Thermo-responsive allele of <i>sucrose synthase 3</i> (<i>Sus3</i>) provides high-temperature tolerance during the ripening stage in rice (<i>Oryza sativa</i> L.)
Kana TakeharaKazumasa MurataTakuya YamaguchiKohei YamaguchiGenki ChayaShintaro KidoYukimoto IwasakiHitoshi OgiwaraTakeshi EbitaniKotaro Miura
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Abstract:
High-temperature stress during the ripening stage leads to quality deterioration due to an increase in chalky grains in brown rice (Oryza sativa L.). In a previous study, we identified a QTL for Appearance quality of brown rice 1 (Apq1) using chromosome segment substitution lines of the indica cultivar 'Habataki' in the japonica cultivar 'Koshihikari' background and narrowed down the locus to a 48-kb region on chromosome 7. To verify the function and mechanisms of this QTL in grain appearance, in this study, we fine-mapped the gene and conducted high-temperature tolerance tests. As a result of the genetic mapping, we narrowed down the candidate region of Apq1 to a 19.4-kb region including three predicted genes. Among these, the temporal expression pattern of sucrose synthase 3 (Sus3) corresponded well with the high temperature-sensitive period during ripening, and expression of the 'Habataki' allele of Sus3 was increased under high-temperature condition. In addition, we transformed the 'Habataki' Sus3 gene into 'Nipponbare', and the transformants obtained high-temperature tolerance. Therefore, we conclude that the causal gene underlying the QTL Apq1 is the thermo-responsive Sus3 allele, and the increase in Sus3 expression under high-temperature condition during ripening leads to high-temperature tolerance in rice.Keywords:
Candidate gene
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Quantitative trait locus mapping and candidate gene analysis for salt tolerance at bud stage in rice
Soil salinization has a serious influence on rice yield and quality. How to enhance salt tolerance in rice is a topical issue. In this study, 120 recombinant inbred line populations were generated through nonstop multi-generation selfing using a male indica rice variety Huazhan ( Oryza sativa L. subsp. indica cv. ‘HZ’) and a female variety of Nekken2 ( Oryza sativa L. subsp. japonica cv. ‘Nekken2’) as the parents. Germination under 80 mM NaCl conditions was measured and analyzed, and quantitative trait locus (QTL) mapping was completed using a genetic map. A total of 16 salt-tolerance QTL ranges were detected at bud stage in rice, which were situated on chromosomes 3, 4, 6, 8, 9, 10, 11, and 12. The maximum limit of detection was 4.69. Moreover, the qST12.3 was narrowed to a 192 kb region on chromosome 12 using map-based cloning strategy. Statistical analysis of the expression levels of these candidate genes under different NaCl concentrations by qRT-PCR revealed that qST12.3 ( LOC_Os12g25200 ) was significantly down-regulated with increasing NaCl concentration, and the expression level of the chlorine-transporter-encoding gene LOC_Os12g25200 in HZ was significantly higher than that of Nekken2 under 0 mM NaCl. Sequencing analysis of LOC_Os12g25200 promoter region indicated that the gene expression difference between parents may be due to eight base differences in the promoter region. Through QTL mining and analysis, a plurality of candidate genes related to salt tolerance in rice was obtained, and the results showed that LOC_Os12g25200 might negatively regulate salt tolerance in rice. The results provide the basis for further screening and cultivation of salt-tolerant rice varieties and have laid the foundation for elucidating further molecular regulation mechanisms of salt tolerance in rice.
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Cold stress is one of the major restraints for stable stand establishment at the early seedling stage of rice (Oryza sativa L.) for much of the production area. A recombinant inbred line population derived from a japonica/indica cross were assessed for cold tolerance at early seedling stage by the paper-roll tests at 10°C. Main-effect QTL for the trait were mapped via composite interval mapping using a linkage map with 198 marker loci. Four putative QTL for the trait were identified, which were mapped to chromosomes 1, 3, 7 and 11, respectively. Among these QTL, qSCT-11 showed a large additive effect on the trait, explaining 26%-30% of the phenotypic variation in the treatment of 13 d at 10℃ with a LOD of 16-19. This QTL was closely linked to SSR marker RM202 and its positive allele came from the parent Lemont. This allele would be useful for the improvement of rice cold tolerance via marker-assisted selection.
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Abstract Tuber shape in potato is commonly regarded as displaying continuous variation, yet at the diploid level phenotypes can be discerned visually, having round or long tubers. Inheritance of qualitative tuber shape can be explained by a single locus Ro, round being dominant to long. With restriction fragment length polymorphisms (RFLPs) the Ro locus was mapped on chromosome 10. Tuber shape was also studied as a quantitative trait, using the length/width ratio as trait value. The estimated broad sense heritability was h2 = 0.80. The morphologically mapped Ro locus explained 75% of the genetic variation, indicating the presence of a major quantitative trait locus (QTL) at the Ro locus and minor genetic factors. RFLP alleles linked with Ro alleles were used to divide the progeny into four genotypic classes: RofemaleRomale:Rofemalero:roRomale:roro = 1:1:1:1. The recessive ro allele is identical by descent in both parents. The significantly different effects (P = 0.0157) of the non-identical alleles Rofemale and Romale provided evidence for multiallelism at the Ro locus. Linkage mapping of the Ro locus was compared with QTL mapping. Only those markers which are polymorphic in both parents allow accurate QTL mapping when genetic factors segregate from both parents. This finding applies to QTL mapping in all outbreeders without homozygous inbred strains.
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By using a doubled haploid population(DH) containing 67 DH lines derived from anther culture of F1 cross between Balilla (japonica) and Nanjing 11 (indica), an RFLP map was constructed, which consisted of 131 RFLP markers covering all 12 linkage groups at an average distance 14. 1 cm. When the cold tolerance was assessed by using died seedling percent in DH lines and their parents at 4 - 5 C as the indicator, a continuous distribution with two peaks was observed in the DHpopulation. The result indicated that the cold tolerance at early seedling stage in rice fitted for quantitative trait model, andwas controlled by a major gene. on the basis of QTL interval analysis with Mapmaker/QTL, 39% of the phenotypic varianceassociated with died seedling percent was explained by the QTL(Cts 7), which was at the interval G379b-RG4 on chromosome7. The mapping of cold tolerance gene Cts 7 can facilitate the rice cold tolerance breeding via marker assisted selection.
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