Excavating single nucleotide polymorphisms (SNPs) significantly associated with rice grain shape and predicting candidate genes through genome-wide association study (GWAS) can provide a theoretical basis for discover...Excavating single nucleotide polymorphisms (SNPs) significantly associated with rice grain shape and predicting candidate genes through genome-wide association study (GWAS) can provide a theoretical basis for discovery and utilization of excellent genetic resources in rice. Based on 16 352 SNPs, 161 natural indica rice varieties with various grain sizes in southern China were used for GWAS of grain shape-related traits, referring to grain length (GL), grain width (GW), 1000-grain weight (TGW), and grain length/width (GLW). Phenotypic statistics showed that coefficient of variation values for these four traits GL, GW, TGW and GLW were 9.92%, 9.09%, 20.20% and 16.38%, respectively. Each trait showed a normal distribution, and there was a certain correlation between these traits. Through general linear model correlation analysis, a total of 38 significant loci were identified, and a range of 100 kb upstream and downstream of the significant loci was identified as the candidate interval. On chromosome 3, GS3 and qGL3 were found to regulate GL. On chromosome 6, TGW6 and GW6a were found to regulate TGW. Also, some QTLs related to grain shape were found on chromosomes 5 and 9. Besides that, using sequenced 3K-germplasm resources, we found that there are 22 overlapped varieties between these two natural populations. Twenty-six SNPs and fourteen haplotypes were identified in five regions of GS3 genes. The detection of multiple candidate genes/QTLs within the candidate interval is beneficial for further excavation of superior rice genetic resources.展开更多
Grain shape as a major determinant of rice yield and quality is widely believed to be controlled by quantitative trait loci(QTL). We have identified a novel gene 'GS2' to largely regulate grain length and widt...Grain shape as a major determinant of rice yield and quality is widely believed to be controlled by quantitative trait loci(QTL). We have identified a novel gene 'GS2' to largely regulate grain length and width in rice. The GS2 allele in the big-grain rice line ‘CDL’functioned in a dominant manner. In the present study, we employed a chromosome walking strategy in the residual heterozygous lines from recombinant inbred population between cultivar 'R1126' and CDL, and located the GS2 gene in an interval of ~33.2 kb flanked by marker GL2-35-1 and GL2-12 in the long arm of rice chromosome 2. According to genome annotations, three putative gene loci, LOC_Os02g47280, LOC_Os02g47290 and LOC_Os02g47300, exist in this candidate region. In addition, allelic analysis with previously reported genes demonstrated that GS2 was novel for regulating rice grain shape. These results will help promote the cloning and functional characterization of the GS2 gene and further develop linked markers to be used in marker-assisted breeding.展开更多
Rice grain shape, grain length （GL）, width （GW）, thickness （GT） and length-to-width ratio （LWR）, are usually controlled by multiple quantitative trait locus （QTL）. To elucidate the genetic basis of extremely...Rice grain shape, grain length （GL）, width （GW）, thickness （GT） and length-to-width ratio （LWR）, are usually controlled by multiple quantitative trait locus （QTL）. To elucidate the genetic basis of extremely large grain shape, QTL analysis was performed using an F2 population derived from a cross between a japonica cuttivar ＇JZI560＇ （extremely large grain） and a contrasting indica cultivar ＇FAZI＇ （small grain）. A total number of 24 QTLs were detected on seven different chromosomes. QTLs for GL, GW, GT and LWR explained 11.6%, 95.62%, 91.5% and 89.9% of total phenotypic variation, respectively. Many QTLs pleiotropically controlled different grain traits, contributing complex traits correlation. GW2 and qSW5/GW5, which have been cloned previously to control GW, showed similar chromosomal locations with qGW2-1/qGT2-1/qLWR2-2 and qGW5-2/qLWR5-1 and should be the right candidate genes. Plants pyramiding GW2 and qSW5/GW5 showed a significant increase in GW compared with those carrying one of the two major QTLs. Furthermore, no significant QTL interaction was observed between GW2 and qSW5/GW5. These results suggested that GW2 and qSW5/GW5 might work in independent pathways to regulate grain traits. ＇JZ1560＇ alleles underlying all QTLs contributed an increase in GW and GT and the accumulation of additive effects generates the extremely large grain shape in ＇JZ1560＇.展开更多
Dear Editor Through the efficient use of heterosis, hybrid rice varieties generally have higher grain yield potential than inbred varieties. With the significant advantage in grain yield, over the past 30 years approx...Dear Editor Through the efficient use of heterosis, hybrid rice varieties generally have higher grain yield potential than inbred varieties. With the significant advantage in grain yield, over the past 30 years approximately half of China＇s total rice-growing area is planted with rice hybrids. However, grain quality has now become one of the most important targets in hybrid rice breeding for meeting consumer demands. Grain shape and chalkiness are two important components of rice grain quality, in which slender grains （typically, grain length-to-width ratio 〉3） with low chatkiness are preferred by most consumers of hybrid rice.展开更多
基金supported by the Natural Science Foundation of China(Grant Nos.31461143014,31771778 and 31801336)the National Key Research and Development Program of China(Grant No.2016YFD0100902-07)+1 种基金the China Postdoctoral Science Foundation(Grant No.2018M641556)the Zhejiang Provincial Natural Science Foundation of China(Grant No.LGN19C130006)
文摘Excavating single nucleotide polymorphisms (SNPs) significantly associated with rice grain shape and predicting candidate genes through genome-wide association study (GWAS) can provide a theoretical basis for discovery and utilization of excellent genetic resources in rice. Based on 16 352 SNPs, 161 natural indica rice varieties with various grain sizes in southern China were used for GWAS of grain shape-related traits, referring to grain length (GL), grain width (GW), 1000-grain weight (TGW), and grain length/width (GLW). Phenotypic statistics showed that coefficient of variation values for these four traits GL, GW, TGW and GLW were 9.92%, 9.09%, 20.20% and 16.38%, respectively. Each trait showed a normal distribution, and there was a certain correlation between these traits. Through general linear model correlation analysis, a total of 38 significant loci were identified, and a range of 100 kb upstream and downstream of the significant loci was identified as the candidate interval. On chromosome 3, GS3 and qGL3 were found to regulate GL. On chromosome 6, TGW6 and GW6a were found to regulate TGW. Also, some QTLs related to grain shape were found on chromosomes 5 and 9. Besides that, using sequenced 3K-germplasm resources, we found that there are 22 overlapped varieties between these two natural populations. Twenty-six SNPs and fourteen haplotypes were identified in five regions of GS3 genes. The detection of multiple candidate genes/QTLs within the candidate interval is beneficial for further excavation of superior rice genetic resources.
基金supported by the National High Technology Research and Development Program of China (2011AA10A101)the Hunan Provincial Natural Science Foundation of China (10JJ2025)
文摘Grain shape as a major determinant of rice yield and quality is widely believed to be controlled by quantitative trait loci(QTL). We have identified a novel gene 'GS2' to largely regulate grain length and width in rice. The GS2 allele in the big-grain rice line ‘CDL’functioned in a dominant manner. In the present study, we employed a chromosome walking strategy in the residual heterozygous lines from recombinant inbred population between cultivar 'R1126' and CDL, and located the GS2 gene in an interval of ~33.2 kb flanked by marker GL2-35-1 and GL2-12 in the long arm of rice chromosome 2. According to genome annotations, three putative gene loci, LOC_Os02g47280, LOC_Os02g47290 and LOC_Os02g47300, exist in this candidate region. In addition, allelic analysis with previously reported genes demonstrated that GS2 was novel for regulating rice grain shape. These results will help promote the cloning and functional characterization of the GS2 gene and further develop linked markers to be used in marker-assisted breeding.
基金supported by grants from the Ministry of Agriculture of China(2009ZX08009-102B)Chinese Academy of Sciences(KSCX3-EW-N-01)+2 种基金the Ministry of Science and Technology of China(2012CB944800)the National Natural Science Foundation of China(31130071)the Zhejiang Provincial Natural Science Foundation of China (Y3110394)
文摘Rice grain shape, grain length （GL）, width （GW）, thickness （GT） and length-to-width ratio （LWR）, are usually controlled by multiple quantitative trait locus （QTL）. To elucidate the genetic basis of extremely large grain shape, QTL analysis was performed using an F2 population derived from a cross between a japonica cuttivar ＇JZI560＇ （extremely large grain） and a contrasting indica cultivar ＇FAZI＇ （small grain）. A total number of 24 QTLs were detected on seven different chromosomes. QTLs for GL, GW, GT and LWR explained 11.6%, 95.62%, 91.5% and 89.9% of total phenotypic variation, respectively. Many QTLs pleiotropically controlled different grain traits, contributing complex traits correlation. GW2 and qSW5/GW5, which have been cloned previously to control GW, showed similar chromosomal locations with qGW2-1/qGT2-1/qLWR2-2 and qGW5-2/qLWR5-1 and should be the right candidate genes. Plants pyramiding GW2 and qSW5/GW5 showed a significant increase in GW compared with those carrying one of the two major QTLs. Furthermore, no significant QTL interaction was observed between GW2 and qSW5/GW5. These results suggested that GW2 and qSW5/GW5 might work in independent pathways to regulate grain traits. ＇JZ1560＇ alleles underlying all QTLs contributed an increase in GW and GT and the accumulation of additive effects generates the extremely large grain shape in ＇JZ1560＇.
文摘Dear Editor Through the efficient use of heterosis, hybrid rice varieties generally have higher grain yield potential than inbred varieties. With the significant advantage in grain yield, over the past 30 years approximately half of China＇s total rice-growing area is planted with rice hybrids. However, grain quality has now become one of the most important targets in hybrid rice breeding for meeting consumer demands. Grain shape and chalkiness are two important components of rice grain quality, in which slender grains （typically, grain length-to-width ratio 〉3） with low chatkiness are preferred by most consumers of hybrid rice.
