Identification and Fine Mapping of a Stably Expressed QTL for Cold Tolerance at the Booting Stage Using an Interconnected Breeding Population in Rice

PLoS One. 2015 Dec 29;10(12):e0145704. doi: 10.1371/journal.pone.0145704. eCollection 2015.

Abstract

Cold stress is one of the major abiotic stresses that impede rice production. A interconnected breeding (IB) population consisted of 497 advanced lines developed using HHZ as the recurrent parent and eight diverse elite indica lines as the donors were used to identify stably expressed QTLs for CT at the booting stage. A total of 41,754 high-quality SNPs were obtained through re-sequencing of the IB population. Phenotyping was conducted under field conditions in two years and three locations. Association analysis identified six QTLs for CT on the chromosomes 3, 4 and 12. QTL qCT-3-2 that showed stable CT across years and locations was fine-mapped to an approximately 192.9 kb region. Our results suggested that GWAS applied to an IB population allows better integration of gene discovery and breeding. QTLs can be mapped in high resolution and quickly utilized in breeding.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromosome Mapping*
  • Cold-Shock Response / genetics*
  • Gene Expression Regulation, Plant*
  • Oryza / genetics*
  • Oryza / physiology*
  • Plant Breeding*
  • Polymorphism, Single Nucleotide
  • Quantitative Trait Loci / genetics*

Grants and funding

This work was funded by Shenzhen Technology Research & Development (http://www.szsti.gov.cn/) (#: JSGG20121026152117750, Recipient: JLX); the "863" Key Project to JLX (2014AA10A601) from the Chinese Ministry of Science & Technology (http://www.863.gov.cn/); the Shenzhen Peacock Plan (http://www.szsti.gov.cn/) (#: 20130415095710361, Recipient: ZKL); the CAAS Innovative Team Award to JL Xu’s team (http://www.caas.net.cn/); and the China Postdoctoral Science Foundation (http://res.chinapostdoctor.org.cn/BshWeb/index.shtml) (#: 2015M571176, Recipient: YJZ). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.