Acacia hybrids offer a great potential for paper industry in Southeast Asia due to their fast growth and ability to grow on abandoned or marginal lands. Breeding Acacia hybrids with desirable traits can be achieved th...Acacia hybrids offer a great potential for paper industry in Southeast Asia due to their fast growth and ability to grow on abandoned or marginal lands. Breeding Acacia hybrids with desirable traits can be achieved through marker assisted selection(MAS) breeding. To develop a MAS program requires development of linkage maps and QTL analysis. Two mapping populations were developed through interspecific hybridization for linkage mapping and QTL analysis. All seeds per pod were cultured initially to improve hybrid yield as quality and density of linkage mapping is affected by the size of the mapping population. Progenies from two mapping populations were field planted for phenotypic and genotypic evaluation at three locations in Malaysia,(1) Forest Research Institute Malaysia field station at Segamat, Johor,(2) Borneo Tree Seeds and Seedlings Supplies Sdn, Bhd.(BTS) field trial site at Bintulu, Sarawak, and(3) Asiaprima RCF field trial site at Lancang, Pahang. During field planting, mislabeling was reported at Segamat, Johor, and a similar problem was suspected for Bintulu, Sarawak. Early screening with two isozymes effectively selected hybrid progenies, and these hybrids were subsequently further confirmed by using species-specific SNPs. During field planting, clonal mislabeling was reported and later confirmed by using a small set of STMS markers. A large set of SNPs were also used to screen all ramets in both populations. A total of 65.36% mislabeled ramets were encountered in the wood density population and 60.34% in the fibre length mapping population. No interpopulation pollen contamination was detected because all ramets found their match within the same population in question.However, mislabeling was detected among ramets of the same population. Mislabeled individuals were identified and grouped as they originated from 93 pods for wood density and 53 pods for fibre length mapping populations.On average 2 meiotically unique seeds per pod(179 seeds/93 pods) for wood density and 3 meiotically unique seeds per p展开更多
A novel method for haplotype phasing in families after joint estimation of recombination fraction and linkage disequilibrium is developed. Results from Monte Carlo computer simulations show that the newly developed E....A novel method for haplotype phasing in families after joint estimation of recombination fraction and linkage disequilibrium is developed. Results from Monte Carlo computer simulations show that the newly developed E.M. algorithm is accurate if true recombination fraction is 0 even for single families of relatively small sizes. Estimates of recombination fraction and linkage disequilibrium were 0.00 （SD 0.00） and 0.19 （SD 0.03） for simulated recombination fraction and linkage disequilibrium of 0.00 and 0.20, respectively. A genome fragmentation phasing strategy was developed and used for phasing haplotypes in a sire and 36 progeny using the 50 k Illumina BeadChip by： a） estimation of the recombination fraction and LD in consecutive SNPs using family information, b） linkage analyses between fragments, c） phasing of haplotypes in parents and progeny and in following generations. Homozygous SNPs in progeny allowed determination of paternal fragment inheritance, and deduction of SNP sequence information of haplotypes from dams. The strategy also allowed detection of genotyping errors. A total of 613 recombination events were detected after linkage analysis was carried out between fragments. Hot and cold spots were identified at the individual （sire level）. SNPs for which the sire and calf were heterozygotes became informative （over 90%） after the phasing of haplotypes. Average of regions of identity between half-sibs when comparing its maternal inherited haplotypes （with at least 20 SNP） in common was 0.11 with a maximum of 0.29 and a minimum of 0.05. A Monte-Carlo simulation of BTA1 with the same linkage disequilibrium structure and genetic linkage as the cattle family yielded a 99.98 and 99.94% of correct phases for informative SNPs in sire and calves, respectively.展开更多
Grapevine(Vitis spp.)contains a wealth of phytochemicals that have received considerable attention due to healthpromoting properties and biological activities as phytoalexins.To date,the genetic basis of the quantitat...Grapevine(Vitis spp.)contains a wealth of phytochemicals that have received considerable attention due to healthpromoting properties and biological activities as phytoalexins.To date,the genetic basis of the quantitative variations for these potentially beneficial compounds has been limited.Here,metabolic quantitative trait locus(mQTL)mapping was conducted using grapevine stems of a segregating F2 population.Metabolic profiling of grapevine stems was performed using liquid chromatography–high-resolution mass spectrometry(LC-HRMS),resulting in the detection of 1317 ions/features.In total,19 of these features matched with literature-reported stilbenoid masses and were genetically mapped using a 1449-SNP linkage map and R/qtl software,resulting in the identification of four mQTLs.Two large-effect mQTLs that corresponded to a stilbenoid dimer and a trimer were mapped on chromosome 18,accounting for phenotypic variances of 29.0%and 38.4%.Functional annotations of these large-effect mQTLs on the VitisNet network database revealed a major hotspot of disease-resistance motifs on chromosome 18.This 2.8-Mbp region contains 48 genes with R-gene motifs,including variants of TIR,NBS,and LRR,that might potentially confer resistance to powdery mildew,downy mildew,or other pathogens.The locus also encompasses genes associated with flavonoid and biosynthetic pathways that are likely involved in the production of secondary metabolites,including phytoalexins.In addition,haplotype dosage effects of the five mQTLs further characterized the genomic regions for differential production of stilbenoids that can be applied in resistance breeding through manipulation of stilbenoid production in planta.展开更多
Saccharina japonica is one of the most important economic brown seaweeds.It is intensively cultivated on large scales in a number of Asian countries.The current annual,global production is about 8 million tons valued ...Saccharina japonica is one of the most important economic brown seaweeds.It is intensively cultivated on large scales in a number of Asian countries.The current annual,global production is about 8 million tons valued as about 4 million US dollars.Considerable efforts have been made to S.japonica in China since the 1950s on its cultivation.To further advance the cultivation of this species,detailed research of genetics and breeding studies are required.Recently,with the advancement of sequencing techniques,the genomics and comparative transcriptomics data were yielded,and quantitative trait locus(QTL)mapping has been conducted,along with genetic linkage maps constructed to this species.New strains have been bred and selected,with better characteristics,e.g.higher seawater temperature resistances and higher yields.In this review,we present the current status of genetic and breeding studies that have been performed to S.japonica in China,and provide guidelines for future developments in the areas of genetic selection and breeding for this species.展开更多
全基因组关联分析(genome-wide association studies,GWAS)是近几年发展起来的解析人类、动物或植物表型多样性遗传基础的有效分析手段。GWAS具有高通量、高精度和高速度等显著优点,其在林木遗传育种中的作用日益凸显。本文从种质材料...全基因组关联分析(genome-wide association studies,GWAS)是近几年发展起来的解析人类、动物或植物表型多样性遗传基础的有效分析手段。GWAS具有高通量、高精度和高速度等显著优点,其在林木遗传育种中的作用日益凸显。本文从种质材料、目标性状的选择和表型鉴定、全基因组SNP位点的获取、群体结构、连锁不平衡分析以及关联作图与候选基因发掘等方面对GWAS在林木育种中的应用进行了综述,并提出后续研究展望。以期为进一步利用GWAS技术进行林木育种中各种性状遗传基础的研究提供参考。展开更多
Molecular screening of major rice blast resistance genes was determined with molecular markers, which showed close-set linkage to 11 major rice blast resistance genes（Pi-d2, Pi-z, Piz-t, Pi-9, Pi-36, Pi-37, Pi5, Pi-b...Molecular screening of major rice blast resistance genes was determined with molecular markers, which showed close-set linkage to 11 major rice blast resistance genes（Pi-d2, Pi-z, Piz-t, Pi-9, Pi-36, Pi-37, Pi5, Pi-b, Pik-p, Pik-h and Pi-ta2）, in a collection of 32 accessions resistant to Magnaporthe oryzae. Out of the 32 accessions, the Pi-d2 and Pi-z appeared to be omnipresent and gave positive express. As the second dominant, Pi-b and Piz-t gene frequencies were 96.9% and 87.5%. And Pik-h and Pik-p gene frequencies were 43.8% and 28.1%, respectively. The molecular marker linkage to Pi-ta2 produced positive bands in eleven accessions, while the molecular marker linkage to Pi-36 and Pi-37 in only three and four accessions, respectively. The natural field evaluation analysis showed that 30 of the 32 accessions were resistant, one was moderately resistant and one was susceptible. Infection types were negatively correlated with the genotype scores of Pi-9, Pi5, Pi-b, Pi-ta2 and Pik-p, although the correlation coefficients were very little. These results are useful in identification and incorporation of functional resistance genes from these germplasms into elite cultivars through marker-assisted selection for improved blast resistance in China and worldwide.展开更多
Simple sequence repeat(SSR)markers have previously been applied to linkage mapping of the pea(Pisum sativum L.)genome.However,the transferability of existing loci to the molecularly distinct Chinese winter pea gene po...Simple sequence repeat(SSR)markers have previously been applied to linkage mapping of the pea(Pisum sativum L.)genome.However,the transferability of existing loci to the molecularly distinct Chinese winter pea gene pool was limited.A novel set of pea SSR markers was accordingly developed.Together with existing SSR sequences,the genome of the G0003973(winter hardy)×G0005527(cold sensitive)cross was mapped using 190 F2individuals.In total,157 SSR markers were placed in 11 linkage groups with an average interval of 9.7 cM and total coverage of 1518 cM.The novel markers and genetic linkage map will be useful for marker-assisted pea breeding.展开更多
基金provided by the Ministry of Science,Technology and Innovation Malaysia(IRPA 01-02-02-0015PR0003/03-02,02-01-02-SF0403)Universiti Kebangsaan Malaysia(UKM-AP-BPB-13-2009,GUP-2013-039)
文摘Acacia hybrids offer a great potential for paper industry in Southeast Asia due to their fast growth and ability to grow on abandoned or marginal lands. Breeding Acacia hybrids with desirable traits can be achieved through marker assisted selection(MAS) breeding. To develop a MAS program requires development of linkage maps and QTL analysis. Two mapping populations were developed through interspecific hybridization for linkage mapping and QTL analysis. All seeds per pod were cultured initially to improve hybrid yield as quality and density of linkage mapping is affected by the size of the mapping population. Progenies from two mapping populations were field planted for phenotypic and genotypic evaluation at three locations in Malaysia,(1) Forest Research Institute Malaysia field station at Segamat, Johor,(2) Borneo Tree Seeds and Seedlings Supplies Sdn, Bhd.(BTS) field trial site at Bintulu, Sarawak, and(3) Asiaprima RCF field trial site at Lancang, Pahang. During field planting, mislabeling was reported at Segamat, Johor, and a similar problem was suspected for Bintulu, Sarawak. Early screening with two isozymes effectively selected hybrid progenies, and these hybrids were subsequently further confirmed by using species-specific SNPs. During field planting, clonal mislabeling was reported and later confirmed by using a small set of STMS markers. A large set of SNPs were also used to screen all ramets in both populations. A total of 65.36% mislabeled ramets were encountered in the wood density population and 60.34% in the fibre length mapping population. No interpopulation pollen contamination was detected because all ramets found their match within the same population in question.However, mislabeling was detected among ramets of the same population. Mislabeled individuals were identified and grouped as they originated from 93 pods for wood density and 53 pods for fibre length mapping populations.On average 2 meiotically unique seeds per pod(179 seeds/93 pods) for wood density and 3 meiotically unique seeds per p
基金support from a Marie Curie International Reintegration Grant from the European Union,project no.PIRG08-GA-2010-277031 "SelectionForWelfare"LGR and WMR acknowledge support from project AGL2012-39137
文摘A novel method for haplotype phasing in families after joint estimation of recombination fraction and linkage disequilibrium is developed. Results from Monte Carlo computer simulations show that the newly developed E.M. algorithm is accurate if true recombination fraction is 0 even for single families of relatively small sizes. Estimates of recombination fraction and linkage disequilibrium were 0.00 （SD 0.00） and 0.19 （SD 0.03） for simulated recombination fraction and linkage disequilibrium of 0.00 and 0.20, respectively. A genome fragmentation phasing strategy was developed and used for phasing haplotypes in a sire and 36 progeny using the 50 k Illumina BeadChip by： a） estimation of the recombination fraction and LD in consecutive SNPs using family information, b） linkage analyses between fragments, c） phasing of haplotypes in parents and progeny and in following generations. Homozygous SNPs in progeny allowed determination of paternal fragment inheritance, and deduction of SNP sequence information of haplotypes from dams. The strategy also allowed detection of genotyping errors. A total of 613 recombination events were detected after linkage analysis was carried out between fragments. Hot and cold spots were identified at the individual （sire level）. SNPs for which the sire and calf were heterozygotes became informative （over 90%） after the phasing of haplotypes. Average of regions of identity between half-sibs when comparing its maternal inherited haplotypes （with at least 20 SNP） in common was 0.11 with a maximum of 0.29 and a minimum of 0.05. A Monte-Carlo simulation of BTA1 with the same linkage disequilibrium structure and genetic linkage as the cattle family yielded a 99.98 and 99.94% of correct phases for informative SNPs in sire and calves, respectively.
基金Funding for this research was provided by the USDA-NIFA Specialty Crops Research Initiative(Award Nos 2011-51181-30635 and 2011-51181-30850)through the VitisGen project and the Northern Grapes Project,as well as by the Minnesota Agricultural Experiment Station and the South Dakota Agricultural Experiment Station through the Hatch projectsFunding was also provided by the National Science Foundation IOS(Award No.1238812).
文摘Grapevine(Vitis spp.)contains a wealth of phytochemicals that have received considerable attention due to healthpromoting properties and biological activities as phytoalexins.To date,the genetic basis of the quantitative variations for these potentially beneficial compounds has been limited.Here,metabolic quantitative trait locus(mQTL)mapping was conducted using grapevine stems of a segregating F2 population.Metabolic profiling of grapevine stems was performed using liquid chromatography–high-resolution mass spectrometry(LC-HRMS),resulting in the detection of 1317 ions/features.In total,19 of these features matched with literature-reported stilbenoid masses and were genetically mapped using a 1449-SNP linkage map and R/qtl software,resulting in the identification of four mQTLs.Two large-effect mQTLs that corresponded to a stilbenoid dimer and a trimer were mapped on chromosome 18,accounting for phenotypic variances of 29.0%and 38.4%.Functional annotations of these large-effect mQTLs on the VitisNet network database revealed a major hotspot of disease-resistance motifs on chromosome 18.This 2.8-Mbp region contains 48 genes with R-gene motifs,including variants of TIR,NBS,and LRR,that might potentially confer resistance to powdery mildew,downy mildew,or other pathogens.The locus also encompasses genes associated with flavonoid and biosynthetic pathways that are likely involved in the production of secondary metabolites,including phytoalexins.In addition,haplotype dosage effects of the five mQTLs further characterized the genomic regions for differential production of stilbenoids that can be applied in resistance breeding through manipulation of stilbenoid production in planta.
基金the National Natural Science Foundation of China(Nos.31772848,31900279)the Joint Research Project between China and Japan(No.2017YFE0130900)。
文摘Saccharina japonica is one of the most important economic brown seaweeds.It is intensively cultivated on large scales in a number of Asian countries.The current annual,global production is about 8 million tons valued as about 4 million US dollars.Considerable efforts have been made to S.japonica in China since the 1950s on its cultivation.To further advance the cultivation of this species,detailed research of genetics and breeding studies are required.Recently,with the advancement of sequencing techniques,the genomics and comparative transcriptomics data were yielded,and quantitative trait locus(QTL)mapping has been conducted,along with genetic linkage maps constructed to this species.New strains have been bred and selected,with better characteristics,e.g.higher seawater temperature resistances and higher yields.In this review,we present the current status of genetic and breeding studies that have been performed to S.japonica in China,and provide guidelines for future developments in the areas of genetic selection and breeding for this species.
文摘全基因组关联分析(genome-wide association studies,GWAS)是近几年发展起来的解析人类、动物或植物表型多样性遗传基础的有效分析手段。GWAS具有高通量、高精度和高速度等显著优点,其在林木遗传育种中的作用日益凸显。本文从种质材料、目标性状的选择和表型鉴定、全基因组SNP位点的获取、群体结构、连锁不平衡分析以及关联作图与候选基因发掘等方面对GWAS在林木育种中的应用进行了综述,并提出后续研究展望。以期为进一步利用GWAS技术进行林木育种中各种性状遗传基础的研究提供参考。
基金supported by the National Natural Science Foundation of China(Grant No.31221004)the Central Academy(Institute)Research Project on Public Welfare(Grant No.2014RG001-3)+2 种基金the Special Fund for Agroscientific Research in the Public Interest(Grant No.20120301400903039-5)the Sichuan Program for Major Crop,Poultry and Livestock Breeding,China(Grant No.2012YZGG-25-3)a fund from the Chinese Academy of Agricultural Sciences to the Scientific and Technical Innovation Team
文摘Molecular screening of major rice blast resistance genes was determined with molecular markers, which showed close-set linkage to 11 major rice blast resistance genes（Pi-d2, Pi-z, Piz-t, Pi-9, Pi-36, Pi-37, Pi5, Pi-b, Pik-p, Pik-h and Pi-ta2）, in a collection of 32 accessions resistant to Magnaporthe oryzae. Out of the 32 accessions, the Pi-d2 and Pi-z appeared to be omnipresent and gave positive express. As the second dominant, Pi-b and Piz-t gene frequencies were 96.9% and 87.5%. And Pik-h and Pik-p gene frequencies were 43.8% and 28.1%, respectively. The molecular marker linkage to Pi-ta2 produced positive bands in eleven accessions, while the molecular marker linkage to Pi-36 and Pi-37 in only three and four accessions, respectively. The natural field evaluation analysis showed that 30 of the 32 accessions were resistant, one was moderately resistant and one was susceptible. Infection types were negatively correlated with the genotype scores of Pi-9, Pi5, Pi-b, Pi-ta2 and Pik-p, although the correlation coefficients were very little. These results are useful in identification and incorporation of functional resistance genes from these germplasms into elite cultivars through marker-assisted selection for improved blast resistance in China and worldwide.
基金supported by the International Cooperation projects(2010DFB33340 and 2010DFR30620)the National Key Technology R&D Program of China from the Ministry of Science and Technology of China(2013BAD01B03-18)+1 种基金the National Natural Science Foundation of China(31371695)supported by the Agricultural Science and Technology Innovation Program(ASTIP)in CAAS
文摘Simple sequence repeat(SSR)markers have previously been applied to linkage mapping of the pea(Pisum sativum L.)genome.However,the transferability of existing loci to the molecularly distinct Chinese winter pea gene pool was limited.A novel set of pea SSR markers was accordingly developed.Together with existing SSR sequences,the genome of the G0003973(winter hardy)×G0005527(cold sensitive)cross was mapped using 190 F2individuals.In total,157 SSR markers were placed in 11 linkage groups with an average interval of 9.7 cM and total coverage of 1518 cM.The novel markers and genetic linkage map will be useful for marker-assisted pea breeding.
