The aim is to develop a liquid chip technique to detect Taura syndrome virus( TSV) and yellow head disease virus( YHDV) on Penaeus orientalis simultaneously. The CP2 gene of TSV and N gene of YHDV in Gen Bank was anal...The aim is to develop a liquid chip technique to detect Taura syndrome virus( TSV) and yellow head disease virus( YHDV) on Penaeus orientalis simultaneously. The CP2 gene of TSV and N gene of YHDV in Gen Bank was analysed by using the software DNAStar 7. 0 to design the TSV-and YHDV-specific primers. The primers were labeled with biotin and subjected to amination modification. They were then coupled with fluorescence-coded microspheres and then used for hybridization with RT- PCR products of TSV and YHDV. The liquid chip detection technique for detection of TSV and YHDV was established by using BD FACSArray to detect fluorescence signal in the reaction system. This assay system had a high sensitivity to TSV and YHDV,with the detection of limit of 100 pg. Moreover,the assay was specific for the detection of TSV,YHDV and was not susceptible to cross with other viruses,including white spot syndrome virus( WSSV),spring viremia of carp virus( SVCV),infectious haematopoietic necrosis virus( IHNV). In conclusion,the liquid chip assay technique established in this study is highly sensitive and specific to TSV and YHDV detection. Moreover,it provides a novel,convenient and rapid approach for the detection of TSV and YHDV.展开更多
High-throughput genotyping tools can effectively promote molecular breeding in crops.In this study,genotyping by target sequencing(GBTS)system was utilized to develop a genome-wide liquid SNP chip for facilitating gen...High-throughput genotyping tools can effectively promote molecular breeding in crops.In this study,genotyping by target sequencing(GBTS)system was utilized to develop a genome-wide liquid SNP chip for facilitating genetics and breeding in melon(Cucumis melo L.),a globally cultivated economically important horticultural crop.Based on over eight million SNPs derived from 823 representative melon accessions,16K,8K,4K,2K,1K,500,250 and 125 informative SNPs were screened and evaluated for their polymorphisms,conservation of flanking sequences,and distributions.The set of 2K SNPs was found to be optimal for representing the maximum diversity with the lowest number of SNPs,and it was selected to develop the liquid chip,named“Melon2K”.Using Melon2K,more than 1500 SNPs were detected across 17 samples of five melon cultivars,and the phylogenetic relationships were clearly constructed.Within the same cultivar,genetic differences were also assessed between different samples.We evaluated the performance of Melon2K in genetic background selection during the breeding process,obtaining the introgression lines of interested trait with more than 97%genetic background of elite variety by only two rounds of backcrossing.These results suggest that Melon2K provides a cost-effective,efficient and reliable platform for genetic analysis and molecular breeding in melon.展开更多
Genotyping platforms,as critical supports for genomics,genetics,and molecular breeding,have been well implemented at national institutions/universities in developed countries and multinational seed companies that poss...Genotyping platforms,as critical supports for genomics,genetics,and molecular breeding,have been well implemented at national institutions/universities in developed countries and multinational seed companies that possess high-throughput,automatic,large-scale,and shared facilities.In this study,we integrated an improved genotyping by target sequencing(GBTS)system with capture-in-solution(liquid chip)technology to develop a multiple single-nucleotide polymorphism(mSNP)approach in which mSNPs can be captured from a single amplicon.From one 40K maize mSNP panel,we developed three types of markers(40K mSNPs,251K SNPs,and 690K haplotypes),and generated multiple panels with various marker densities(1K–40K mSNPs)by sequencing at different depths.Comparative genetic diversity analysis was performed with genic versus intergenic markers and di-allelic SNPs versus non-typical SNPs.Compared with the one-amplicon-one-SNP system,mSNPs and within-mSNP haplotypes are more powerful for genetic diversity detection,linkage disequilibrium decay analysis,and genome-wide association studies.The technologies,protocols,and application scenarios developed for maize in this study will serve as a model for the development of mSNP arrays and highly efficient GBTS systems in animals,plants,and microorganisms.展开更多
研究旨在通过全基因组选择信号分析,挖掘宁蒗高原鸡品种重要的种质特性基因。研究使用“神农一号”地方鸡液相基因芯片对3个地方鸡品种(30只宁蒗高原鸡,30只正阳三黄鸡及33只固始鸡)进行基因分型。试验首先通过构建系统发育树、主成分...研究旨在通过全基因组选择信号分析,挖掘宁蒗高原鸡品种重要的种质特性基因。研究使用“神农一号”地方鸡液相基因芯片对3个地方鸡品种(30只宁蒗高原鸡,30只正阳三黄鸡及33只固始鸡)进行基因分型。试验首先通过构建系统发育树、主成分分析、祖先成分分析等方法,探究品种的种群遗传结构;然后,结合群体遗传分化指数(Pattern of genetic differentiation,FST)和跨群体单倍型统计(Cross-population haplotype-based statistic,XP-nSL)等比较基因组方法鉴定宁蒗高原鸡全基组选择信号;最后,对宁蒗高原鸡进行连续性纯合片段(Run of homozygosity,ROH)分析,以进一步探究其受到的人工和自然选择足迹。结果显示:选择信号分析发现宁蒗高原鸡在高海拔适应、骨骼和肌肉发育、生长及体型大小等性状经历了更高强度选择;ROH分析共鉴定到7个ROH岛,对其进行基因注释发现,与生长、体型大小、骨骼发育及高海拔适应等相关的基因受到了选择。研究表明,3个品种间有明显的群体分化,两个河南地方鸡品种遗传距离较近,而宁蒗高原鸡与两者明显分离,该结果与现实中分群结果一致,结果为宁蒗高原鸡遗传资源保护、开发利用与评价工作提供参考。展开更多
基金Supported by Science and Technology Project of General Administration of Quality Supervision,Inspection and Quarantine of the People's Republic of China(2012IK018)Special Fund for Scientific Research in the Public Welfare(201210055-4)
文摘The aim is to develop a liquid chip technique to detect Taura syndrome virus( TSV) and yellow head disease virus( YHDV) on Penaeus orientalis simultaneously. The CP2 gene of TSV and N gene of YHDV in Gen Bank was analysed by using the software DNAStar 7. 0 to design the TSV-and YHDV-specific primers. The primers were labeled with biotin and subjected to amination modification. They were then coupled with fluorescence-coded microspheres and then used for hybridization with RT- PCR products of TSV and YHDV. The liquid chip detection technique for detection of TSV and YHDV was established by using BD FACSArray to detect fluorescence signal in the reaction system. This assay system had a high sensitivity to TSV and YHDV,with the detection of limit of 100 pg. Moreover,the assay was specific for the detection of TSV,YHDV and was not susceptible to cross with other viruses,including white spot syndrome virus( WSSV),spring viremia of carp virus( SVCV),infectious haematopoietic necrosis virus( IHNV). In conclusion,the liquid chip assay technique established in this study is highly sensitive and specific to TSV and YHDV detection. Moreover,it provides a novel,convenient and rapid approach for the detection of TSV and YHDV.
基金supported by the National Natural Science Foundation of China(Grant Nos.32102383,32225044 and 32130093)the Natural Science Foundation of Shandong Province(Grant No.ZR2021QC075)+1 种基金the Taishan Scholar Foundation of the People's Government of Shandong Province(Grant No.ts20190947)the Qingdao Agricultural University Doctoral Start-Up Fund。
文摘High-throughput genotyping tools can effectively promote molecular breeding in crops.In this study,genotyping by target sequencing(GBTS)system was utilized to develop a genome-wide liquid SNP chip for facilitating genetics and breeding in melon(Cucumis melo L.),a globally cultivated economically important horticultural crop.Based on over eight million SNPs derived from 823 representative melon accessions,16K,8K,4K,2K,1K,500,250 and 125 informative SNPs were screened and evaluated for their polymorphisms,conservation of flanking sequences,and distributions.The set of 2K SNPs was found to be optimal for representing the maximum diversity with the lowest number of SNPs,and it was selected to develop the liquid chip,named“Melon2K”.Using Melon2K,more than 1500 SNPs were detected across 17 samples of five melon cultivars,and the phylogenetic relationships were clearly constructed.Within the same cultivar,genetic differences were also assessed between different samples.We evaluated the performance of Melon2K in genetic background selection during the breeding process,obtaining the introgression lines of interested trait with more than 97%genetic background of elite variety by only two rounds of backcrossing.These results suggest that Melon2K provides a cost-effective,efficient and reliable platform for genetic analysis and molecular breeding in melon.
基金This research is supported by the National Key Research and Development Program of China(2016YFD0101803 and 2017YFD0101201)the Central Public-interest Scientific Institution Basal Research Fund(Y2020PT20)+4 种基金the Agricultural Science and Technology Innovation Program(ASTIP)of the Chinese Academy of Agricultural Sciences(CAAS)(CAAS-XTCX2016009)the Key Research Area and Development Program of Guangdong Province(2018B020202008)the Shijiazhuang Science and Technology Incubation Program(191540089A)the Hebei Innovation Capability Enhancement Project(19962911D)Research activities at CIMMYT were supported by the Bill and Melinda Gates Foundation and the CGIAR Research Program MAIZE.
文摘Genotyping platforms,as critical supports for genomics,genetics,and molecular breeding,have been well implemented at national institutions/universities in developed countries and multinational seed companies that possess high-throughput,automatic,large-scale,and shared facilities.In this study,we integrated an improved genotyping by target sequencing(GBTS)system with capture-in-solution(liquid chip)technology to develop a multiple single-nucleotide polymorphism(mSNP)approach in which mSNPs can be captured from a single amplicon.From one 40K maize mSNP panel,we developed three types of markers(40K mSNPs,251K SNPs,and 690K haplotypes),and generated multiple panels with various marker densities(1K–40K mSNPs)by sequencing at different depths.Comparative genetic diversity analysis was performed with genic versus intergenic markers and di-allelic SNPs versus non-typical SNPs.Compared with the one-amplicon-one-SNP system,mSNPs and within-mSNP haplotypes are more powerful for genetic diversity detection,linkage disequilibrium decay analysis,and genome-wide association studies.The technologies,protocols,and application scenarios developed for maize in this study will serve as a model for the development of mSNP arrays and highly efficient GBTS systems in animals,plants,and microorganisms.
文摘研究旨在通过全基因组选择信号分析,挖掘宁蒗高原鸡品种重要的种质特性基因。研究使用“神农一号”地方鸡液相基因芯片对3个地方鸡品种(30只宁蒗高原鸡,30只正阳三黄鸡及33只固始鸡)进行基因分型。试验首先通过构建系统发育树、主成分分析、祖先成分分析等方法,探究品种的种群遗传结构;然后,结合群体遗传分化指数(Pattern of genetic differentiation,FST)和跨群体单倍型统计(Cross-population haplotype-based statistic,XP-nSL)等比较基因组方法鉴定宁蒗高原鸡全基组选择信号;最后,对宁蒗高原鸡进行连续性纯合片段(Run of homozygosity,ROH)分析,以进一步探究其受到的人工和自然选择足迹。结果显示:选择信号分析发现宁蒗高原鸡在高海拔适应、骨骼和肌肉发育、生长及体型大小等性状经历了更高强度选择;ROH分析共鉴定到7个ROH岛,对其进行基因注释发现,与生长、体型大小、骨骼发育及高海拔适应等相关的基因受到了选择。研究表明,3个品种间有明显的群体分化,两个河南地方鸡品种遗传距离较近,而宁蒗高原鸡与两者明显分离,该结果与现实中分群结果一致,结果为宁蒗高原鸡遗传资源保护、开发利用与评价工作提供参考。
