Abstract
Common wild rice contains valuable resources of novel alleles for rice improvement. It is well known that genetic populations provide the basis for a wide range of genetic and genomic studies. In particular, chromosome segment substitution lines (CSSLs) ais a powerful tool for fine mapping of quantitative traits, new gene discovery and marker-assisted breeding. In this study, 132 CSSLs were developed from a cultivated rice (Oryza sativa) cultivar (93-11) and common wild rice (Oryza rufipogon Griff. DP30) by selfing-crossing, backcrossing and marker-assisted selection (MAS). Based on the high-throughput sequencing of the 93-11 and DP30, 285 pairs of Insertion-deletions (InDel) markers were selected with an average distance of 1.23 Mb. The length of this DP30-CSSLs library was 536.4 cM. The coverage rate of substitution lines cumulatively overlapping the whole genome of DP30 was about 91.55%. DP30-CSSLs were used to analyze the variation for 17 traits leading to the detection of 36 quantitative trait loci (QTLs) with significant phenotypic effects. A cold-tolerant line (RZ) was selected to construct a secondary mapping F2 population, which revealed that qCT2.1 is in the 1.7 Mb region of chromosome 2. These CSSLs may, therefore, provide powerful tools for genome wide large-scale gene discovery in wild rice. This research will also facilitate fine mapping and cloning of QTLs and genome-wide study of wild rice. Moreover, these CSSLs will provide a foundation for rice variety improvement.
Highlights
Wild rice (Oryza rufipogon Griff.) contains many novel and useful alleles that control tiller number, shattering, dormancy, pericarp color, mating type, panicle architecture and grain size and number [1]
We evaluated the variation in plant architecture, agronomic and cold tolerance traits (DP30, DP30-chromosome segment substitution lines (CSSLs) and 93-11) and calculated the phenotypic values of these traits during two seasons
We speculated that the biased distribution was due to continuous backcrossing, that the CSSLs without related trait substitution segments were similar to 93-11
Summary
Wild rice (Oryza rufipogon Griff.) contains many novel and useful alleles that control tiller number, shattering, dormancy, pericarp color, mating type, panicle architecture and grain size and number [1]. Single segment substitution lines (SSSLs) libraries has been utilized to detect several QTLs related to plant height, heading date, seed setting rate and 1000-grain weight [10]. These achievements have undoubtedly enhanced the understanding of complex traits and encouraged plant genomic studies. A cold-tolerant line (RZ) was selected to construct a secondary mapping F2 population, which revealed that qCT2.1 is in the 1.7 Mb region of chromosome 2 These CSSLs may, provide powerful tools for genome wide large-scale gene discovery in wild rice. These CSSLs will provide a foundation for rice variety improvement
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