High-density markers are necessary for map-based cloning of rice genes, but the currently available markers are not satisfactory enough. InDel (insertion-deletion length polymorphism) and SNP (single nucleotide polymo...High-density markers are necessary for map-based cloning of rice genes, but the currently available markers are not satisfactory enough. InDel (insertion-deletion length polymorphism) and SNP (single nucleotide polymorphism) are the new generation of molecular markers and can basically meet the need of fine mapping. InDel and SNP markers can be developed through bioinformatics. These markers are valuable markers with the characters of low cost, high specificity and stability. This article introduced the methods for designing InDel and SNP markers, taking the mapping of a rice rolled leaf gene as an example. In addition, some key factors in improving the design efficiency were also discussed.展开更多
The discovery of thermo-sensitive genic male sterility(TGMS) has led to development of a simple and highly efficient two-line breeding system. In this study, genetic analysis was conducted using three F_2 populations ...The discovery of thermo-sensitive genic male sterility(TGMS) has led to development of a simple and highly efficient two-line breeding system. In this study, genetic analysis was conducted using three F_2 populations derived from crosses between IR68301 S, an indica TGMS rice line, and IR14632(tropical japonica), Supanburi 91062(indica) and IR67966-188-2-2-1(tropical japonica), respectively.Approximately 1:3 ratio between sterile and normal pollen of F_2 plants from the three populations revealed that TGMS is controlled by a single recessive gene. Bulked segregant analysis using simple sequence repeat(SSR) and insertion-deletion(InDel) markers were used to identify markers linked to the tms gene. The linkage analysis based on the three populations indicated that the tms locus was located on chromosome 2 covering the same area. Using IR68301S × IR14632 F_2 population, the results showed that the tms locus was located between SSR marker RM12676 and InDel marker 2gAP0050058. The genetic distance from the tms gene to these two flanking markers were 1.10 and 0.82 cM, respectively.InDel marker 2gAP004045 located between these two markers showed complete co-segregation with the TGMS phenotype. In addition, InDel marker vf0206114052 showed 2.94 cM linked to the tms gene using F_2 populations of IR68301S × Supanburi 91062. These markers are useful tool for developing new TGMS lines by marker-assisted selection. There were ten genes located between the two flanking markers RM12676 and 2gAP0050058. Using quantitative real-time PCR for expression analysis, 7 of the 10 genes showed expression in panicles, and response to temperatures. These genes could be the candidate gene controlling TGMS in IR68301S.展开更多
A rice heading-date-related mutant was isolated from a ^60Co-y-ray-induced mutation pool of Zhejing 22, a conventional japonica cultivar in Zhejiang Province, China. The mutant was characterized by a delayed heading d...A rice heading-date-related mutant was isolated from a ^60Co-y-ray-induced mutation pool of Zhejing 22, a conventional japonica cultivar in Zhejiang Province, China. The mutant was characterized by a delayed heading date of almost 20 d longer than the wild type plant. Genetic analysis revealed that the mutation was controlled by a single nuclear-encoded recessive gene that was designed as HD（t） （heading date tentatively）. To isolate the HD（t） gene, a map-based cloning approach was employed using 479 F2 mutant individual plants derived from the cross between the hd（t） mutant （japonica） x Zhenshan 97 （indica）. Finally, the HD（t） gene was mapped to an approximate 53 kb region between the insertion and deletion （InDel） markers of 10-61W and 10-66W on chromosome 10. According to the genome sequence of Nipponbare, the target region contains 11 annotated genes. It is helpful for future cloning of HD（t） gene based on this fine mapping results.展开更多
The eastern Himalayan region of Northeast （NE） India is home to a large number of indigenous rice varieties, which are traditionally classified as Oryza sativa subspecies indica, japonica or intermediate types. The ...The eastern Himalayan region of Northeast （NE） India is home to a large number of indigenous rice varieties, which are traditionally classified as Oryza sativa subspecies indica, japonica or intermediate types. The classification based on traditional Cheng’s index is often inconclusive due to phenotypic plasticity of morphological characters, which are influenced by environmental conditions. We used molecular markers specific for indica and japonica subspecies to assess the degree of genetic relatedness of indigenous rice varieties in NE India. The results revealed that majority of upland （jum） and glutinous rice varieties, traditionally considered as japonica, were genetically close to the subspecies indica. All varieties of boro ecotype were found to be indica type, and only a few varieties cultivated in lowland and upland areas were japonica type. Some of the lowland varieties of the sali ecotype were intermediate between indica and japonica, and they showed a closer genetic affinity to O. rufipogon.展开更多
文摘High-density markers are necessary for map-based cloning of rice genes, but the currently available markers are not satisfactory enough. InDel (insertion-deletion length polymorphism) and SNP (single nucleotide polymorphism) are the new generation of molecular markers and can basically meet the need of fine mapping. InDel and SNP markers can be developed through bioinformatics. These markers are valuable markers with the characters of low cost, high specificity and stability. This article introduced the methods for designing InDel and SNP markers, taking the mapping of a rice rolled leaf gene as an example. In addition, some key factors in improving the design efficiency were also discussed.
基金supported by Center for Agricultural Biotechnology, Kasetsart University, Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDOCHE)Agricultural Research Development Agency (ARDA)National Science and Technology Development Agency, Thailand
文摘The discovery of thermo-sensitive genic male sterility(TGMS) has led to development of a simple and highly efficient two-line breeding system. In this study, genetic analysis was conducted using three F_2 populations derived from crosses between IR68301 S, an indica TGMS rice line, and IR14632(tropical japonica), Supanburi 91062(indica) and IR67966-188-2-2-1(tropical japonica), respectively.Approximately 1:3 ratio between sterile and normal pollen of F_2 plants from the three populations revealed that TGMS is controlled by a single recessive gene. Bulked segregant analysis using simple sequence repeat(SSR) and insertion-deletion(InDel) markers were used to identify markers linked to the tms gene. The linkage analysis based on the three populations indicated that the tms locus was located on chromosome 2 covering the same area. Using IR68301S × IR14632 F_2 population, the results showed that the tms locus was located between SSR marker RM12676 and InDel marker 2gAP0050058. The genetic distance from the tms gene to these two flanking markers were 1.10 and 0.82 cM, respectively.InDel marker 2gAP004045 located between these two markers showed complete co-segregation with the TGMS phenotype. In addition, InDel marker vf0206114052 showed 2.94 cM linked to the tms gene using F_2 populations of IR68301S × Supanburi 91062. These markers are useful tool for developing new TGMS lines by marker-assisted selection. There were ten genes located between the two flanking markers RM12676 and 2gAP0050058. Using quantitative real-time PCR for expression analysis, 7 of the 10 genes showed expression in panicles, and response to temperatures. These genes could be the candidate gene controlling TGMS in IR68301S.
基金supported by the Chinese Ministry of Agriculture(Grant Nos.200803034 and 2011ZX08001001)the Zhejiang Provincial and the National Natural Science Foundation of China(Grant Nos.Y3080361 and 31071207)+2 种基金the Science and Technology Department of Zhejiang Province,China(Grant No.2004C12020)the Special Fund for Agro-scientific Research in the Public Interest(Grant No.201103007)the Special Fund of Zhejiang Academy of Agricultural Science,China
文摘A rice heading-date-related mutant was isolated from a ^60Co-y-ray-induced mutation pool of Zhejing 22, a conventional japonica cultivar in Zhejiang Province, China. The mutant was characterized by a delayed heading date of almost 20 d longer than the wild type plant. Genetic analysis revealed that the mutation was controlled by a single nuclear-encoded recessive gene that was designed as HD（t） （heading date tentatively）. To isolate the HD（t） gene, a map-based cloning approach was employed using 479 F2 mutant individual plants derived from the cross between the hd（t） mutant （japonica） x Zhenshan 97 （indica）. Finally, the HD（t） gene was mapped to an approximate 53 kb region between the insertion and deletion （InDel） markers of 10-61W and 10-66W on chromosome 10. According to the genome sequence of Nipponbare, the target region contains 11 annotated genes. It is helpful for future cloning of HD（t） gene based on this fine mapping results.
基金financially supported by NSERC-Canada,FRQNT and Concordia University
文摘The eastern Himalayan region of Northeast （NE） India is home to a large number of indigenous rice varieties, which are traditionally classified as Oryza sativa subspecies indica, japonica or intermediate types. The classification based on traditional Cheng’s index is often inconclusive due to phenotypic plasticity of morphological characters, which are influenced by environmental conditions. We used molecular markers specific for indica and japonica subspecies to assess the degree of genetic relatedness of indigenous rice varieties in NE India. The results revealed that majority of upland （jum） and glutinous rice varieties, traditionally considered as japonica, were genetically close to the subspecies indica. All varieties of boro ecotype were found to be indica type, and only a few varieties cultivated in lowland and upland areas were japonica type. Some of the lowland varieties of the sali ecotype were intermediate between indica and japonica, and they showed a closer genetic affinity to O. rufipogon.
