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Finding new addictive QTL for yield traits based on a high-density genetic map in hybrid rice

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Abstract

Rice is one of the most important food crops in the world. To discover the genetic basis of yield components in super hybrid rice Nei2You No.6, 386 recombinant inbred sister lines (RISLs) were obtained for mapping quantitative trait loci (QTL) responsible for grain yield per plant, number of panicles per plant, grain number per panicle and 1000-grain weight. Using whole genome re-sequencing, a high-density linkage map consisting of 3203 Bin markers was constructed with total genetic coverage of 1951.1 cM and average density of 0.61 cM. A total of 43 yield-related QTL were mapped to all 12 chromosomes, and each explained 2.40–10.17% phenotypic variance, indicating that the medium and minor effect QTL are genetic basis for high yield of Nei2You No.6. With positive effect, 28 out of the 43 QTL are inherited from the maintainer line (Nei2B). Nine loci, qGYP-6b, qGNP-6c, qNP-7, qTGW-1a, qTGW-5, qTGW-7, qTGW-10b, qTGW-10c and qTGW-12 showed stable effects across multiple environments. Five of these nine QTL were co-located with previously reported QTL, and four novel locus, qNP-7, qGNP-6c, qTGW-7 and qTGW-12, were firstly identified in the present study. Subsequently, qNP-7, qTGW-7 and qTGW-12 were validated using corresponding paired sister lines which differed only in the target genome region. The recombinant inbred sister lines is an effective tool for mapping and confirming QTL of yield-associated traits. Newly detected QTL provide new resource for investigating genetics of yield components and will accelerate molecular breeding in rice.

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Abbreviations

FY:

Fuyang

LS:

Lingshui

RISL:

Recombinant inbred sister line

GNP:

Grain number per panicle

GYP:

Grain yield per plant

NP:

The number of panicles

QTL:

Quantitative trait loci

SNP:

Single nucleotide polymorphism

TGW:

Thousand grain weight

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Acknowledgements

This research was supported by the National Key Research and Development Program (2016YFD0101801), the Fundamental Research Funds of Central Public Welfare Research Institutions (2017RG001-1), the Chinese Academy of Agricultural Sciences Innovation Project (CAAS-ASTIP-2013-CNRRI), and the Natural Science Foundation of Innovation Research Group (31521064). Funding bodies played no role in the design of the study in collection, analysis, interpretation of data or in writing the manuscript or decision to submit the article for publication. Thanks to Galal Bakr Anis for grammatically polishing this article.

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  1. Miao Zhang and Zheng-ping Zhou have contributed equally to this work.

Authors and Affiliations

  1. State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China

    Miao Zhang, Zheng-ping Zhou, Yu-yu Chen, Yong-run Cao, Chen-wei Deng, Pao Xue, Xiao-deng Zhan, Shi-hua Cheng, Li-yong Cao & Ying-xin Zhang

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  1. Miao Zhang
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Correspondence to Li-yong Cao or Ying-xin Zhang.

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Electronic supplementary material

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Electronic supplementary material 1 (TIF 91 kb)

Supplementary Figure 1. Work flow for RISL population development in the present study. LS, Lingshui; FY, Fuyang.

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Supplementary Figure 2. Phylogenetic analysis of RISLs.

Electronic supplementary material 3 (XLSX 4203 kb)

Supplementary Table 1. The number of paired RISLs in each bin. Supplementary Table 2. Comparison of QTL identified from this and previous studies. Supplementary Table 3. The bin map of the RISL population. Supplementary Table 4. The linkage map of the RISL population.

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Zhang, M., Zhou, Zp., Chen, Yy. et al. Finding new addictive QTL for yield traits based on a high-density genetic map in hybrid rice. Plant Growth Regul 93, 105–115 (2021). https://doi.org/10.1007/s10725-020-00669-2

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