This review updates the present status of the field of molecular markers and marker-assisted selection(MAS),using the example of drought tolerance in barley.The accuracy of selected quantitative trait loci(QTLs),candi...This review updates the present status of the field of molecular markers and marker-assisted selection(MAS),using the example of drought tolerance in barley.The accuracy of selected quantitative trait loci(QTLs),candidate genes and suggested markers was assessed in the barley genome cv.Morex.Six common strategies are described for molecular marker development,candidate gene identification and verification,and their possible applications in MAS to improve the grain yield and yield components in barley under drought stress.These strategies are based on the following five principles:(1)Molecular markers are designated as genomic‘tags’,and their‘prediction’is strongly dependent on their distance from a candidate gene on genetic or physical maps;(2)plants react differently under favourable and stressful conditions or depending on their stage of development;(3)each candidate gene must be verified by confirming its expression in the relevant conditions,e.g.,drought;(4)the molecular marker identified must be validated for MAS for tolerance to drought stress and improved grain yield;and(5)the small number of molecular markers realized for MAS in breeding,from among the many studies targeting candidate genes,can be explained by the complex nature of drought stress,and multiple stress-responsive genes in each barley genotype that are expressed differentially depending on many other factors.展开更多
Evaluation of agronomic traits in Prunus breeding programs is a tedious process because of the long juvenile period of trees, the influence of juvenility and the existence of climatic factors affecting the expression ...Evaluation of agronomic traits in Prunus breeding programs is a tedious process because of the long juvenile period of trees, the influence of juvenility and the existence of climatic factors affecting the expression of the trait. For these reasons, marker-assisted selection (MAS) strategies are particularly useful in these cases. The objective of this work is the analysis of alternative low- cost strategies for development of molecular markers linked to agronomic traits in Prunus including the application of modified Bulked segregant analysis (BSA) using Simple sequence repeat (SSRs) markers and the application of Random amplified polymorphism microsatellite (RAMP) markers. First BSA results showed that two SSR loci were found to be tightly linked to flowering time in almond. On the other hand, RAMP analysis has been demonstrated to be a potentially valuable molecular marker for the study of genetic relationships in Prunus. Results showed the dominant nature of these markers with a great abundance and transferability although with a reduced polymorphism. In addition, RAMP application in F1 progenies showed its suitability for molecular characterization and mapping, and later Quantitative trait loci (QTL) or BSA analysis.展开更多
The translucent endosperm trait in a japonica rice variety ＇Kantou 194＇ is controlled by a Wx-mq gene which is allelic to Wx locus by genetic analysis and allelic test. The amylose content analysis showed that an in...The translucent endosperm trait in a japonica rice variety ＇Kantou 194＇ is controlled by a Wx-mq gene which is allelic to Wx locus by genetic analysis and allelic test. The amylose content analysis showed that an intermediate amylose content between those of glutinous and non-glutinous rice existed in endosperm of homozygous Wx-mq genotype. The slight changes of amylose content in different varieties and F1 grains with an identical Wx-mq genotype might be influenced by dissimilar genetic background. To identify the Wx-mq genotype simply and rapidly, a cleaved amplified polymorphic sequence （CAPS） marker was designed. The result from the molecular detection indicated that it could be used for marker-assisted selection for low amylose content varieties in rice breeding.展开更多
Although long-term genetic gain has been achieved through increasing use of modern breeding methods and technologies,the rate of genetic gain needs to be accelerated to meet humanity’s demand for agricultural product...Although long-term genetic gain has been achieved through increasing use of modern breeding methods and technologies,the rate of genetic gain needs to be accelerated to meet humanity’s demand for agricultural products.In this regard,genomic selection(GS)has been considered most promising for genetic improvement of the complex traits controlled by many genes each with minor effects.Livestock scientists pioneered GS application largely due to livestock’s significantly higher individual values and the greater reduction in generation interval that can be achieved in GS.Large-scale application of GS in plants can be achieved by refining field management to improve heritability estimation and prediction accuracy and developing optimum GS models with the consideration of genotype-by-environment interaction and non-additive effects,along with significant cost reduction.Moreover,it would be more effective to integrate GS with other breeding tools and platforms for accelerating the breeding process and thereby further enhancing genetic gain.In addition,establishing an open-source breeding network and developing transdisciplinary approaches would be essential in enhancing breeding efficiency for small-and medium-sized enterprises and agricultural research systems in developing countries.New strategies centered on GS for enhancing genetic gain need to be developed.展开更多
Powdery mildew(PM),caused by Blumeria graminis f.sp.tritici(Bgt),is one of the destructive wheat diseases worldwide.Wild emmer wheat(Triticum turgidum ssp.dicoccoides,WEW),a tetraploid progenitor of common wheat,is a ...Powdery mildew(PM),caused by Blumeria graminis f.sp.tritici(Bgt),is one of the destructive wheat diseases worldwide.Wild emmer wheat(Triticum turgidum ssp.dicoccoides,WEW),a tetraploid progenitor of common wheat,is a valuable genetic resource for wheat disease resistance breeding programs.We developed three hexaploid pre-breeding lines with PM resistance genes derived from three WEW accessions.These resistant pre-breeding lines were crossed with susceptible common wheat accessions.Segregations in the F2populations were 3 resistant:1 susceptible,suggesting a single dominant allele in each resistant parent.Mapping of the resistance gene in each line indicated a single locus on the long arm of chromosome 7A,at the approximate location of previously cloned Pm60 from T.urartu.Sanger sequencing revealed three different Pm60 haplotypes(Hap 3,Hap 5,and Hap 6).Co-segregating diagnostic markers were developed for identification and selection of each haplotype.The resistance function of each haplotype was verified by the virus-induced gene silencing(VIGS).Common wheat lines carrying each of these Pm60 haplotypes were resistant to most Bgt isolates and differences in the response arrays suggested allelic variation in response.展开更多
【目的】通过筛选与鹅蛋品质性状相关的分子标记和候选基因,为解析蛋品质性状的遗传机制及分子标记辅助选择提供理论支撑。【方法】采用同批次健康四川白鹅群体(209只)作为研究对象。收集了每只鹅在产蛋高峰期连续生产的5枚蛋,并测定了...【目的】通过筛选与鹅蛋品质性状相关的分子标记和候选基因,为解析蛋品质性状的遗传机制及分子标记辅助选择提供理论支撑。【方法】采用同批次健康四川白鹅群体(209只)作为研究对象。收集了每只鹅在产蛋高峰期连续生产的5枚蛋,并测定了蛋重、蛋形指数、蛋壳强度、蛋壳厚度、蛋壳重和蛋黄重量等6个蛋品质性状。基于前期209只四川白鹅(母鹅)2.896 Tb全基因组重测序数据(12.44×/个体),采用全基因组关联分析的方法,筛选与蛋品质性状相关的SNP位点和重要候选基因,并通过核酸飞行时间质谱方法检测了这些SNP位点的基因型频率。【结果】经过筛选过滤,共有9279339个SNPs和209个个体用于后续研究。GWAS研究发现,48个SNP位点与6个鹅蛋品质性状显著或建议性显著相关(阈值分别为5.43×10-9和1.09×10-7),并注释出27个蛋品质性状相关的候选基因,包括妊娠相关血浆蛋白A(pappalysin1,PAPPA)、蛋白丝氨酸/苏氨酸磷酸酶调节亚基2基因(serine/threonine-protein phosphatase 4 regulatory subunit 2,PP4R2)、乙醇胺磷酸转移酶1(ethanolamine phosphotransferase 1,EPT1)和离子型谷氨酸受体K2(glutamate receptor ionotropic,kainate 2,GRIK2)等,其中候选基因PAPPA参与蛋白质代谢,促进生长因子IGF生成,在PP4R2的11bp范围内存在5个SNPs与蛋壳厚度显著相关,另外在GRIK2上有6个SNPs与蛋黄重量显著相关,GRIK2和PP4R2分别与机体血钙维持功能以及胆固醇代谢相关。功能富集研究发现,候选基因主要参与了response to growth factor(GO:0070848)、intracellular chemical homeostasis(GO:0055082)、response to hormone(GO:0009725)和regulation of the monoatomic ion transport(GO:43269)等代谢通路。【结论】经GWAS方法筛选出PAPPA、GRIK2、ASCC3和EPT1分别作为蛋重、蛋黄重、蛋壳强度等蛋品质性状潜在功能基因,为鹅蛋品质性状的改良提供了分子遗传标记的理论参考。展开更多
基金supported by Bolashak International Fellowships,Center for International Programs,Ministry of Education and Science,KazakhstanAP14869777 supported by the Ministry of Education and Science,KazakhstanResearch Projects BR10764991 and BR10765000 supported by the Ministry of Agriculture,Kazakhstan。
文摘This review updates the present status of the field of molecular markers and marker-assisted selection(MAS),using the example of drought tolerance in barley.The accuracy of selected quantitative trait loci(QTLs),candidate genes and suggested markers was assessed in the barley genome cv.Morex.Six common strategies are described for molecular marker development,candidate gene identification and verification,and their possible applications in MAS to improve the grain yield and yield components in barley under drought stress.These strategies are based on the following five principles:(1)Molecular markers are designated as genomic‘tags’,and their‘prediction’is strongly dependent on their distance from a candidate gene on genetic or physical maps;(2)plants react differently under favourable and stressful conditions or depending on their stage of development;(3)each candidate gene must be verified by confirming its expression in the relevant conditions,e.g.,drought;(4)the molecular marker identified must be validated for MAS for tolerance to drought stress and improved grain yield;and(5)the small number of molecular markers realized for MAS in breeding,from among the many studies targeting candidate genes,can be explained by the complex nature of drought stress,and multiple stress-responsive genes in each barley genotype that are expressed differentially depending on many other factors.
文摘Evaluation of agronomic traits in Prunus breeding programs is a tedious process because of the long juvenile period of trees, the influence of juvenility and the existence of climatic factors affecting the expression of the trait. For these reasons, marker-assisted selection (MAS) strategies are particularly useful in these cases. The objective of this work is the analysis of alternative low- cost strategies for development of molecular markers linked to agronomic traits in Prunus including the application of modified Bulked segregant analysis (BSA) using Simple sequence repeat (SSRs) markers and the application of Random amplified polymorphism microsatellite (RAMP) markers. First BSA results showed that two SSR loci were found to be tightly linked to flowering time in almond. On the other hand, RAMP analysis has been demonstrated to be a potentially valuable molecular marker for the study of genetic relationships in Prunus. Results showed the dominant nature of these markers with a great abundance and transferability although with a reduced polymorphism. In addition, RAMP application in F1 progenies showed its suitability for molecular characterization and mapping, and later Quantitative trait loci (QTL) or BSA analysis.
基金supported by the National High Technology Research and Development Program of China(Grant No.2006AA100101)National Science and Technology Support Program of China(Grant No. 2006BAD01A01-5)+1 种基金Special Program for Rice Scientific Research,Ministry of Agriculture,China(Grant No. nyhyzx 07-001-006)Super Rice Breeding and Demonstration Program,Ministry of Agriculture,China and Jiangsu Agricultural Scientific Self-innovation Fund,China(Grant No.CX[07]603)
文摘The translucent endosperm trait in a japonica rice variety ＇Kantou 194＇ is controlled by a Wx-mq gene which is allelic to Wx locus by genetic analysis and allelic test. The amylose content analysis showed that an intermediate amylose content between those of glutinous and non-glutinous rice existed in endosperm of homozygous Wx-mq genotype. The slight changes of amylose content in different varieties and F1 grains with an identical Wx-mq genotype might be influenced by dissimilar genetic background. To identify the Wx-mq genotype simply and rapidly, a cleaved amplified polymorphic sequence （CAPS） marker was designed. The result from the molecular detection indicated that it could be used for marker-assisted selection for low amylose content varieties in rice breeding.
基金The research involved in this report was supported by the National Key Research and Development Program of China(2016YFD0101803)the National Key Basic Research Program of China(2014 CB138206)+1 种基金the Agricultural Science and Technology Innovation Program of CAAS,and Fundamental Research Funds for Central Non-Profit of Institute of Crop Sciences,CAAS(1610092016124)Research activities of CIMMYT staff have been supported by the Bill and Melinda Gates Foundation and the CGIAR Research Program MAIZE.
文摘Although long-term genetic gain has been achieved through increasing use of modern breeding methods and technologies,the rate of genetic gain needs to be accelerated to meet humanity’s demand for agricultural products.In this regard,genomic selection(GS)has been considered most promising for genetic improvement of the complex traits controlled by many genes each with minor effects.Livestock scientists pioneered GS application largely due to livestock’s significantly higher individual values and the greater reduction in generation interval that can be achieved in GS.Large-scale application of GS in plants can be achieved by refining field management to improve heritability estimation and prediction accuracy and developing optimum GS models with the consideration of genotype-by-environment interaction and non-additive effects,along with significant cost reduction.Moreover,it would be more effective to integrate GS with other breeding tools and platforms for accelerating the breeding process and thereby further enhancing genetic gain.In addition,establishing an open-source breeding network and developing transdisciplinary approaches would be essential in enhancing breeding efficiency for small-and medium-sized enterprises and agricultural research systems in developing countries.New strategies centered on GS for enhancing genetic gain need to be developed.
基金supported by grants from the National Key Research and Development Program of China(2023YFF1000404,2022YFF10001501)the National Natural Science Foundation of China(32171971)。
文摘Powdery mildew(PM),caused by Blumeria graminis f.sp.tritici(Bgt),is one of the destructive wheat diseases worldwide.Wild emmer wheat(Triticum turgidum ssp.dicoccoides,WEW),a tetraploid progenitor of common wheat,is a valuable genetic resource for wheat disease resistance breeding programs.We developed three hexaploid pre-breeding lines with PM resistance genes derived from three WEW accessions.These resistant pre-breeding lines were crossed with susceptible common wheat accessions.Segregations in the F2populations were 3 resistant:1 susceptible,suggesting a single dominant allele in each resistant parent.Mapping of the resistance gene in each line indicated a single locus on the long arm of chromosome 7A,at the approximate location of previously cloned Pm60 from T.urartu.Sanger sequencing revealed three different Pm60 haplotypes(Hap 3,Hap 5,and Hap 6).Co-segregating diagnostic markers were developed for identification and selection of each haplotype.The resistance function of each haplotype was verified by the virus-induced gene silencing(VIGS).Common wheat lines carrying each of these Pm60 haplotypes were resistant to most Bgt isolates and differences in the response arrays suggested allelic variation in response.
文摘全基因组SNP变异检测是开展基因组育种(Genomic selection)和准确度量群体遗传多样性的基础。继国外开发出60 K和600 K鸡SNP芯片后,中国农业科学院北京畜牧兽医研究所等单位,针对国产化鸡育种和地方种质资源保护的现状和需求,自主研发出了"京芯一号"55 K SNP芯片等高性价比的检测芯片。芯片特点包括:(1)包含中国地方鸡种特有遗传变异信息,兼顾国外商业化鸡种基因组信息;(2)整合大量的功能基因相关SNP位点;(3)在基因组上均匀分布;(4)密度适中,性价比高等。应用实践证明,鸡基因组SNP芯片在基因组选择育种、种质资源多样性分析、亲缘关系鉴定、基因组关联研究、基因定位等方面可发挥重要作用。文章以"京芯一号"55 K SNP芯片为重点,对鸡全基因组SNP芯片研发和应用的最新进展进行了综述。
文摘【目的】通过筛选与鹅蛋品质性状相关的分子标记和候选基因,为解析蛋品质性状的遗传机制及分子标记辅助选择提供理论支撑。【方法】采用同批次健康四川白鹅群体(209只)作为研究对象。收集了每只鹅在产蛋高峰期连续生产的5枚蛋,并测定了蛋重、蛋形指数、蛋壳强度、蛋壳厚度、蛋壳重和蛋黄重量等6个蛋品质性状。基于前期209只四川白鹅(母鹅)2.896 Tb全基因组重测序数据(12.44×/个体),采用全基因组关联分析的方法,筛选与蛋品质性状相关的SNP位点和重要候选基因,并通过核酸飞行时间质谱方法检测了这些SNP位点的基因型频率。【结果】经过筛选过滤,共有9279339个SNPs和209个个体用于后续研究。GWAS研究发现,48个SNP位点与6个鹅蛋品质性状显著或建议性显著相关(阈值分别为5.43×10-9和1.09×10-7),并注释出27个蛋品质性状相关的候选基因,包括妊娠相关血浆蛋白A(pappalysin1,PAPPA)、蛋白丝氨酸/苏氨酸磷酸酶调节亚基2基因(serine/threonine-protein phosphatase 4 regulatory subunit 2,PP4R2)、乙醇胺磷酸转移酶1(ethanolamine phosphotransferase 1,EPT1)和离子型谷氨酸受体K2(glutamate receptor ionotropic,kainate 2,GRIK2)等,其中候选基因PAPPA参与蛋白质代谢,促进生长因子IGF生成,在PP4R2的11bp范围内存在5个SNPs与蛋壳厚度显著相关,另外在GRIK2上有6个SNPs与蛋黄重量显著相关,GRIK2和PP4R2分别与机体血钙维持功能以及胆固醇代谢相关。功能富集研究发现,候选基因主要参与了response to growth factor(GO:0070848)、intracellular chemical homeostasis(GO:0055082)、response to hormone(GO:0009725)和regulation of the monoatomic ion transport(GO:43269)等代谢通路。【结论】经GWAS方法筛选出PAPPA、GRIK2、ASCC3和EPT1分别作为蛋重、蛋黄重、蛋壳强度等蛋品质性状潜在功能基因,为鹅蛋品质性状的改良提供了分子遗传标记的理论参考。
