Abstract
Common wild rice (Oryza rufipogon Griff.) represents an important resource for rice improvement. Genetic populations provide the basis for a wide range of genetic and genomic studies. In particular, chromosome segment substitution lines (CSSLs) are most powerful tools for the detection and precise mapping of quantitative trait loci (QTLs). In this study, 146 CSSLs were produced; they were derived from the crossing and back-crossing of two rice cultivars: Dongnanihui 810 (Oryza sativa L.), an indica rice cultivar as the recipient, and ZhangPu wild rice, a wild rice cultivar as the donor. First, a physical map of the 146 CSSLs was constructed using 149 molecular markers. Based on this map, the total size of the 147 substituted segments in the population was 1145.65 Mb, or 3.04 times that of the rice genome. To further facilitate gene mapping, heterozygous chromosome segment substitution lines (HCSSLs) were also produced, which were heterozygous in the target regions. Second, a physical map of the 244 HCSSLs was produced using 149 molecular markers. Based on this map, the total length of substituted segments in the HCSSLs was 1683.75 Mb, or 4.47 times the total length of the rice genome. Third, using the 146 CSSLs, two QTLs for plant height, and one major QTL for apiculus coloration were identified. Using the two populations of HCSSLs, the qPa-6-2 gene was precisely mapped to an 88 kb region. These CSSLs and HCSSLs may, therefore, provide powerful tools for future whole genome large-scale gene discovery in wild rice, providing a foundation enabling the development of new rice varieties. This research will also facilitate fine mapping and cloning of quantitative trait genes, providing for the development of superior rice varieties.
Highlights
Given the rapid increase in world population, the century may witness serious global food shortage problems
Sun et al (2002) compared the genetic diversity between common wild rice and cultivated rice, and the results showed that the number of alleles of cultivated rice was only 60% that of wild rice, indicating that many alleles were lost during the course of domestication from wild to cultivated rice
A lot of 302 simple sequence repeats (SSR) markers were selected from dense rice microsatellite maps (McCouch et al, 2002), and 206 InDel markers were developed using Primer Premier 5.0 software according to the publicly available rice genome sequence comparisons between Nipponbare and 93112
Summary
Given the rapid increase in world population, the century may witness serious global food shortage problems. Rice is one of the most important crops in the world, and in order to meet the growing demand for food driven by population growth and economic development, global rice production must double by 2050 (Arbelaez et al, 2015) This signals the importance of identifying, transferring, and utilizing beneficial allele genes from wild and cultivated rice. Several CSSLs in rice have been developed and many QTLs for traits of biological and economic interest have been detected (Kubo et al, 2002; Ebitani et al, 2005; Mei et al, 2006; Takai et al, 2007; Zhu et al, 2009; Xu et al, 2010; Chen et al, 2014; Nagata et al, 2015; Subudhi et al, 2015) These achievements have undoubtedly enhanced the understanding of complex traits and promoted plant genomic studies. It will be possible to illustrate the genetic mechanisms of complex traits in plant functional genomics
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