Development of Chromosome Segment Substitution Lines Derived from Backcross between Two Sequenced Rice Cultivars, Indica Recipient 93-11 and Japonica Donor Nipponbare

Abstract

Chromosome segment substitution lines (CSSLs) are powerful tools for detecting and precisely mapping quantitative trait loci (QTLs) and evaluating gene action as a single factor. In this study, 103 CSSLs were produced using two sequenced rice cultivars: 93-11, an elite restorer indica cultivar as recipient, and Nipponbare, a japonica cultivar, as donor. Each CSSL carried a single chromosome substituted segment. The total length of the substituted segments in the CSSLs was 2,590.6 cM, which was 1.7 times of the rice genome. To evaluate the potential application of these CSSLs for QTL detection, phenotypic variations of seed shattering, grain length and grain width in 10 CSSLs were observed. Two QTLs for seed shattering and three for grain length and grain width were identified and mapped on rice chromosomes. The results demonstrate that CSSLs are excellent genetic materials for dissecting complex traits into a set of monogenic loci. These CSSLs are of great potential value for QTL mapping and plant marker-assisted breeding (MAB).

Chromosome Segment Substitution Lines: A Powerful Tool for the Introgression of Valuable Genes from Oryza Wild Species into Cultivated Rice (O. sativa)

“…Using multiple 384-SNP assays, a large number of SNP markers can be employed for genotyping which will allow more precise identification of the genome-wide introgression lines. The SNP-linked genes/QTLs on the introgressed segments can also be mapped and cloned with relative ease, due to the small size of the substituted chromosome segments in the CSSLs, and the known physical locations of SNPs (Zhu et al 2009). Even larger numbers of polymorphic SNP markers with uniform distribution over the 12 rice chromosomes can be chosen from the newly constructed high density 44K-SNP array or 1 million SNP array (a future endeavor) after genotyping the parental lines (Tung et al 2010).…”

“…With similar objectives as described above, CSSLs have also been developed in the background of an indica cultivar with donor segments from japonica varieties. These populations include HJX74 (indica, recurrent parent) × four japonica donors (Suyunuo, IRAT261, Lemont, and JAPAR9) developed to map QTLs for different traits including days to heading and grain length (Xi et al 2006); Zhenshen 97B (indica recurrent parent) × Nipponbare (japonica donor) to map QTL alleles enhancing the culturability of indica rice ); and '93-11' (indica recurrent parent) × Nipponbare (Japonica donor) to detect QTLs for panicle number per plant and grain yield under low nitrogen and phosphorus conditions (Wang et al 2009) and seed shattering, grain length, and grain width (Zhu et al 2009). …”

“…As differences between CSSLs and their parental lines must be due to the genes and QTLs located in the introgressed regions (Aida et al 1998;Eshed and Zamir 1994), CSSLs are considered excellent starting materials for dissecting complex traits into a set of monogenic loci (Zhu et al 2009). Through additional backcrossing and selfing of CSSLs, NILs can be generated for fine mapping genes, as well as, for precise estimation of the effect of each gene after testing in multiple environments.…”

Root responses in chromosome segment substitution lines of rice 'KDML105' under early drought stress

“…In recent years, the use of genotypic variation for genomic research on drought tolerance mechanisms has been enhanced by the development of introgression lines from the segregating populations (Chen et al, 2006;Zhu et al, 2009;Xu et al, 2010;Shim et al, 2010;Furuta et al, 2014). Chromosome segment substitution lines (CSSLs) are a genetic resource that contains the genetic background of the recurrent parent, with overlapping chromosome segments of the donor parent.…”

Fine Mapping of qHD4-1, a QTL Controlling the Heading Date, to a 20.7-kb DNA Fragment in Rice (Oryza sativa L.)

“…Hence several sets of secondary mapping populations for various crops have already been developed, such as introgression lines in tomato (Eshed and Zamir 1995;Chetelat et al 2000), Chromosome-segment substitution lines (CSSLs) in rice (Doi et al 1997;Kubo et al 2002;Ebitani et al 2005;Zhu et al 2009), recombinant chromosome substitution lines in barley and maize (Matus et al 2003;Xu et al 2009), and backcross inbred lines in lettuce and Cucurbita pepo L. (Jeuken and Lindhout 2004;Guo et al 2010). Secondary segregation populations as like F 2 and F 3 can be developed from a cross between a near isogenic line (NIL) with target QTL and the recurrent parent, which can be used to identify recombinants with the introgression segment using flanking markers (Yamamoto et al 1998;Yano et al 2000a, b).…”