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Mapping quantitative trait loci (QTL) determining seed-shattering in weedy rice: evolution of seed shattering in weedy rice through de-domestication

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Abstract

Seed shattering is an important trait that distinguishes domesticated plants from their wild and weedy counterparts. This trait is essential for seed harvesting in the production of cereal crops, and therefore has attracted great attention of scientists to study the underlying genetic mechanisms of seed persistence/shattering during crop domestication. To study seed shattering in weedy rice, we analyzed the F2 offspring derived from artificial crosses between a non-shattering rice variety Minghui86 and a weedy rice accession WD1292 with strong seed shattering. We identified three seed-shattering associated quantitative trait loci (QTL), wd-qsh1, wd-qsh3, and wd-qsh5 located on chromosome-1, -3 and -5, respectively, based on the microsatellite (SSR) variation pattern of the crop-weed F2 offspring. The wd-qsh3 had the greatest contribution to seed shattering by explaining 31.41 % of the phenotypic variance, and the two remaining QTLs had relatively minor effects on phenotypic variation, ranging from 11.61 to 16.85 %. Comparative analysis indicated that the mapped QTLs (wd-qsh1, wd-qsh3 and wd-qsh5) from this study had no overlaps with any of the previously reported major shattering loci (e.g., SH4, qSH1, sh-h, and SHAT1) identified using a diverse set of rice germplasm, including cultivated, wild, and weedy rice lines. These results suggest that distinct genetic mechanisms should be evolved independently in different weedy rice groups, which allows weedy rice to adapt to the diverse agricultural environments. De-domestication plays a significant role in generating weedy rice without the involvement of wild rice in agro-ecosystems.

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Acknowledgments

This study was funded by the “973” program (2011CB100401) and the Natural Science Foundation of China (31271683, 31330014).

Conflict of interest

The authors have no conflicts of interest to declare.

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Authors and Affiliations

  1. School of Life Science, Chongqing University, Chongqing, China

    Nan Yao & Yongsheng Liu

  2. Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, 200433, China

    Lei Wang, Huanxin Yan & Bao-Rong Lu

  3. School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, China

    Yongsheng Liu

Authors
  1. Nan Yao
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  2. Lei Wang
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  3. Huanxin Yan
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  4. Yongsheng Liu
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  5. Bao-Rong Lu
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Corresponding authors

Correspondence to Yongsheng Liu or Bao-Rong Lu.

Electronic supplementary material

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10681_2014_1331_MOESM1_ESM.tif

Supplementary material 1 (TIFF 635 kb) Figure S1 The partial sequences of the SH4 gene in the sampled rice cultivar (Minghui86) and weedy rice (WD1292) parents. Sequence comparison demonstrates the identical mutational nucleotide (T) at the functional nucleotide polymorphism (FNP) site of the cultivar and weedy parents, as indicated by a grey box, suggesting that both parents are non-shattering type for the SH4 gene. The straight long-line represents the untranslated region of SH4. The black box at the right side of the long-line represents the first exon of SH4. The stripped box represents a part of intron. The broken lines indicate the compared region included in the partial sequences (ca. 240 bp). The method for sequencing the partial SH4 gene followed the description of Zhu et al. (2012)

Supplementary material 2 (DOC 69 kb)

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Yao, N., Wang, L., Yan, H. et al. Mapping quantitative trait loci (QTL) determining seed-shattering in weedy rice: evolution of seed shattering in weedy rice through de-domestication. Euphytica 204, 513–522 (2015). https://doi.org/10.1007/s10681-014-1331-x

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