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A SNP-Based High-Density Genetic Map Reveals Reproducible QTLs for Tassel-Related Traits in Maize (Zea mays L.)

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Abstract

The tassel architecture of maize (Zea mays L.), which plays an important role in F1 hybrid seed production and yield performance, is genetically controlled by quantitative trait loci (QTLs). Here, we constructed a high-density SNP-based genetic map using an F2 population containing 148 individuals. This genetic map included 7613 SNPs whose average genetic distance was 0.19 cM. On account of the F2 population, we detected 14 QTLs responsible for tassel branch number (TBN), tassel weight (TW), central spike length (CSL), and meristem length (ML); eight of these QTLs demonstrated a relatively high level of phenotypic variation explanation (PVE) (PVE ≥ 10%), at a high level of significance. qTW-2 was a major QTL (LOD = 10.11 and PVE = 28.82%), and this QTL and qTBN-2 shared the same region, indicating a possible pleiotropic effect. An F2:3 population was developed to further verify QTLs in the F2 population. Finally, qTBN-5, qTW-2 and qCSL_N-10 were detected reproducibly. To help screen potential candidate genes, we chose 12 genes within the regions of qTBN-5, qML-6, qCSL_N-7 and qTW-2 and that were possibly involved in tassel morphogenesis according to Gene Ontology (GO) annotation analysis and performed quantitative real-time polymerase chain reaction (qRT-PCR). The expression of eight of the 12 genes was significantly (P < 0.05) or extremely significantly different (P < 0.01) between parents of the F2 population during the young tassel development stage, suggesting that those eight were possible candidate genes. These results provide insights into the genetic mechanisms controlling tassel architecture and will benefit both tassel-related QTL fine mapping and causal gene cloning in maize.

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Abbreviations

SNP:

Single Nucleotide Polymorphism

QTL:

quantitative trait locus

TBN:

tassel branch number

TW:

tassel weight

CSL_T:

central spike length (from top branch to tip of central spikelet)

CSL_N:

central spike length (from the tip of central spike to the non- branching node present below the lowermost primary branch)

ML:

meristem length

PVE:

phenotypic variation explanation

SLAF-seq:

Specific-Locus Amplified Fragment Sequencing

SD:

standard deviation.

RIL:

recombinant inbred line

qRT-PCR:

Quantitative real-time PCR

ADD:

additive effect

LOD:

logarithm of odds.

LD:

linkage disequilibrium

CTAB:

cetyl-trimethylammonium bromide

DOM:

dominant effect

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Acknowledgments

This work was supported by the China Department for Ministry of Science and Technology Spark Program (2015GA660007) and by the Jilin Provincial Agriculture Committee Promotion Project (ntg1807).

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Authors and Affiliations

  1. Waxy Corn Research Center, Jilin Agricultural University, No. 2888 Xincheng Street, Changchun, Jilin, 130000, China

    Yanning Xie, Xiaoci Ren & Rengui Zhao

  2. Institute of Maize, Jilin Academy of Agricultural Sciences, No.303 Kemaoxi Street, Gongzhuling, Jilin, 136100, China

    Xinqi Wang

  3. Institute of Peanut, Jilin Academy of Agricultural Sciences, No.303 Kemaoxi Street, Gongzhuling, Jilin, 136100, China

    Xiangyu Yang

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  1. Yanning Xie
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  2. Xinqi Wang
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  3. Xiaoci Ren
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  4. Xiangyu Yang
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  5. Rengui Zhao
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Contributions

R.Z. conceived and supervised the project. Y.N.X. participated in experimental design, carried out phenotypic data analysis and drafted the manuscript. X.Y.Y. and X.C.R. prepared the experiment materials. X.Q.W. contributed to linkage map construction and QTL mapping. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Rengui Zhao.

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The authors declare that they have no competing interests.

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Communicated by: Ray Ming

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Xie, Y., Wang, X., Ren, X. et al. A SNP-Based High-Density Genetic Map Reveals Reproducible QTLs for Tassel-Related Traits in Maize (Zea mays L.). Tropical Plant Biol. 12, 244–254 (2019). https://doi.org/10.1007/s12042-019-09227-1

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