Research articleConstruction of chromosome segment substitution lines of Dongxiang common wild rice (Oryza rufipogon Griff.) in the background of the japonica rice cultivar Nipponbare (Oryza sativa L.)
Introduction
Rice breeding in China has undergone two major changes: from dwarf breeding to heterosis utilization in the last century and then to super rice cultivation, which is the approach used today. Every change in breeding practices has resulted from the exploration and utilization of important rice germplasm resources, but the homogenization of rice varieties is becoming increasingly severe. For example, the gene pool used for the breeding of parent materials of japonica rice varieties in northern China has narrowed, and the genetic diversity has declined sharply. Rice production is an eternal theme in the development of the rice industry. By 2050, the production of rice will need to increase by 60–70% to meet the needs of population growth in Asia (Tester and Langridge, 2010). In addition, in some countries, such as China, the improvement of living standards over the past decade has resulted in an increased demand for high-quality rice. Panicle-related traits, such as panicle length, grain number, grain length and width, are related to rice yield and play important roles in rice grain quality. However, the identification of new resources of existing varieties to further improve both rice yield and quality has proven difficult. Wild rice species are wild relatives of cultivated rice and contain large numbers of genes related to traits such as disease resistance, stress resistance, rice yield and grain quality. The use of wild rice species to expand the gene pool of cultivated rice and increase the genetic diversity of varieties is an effective approach for improving rice breeding and production (Huang et al., 2012).
The genus Oryza includes cultivated rice and wild rice species. Cultivated rice comprises two species (O. sativa and O. glaberrima) with the AA genome type (2n = 24), whereas wild Oryza comprises 22 species (O. barthii, O. glumaepatula, O. longistaminata, O. meridionalis, O. nivara, O. rufipogon, O. punctata, O. officinalis, O. rhizomatis, O. minuta, O. eichingeri, O. alta, O. grandiglumis, O. latifolia, O. australiensis, O. brachyantha, O. longiglumis, O. ridleyi, O. schlechteri, O. granulata, O. meyeriana, and O. coarctata) with the AA, BB, CC, BBCC, CCDD, EE, FF, GG, HHJJ, and HHKK genome types (2n = 24 or 48) (Vaughan, 1994; Ge et al., 1999; Sanchez et al., 2013). Cultivated rice was domesticated from wild Oryza species, and during this domestication process, the diversity of morphological traits, including plant height, tillering number, flowering behavior, and panicle, leaf and seed characteristics, in cultivated rice was reduced by 40% relative to that in wild Oryza species. In addition, the domestication process of rice resulted in the loss of several biotic and abiotic stress-related genes (Sun et al., 2001; Xie et al., 2008). Due to a research emphasis on the identification of wild rice resources, many rice disease-resistance and stress-tolerance genes have been discovered in recent years. For example, many bacterial blight-resistance genes have been identified in wild rice, including Xa21 from O. longistaminata (Ronald et al., 1992; Song et al., 1995), Xa23 from O. rufipogon (Wang et al., 2015), Xa33 and Xa38 from O. nivara (Hemal et al., 2012; Kumar et al., 2012), Xa27 from the tetraploid wild rice species O. minuta (Gu et al., 2004), and Xa32(t) from O. australiensis (Zheng et al., 2009). Furthermore, genes related to insect resistance, cold tolerance and male fertility have been found in wild rice (He et al., 2012; Huang et al., 2013; Xiao et al., 2015; Hu et al., 2016).
Three species of wild rice are distributed in China: O. rufipogon, O. officinalis and O. meyeriana. O. rufipogon and O. sativa share the AA genome type and are very closely related, and O. rufipogon is an ancestor of modern rice. To date, most varieties bred using conventional methods, hybridization and high-yield- and high-grain-quality-targeted breeding have O. rufipogon as one parent. China is rich in wild rice resources, which are widely distributed in six onshore provinces (Guangdong, Guangxi, Yunnan, Hunan, Fujian and Jiangxi) and two island provinces (Hainan and Taiwan) (Gao et al., 2000). One of these resources, O. rufipogon is believed to have the northernmost distribution of any species of wild rice (N 28°14’) (Luo et al., 2012). Because this species was discovered in Dongxiang County, Jiangxi Province, in 1978, it is called Dongxiang common wild rice. This rice species exhibits abundant genetic diversity and is a potential source of many genes related to cold and drought tolerance, disease and insect resistance, wide cross-compatibility, fertility restoration, cytoplasmic male sterility, and high grain yield. Dongxiang wild rice plays important roles in basic rice research and industrial development and is known as “the panda of wild plants” (Tian et al., 2006; Xie et al., 2010).
Although common wild rice and cultivated rice have the same genome type, they exhibit substantial differences in their genome sequences. A stable and reliable genetic population is important for utilizing or studying common wild rice. The construction of temporary genetic populations, such as F2 or BC1 populations, and permanent primary genetic populations, such as doubled-haploid and recombinant inbred lines, is easy. However, due to interference from genetic background noise, such populations exhibit not only a low QTL detection efficiency but also poor stability, and QTL detection with fine mapping requires the construction of near-isogenic lines and secondary segregating populations (Yano, 2001). Chromosome segment substitution lines (CSSLs, also called introgression lines (ILs)) are not subject to the limitations of the abovementioned genetic populations. A CSSL population is generally developed through crossing, advanced backcrossing with marker-assisted selection (MAS) and self-crossing. Each final CSSL carries a single or a few chromosomal segments from the donor parent in the background of the recurrent parent and can thus be regarded as a near-isogenic line of the recurrent parent. Using O. rufipogon, O. glumaepatula and some improved cultivars as the donor parent, many sets of CSSLs and ILs have been constructed in rice (Tian et al., 2006; Tan et al., 2007; Hirabayashi et al., 2010; Qiao et al., 2016; Takai et al., 2014; Nagata et al., 2015; Uga et al., 2015). The CSSL strategy is particularly suitable for the construction of a genetic population with wild rice as the donor parent. CSSLs can solve the problem of the extreme distance between the early-generation populations of wild rice plants and their cultivated rice offspring (Kubo et al., 2002; Furuta et al., 2014). In addition, CSSLs can also minimize linkage drag, facilitate the map-based cloning of QTLs and produce new resources for CSSL-based rice breeding (Yamamoto et al., 2000).
In this study, we used Dongxiang wild rice as the donor and the japonica rice cultivar Nipponbare as the recurrent parent to construct a set of CSSLs comprising 104 families. The CSSL genotypes were analyzed using 203 molecular markers that uniformly covered the 12 chromosomes, and the set of constructed CSSLs covered 87.94% of the genome of Dongxiang wild rice. The subsequent characterization of CSSLs associated with the transmission of panicle-related traits from common wild rice to cultivated rice revealed several novel QTLs.
Section snippets
Plant materials and construction of CSSLs
A Chinese common wild rice (O. rufipogon Griff.) accession (C35) collected from Dongxiang, Jiangxi Province, was used as the donor parent. Nipponbare, a typical japonica rice cultivar (O. sativa L.) used in the International Rice Genome Sequencing Project (IRGSP), was used as the recurrent parent. Extensive genomic information is available for Nipponbare, and this cultivar is used worldwide in rice functional genomics research. All materials, including plants of different generations during the
Development of CSSLs
To construct the CSSLs, the F1 plant derived from a cross between Nipponbare and Dongxiang wild rice was successively backcrossed three times with Nipponbare, and 187 BC3F1 lines were obtained. The genotypes of the BC3F1 lines were surveyed using 203 markers, and 101 plants were selected for backcrossing. MAS resulted in the identification of 87 and 79 CSSLs from BC4F1 and BC5F1, respectively, and the BC5F1 plants were self-crossed five times to obtain the BC5F6 population. The genotypes of 368
Discussion
In this study, we used an accession of O. rufipogon as a donor parent with MAS to screen 104 individuals from a 368-line BC5F6 population and constructed a set of CSSLs. The average coverage of the Dongxiang wild rice genome in the CSSLs was 87.94%. A few chromosomal regions (nine molecular markers) were not covered by the CSSLs, consistent with results obtained in previous studies (Tian et al., 2006; Qiao et al., 2016; Kubo et al., 2002). Using the same Dongxiang wild rice accession as the
Conclusions
In conclusion, we constructed 104 CSSLs of O. rufipogon in a japonica rice background. The CSSL population covered approximately 87.94% of the wild rice genome, and the average introgressed segment length was 3.3 Mb. Each CSSL contained an average of four introgressed segments. In addition, we identified 18 panicle trait-related QTLs from the O. rufipogon donor. The genes of some of these QTLs have been cloned (qGL3-2 and qGW8), and some of the QTLs were previously reported (qPNL1-2 and qPNL1-3
Contributions
XM, LH and ML designed the study. BH and JT analyzed the phenotypic data. BH, JT, JZ, DC and LG contributed to genotype analysis. ML and HZ made crossing and backcrossing. XM, BH and JT performed QTL analysis and wrote the manuscript. All authors read and approved the final manuscript.
Declaration of competing interestCOI
The authors declare that there is no conflict of interest.
Acknowledgments
This work was supported by the National Key Research and Development Program of China (2016YFD0100101, 2016YFD0100301), the National Science and Technology Support Program of China (2015BAD01B01-1), the CAAS Science and Technology Innovation Program, National Infrastructure for Crop Germplasm Resources (NICGR 2017-01), and the Protective Program of Crop Germplasm of China (2017NWB 036-01, 2017NWB036-12-2).
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2021, Crop JournalCitation Excerpt :Most were generated between indica and japonica subspecies using either indica [26,27,30,31,45–53] or japonica [27,28,52–64] as recipient parents. CSSLs or ILs were also created by introgression of chromosome segments from African cultivated rice (O. glaberrima) [65–72] or Oryza wild species such as O. nivara [73,74], O. rufipogon [75–85], O. barthii [86,87], O. meridionalis [88,89], and O. glumaepatula [81,87,90,91] into cultivars. In addition, a set of CSSLs has been created in weedy rice [92].
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Xiaoding Ma and Bing Han contributed equally to this work.