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Mapping of qChalk1 controlling grain chalkiness in japonica rice

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Abstract

Background

Rice grain chalkiness is an undesirable characteristic that affects grain quality. The aim of this study was to map QTLs controlling grain chalkiness in japonica rice.

Methods and results

In this study, two japonica rice cultivars with similar grain shapes but different grain chalkiness rates were crossed and the F2 and BC1F2 populations were subjected to QTL-seq analysis to map the QTLs controlling the grain chalkiness rate. QTL-seq analysis revealed SNP index differences on chromosome 1 in both of the segregating populations. Using polymorphic markers between the two parents, QTL mapping was conducted on 213 individual plants in the BC1F2 population. QTL mapping confined a QTL controlling grain chalkiness, qChalk1, to a 1.1 Mb genomic region on chromosome 1. qChalk1 explained 19.7% of the phenotypic variation.

Conclusion

A QTL controlling grain chalkiness qChalk1 was detected in both F2 and BC1F2 segregating populations by QTL-Seq and QTL mapping methods. This result would be helpful for further cloning of the genes controlling grain chalkiness in japonica rice.

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Data availability

The datasets used and/or analyzed during the current study are available from the corresponding author upon reasonable request.

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Acknowledgements

The authors are grateful to all the members in rice group of Henan Agricultrual University.

Funding

This work was supported by the Key Research Project of Henan Higher Education (Grant No. 21A210019), Mordern Agricultural Technology System of Henan Province (Grant No. S2012-04-G02) and Central Plains Talents Program of Henan Province (Talent Training Series)—Top Young Talents in Central Plains (ZYYCYU202012170).

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Authors and Affiliations

  1. College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, People’s Republic of China

    Hongzheng Sun, Fuhao Li, Ting Peng, Junzhou Li & Yanxiu Du

  2. Henan Zhumadian Agricultural School, Zhumadian, 463000, People’s Republic of China

    Zeke Yuan

  3. Xinxiang Academy of Agricultural Sciences, Xinxiang, 453004, People’s Republic of China

    Qianqian Zhang

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  1. Hongzheng Sun
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  2. Zeke Yuan
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  3. Fuhao Li
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  5. Ting Peng
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  6. Junzhou Li
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  7. Yanxiu Du
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Contributions

HS and YD contributed to the study’s conception and design. Experiments was done by ZY, FL and QZ. TP and JL helped in data analysis. HS wrote the manuscript. All authors read and approved the final manuscript.

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Correspondence to Yanxiu Du.

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Supplementary Information

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11033_2023_8537_MOESM1_ESM.pdf

Supplementary file1 (PDF 163 KB) Fig. S1 Chromosome distribution of polymorphic SNPs and InDels between japonica rice varieties Shuijing3 and Lamujia. The color indicated numbers of polymorphic sites in each 10kb window size.

11033_2023_8537_MOESM2_ESM.pdf

Supplementary file2 (PDF 187 KB) Fig. S2 SNP index of the BC1F2 population QTL-seq. A, SNP index of high chalkiness bulk; B, SNP index of low chalkiness bulk; C, delta SNP index between high and low chalkiness bulk.

Supplementary file3 (DOCX 18 KB)

Supplementary file4 (XLSX 478 KB)

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Sun, H., Yuan, Z., Li, F. et al. Mapping of qChalk1 controlling grain chalkiness in japonica rice. Mol Biol Rep 50, 5879–5887 (2023). https://doi.org/10.1007/s11033-023-08537-8

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