Science China Life Sciences

, Volume 62, Issue 4, pp 507–516 | Cite as

Genome-wide dissection of segregation distortion using multiple inter-subspecific crosses in rice

  • Guangwei Li
  • Jiye Jin
  • Yan Zhou
  • Xufeng Bai
  • Donghai Mao
  • Cong Tan
  • Gongwei Wang
  • Yidan OuyangEmail author
Research Paper


Mendelian inheritance can ensure equal segregation of alleles from parents to offspring, which provides fundamental basis for genetics and molecular biology. Segregation distortion (SD) leads to preferential transmission of certain alleles from generation to generation. Such violation of Mendelian genetic principle is often accompanied by reproductive isolation and eventually speciation. Although SD is observed in a wide range of species from plants to animals, genome-wide dissection of such biased transmission of gametes is rare. Using nine inter-subspecific rice crosses, a genome-wide screen for SD loci is performed, which reveals 61 single-locus quantitative trait loci and 194 digenic interactions showing distorted transmission ratio, among which 24 new SD loci are identified. Biased transmission of alleles is observed in all nine crosses, suggesting that SD exists extensively in rice populations. 72.13% distorted regions are repeatedly detected in multiple populations, and the most prevalent SD hotspot that observed in eight populations is mapped to chromosome 3. Xian alleles are transmitted at higher frequencies than geng alleles in inter-subspecific crosses, which change the genetic composition of the rice populations. Epistatic interaction contributes significantly to the deviation of Mendelian segregation at the whole-genome level in rice, which is distinct from that in animals. These results provide an extensive archive for investigating the genetic basis of SD in rice, which have significant implications in understanding the reproductive isolation and formation of inter-subspecific barriers during the evolution.


Oryza sativa xian/indica geng/japonica segregation distortion reproductive isolation allele frequency 


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We thank Profs. Yongzhong Xing and Shiping Wang for providing the genotype data of the populations. We also thank Yuan Wang and Xu Li for checking the data. This work was supported by grants from the National Natural Science Foundation of China (31771873 and 30800678), the National Program for Support of Top-notch Young Professionals, and the Fundamental Research Funds for the Central Universities (2662017QD033).

Supplementary material

11427_2018_9452_MOESM1_ESM.xlsx (15 kb)
Table S1 Interacting bin clusters showing significant χ2 independence test values in Nip × 9311 and XZ2 × ZS97 RIL populations.
11427_2018_9452_MOESM2_ESM.xlsx (17 kb)
Table S2 Segregation distortion regions detected in nine inter-subspecific populations in rice.


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Copyright information

© Science China Press and Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Guangwei Li
    • 1
  • Jiye Jin
    • 1
  • Yan Zhou
    • 1
  • Xufeng Bai
    • 1
  • Donghai Mao
    • 1
  • Cong Tan
    • 1
  • Gongwei Wang
    • 1
  • Yidan Ouyang
    • 1
    Email author
  1. 1.National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina

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