Plant height is an important agronomic trait, which is governed by multiple genes with major or minor effects. Of numerous QTLs for plant height reported in soybean, most are in large genomic regions, which results in...Plant height is an important agronomic trait, which is governed by multiple genes with major or minor effects. Of numerous QTLs for plant height reported in soybean, most are in large genomic regions, which results in a still unknown molecular mechanism for plant height. Increasing the density of molecular markers in genetic maps will significantly improve the efficiency and accuracy of QTL mapping. This study constructed a high-density genetic map using 4 011 recombination bin markers developed from whole genome re-sequencing of 241 recombinant inbred lines(RILs) and their bi-parents, Zhonghuang 13(ZH) and Zhongpin 03-5373(ZP). The total genetic distance of this bin map was 3 139.15 cM,with an average interval of 0.78 cM between adjacent bin markers. Comparative genomic analysis indicated that this genetic map showed a high collinearity with the soybean reference genome. Based on this bin map, nine QTLs for plant height were detected across six environments, including three novel loci(qPH-b_11, qPH-b_17 and qPH-b_18). Of them, two environmentally stable QTLs qPH-b_13 and qPH-b_19-1 played a major role in plant height, which explained 10.56-32.7% of the phenotypic variance. They were fine-mapped to 440.12 and 237.06 kb region, covering 54 and 28 annotated genes, respectively. Via the function of homologous genes in Arabidopsis and expression analysis, two genes of them were preferentially predicted as candidate genes for further study.展开更多
The construction of high density genetic linkage map provides a powerful tool to detect and map quantitative trait loci(QTLs) controlling agronomically important traits. In this study, simple sequence repeat(SSR) mark...The construction of high density genetic linkage map provides a powerful tool to detect and map quantitative trait loci(QTLs) controlling agronomically important traits. In this study, simple sequence repeat(SSR) markers and Illumina 9K i Select single nucleotide polymorphism(SNP) genechip were employed to construct one genetic linkage map of common wheat(Triticum aestivum L.) using 191 recombinant inbred lines(RILs) derived from cross Yu 8679×Jing 411. This map included 1 901 SNP loci and 178 SSR loci, covering 1 659.9 c M and 1 000 marker bins, with an average interval distance of 1.66 c M. A, B and D genomes covered 719.1, 703.5 and 237.3 c M, with an average interval distance of 1.66, 1.45 and 2.9 c M, respectively. Notably, the genetic linkage map covered 20 chromosomes, with the exception of chromosome 5D. Bioinformatics analysis revealed that 1 754(92.27%) of 1 901 mapped SNP loci could be aligned to 1 215 distinct wheat unigenes, among which 1 184(97.4%) were located on o ne single chromosome, and the rest 31(2.6%) were located on 2 to 3 chromosomes. By performing in silico comparison, 214 chromosome deletion bin-mapped expressed sequence tags(ESTs), 1 043 Brachypodium genes and 1 033 rice genes were further added onto the genetic linkage map. This map not only integrated genetic and physical maps, SSR and SNP loci, respectively, but also provided the information of Brachypodium and rice genes corresponding to 1 754 SNP loci. Therefore, it will be a useful tool for comparative genomics analysis, fine mapping of QTL/gene controlling agronomically important traits and marker-assisted selection breeding in wheat.展开更多
High-throughput SNP genotyping is widely used for plant genetic studies. Recently, a RICE6K SNP array has been developed based on the Illumina Bead Array platform and Infinium SNP assay technology for genome-wide eval...High-throughput SNP genotyping is widely used for plant genetic studies. Recently, a RICE6K SNP array has been developed based on the Illumina Bead Array platform and Infinium SNP assay technology for genome-wide evaluation of allelic variations and breeding applications. In this study, the RICE6K SNP array was used to genotype a recombinant inbred line （RIL） population derived from the cross between the indica variety, Zhenshan 97, and the japonica variety, Xizang 2. A total of 3324 SNP markers of high quality were identified and were grouped into 1495 recombination bins in the RIL population. A high-density linkage map, consisting of the 1495 bins, was developed, covering 1591.2 cM and with average length ofl.1 cM per bin. Segregation distortions were observed in 24 regions of the 11 chromosomes in the RILs. One half of the distorted regions contained fertility genes that had been previously reported. A total of 23 QTLs were identified for yield. Seven QTLs were firstly detected in this study. The positive alleles from about half of the identified QTLs came from Zhenshan 97 and they had lower phenotypic values than Xizang 2. This indicated that favorable alleles for breeding were dispersed in both parents and pyramiding favorable alleles could develop elite lines. The size of the mapping population for QTL analysis using high throughput SNP genotyping platform is also discussed.展开更多
Maize（Zea mays） root system architecture（RSA）mediates the key functions of plant anchorage and acquisition of nutrients and water. In this study,a set of 204 recombinant inbred lines（RILs） was derived from the w...Maize（Zea mays） root system architecture（RSA）mediates the key functions of plant anchorage and acquisition of nutrients and water. In this study,a set of 204 recombinant inbred lines（RILs） was derived from the widely adapted Chinese hybrid ZD958（Zheng58 Chang7-2）,genotyped by sequencing（GBS） and evaluated as seedlings for 24 RSA related traits divided into primary,seminal and total root classes. Signi ficant differences between the means of the parental phenotypes were detected for 18 traits,and extensive transgressive segregation in the RIL population was observed for all traits. Moderate to strong relationships among the traits were discovered. A total of 62 quantitative trait loci（QTL） were identi fied that individually explained from1.6% to 11.6%（total root dry weight/total seedling shoot dry weight） of the phenotypic variation. Eighteen,24 and 20 QTL were identi fied for primary,seminal and total root classes of traits,respectively. We found hotspots of 5,3,4 and 12 QTL in maize chromosome bins 2.06,3.02-03,9.02-04,and 9.05-06,respectively,implicating the presence of root gene clusters or pleiotropic effects. These results characterized the phenotypic variation and genetic architecture of seedling RSA in a population derived from a successful maize hybrid.展开更多
基金supported by the National Key R&D Program of China(2016YFD0100201)the Agricultural Science and Technology Innovation Program(ASTIP)of Chinese Academy of Agricultural Sciences。
文摘Plant height is an important agronomic trait, which is governed by multiple genes with major or minor effects. Of numerous QTLs for plant height reported in soybean, most are in large genomic regions, which results in a still unknown molecular mechanism for plant height. Increasing the density of molecular markers in genetic maps will significantly improve the efficiency and accuracy of QTL mapping. This study constructed a high-density genetic map using 4 011 recombination bin markers developed from whole genome re-sequencing of 241 recombinant inbred lines(RILs) and their bi-parents, Zhonghuang 13(ZH) and Zhongpin 03-5373(ZP). The total genetic distance of this bin map was 3 139.15 cM,with an average interval of 0.78 cM between adjacent bin markers. Comparative genomic analysis indicated that this genetic map showed a high collinearity with the soybean reference genome. Based on this bin map, nine QTLs for plant height were detected across six environments, including three novel loci(qPH-b_11, qPH-b_17 and qPH-b_18). Of them, two environmentally stable QTLs qPH-b_13 and qPH-b_19-1 played a major role in plant height, which explained 10.56-32.7% of the phenotypic variance. They were fine-mapped to 440.12 and 237.06 kb region, covering 54 and 28 annotated genes, respectively. Via the function of homologous genes in Arabidopsis and expression analysis, two genes of them were preferentially predicted as candidate genes for further study.
基金financially supported by the National Natural Science Foundation of China (91435204, 31271710)the National 863 Program of China (2012AA10A309)the Program of Conservation and Sustainable Utilization of Wild Relatives of Crops by the Ministry of Agriculture of China (201003021)
文摘The construction of high density genetic linkage map provides a powerful tool to detect and map quantitative trait loci(QTLs) controlling agronomically important traits. In this study, simple sequence repeat(SSR) markers and Illumina 9K i Select single nucleotide polymorphism(SNP) genechip were employed to construct one genetic linkage map of common wheat(Triticum aestivum L.) using 191 recombinant inbred lines(RILs) derived from cross Yu 8679×Jing 411. This map included 1 901 SNP loci and 178 SSR loci, covering 1 659.9 c M and 1 000 marker bins, with an average interval distance of 1.66 c M. A, B and D genomes covered 719.1, 703.5 and 237.3 c M, with an average interval distance of 1.66, 1.45 and 2.9 c M, respectively. Notably, the genetic linkage map covered 20 chromosomes, with the exception of chromosome 5D. Bioinformatics analysis revealed that 1 754(92.27%) of 1 901 mapped SNP loci could be aligned to 1 215 distinct wheat unigenes, among which 1 184(97.4%) were located on o ne single chromosome, and the rest 31(2.6%) were located on 2 to 3 chromosomes. By performing in silico comparison, 214 chromosome deletion bin-mapped expressed sequence tags(ESTs), 1 043 Brachypodium genes and 1 033 rice genes were further added onto the genetic linkage map. This map not only integrated genetic and physical maps, SSR and SNP loci, respectively, but also provided the information of Brachypodium and rice genes corresponding to 1 754 SNP loci. Therefore, it will be a useful tool for comparative genomics analysis, fine mapping of QTL/gene controlling agronomically important traits and marker-assisted selection breeding in wheat.
基金supported by the grants from the National High-tech R&D Program(863 Program) on functional genomics of stress resistance and nutrient utility in rice(No.2012AA10A303)the National Basic Research Program(No.2007CB109001)+1 种基金Agriculture Public Welfare Scientific Research Project(No.201303008)the National Special Program for Research of Transgenic Plants of China(No.2011ZX08009-001)
文摘High-throughput SNP genotyping is widely used for plant genetic studies. Recently, a RICE6K SNP array has been developed based on the Illumina Bead Array platform and Infinium SNP assay technology for genome-wide evaluation of allelic variations and breeding applications. In this study, the RICE6K SNP array was used to genotype a recombinant inbred line （RIL） population derived from the cross between the indica variety, Zhenshan 97, and the japonica variety, Xizang 2. A total of 3324 SNP markers of high quality were identified and were grouped into 1495 recombination bins in the RIL population. A high-density linkage map, consisting of the 1495 bins, was developed, covering 1591.2 cM and with average length ofl.1 cM per bin. Segregation distortions were observed in 24 regions of the 11 chromosomes in the RILs. One half of the distorted regions contained fertility genes that had been previously reported. A total of 23 QTLs were identified for yield. Seven QTLs were firstly detected in this study. The positive alleles from about half of the identified QTLs came from Zhenshan 97 and they had lower phenotypic values than Xizang 2. This indicated that favorable alleles for breeding were dispersed in both parents and pyramiding favorable alleles could develop elite lines. The size of the mapping population for QTL analysis using high throughput SNP genotyping platform is also discussed.
基金supported by 863 Project (2012AA10A305)Chinese Universities Scientific Fund (2014XJ036)+1 种基金NSF (31301321)948 Project (2011-G15)
文摘Maize（Zea mays） root system architecture（RSA）mediates the key functions of plant anchorage and acquisition of nutrients and water. In this study,a set of 204 recombinant inbred lines（RILs） was derived from the widely adapted Chinese hybrid ZD958（Zheng58 Chang7-2）,genotyped by sequencing（GBS） and evaluated as seedlings for 24 RSA related traits divided into primary,seminal and total root classes. Signi ficant differences between the means of the parental phenotypes were detected for 18 traits,and extensive transgressive segregation in the RIL population was observed for all traits. Moderate to strong relationships among the traits were discovered. A total of 62 quantitative trait loci（QTL） were identi fied that individually explained from1.6% to 11.6%（total root dry weight/total seedling shoot dry weight） of the phenotypic variation. Eighteen,24 and 20 QTL were identi fied for primary,seminal and total root classes of traits,respectively. We found hotspots of 5,3,4 and 12 QTL in maize chromosome bins 2.06,3.02-03,9.02-04,and 9.05-06,respectively,implicating the presence of root gene clusters or pleiotropic effects. These results characterized the phenotypic variation and genetic architecture of seedling RSA in a population derived from a successful maize hybrid.
