Theoretical and Applied Genetics

, Volume 132, Issue 7, pp 1931–1941 | Cite as

QTL mapping for maize starch content and candidate gene prediction combined with co-expression network analysis

  • Feng Lin
  • Ling Zhou
  • Bing He
  • Xiaolin Zhang
  • Huixue Dai
  • Yiliang Qian
  • Long Ruan
  • Han ZhaoEmail author
Original Article


Key message

A major QTL Qsta9.1 was identified on chromosome 9, combined with GWAS, and co-expression network analysis showed that GRMZM2G110929 and GRMZM5G852704 are the potential candidates for association with maize kernel starch content.


Increasing maize kernel starch content may not only lead to higher maize kernel yields and qualities, but also help meet industry demands. By using the intermated B73 × Mo17 population, QTLs were mapped for starch content in this study. A major QTL Qsta9.1 was detected in a 1.7 Mb interval on chromosome 9 and validated by allele frequency analysis in extreme tails of a newly constructed segregating population. According to genome-wide association study (GWAS) based on genotyping of a natural population, we identified a significant SNP for starch content within the ORF region of GRMZM5G852704_T01 colocalized with QTL Qsta9.1. Co-expression network analysis was also conducted, and 28 modules were constructed during six seed developmental stages. Functional enrichment was performed for each module, and one module showed the most possibility for the association with carbohydrate-related processes. In this module, one transcripts GRMZM2G110929_T01 located in the Qsta9.1 assigned 1.7 Mb interval encoding GLABRA2 expression modulator. Its expression level in B73 was lower than that in Mo17 across all seed developmental stages, implying the possibility for the candidate gene of Qsta9.1. Our studies combined GWAS, mRNA profiling, and traditional QTL analyses to identify a major locus for controlling seed starch content in maize.



This work was supported by Grant from National key research and development program of China (2017YFD0102005), Natural Science Foundation of Jiangsu Province, China (BK20160582), National Natural Science Foundation of China (31601315), Key Research and Development Program of Jiangsu Province (BE2017365), and Project of Science and Technology of Anhui Province (1604a0702021).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standards

The experiments carried out in this study comply with the ethical standards in China.

Supplementary material

122_2019_3326_MOESM1_ESM.pdf (32 kb)
Supplementary Table S1 The list of 149 maize inbred lines used in association study (PDF 32 kb)
122_2019_3326_MOESM2_ESM.pdf (49 kb)
Supplementary Table S2 The list of 116 transcripts predicted at the major QTL Qsta9.1 region (PDF 48 kb)
122_2019_3326_MOESM3_ESM.pdf (3 mb)
Supplementary Table S3 The list of 28 modules constructed by WGCNA involving 16,808 transcripts (PDF 3078 kb)
122_2019_3326_MOESM4_ESM.pdf (88 kb)
Supplementary Table S4 Functions enriched in each module analyzed by using SEA tool (PDF 87 kb)
122_2019_3326_MOESM5_ESM.pdf (65 kb)
Supplementary Fig. S1 Cross-validation error plot indicating the choice of the appropriate K value (PDF 64 kb)
122_2019_3326_MOESM6_ESM.pdf (234 kb)
Supplementary Fig. S2 The population structure of 149 maize inbred lines. A: Population structure analysis using ADMIXTURE. Each color represents a single population. The numbers of clusters (K) were set from 2–10. The 149 lines were divided into seven groups. B: PCA of the 149 lines. Individuals from the same group are represented by the same color. C: A neighbor-joining tree of the 149 lines (PDF 233 kb)
122_2019_3326_MOESM7_ESM.pdf (203 kb)
Supplementary Fig. S3 Quantile–quantile plot of SNPs for both general linear model (GLM) and mixed linear model (MLM) (PDF 203 kb)
122_2019_3326_MOESM8_ESM.pdf (54 kb)
Supplementary Fig. S4 Manhattan plots of the association of SNPs with starch content with GLM analysis. Genome position is shown along the x-axis divided by chromosome, and the − log10P for association is shown on the y-axis (PDF 53 kb)
122_2019_3326_MOESM9_ESM.pdf (98 kb)
Supplementary Fig. S5 Comparison of the protein sequences of GRMZM5G852704_T01 between B73 and Mo17. Query: B73, Sbjct: Mo17 (PDF 97 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Feng Lin
    • 1
  • Ling Zhou
    • 1
  • Bing He
    • 1
  • Xiaolin Zhang
    • 1
  • Huixue Dai
    • 2
  • Yiliang Qian
    • 3
  • Long Ruan
    • 3
  • Han Zhao
    • 1
    Email author
  1. 1.Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and BiotechnologyJiangsu Academy of Agricultural SciencesNanjingChina
  2. 2.Nanjing Institute of Vegetable SciencesNanjingChina
  3. 3.Anhui Academy of Agricultural SciencesHefeiChina

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