model has the greatest success in reducing false positive (type I errors) than other two models. Based on the result of K model, a total of 18 loci involving in 29 significantly SNP-traits associations were detected (P≤3.99×10 -6), and 76 candidate genes were found, including 42 genes that have functional annotation that involved in energy metabolism, biosynthetic regulation and material transportation and metabolic pathways. Of which, 85.5% (65/76) of the candidate genes have eQTLs and 11.8% (9/76) of the candidate genes were significantly associated with the corresponding phenotype (P<0.05), indicating that these nine genes may affect phenotypic variation by regulating their expression. Moreover, two loci were found to be co-localized in two environments or leaves, the gene GRMZM2G074759 within the co-localized locus, encodes an acyl-activating enzyme, highly similar to AAE3. It can increase the lysine content and improve maize quality by increasing the content of α-ketoglutarate (ALA) and oxaloacetate, in addition, ALA could promote chlorophyll biosynthesis and improve crop yield, this gene was considered as the most likely candidate gene. 【Conclusion】 The results indicated that K model having the best result in reducing the false positive. Based on the K model, a total of 18 loci associated with chlorophyll content and several candidate genes may be involved in chlorophyll synthesis pathway were identified.

Key words: maize (Zea mays L.), chlorophyll content, genome-wide association study, high photosynthetic efficiency