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作物学报 ›› 2019, Vol. 45 ›› Issue (4): 499-507.doi: 10.3724/SP.J.1006.2019.83068

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

玉米开花期相关的Indeterminate domain (IDD)蛋白家族基因的鉴定

李云富1,2,王静贤1,杜艳芳1,邹华文2,张祖新1,*()   

  1. 1 华中农业大学 / 作物遗传改良国家重点实验室, 湖北武汉430070
    2 长江大学农学院, 湖北荆州434000
  • 收稿日期:2018-11-01 接受日期:2019-01-12 出版日期:2019-04-12 网络出版日期:2019-01-31
  • 通讯作者: 张祖新
  • 作者简介:1109704146@qq.com; Tel: +86 027-87282689
  • 基金资助:
    本研究由国家自然科学基金项目(31871628)

Identification of indeterminate domain protein family genes associated with flowering time in maize

Yun-Fu LI1,2,Jing-Xian WANG1,Yan-Fang DU1,Hua-Wen ZOU2,Zu-Xin ZHANG1,*()   

  1. 1 National Key Laboratory of Crop Genetic Improvement / Huazhong Agricultural University, Wuhan 430070, Hubei, China
    2 College of Agronomy, Yangtze University, Jingzhou 434000, Hubei, China
  • Received:2018-11-01 Accepted:2019-01-12 Published:2019-04-12 Published online:2019-01-31
  • Contact: Zu-Xin ZHANG
  • Supported by:
    This study was supported by the National Natural Science Foundation of China(31871628)

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摘要：

开花期是影响玉米产量的重要因子之一。Indeterminate1 (ID1)编码玉米Indeterminate domain (IDD)家族蛋白, 是玉米开花期的重要调控因子。然而, 其他玉米IDD蛋白家族基因及其生物学功能有待深入研究。本文利用生物信息学技术在玉米基因组中鉴定并分离了37个IDD家族基因, 记作ZmIDD。表达分析发现这些ZmIDD基因在8个玉米组织中显示出多种表达模式。为进一步探讨ZmIDD基因在调控玉米开花期上的作用, 检测了37个ZmIDD在172个自交系中的遗传多样性, 发现35个ZmIDD基因在自交系间具有多态性, 平均每个基因具有37.8个多态性位点。关联分析鉴定到包含ID1在内的7个ZmIDD基因在多个环境下与开花期性状显著关联。对Zm00001d020683基因2 kb的启动子区和600 bp编码区重测序, 共鉴定到64个多态性位点。候选基因关联分析鉴定到2个启动子区的插入缺失(In/Del)位点与开花期显著关联, 其中2个位点分别插入3 bp和2 bp的单倍型为一种提早开花的基因型。研究结果为玉米开花期相关基因的分离和利用研究提供了候选基因和选择靶点。

关键词: 玉米(Zea mays L.), 开花期, IDD蛋白家族, 关联分析, 重测序

Abstract:

Flowering time is one of the important factors affecting grain yield in maize (Zea mays L.). Indeterminate1 (ID1) is a known gene encoding indeterminate domain (IDD) protein which controls flowering time of maize. However, biological functions of the other IDD family genes are little known. In this study, we identified 37 IDD family genes, referred to as ZmIDDs by searching conserved IDD domains using bioinformatics strategy, and we then isolated these ZmIDDs by amplifying B73 genome using PCR. Diverse expression patterns of these ZmIDDs were revealed in eight tissues using B73 transcriptome data deposited in public database MaizeGDB (www.maizeGDB.org). In addition, we found that 35 ZmIDDs showed abundant genetic diversity with an average of 37.8 polymorphic loci per gene in 172 inbred lines, and seven ZmIDDs including ID1 were significantly associated with three flowering time-traits: days to tassel, days to anthesis and days to silking under multiple environments. We resequenced a 2 kb promoter region and 600 bp coding region of Zm00001d020683, and found 64 variants within 172 inbred lines. Candidate gene association analysis identified that two variants at promoter region were significantly associated with flowering time, and the haplotype composed of 3 bp and 2 bp insertion at the two associated loci showed an effect of shortening flowering time. The results provide a subset of flowering time-related candidate genes for further function assay and genetic improvement of flowering time in maize.

Key words: maize (Zea mays L.), flowering time, indeterminate domain (IDD) protein, association analysis, resequencing

图1

玉米IDD家族基因及其保守基序特征 通过GSDS2.0软件展示基因结构。直线表示内含子, 黑色矩形表示外显子。通过MEME程序分析保守基序。黑色方框: motif 1; 灰色方框: motif 2; 白色方框: motif 3。"

图2

玉米和拟南芥IDD家族蛋白的系统进化树 系统进化树采用邻接法构建, 自举检验1000次。"

图3

37个玉米IDD家族基因表达模式 方框内颜色显示基因表达水平, RNA-seq数据用FPKM表示。"

表1

玉米IDD家族基因的遗传变异及其与开花期的关联分析"

基因
Gene		 染色体
Chr.		 数目
No.		 显著性水平Significance level P<0.01 显著性水平Significance level P<0.00075 P<0.00075
环境1 Env1 环境2 Env2 环境2 Env2 BLUP 环境1 Env1 环境2 Env2 环境2 Env2 BLUP
Zm00001d032922 1 18 5/7/5 7/7/7 7/8/8 3/3/3 1/1/1 1/1/1 5/3/5 2/2/1
Zm00001d005566 2 14 7/7/7 7/7/6 6/7/6 1/1//1 6/2/6 4/2/5 5/0/5 0
Zm00001d039467 3 36 7/4/4 6/3/3 6/2/2 2/2/0 6/2/0 5/1/1 0 0
Zm00001d044261 3 25 4/2/2 3/3/3 3/3/3 0 2/2/0 2/2/2 0 0
Zm00001d020683 7 31 4/3/3 3/5/5 7/4/5 3/3/3 2/2/2 3/3/3 1/1/1 1/1/1
Zm00001d011223 8 39 0 2/3/3 4/4/4 0 0 1/1/0 0/1/1 0
Zm00001d023558 10 80 12/11/13 10/9/9 9/9/9 1/1/2 4/4/2 3/4/2 7/2/5 0/1/1

图4

候选基因关联分析 A) Zm00001d020683变异位点与开花期的关联及多态性位点的连锁不平衡关系。B) 3种单倍型自交系的开花期比较。Hap1为0 + 0单倍型; Hap3为3 bp + 0单倍型; Hap4为3 bp + 2 bp单倍型。DTT为抽雄期; DTS为吐丝期; DTA为散粉期。*P < 0.05; **P < 0.01."

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