Genetic Resources and Crop Evolution

, Volume 66, Issue 7, pp 1557–1571 | Cite as

Fine mapping and identification of ub4 as a candidate gene associated with tassel branch number in maize (Zea mays L.)

  • Jianbo Li
  • Dexuan Meng
  • Hongwei Yu
  • Kuangye Zhang
  • Kangning Zhu
  • Jingbo Lv
  • Zixiang Cheng
  • Jianfeng Weng
  • Wanli Du
  • Xiangling LvEmail author
  • Fenghai LiEmail author
Research Article


The tassel branch number in maize is an important agronomic trait and it has been increasingly investigated in maize breeding programs. In this study, we isolated a pair of sister lines (Lx1 and Lx2) associated with the tassel branch trait. Lx1 showed unbranched tassel phenotype whereas Lx2 had 5–8 tassel branches. Genetic analysis showed that the unbranched tassel trait was controlled by a recessive gene designated as unbranched tassel 4 (ub4). An F2 population comprising 6782 individuals was developed to fine map ub4. Finally, ub4 was mapped to an 88.2-kb region on chromosome 6, which harbored five candidate genes. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed that the unique Zm00001d038546 gene in this region exhibited significantly different expression between Lx1 and Lx2. Sequence analysis of Zm00001d038546 from Lx1 showed that an 8-bp deletion in the third exon generated a premature stop codon, thereby leading to the termination of transcription. Moreover, Zm00001d038546 co-segregated with ub4 according to an InDel marker (InDel546) within the 8-bp deletion among the 1671 individuals without tassel branches in the F2 population. Therefore, Zm00001d038546 was considered as the most likely candidate gene for ub4. These findings might be useful for reducing tassel branches and increasing grain yield in the maize breeding.


ub4 Tassel branch number Candidate gene Fine mapping Maize 



This study was supported by funds from the National Key Research and Development Program of China (2017YFD0101103-3).

Author contribution

Jianbo Li, Xiangling Lv, and Fenghai Li designed the experiments. Jianbo Li performed the experiments. Jianbo Li, Xiangling Lv, and Dexuan Meng analyzed the results. Jianbo Li wrote the manuscript, and Dexuan Meng and Jianfeng Weng revised the manuscript. Jianbo Li, Jingbo Lv, Kangning Zhu, Hongwei Yu, and Zixiang Cheng contributed to phenotyping. Kuangye Zhang and Wanli Du contributed to the production of images. All of the authors read and approved the manuscript.

Compliance with ethical standards

Conflict of interest

On behalf of all authors, the corresponding author states that there are no conflicts of interest related to this research.

Supplementary material

10722_2019_805_MOESM1_ESM.xlsx (9 kb)
Information integration of maize QTL related to the tassel branch number (XLSX 9 kb)
10722_2019_805_MOESM2_ESM.tif (15.1 mb)
The construction of the sister lines Lx1 and Lx2 (TIFF 15472 kb)
10722_2019_805_MOESM3_ESM.tif (3.8 mb)
The distribution of the differential SNP and SSR on chromosomes. Utilize total of 5259 SNPs and 994 SSRs to analysis the polymorphic markers between the pair of sister lines Lx1 and Lx2, and obtained 406 differential SNPs and 21 differential SSRs. The distribution of polymorphic markers on chromosomes were 63 SNPs and 3 SSRs on chromosome 1, 22 SNPs and 2 SSRs on chromosome 2, 67 SNPs on chromosome 3, 2 SNPs on chromosome 4, 78 SNPs on chromosome 5, 74 SNPs and 11 SSRs on chromosome 6, 30 SNPs and 4 SSRs on chromosome 7, 37 SNPs on chromosome 9, 16 SNPs and 2 SSRs on chromosome 9, 17 SNPs on chromosome 10, respectively. The genetic background similarity between Lx1 and Lx2 reached to 93.17% (TIFF 3894 kb)
10722_2019_805_MOESM4_ESM.xlsx (11 kb)
The difference between the pair of sister lines on the agronomic traits (XLSX 10 kb)
10722_2019_805_MOESM5_ESM.xlsx (12 kb)
Primers used in this study (XLSX 11 kb)
10722_2019_805_MOESM6_ESM.tif (10.8 mb)
Gel image of the polymorphism markers that showed polymorphisms between two bulks which were made up by two extremes. Note: Four channels consist of a group, channel 1: Lx1; channel 2: Lx2; channel 3: Bulk1; channel 4: Bulk2. 1-21 stand for mmc0241, bnlg1759a, phi123, umc2323, bnlg345, umc2320, umc2375, umc1490, bnlg1174a, bnlg1740, umc2165, phi090, phi260485, phi082, umc2396, umc2237, umc2225, umc2333, umc1406, umc2213 and phi448880, respectively (TIFF 11105 kb)
10722_2019_805_MOESM7_ESM.pdf (1.5 mb)
The cDNA sequence of the candidate genes Zm00001d038542 - Zm00001d038546 in Lx1, Lx2 and B73. a, b, c, d and e stand for Zm00001d038542, Zm00001d038543, Zm00001d038544, Zm00001d038545 and Zm00001d038545, respectively. The red boxes on Zm00001d038544 were synonymous mutation, and in the Zm00001d038546 was the 8 bp deletion (PDF 1565 kb)
10722_2019_805_MOESM8_ESM.tif (2.3 mb)
Alignment of multiple gDNA sequence of Zm00001d038546 from Lx1, Lx2 and 15 inbred lines. The amino acid sequence is from initial codon to termination codon. The red box section was the 8 bp deletion (TIFF 2319 kb)
10722_2019_805_MOESM9_ESM.tif (7.7 mb)
Gel images of the InDel marker InDel546 of the bands co-segregated with the absent TBN phenotype. Note: M: Marker; P1: Lx1; P2: Lx2 (TIFF 7841 kb)
10722_2019_805_MOESM10_ESM.tif (39 kb)
Compared the genotype of Xianyu335 and Zheng58 with Lx1 and Lx2 used by the primer of InDel546 (TIFF 39 kb)
10722_2019_805_MOESM11_ESM.xlsx (10 kb)
Informations of the previously QTLs on chromosome 6 (XLSX 10 kb)
10722_2019_805_MOESM12_ESM.tif (3 mb)
Integrative information of the dtbn1 gene location and other previously published literature of tassel branch locus on chromosome 6. The light green, purple, hot pink, orange, red, light blue, green and aqua bars represent the classification of QTLs on chromosome 6 of Group I, Group II, Group III, Group IV, Group V, Group VI, Group VII and Group VIII, respectively (TIFF 3112 kb)


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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  • Jianbo Li
    • 1
  • Dexuan Meng
    • 1
  • Hongwei Yu
    • 1
  • Kuangye Zhang
    • 1
  • Kangning Zhu
    • 1
  • Jingbo Lv
    • 1
  • Zixiang Cheng
    • 2
  • Jianfeng Weng
    • 2
  • Wanli Du
    • 1
  • Xiangling Lv
    • 1
    Email author
  • Fenghai Li
    • 1
    Email author
  1. 1.College of AgronomyShenyang Agricultural UniversityShenyangPeople’s Republic of China
  2. 2.Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingPeople’s Republic of China

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