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Acta Agronomica Sinica ›› 2019, Vol. 45 ›› Issue (4): 499-507.doi: 10.3724/SP.J.1006.2019.83068


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 Online:2019-04-12 Published:2019-01-31
  • Contact: Zu-Xin ZHANG E-mail:zuxinzhang@mail.hza
  • Supported by:
    This study was supported by the National Natural Science Foundation of China(31871628)


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

Fig. 1

Gene structures and putative conserved motifs of IDD family genes in maize Gene structures are showed by the GSDS2.0. Putative conserved motifs of IDD family proteins are predicted by the MEME program. Black box: motif 1; gray box: motif 2; white box: motif 3."

Fig. 2

Phylogenetic tree of IDD proteins in Zea mays and Arabidopsis thaliana The phylogenetic tree is constructed by Neighbor-Joining method with 1000 bootstraps based on the amino acid sequence of IDD proteins in Zea mays and Arabidopsis thaliana."

Fig. 3

Expression patterns of 37 maize IDD family genes Color boxes show the expression level of maize IDD family genes. RNA-sequencing is showed by FPKM (fragments per kilobase of exon per million fragments mapped)."

Table 1

Genetic variations of IDD family genes and their associations with flowering time in maize"

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

Fig. 4

Association analysis of candidate gene A) Association of variants at Zm00001d020683 with maize flowering time in the association panel, and linkage disequilibrium block among variants at Zm00001d020683. B) Comparison of flowering time between haplotypes. Hap1: 0 + 0 haplotype. Hap3: 3 bp + 0 haplotype. Hap4: 3 bp + 2 bp haplotype. DTT: days to tassel; DTA: days to anthesis; DTA: days to silking. * P < 0.05; **P < 0.01."

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