Abstract
Heading date is an important agronomic trait in rice (Oryza sativa L.); it determines the geographical and seasonal adaptability of the crop. Single segment substitution lines (SSSLs) have become the preferred experimental materials in mapping functional genetic variations as the particular chromosome segments from donor genotypes can be evaluated for their impact on the phenotype in a recurrent recipient background. The phenotypic differences can be attributed to the control of quantitative trait loci (QTLs). Here, we evaluated a library consisting of 1,123 SSSLs in the same genetic background of an elite rice variety, Huajingxian74 (HJX74), and revealed four SSSLs, W05-1-11-2-7-6 (W05), W08-16-3-2 (W08), W12-28-58-03-19-1 (W12), and W22-9-5-2-4-9-3 (W22), which had a significantly different heading date compared to HJX74. To further genetically dissect the QTLs controlling heading date on chromosomes 3, 6, and 10, four SSSLs were used to develop 15 secondary SSSLs with the smaller substituted segments. The qHD-3 heading date QTL detected in W05 and W08 was delimited to an interval of 4.15 cM, whereas qHD-6-1 and qHD-6-2 heading date QTLs dissected from the substituted segments in W12 were mapped to the intervals of 2.25-cM and 2.55-cM, respectively. The qHD-10 QTL detected on the substituted segment in W22 was mapped to an interval of 6.85-cM. The nucleotide and amino acid sequence changes for those genes in the secondary SSSLs were also revealed. The allele variations of those genes might contribute to the heading date QTLs on chromosome 3 (DTH3, OsDof12, and EHD4), chromosome 6 (Hd3a, Hd17, and RFT1), and chromosome 10 (Ehd1 and Ehd2). These sequence variations in heading date genes would be useful resources for further studying the function of genes, and would be important for rice breeding. Overall, our results indicate that secondary SSSLs were powerful tools for genetic dissection of QTLs and identification of differentiation in the genes.
Highlights
Rice (Oryza sativa L.) is a cereal crop used as a staple food for more than half of the population in the world, and is important for global food security [1, 2]
The heading time for W22 was 113 days; this segment substitution lines (SSSLs) has an estimated 16.25-cM long substituted segment from its donor, Khazar, on chromosome 10. These results indicated that at least one QTL for heading date was located on the substituted segments in each of the four SSSLs
A library of 1,123 SSSLs has been constructed in rice, using the cultivar HJX74 as the recipient parent and 24 other varieties as donors of substituted chromosome segments, which had an average of 19.3 cM in size [20]
Summary
Rice (Oryza sativa L.) is a cereal crop used as a staple food for more than half of the population in the world, and is important for global food security [1, 2]. Several genes and genetic loci that regulate heading date have been identified in past decades using molecular genetics [3,4,5,6,7,8]. Many important traits in rice, such as yield, heading date, grain quality, and culm length, are regulated by multiple genes, representing quantitative traits with complex inheritances. Secondary segregation materials like F2 and F3 populations can be developed from a cross between a near isogenic line (NIL) with the target QTL and the recurrent parent, which can be used to identify recombinants with the introgression segment using flanking markers [16]. Each SSSL contained homozygous genetic background from its recipient except the substituted segment from a donor, and could be used to dissect polygenic traits into a set of monogenic loci. SSSLs developed recently are powerful tools for analyzing genetic mechanisms of QTLs and elucidating gene functions in plants [17,18,19]
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