以特大粒水稻品系TD70和小粒籼稻品种Kasalath不同发育时期的幼穗为材料,进行转录组测序。将获得的干净读长(Clean read)以日本晴(Nipponbare)基因组序列为参考序列进行比对得到唯一读长(即特异比对到参考基因组的read),利用FPKM(Fragme...以特大粒水稻品系TD70和小粒籼稻品种Kasalath不同发育时期的幼穗为材料,进行转录组测序。将获得的干净读长(Clean read)以日本晴(Nipponbare)基因组序列为参考序列进行比对得到唯一读长(即特异比对到参考基因组的read),利用FPKM(Fragments per kilobase of transcript per million fragments mapped)法计算基因的表达水平,用GO和KEGG数据库对差异表达基因(Differentially expressed genes,DEGs)进行功能注释、富集和代谢通路分析。结果表明,在水稻幼穗发育的早、中、后3个时期分别获得3618个、4183个和5254个差异表达基因,共有4374个差异表达基因得到基因本体(Gene ontology,GO)功能注释,主要涉及DNA结合、细胞进程、信号转导、细胞增殖、物质转运等方面。KEGG数据库分析结果显示,差异表达基因共涉及119条代谢通路,主要包括淀粉和蔗糖代谢通路、内质网中的蛋白质加工通路、激素信号转导通路、细胞周期蛋白通路等。展开更多
To understand the effect of nitrogen(N) fertilizer on rice(Oryza sativa L.) eating and cooking quality(ECQ). Here, we investigated the ECQ attributes, physicochemical foundation of ECQ, and amylopectin fine structure ...To understand the effect of nitrogen(N) fertilizer on rice(Oryza sativa L.) eating and cooking quality(ECQ). Here, we investigated the ECQ attributes, physicochemical foundation of ECQ, and amylopectin fine structure of two Waxy(Wx) alleles japonica rice cultivars Nanjing 9108(NJ9108) and Huaidao 5(HD5) under four N rates(0, 150, 300, and 450 kg ha^-1). Sensory and pasting properties of the two cultivars varied depending on N rates. Compared with the control(0 kg ha^-1), the overall eating quality and sensory value were significantly decreased under the N rates of 300 and 450 kg ha^-1. Further, conventional descriptive analysis showed that the stickiness and retrogradation of cooked rice were significantly decreased. These results indicated that application of N fertilizer seems to affect the texture of cooked rice, causing it to be less sticky, lowering its retrogradation, and consequently reducing its palatability. Results from rapid visco analyzer(RVA) revealed that the peak and breakdown viscosities significantly decreased, while the setback viscosity and peak time increased under the N rates of 300 and 450 kg ha^-1. However, no significant difference was observed when the N rate was 150 kg ha^-1, indicating that less N fertilization can maintain rice ECQ. As the N rate increasing, protein content increased, whereas apparent amylose content, starch content, and gel consistency almost unchanged. Interestingly, compared with the control, under N treatments, the percentage of short amylopectin branches in NJ9108 was decreased, but increased in HD5, as controlled by amylopectin synthesis-related genes. Notably, SSI and BEIIb were down-regulated in NJ9108, whereas BEIIb was up-regulated in HD5. Thus, the palatability of both rice cultivars was significantly decreased under excessive N fertilization as a consequence of reduced stickiness and retrogradation of the cooked rice, which might have resulted from an elevated protein content and altered amylopectin fine structure. In addition, amylopectin synthesis appeared to be affected by N fertilizer and the genotype of the rice cultivar.展开更多
In this study we report the results of a decade-long breeding program for japonica super rice made by Nanjing Branch of Chinese National Center for Rice Improvement in Jiangsu Academy of Agricultural Sciences. We conc...In this study we report the results of a decade-long breeding program for japonica super rice made by Nanjing Branch of Chinese National Center for Rice Improvement in Jiangsu Academy of Agricultural Sciences. We concluded that selection of parents with good comprehensive traits and complementary advantages and disadvantages of both parents in the hybrid combination, and early selection of high heritability traits in earlier segregating generations could significantly improve the breeding efficiency. The use of closely-linked functional markers in pyramiding of multiple genes could greatly increase breeding efficiency, avoiding time-consuming and laborious steps that were used in traditional breeding program. It is also important to coordinate the yield components with variety characteristics such as yield stability, wide adaptability, lodging resistance, and an attractive grain appearance during late growth stage of rice.展开更多
Diversity of 60 conventional japonica rice accessions with good eating quality at home and abroad was analyzed using SSR molecular markers, agronomic traits and taste characteristics. A total of 290 alleles were detec...Diversity of 60 conventional japonica rice accessions with good eating quality at home and abroad was analyzed using SSR molecular markers, agronomic traits and taste characteristics. A total of 290 alleles were detected in the 60 accessions at 72 SSR loci with the high similarity coefficients varying between 0.600 and 0.924. The loci on chromosome 5 showed the greatest value in average allele number. Additionally, most of the SSR loci could detect 3 to 4 alleles. An UPGMA dendrogram based on the cluster analysis of the genetic similarity coefficients showed that the grouping trend of part of the rice accessions was geographic-related and most of the rice accessions in Jiangsu Province, China were clustered together. Furthermore, many domestic accessions from south and north origins in China were close to the foreign japonica rice varieties, as proved by their pedigree origin from the foreign high-quality sources. For taste characteristics, part of the accessions with excellent taste were clearly clustered into one category though they came from different geographical regions, which indicates that taste characteristics of some varieties were mainly genetically determined. In addition, the agronomic traits of japonica rice with good taste might be closely related with their geographical origins, but the relationship between superior taste characteristics and agronomic traits should be further clarified.展开更多
Japonica rice variety Kanto 194 as the donor of resistance gene Stv-b^i and Iow-amylose content gene Wx-mq was used to improve the resistance and eating quality of Wuyujing 3 by the breeding strategy of backcross. In ...Japonica rice variety Kanto 194 as the donor of resistance gene Stv-b^i and Iow-amylose content gene Wx-mq was used to improve the resistance and eating quality of Wuyujing 3 by the breeding strategy of backcross. In continuous backcross and selfcross generations, the related molecular markers with Stvobi and Wx-mq genes were utilized for genotypic detection by associated with resistance identification of rice stripe disease and agronomic traits selection. Finally, 10 improved lines with homozygous genotype Stv-b^i Stv-b^iWx-mqWx-mq were obtained from BC3F4 generation. The results of comparative analysis indicated that most characters of these lines were consistent with those of recipient parent Wuyujing 3, except for the improved resistance, appearance and eating quality. By evaluation of the comprehensive performance of them, two excellent lines K01 and K04 were selected for further experiments.展开更多
The rice starch viscosity characteristics, which can be indicated by Rapid Visco Analyzer profile (RVA profile), have been proved useful for the evaluation of cooking and eating quality in rice breeding program. To ...The rice starch viscosity characteristics, which can be indicated by Rapid Visco Analyzer profile (RVA profile), have been proved useful for the evaluation of cooking and eating quality in rice breeding program. To study the inheritance of the RVA profile, an F2 population of Wuyujing 3/Aichi 106 was used. The results indicated that the peak viscosity (PKV) was a typical quantitative character, and the hot paste viscosity (HPV), cool paste viscosity (CPV), setback viscosity (SBV), breakdown viscosity (BDV), and consistence viscosity (CSV) might be controlled by one major gene and several minor genes To elucidate the genetic basis of the paste viscosity characteristics, a recombinant inbred line (RIL) population derived from Nikken 2/Milyang 23 and its genetic linkage map were used to map the QTLs controlling RVA profiles in 2005 and 2006. A total of 34 QTLs distributed on chromosomes 1,2, 3, 4, 6, 7 and 8 were detected, including 19 and 15 QTLs in 2005 and 2006 respectively. Eight QTLs were both detected in the two years, qHPV6, qCPV6, qCSV6, qSBV6, and qBDV6 were located on chromosome 6, while qHPV2, qCSV2, and qCPV2were on chromosome 2.展开更多
Grain size traits, including grain length, grain width and grain thickness, are controlled by quantitative trait loci (QTLs). Many QTLs relating to rice grain size traits had been reported, but their control mechani...Grain size traits, including grain length, grain width and grain thickness, are controlled by quantitative trait loci (QTLs). Many QTLs relating to rice grain size traits had been reported, but their control mechanisms have not yet been elucidated. A recombinant inbred line (RIL) population of 240 lines, deriving from a cross between TD70, an extra-large grain size japonica line with 80 g of 1000-grain weight, and Kasalath, a small grain size indica variety, were constructed and used to map grain size QTLs to a linkage map by using 141 SSR markers in 2010 and 2011. Five QTLs for grain length, six for grain width and seven for grain thickness were detected distributing over chromosomes 2, 3, 5, 7, 9 and 12. Seven QTLs, namely qGL3.1, qGW2, qGW2.2, qGW5.1, qGW5.2, qGT2.3 and qGT3.1, were detected in either of the two years and explained for 56.19%, 4.42%, 29.41%, 10.37%, 7.61%, 21.19% and 17.06% of the observed phenotypic variances on average, respectively. The marker interval RM1347-RM5699 on chromosome 2 was found common for grain length, grain width and grain thickness; qGL3.1 and qGT3.1 were mapped to the same interval RM6080-RM6832 on chromosome 3. All 18 QTL alleles were derived from the large grain parent TD70. Most of the QTLs mapped in the present study were found the same as the genes previously cloned (GW2, GS3 or qGL3, GW5 and GS5), and several were the same as the QTLs (GS7 and qGL-7) previously mapped. Three QTLs, qGL2.2 on chromosome 2, qGW9 and qGT9 on chromosome 9, were first detected. These results laid a foundation for further fine mapping or cloning of these QTLs.展开更多
A high-yielding japonica rice variety, Wuyunjing 7, bred in Jiangsu Province, China as a female parent was crossed with a Japanese rice variety Kantou 194, which carries a rice stripe disease resistance gene Stv-b' a...A high-yielding japonica rice variety, Wuyunjing 7, bred in Jiangsu Province, China as a female parent was crossed with a Japanese rice variety Kantou 194, which carries a rice stripe disease resistance gene Stv-b' and a translucent endosperm mutant gene Wx-mq. From F2 generations, a sequence characterized amplified region (SCAR) marker tightly linked with Stv-b' and a cleaved amplified polymorphic sequence (CAPS) marker for Wx-mq were used for marker-assisted selection. Finally, a new japonica rice line, Ning 9108, with excellent agronomic traits was obtained by multi-generational selection on stripe disease resistance and endosperm appearance. The utilization of the markers from genes related to rice quality and disease resistance was helpful not only for establishing a marker-assisted selection system of high-quality and disease resistance for rice but also for providing important intermediate materials and rapid selection method for good quality, disease resistance and high yield in rice breeding.展开更多
文摘以特大粒水稻品系TD70和小粒籼稻品种Kasalath不同发育时期的幼穗为材料,进行转录组测序。将获得的干净读长(Clean read)以日本晴(Nipponbare)基因组序列为参考序列进行比对得到唯一读长(即特异比对到参考基因组的read),利用FPKM(Fragments per kilobase of transcript per million fragments mapped)法计算基因的表达水平,用GO和KEGG数据库对差异表达基因(Differentially expressed genes,DEGs)进行功能注释、富集和代谢通路分析。结果表明,在水稻幼穗发育的早、中、后3个时期分别获得3618个、4183个和5254个差异表达基因,共有4374个差异表达基因得到基因本体(Gene ontology,GO)功能注释,主要涉及DNA结合、细胞进程、信号转导、细胞增殖、物质转运等方面。KEGG数据库分析结果显示,差异表达基因共涉及119条代谢通路,主要包括淀粉和蔗糖代谢通路、内质网中的蛋白质加工通路、激素信号转导通路、细胞周期蛋白通路等。
基金funded by the China Postdoctoral Science Foundation(2017M611753)the earmarked fund for Agriculture Research System of China(CARS-01-62)+3 种基金the National Key R&D Program of China(2015BAD01B02)the Natural Science Foundation of Jiangsu Province,China(BK20180302)the Jiangsu Agriculture Science and Technology Innovation Fund,China(CX[17]3009)the Project of Henan Key Laboratory of Tea Plant Comprehensive Utilization in South Henan,China(HNKLTCU2018004)。
文摘To understand the effect of nitrogen(N) fertilizer on rice(Oryza sativa L.) eating and cooking quality(ECQ). Here, we investigated the ECQ attributes, physicochemical foundation of ECQ, and amylopectin fine structure of two Waxy(Wx) alleles japonica rice cultivars Nanjing 9108(NJ9108) and Huaidao 5(HD5) under four N rates(0, 150, 300, and 450 kg ha^-1). Sensory and pasting properties of the two cultivars varied depending on N rates. Compared with the control(0 kg ha^-1), the overall eating quality and sensory value were significantly decreased under the N rates of 300 and 450 kg ha^-1. Further, conventional descriptive analysis showed that the stickiness and retrogradation of cooked rice were significantly decreased. These results indicated that application of N fertilizer seems to affect the texture of cooked rice, causing it to be less sticky, lowering its retrogradation, and consequently reducing its palatability. Results from rapid visco analyzer(RVA) revealed that the peak and breakdown viscosities significantly decreased, while the setback viscosity and peak time increased under the N rates of 300 and 450 kg ha^-1. However, no significant difference was observed when the N rate was 150 kg ha^-1, indicating that less N fertilization can maintain rice ECQ. As the N rate increasing, protein content increased, whereas apparent amylose content, starch content, and gel consistency almost unchanged. Interestingly, compared with the control, under N treatments, the percentage of short amylopectin branches in NJ9108 was decreased, but increased in HD5, as controlled by amylopectin synthesis-related genes. Notably, SSI and BEIIb were down-regulated in NJ9108, whereas BEIIb was up-regulated in HD5. Thus, the palatability of both rice cultivars was significantly decreased under excessive N fertilization as a consequence of reduced stickiness and retrogradation of the cooked rice, which might have resulted from an elevated protein content and altered amylopectin fine structure. In addition, amylopectin synthesis appeared to be affected by N fertilizer and the genotype of the rice cultivar.
基金supported by the National Key Technologies R&D Program of China during the 12th Five-Year Plan period(2015BAD01B02)the Special Program for Rice Scientific Research,Ministry of Agriculture,China(201603002-5-1)the Construction of Modern Agricultural and Industrial Technology System Project special fund,China(CARS01-47)
文摘In this study we report the results of a decade-long breeding program for japonica super rice made by Nanjing Branch of Chinese National Center for Rice Improvement in Jiangsu Academy of Agricultural Sciences. We concluded that selection of parents with good comprehensive traits and complementary advantages and disadvantages of both parents in the hybrid combination, and early selection of high heritability traits in earlier segregating generations could significantly improve the breeding efficiency. The use of closely-linked functional markers in pyramiding of multiple genes could greatly increase breeding efficiency, avoiding time-consuming and laborious steps that were used in traditional breeding program. It is also important to coordinate the yield components with variety characteristics such as yield stability, wide adaptability, lodging resistance, and an attractive grain appearance during late growth stage of rice.
基金supported by the National Science and Technology Support Program(Grant No.2006BAD01A01-5)the Key Program of the Development of Variety of Genetically Modified Organisms(Grant No.2008ZX08001-006)+2 种基金Special Program for Rice Scientific Research,Ministry of Agriculture,China(Grant No.nyhyzx 07-001-006)the Key Support Program of Jiangsu Science and Technology(Grant No.BE2008354)Jiangsu Self-innovation Fund for Agricultural Science and Technology,China(GrantNo.CX[08]603)
文摘Diversity of 60 conventional japonica rice accessions with good eating quality at home and abroad was analyzed using SSR molecular markers, agronomic traits and taste characteristics. A total of 290 alleles were detected in the 60 accessions at 72 SSR loci with the high similarity coefficients varying between 0.600 and 0.924. The loci on chromosome 5 showed the greatest value in average allele number. Additionally, most of the SSR loci could detect 3 to 4 alleles. An UPGMA dendrogram based on the cluster analysis of the genetic similarity coefficients showed that the grouping trend of part of the rice accessions was geographic-related and most of the rice accessions in Jiangsu Province, China were clustered together. Furthermore, many domestic accessions from south and north origins in China were close to the foreign japonica rice varieties, as proved by their pedigree origin from the foreign high-quality sources. For taste characteristics, part of the accessions with excellent taste were clearly clustered into one category though they came from different geographical regions, which indicates that taste characteristics of some varieties were mainly genetically determined. In addition, the agronomic traits of japonica rice with good taste might be closely related with their geographical origins, but the relationship between superior taste characteristics and agronomic traits should be further clarified.
基金supported by the Special Fund of Construction of Modern Agricultural and Industrial Technology System Project (Grant No. CARS-01-47)the Special Fund for Agro-scientific Research in the Public Interest (Grant No. 201503002-5-1)the Key Research & Development Program of Jiangsu Province (Grant No. BE2015363-3) in China
文摘Japonica rice variety Kanto 194 as the donor of resistance gene Stv-b^i and Iow-amylose content gene Wx-mq was used to improve the resistance and eating quality of Wuyujing 3 by the breeding strategy of backcross. In continuous backcross and selfcross generations, the related molecular markers with Stvobi and Wx-mq genes were utilized for genotypic detection by associated with resistance identification of rice stripe disease and agronomic traits selection. Finally, 10 improved lines with homozygous genotype Stv-b^i Stv-b^iWx-mqWx-mq were obtained from BC3F4 generation. The results of comparative analysis indicated that most characters of these lines were consistent with those of recipient parent Wuyujing 3, except for the improved resistance, appearance and eating quality. By evaluation of the comprehensive performance of them, two excellent lines K01 and K04 were selected for further experiments.
基金supported by the National High- tech Research and Development Program of China (Grant No. 2006AA100101)the Super-rice Breeding and Demonstration Program of Chinese Ministry of Agriculture+1 种基金the Special Research Program on Key Technology of Agricultural Structure Adjustment (Grant No. 05-01-05B),ChinaJiangsu High Technology Program , China (Grant No. BG2004304)
文摘The rice starch viscosity characteristics, which can be indicated by Rapid Visco Analyzer profile (RVA profile), have been proved useful for the evaluation of cooking and eating quality in rice breeding program. To study the inheritance of the RVA profile, an F2 population of Wuyujing 3/Aichi 106 was used. The results indicated that the peak viscosity (PKV) was a typical quantitative character, and the hot paste viscosity (HPV), cool paste viscosity (CPV), setback viscosity (SBV), breakdown viscosity (BDV), and consistence viscosity (CSV) might be controlled by one major gene and several minor genes To elucidate the genetic basis of the paste viscosity characteristics, a recombinant inbred line (RIL) population derived from Nikken 2/Milyang 23 and its genetic linkage map were used to map the QTLs controlling RVA profiles in 2005 and 2006. A total of 34 QTLs distributed on chromosomes 1,2, 3, 4, 6, 7 and 8 were detected, including 19 and 15 QTLs in 2005 and 2006 respectively. Eight QTLs were both detected in the two years, qHPV6, qCPV6, qCSV6, qSBV6, and qBDV6 were located on chromosome 6, while qHPV2, qCSV2, and qCPV2were on chromosome 2.
基金supported by the National Natural Science Foundation of China (Grant No. 31271678)the Jiangsu Agricultural Scientific Self-Innovation Fund (Grant No. CX[11]4023)the Super Rice Breeding and Demonstration Program of the Ministry of Agriculture in China
文摘Grain size traits, including grain length, grain width and grain thickness, are controlled by quantitative trait loci (QTLs). Many QTLs relating to rice grain size traits had been reported, but their control mechanisms have not yet been elucidated. A recombinant inbred line (RIL) population of 240 lines, deriving from a cross between TD70, an extra-large grain size japonica line with 80 g of 1000-grain weight, and Kasalath, a small grain size indica variety, were constructed and used to map grain size QTLs to a linkage map by using 141 SSR markers in 2010 and 2011. Five QTLs for grain length, six for grain width and seven for grain thickness were detected distributing over chromosomes 2, 3, 5, 7, 9 and 12. Seven QTLs, namely qGL3.1, qGW2, qGW2.2, qGW5.1, qGW5.2, qGT2.3 and qGT3.1, were detected in either of the two years and explained for 56.19%, 4.42%, 29.41%, 10.37%, 7.61%, 21.19% and 17.06% of the observed phenotypic variances on average, respectively. The marker interval RM1347-RM5699 on chromosome 2 was found common for grain length, grain width and grain thickness; qGL3.1 and qGT3.1 were mapped to the same interval RM6080-RM6832 on chromosome 3. All 18 QTL alleles were derived from the large grain parent TD70. Most of the QTLs mapped in the present study were found the same as the genes previously cloned (GW2, GS3 or qGL3, GW5 and GS5), and several were the same as the QTLs (GS7 and qGL-7) previously mapped. Three QTLs, qGL2.2 on chromosome 2, qGW9 and qGT9 on chromosome 9, were first detected. These results laid a foundation for further fine mapping or cloning of these QTLs.
基金supported by the Key Program of the Development of Variety of Genetically Modified Organisms(Grant Nos.2009ZX08001-019B and 2008ZX08001-006)the Special Program for Rice Scientific Research of Ministry of Agriculture(Grant No.nyhyzx 07-001-006)+1 种基金the Key Support Program of Science and Technology of Jiangsu Province(Grant No.BE2008354)the Self-directed Innovation Fund of Agricultural Science and Technology in Jiangsu Province,China(Grant No.CX[09]634)
文摘A high-yielding japonica rice variety, Wuyunjing 7, bred in Jiangsu Province, China as a female parent was crossed with a Japanese rice variety Kantou 194, which carries a rice stripe disease resistance gene Stv-b' and a translucent endosperm mutant gene Wx-mq. From F2 generations, a sequence characterized amplified region (SCAR) marker tightly linked with Stv-b' and a cleaved amplified polymorphic sequence (CAPS) marker for Wx-mq were used for marker-assisted selection. Finally, a new japonica rice line, Ning 9108, with excellent agronomic traits was obtained by multi-generational selection on stripe disease resistance and endosperm appearance. The utilization of the markers from genes related to rice quality and disease resistance was helpful not only for establishing a marker-assisted selection system of high-quality and disease resistance for rice but also for providing important intermediate materials and rapid selection method for good quality, disease resistance and high yield in rice breeding.