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Identification of genome-wide SNPs associated with combining ability for grain quality traits in parents of hybrid japonica rice (Oryza sativa L.)

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Abstract

Improving the combining ability for grain quality traits of the parents is the key factor to enhance averaged bulk grain quality of hybrid japonica rice. Eight quality traits including brown rice rate, milled rice rate (MRR), head rice rate (HRR), chalkiness degree (CD), percentage of chalky grain (PCG), alkali spreading value (ASV), gel consistency (GC) and amylose content (AC) of the bulked sample of rough rice harvested from the 81 F1 hybrid plants were investigated in 2014 and 2015. By combining the phenotypic data of general combining ability (GCA) for the quality traits with genotypic data of single nucleotide polymorphism (SNP) obtained by genotyping by sequencing method, CAScreen1.0 program compiled by MATLAB language was conducted to identify the elite SNP genotype associated with combining ability of quality traits in parents. Totally 35 elite SNP genotypes involving 22 genes (genotypes) were detected associated with GCA of seven quality traits (P < 0.05) in both 2014 and 2015. Seven and four SNPs were detected associated with combining ability for MRR and HRR, respectively. For PCG and CD, six and ten SNPs were detected associated with combining ability of parents, respectively. Six SNPs involving two genes were detected for combining ability of GC. Only two SNPs were detected which associated with combining ability for ASV. For combining ability of AC, six elite SNPs genotype were detected. Among them, elite SNP genotype of LOC_Os08g25220 (T/C) located on chromosome 8 could significantly reduce AC content in mixed rice samples of hybrid japonica rice.

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Abbreviations

BRR:

Brown rice rate

MRR:

Milled rice rate

HRR:

Head rice rate

ASV:

Alkali spreading value

GC:

Gel consistency

CD:

Chalkiness degree

PCG:

Percentage of chalky grain

AC:

Amylose content

SSR:

Simple sequence repeat

SNP:

Single nucleotide polymorphism

GBS:

Genotyping by sequencing

GCA:

General combining ability

SCA:

Special combining ability

CMS:

Cytoplasmic male sterile line

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Acknowledgements

We thank all the breeding institutions including Jiangsu Academy of Agricultural Sciences, Changshu Institute of Agricultural Sciences, Agricultural Science Institute of Huaiyin District, Zhejiang Academy of Agricultural Sciences, China National Rice Research Institute, Xinjiang Academy of Agricultural Sciences, Agricultural Reasearch Institute of Yandu District, Tianjin Tianlong Seeds Science and Technology Co.,Ltd, Shanghai Academy of Agricultural Sciences, and Liaoning Academy of Agricultural Sciences for providing the seeds of CMS lines and restorer lines.

Funding

This work was supported by the National Natural Science Foundation of China (31571743), a grant from the doctoral fund of the Educational Ministry of China (20130097110001), a special programme of scientific research belonging to the Educational Ministry of China (KYZ2012-9) and a grant from the China Postdoctoral Science Foundation (2016M601830).

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Authors and Affiliations

  1. State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China

    Erbao Liu, Shangshang Zhu, Siyuan Zeng, Xiaoxiao Hu, Dalu Li, Guocan Wu, Jie Ji, Yang Liu & Delin Hong

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  1. Erbao Liu
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  2. Shangshang Zhu
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  3. Siyuan Zeng
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  4. Xiaoxiao Hu
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  5. Dalu Li
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  7. Jie Ji
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  8. Yang Liu
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  9. Delin Hong
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Contributions

DH and EL conceived and designed the experiments. EL, SSZ, YSZ, GW, DL, JJ and YL conducted the experiments. EL analysed the data and wrote the manuscript. All authors read and approved the final manuscript.

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Correspondence to Delin Hong.

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The authors declare that the research was conducted in the absence of any commercial or financial relationship that could be construed as a potential conflict of interest.

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Liu, E., Zhu, S., Zeng, S. et al. Identification of genome-wide SNPs associated with combining ability for grain quality traits in parents of hybrid japonica rice (Oryza sativa L.). Euphytica 214, 217 (2018). https://doi.org/10.1007/s10681-018-2301-5

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  • DOI: https://doi.org/10.1007/s10681-018-2301-5

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