Agronomic traits are important determinants to rice yield, which are controlled by complex genetic factors as well as genotype by environment （G × E） interaction effects. The G × E effects for agronomic tr...Agronomic traits are important determinants to rice yield, which are controlled by complex genetic factors as well as genotype by environment （G × E） interaction effects. The G × E effects for agronomic traits of rice have been dissected with various approaches, but not with the current available approach, the association studies. In this study, a total of 32 655 single nucleotide polymorphisms were used to carry out associations with 14 agronomic traits among 20 rice accessions in two environments. The G × E interaction effects for all the agronomic traits were at highly significant levels （P〈0.01）, accounting for 3.4%-22.3% of the total sum of squares except for the length of brown rice. Twenty three putative quantitative trait loci （QTLs）, including five previously known and several new promising associations, were identified for 10 of 14 traits. Analysis of the relationships between the traits for which QTLs and the genotype effects could be identified suggested that the higher the genotypic effect, the higher the possibility to identify QTLs for the given trait. The new QTLs detected in this study will facilitate dissection of the complex agronomic traits and may give insight into the G × E effects with association mapping.展开更多
The objectives of the present study were to estimate genetic diversity and genetic changes of introgression lines （ILs） which derived from cultivated rice （Oryza sativa L. cv. Xieqingzao B, XB） mating with common ...The objectives of the present study were to estimate genetic diversity and genetic changes of introgression lines （ILs） which derived from cultivated rice （Oryza sativa L. cv. Xieqingzao B, XB） mating with common wild rice （O. rufipogon Griff., CWR）. The genetic data of 239 ILs were based on a total of 131 polymorphic microsatellite （SSR） markers distributed across the 12 chromosomes of rice. On average, these ILs possessed 77.1 and 14.31% homozygous bands from XB and CWR, respectively. Most of the ILs were clustered together with XB individual, which was revealed by principal coordinate analysis （PCA） and the program STRUCTURE analysis. The result from PCA demonstrated that some intermediate genotypes between XB and CWR were also found. Moreover, there were some genomic sequence changes including parental bands elimination and novel bands emergence in the ILs. The average Nei＇s gene diversity （He） was 0.296, which was higher than that of cultivated rice. It suggested that interspecific hybridization and gene introgression could broaden the base of genetic variation and lay an important foundation for rice genetic improvement. These different genotypic ILs would provide a better experimental system for understanding the evolution of rice species and the mechanism of alien gene introgression.展开更多
Osmanthus fragrans is well-known as an ornamental and agricultural plant noted for its unique fragrance.We investigated the genetic relationships between two new colorful O.fragrans cultivars,Ziyan Gongzhu and Qiannan...Osmanthus fragrans is well-known as an ornamental and agricultural plant noted for its unique fragrance.We investigated the genetic relationships between two new colorful O.fragrans cultivars,Ziyan Gongzhu and Qiannan Guifei,and their relationships with other O.fragrans using amplified fragment length polymorphism(AFLP)and simple sequence repeat(SSR),compared to the Changye Muxi species.55 AFLP primer pairs and 17 SSRs were screened;1103 and 45 amplification products were produced,of which 92.29%of the AFLP and 62.20%of the SSRs were polymorphic.At the population level,the number of effective alleles varied from 0.76 to 1.11,and the Shannon index(I)ranged from 0 to 0.11,indicating a narrow genetic base of O.fragrans cultivars.The genetic similarity varied from 0.61 to 0.80 between Ziyan Gongzhu and other O.fragrans cultivars,and 0.57 to 0.67 in the Qiannan Guifei and other cultivars.The unweighted pair group method with arithmetic mean(UPGMA)clustering revealed that Ziyan Gongzhu may belong to the O.fragrans Albus group.However,the Qiannan Guifei cultivar was clustered into a group,showing that it has great genetic variation.These results provide new molecular evidence for germplasm resources protection,and new cultivars for breeding.展开更多
Cold stress is a major problem in rice production. To rapidly identify genes for cold tolerance in Dongxiang wild rice（DWR, Oryza rufipogon Griff.）, sequencing-based bulked segregant analysis of QTL-seq method was u...Cold stress is a major problem in rice production. To rapidly identify genes for cold tolerance in Dongxiang wild rice（DWR, Oryza rufipogon Griff.）, sequencing-based bulked segregant analysis of QTL-seq method was used to resequence the extremely resistant（R） and susceptible（S） bulks of a backcross inbred lines（BILs） population（derived from Oryza sativa×O. rufipogon） and their parents. Single nucleotide polymorphisms（SNP）-index graphs and corresponding Δ（SNPindex） graphs（at 99 and 95% confidence levels） for R-and S-bulks detected a total of 2 609 candidate SNPs, including 58 candidate cold-tolerance genes. Quantitative real-time PCR analysis revealed that 5 out of the 58 candidate genes had significant differences in expression between O. sativa and O. rufipogon. Structural variation and functional annotations of the 5 candidate genes were also analyzed, and allowed us to identify 2 insertion-deletion（InDel） markers（12-7 and 12-16） that were linked with candidate genes on chromosome 12 in DWR. These results are helpful for cloning and using cold tolerance genes from common wild rice in cultivated rice.展开更多
基金supported by the Special Fund for Agro-Scientific Research in the Public Interest from the Ministry of Agriculture, China (Grant No. 201103007)
文摘Agronomic traits are important determinants to rice yield, which are controlled by complex genetic factors as well as genotype by environment （G × E） interaction effects. The G × E effects for agronomic traits of rice have been dissected with various approaches, but not with the current available approach, the association studies. In this study, a total of 32 655 single nucleotide polymorphisms were used to carry out associations with 14 agronomic traits among 20 rice accessions in two environments. The G × E interaction effects for all the agronomic traits were at highly significant levels （P〈0.01）, accounting for 3.4%-22.3% of the total sum of squares except for the length of brown rice. Twenty three putative quantitative trait loci （QTLs）, including five previously known and several new promising associations, were identified for 10 of 14 traits. Analysis of the relationships between the traits for which QTLs and the genotype effects could be identified suggested that the higher the genotypic effect, the higher the possibility to identify QTLs for the given trait. The new QTLs detected in this study will facilitate dissection of the complex agronomic traits and may give insight into the G × E effects with association mapping.
基金partially supported by the National Natural Science Foundation of China (30860120 and 30900781)the Natural Science Foundation of Jiangxi Province, China(2008GQN0059)the Development Program for Young Scientists of Jiangxi Province, China (20112BCB23007)
文摘The objectives of the present study were to estimate genetic diversity and genetic changes of introgression lines （ILs） which derived from cultivated rice （Oryza sativa L. cv. Xieqingzao B, XB） mating with common wild rice （O. rufipogon Griff., CWR）. The genetic data of 239 ILs were based on a total of 131 polymorphic microsatellite （SSR） markers distributed across the 12 chromosomes of rice. On average, these ILs possessed 77.1 and 14.31% homozygous bands from XB and CWR, respectively. Most of the ILs were clustered together with XB individual, which was revealed by principal coordinate analysis （PCA） and the program STRUCTURE analysis. The result from PCA demonstrated that some intermediate genotypes between XB and CWR were also found. Moreover, there were some genomic sequence changes including parental bands elimination and novel bands emergence in the ILs. The average Nei＇s gene diversity （He） was 0.296, which was higher than that of cultivated rice. It suggested that interspecific hybridization and gene introgression could broaden the base of genetic variation and lay an important foundation for rice genetic improvement. These different genotypic ILs would provide a better experimental system for understanding the evolution of rice species and the mechanism of alien gene introgression.
基金Supported by Science and Technology Planning Project of Jiangxi Province(20161BBF60032)Jiangxi Modern Agricultural Research Collaborative Innovation Project(JXXTCX2015006-005)Jiangxi Modern Agricultural Industry Technology System Construction Special Funds(JXARS-17)~~
文摘Osmanthus fragrans is well-known as an ornamental and agricultural plant noted for its unique fragrance.We investigated the genetic relationships between two new colorful O.fragrans cultivars,Ziyan Gongzhu and Qiannan Guifei,and their relationships with other O.fragrans using amplified fragment length polymorphism(AFLP)and simple sequence repeat(SSR),compared to the Changye Muxi species.55 AFLP primer pairs and 17 SSRs were screened;1103 and 45 amplification products were produced,of which 92.29%of the AFLP and 62.20%of the SSRs were polymorphic.At the population level,the number of effective alleles varied from 0.76 to 1.11,and the Shannon index(I)ranged from 0 to 0.11,indicating a narrow genetic base of O.fragrans cultivars.The genetic similarity varied from 0.61 to 0.80 between Ziyan Gongzhu and other O.fragrans cultivars,and 0.57 to 0.67 in the Qiannan Guifei and other cultivars.The unweighted pair group method with arithmetic mean(UPGMA)clustering revealed that Ziyan Gongzhu may belong to the O.fragrans Albus group.However,the Qiannan Guifei cultivar was clustered into a group,showing that it has great genetic variation.These results provide new molecular evidence for germplasm resources protection,and new cultivars for breeding.
基金partially supported by the National Natural Science Foundation of China (31260255, 31360147 and 31660384)the Natural Science Foundation of Jiangxi Province, China (20151BAB204008)+1 种基金the Scientific Planning Project of Jiangxi Provincial Education Department, China (GJJ12184 and KJLD12059)the Major Projects in Jiangxi Province, China (20161ACF60022)
文摘Cold stress is a major problem in rice production. To rapidly identify genes for cold tolerance in Dongxiang wild rice（DWR, Oryza rufipogon Griff.）, sequencing-based bulked segregant analysis of QTL-seq method was used to resequence the extremely resistant（R） and susceptible（S） bulks of a backcross inbred lines（BILs） population（derived from Oryza sativa×O. rufipogon） and their parents. Single nucleotide polymorphisms（SNP）-index graphs and corresponding Δ（SNPindex） graphs（at 99 and 95% confidence levels） for R-and S-bulks detected a total of 2 609 candidate SNPs, including 58 candidate cold-tolerance genes. Quantitative real-time PCR analysis revealed that 5 out of the 58 candidate genes had significant differences in expression between O. sativa and O. rufipogon. Structural variation and functional annotations of the 5 candidate genes were also analyzed, and allowed us to identify 2 insertion-deletion（InDel） markers（12-7 and 12-16） that were linked with candidate genes on chromosome 12 in DWR. These results are helpful for cloning and using cold tolerance genes from common wild rice in cultivated rice.
