QTL and QTL networks for cold tolerance at the reproductive stage detected using selective introgression in rice

PLoS One. 2018 Sep 17;13(9):e0200846. doi: 10.1371/journal.pone.0200846. eCollection 2018.

Abstract

Low temperature stress is one of the major abiotic stresses limiting the productivity of Geng (japonica) rice grown the temperate regions as well as in tropical high lands worldwide. To develop rice varieties with improved cold tolerance (CT) at the reproductive stage, 84 BC2 CT introgression lines (ILs) were developed from five populations through backcross breeding. These CT ILs plus 310 random ILs from the same BC populations were used for dissecting genetic networks underlying CT in rice by detecting QTLs and functional genetic units (FGUs) contributing to CT. Seventeen major QTLs for CT were identified using five selective introgression populations and the method of segregation distortion. Of them, three QTLs were confirmed using the random populations and seven others locate in the regions with previously reported CT QTLs/genes. Using multi-locus probability tests and linkage disequilibrium (LD) analyses, 46 functional genetic units (FGUs) (37 single loci and 9 association groups or AGs) distributed in 37 bins (~20%) across the rice genome for CT were detected. Together, each of the CT loci (bins) was detected in 1.7 populations, including 18 loci detected in two or more populations. Putative genetic networks (multi-locus structures) underlying CT were constructed based on strong non-random associations between or among donor alleles at the unlinked CT loci/FGUs identified in the CT ILs, suggesting the presence of strong epistasis among the detected CT loci. Our results demonstrated the power and usefulness of using selective introgression for simultaneous improvement and genetic dissection of complex traits such as CT in rice.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acclimatization / physiology*
  • Cold Temperature*
  • Crosses, Genetic
  • Epistasis, Genetic / physiology*
  • Linkage Disequilibrium / physiology*
  • Oryza / genetics*
  • Quantitative Trait Loci / physiology*

Grants and funding

This work was supported by The "863" Key Project to JX (2014AA10A601) from the Chinese Ministry of Science & Technology (http://www.rmbreeding.cn/Index/). The funder had roles in study design, data collection and analysis, and preparation of the manuscript. This work was supported by Fundamental Research Funds for Central Non-profit Scientific Institution to JX (Y2016PT53) (http://www.caas.net.cn/). The funder had a role in data collection and analysis. This work was supported by The Shenzhen Peacock Plan to ZL (20130415095710361) (http://www.szsti.gov.cn/). The funder had roles in data collection and analysis, and preparation of the manuscript. This work was supported by Bill and Melinda Gates Foundation project to ZL (No. OPP1130530) (https://www.gatesfoundation.org/). The funder had a role in decision to publish. This work was supported by Dapeng district industry development special funds to LM (No. KY20150203) (http://www.dpxq.gov.cn/). The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. This work was supported by The National Natural Science Foundation of China to LM (No. 31601286) (https://isisn.nsfc.gov.cn/). The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.