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Genetic analysis for rice grain quality traits in the YVB stable variant line using RAD-seq

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Abstract

The future of rice breeding will likely be built on the basis of the further utilization of heterosis between elite cultivars and genetic resources from distant subspecies of rice. Previous studies have proved that exogenous genomic DNA transformation methods can be used to transfer genetic information from distant relatives (donor) into cultivated rice (recipient). However, the mechanism underlying this form of genetic transfer is poorly characterized, and the genes that cause the phenotypic changes in these variants are typically difficult to identify. This study examined YVB, a stable variant line with greatly improved grain quality traits that was derived from an indica variety (V20B) by transferring genomic DNA of O.minuta through the “spike-stalk injection method (SIM)”. We used restriction-site associated DNA sequencing technology (RAD-seq) to evaluate a population of BC1F5 backcross lines (YVB × V20B); the RAD-seq data were used to construct a genetic linkage map with high-density SNPs for use in association analysis exploring genotype–phenotype relationships at the whole-genome level. A total of 17 quantitative trait loci (QTLs) for rice quality traits were mapped to chromosomes 3, 5, 6, 8, and 9. 8 major QTLs controlling different phenotypic variations were mapped to the same region of chromosome 5. This region contained the GS5 gene for grain weight and the qSW5/GW5 gene for grain width. This study provides new resources and insights into the molecular mechanisms of grain trait phenotypic variation and the transmission of genetic information via the introduction of genomic DNA to a distantly related crop relative species.

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Abbreviations

RAD-seq:

Restriction site-associated DNA sequencing

SNP:

Single nucleotide polymorphism

InDel:

Insertion and deletion

QTL:

Quantitative trait loci

SIM:

Spike-stalk injection method

NGS:

Next-generation sequencing techniques

SSR:

Simple sequence repeat

RFLP:

Restriction fragment length polymorphism

TGW:

Thousand-grain weight

GL:

Grain length

GW:

Grain width

LWR:

Length/width ratio

MR:

Milled rice ratio

HR:

Head rice ratio

CA:

Chalkiness area

CR:

Chalkiness rate

AC:

Amylose content

GC:

Gel consistency

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Acknowledgments

We thank Zhicheng Yuan, Chengshu Zhou, and Wuzhong Luo of the China National Hybrid Rice Research and Development Center for the management of our field plantings. This research was financially supported by the National Natural Science Foundation of China (31471465; 31301291; 31501289) and the earmarked fund for Modern Agro-industry Technology Research Systems (CARS-01-05).

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    Authors and Affiliations

    1. State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, 736 Yuanda Erlu, Changsha, 410125, China

      Yan Peng, Yuanyi Hu, Bigang Mao, Ye Shao, Xiabing Sheng, Yaokui Li, Yumei Xia, Longping Yuan & Bingran Zhao

    2. Key Lab of Genomics, BGI-Shenzhen, Chinese Ministry of Agriculture, Shenzhen, 518083, China

      Haitao Xiang, Xuemei Ni, Gengyun Zhang & Zhiwu Quan

    3. Longping Branch, Graduate School of Central South University, Changsha, 410125, China

      Yinlin Pan

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    1. Yan Peng
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    Correspondence to Zhiwu Quan or Bingran Zhao.

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    The authors declare that they have no conflict of interest.

    Ethical standards

    The experiments complied with the current laws of the country in which they were performed.

    Additional information

    Communicated by B. Yang.

    Y. Peng and Y. Hu have contributed equally to this work.

    Electronic supplementary material

    Below is the link to the electronic supplementary material.

    Supplementary material Fig. S1 Detailed presentation of the genetic map for the BC1F5 population (TIFF 1375 kb)

    Supplementary material Fig. S2. Genome-wide scan of the BC1F5 population and QTL trait mapping (TIFF 3243 kb)

    438_2015_1104_MOESM3_ESM.doc

    Supplementary material Table S1. Statistics of the sequencing data, unique coverage, and sequencing depth for the 100 BC1F5 lines (DOC 147 kb)

    438_2015_1104_MOESM4_ESM.doc

    Supplementary material Table S2. Detection and annotation of the SNPs and InDels in V20B, YVB, and O.minuta for the qSW5, GS5, Wx, GW8, ALK, and Chalk5 genes (DOC 40 kb)

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    Peng, Y., Hu, Y., Mao, B. et al. Genetic analysis for rice grain quality traits in the YVB stable variant line using RAD-seq. Mol Genet Genomics 291, 297–307 (2016). https://doi.org/10.1007/s00438-015-1104-9

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