Echinotriton chinhaiensis is a critically endangered salamander and its distribution is restricted to Ningbo, Zhejiang Province of China. In this study, we developed and characterized fifteen polymorphic microsatellit...Echinotriton chinhaiensis is a critically endangered salamander and its distribution is restricted to Ningbo, Zhejiang Province of China. In this study, we developed and characterized fifteen polymorphic microsatellite loci for E. ehinhaiensis from dinucleotide- and tetranucleotide- enriched library. The number of alleles ranges from 4 to 12 with an average of 7.27 alleles per locus. The observed and expected heterozygosities values were from 0.250 to 0.844 and 0.511 to 0.872 with an average value of 0.596 and 0.722; respectively. The polymorphic microsatellite loci described in this paper are useful in the further study on genetic diversity and gene flow, which would be helpful to formulate effective conservation strategies for the E. chinhaiensis.展开更多
目的评价Microreader^(TM)23HS Plex ID System试剂盒中包含的23个常染色体STR基因座在中国北方汉族人群中等位基因频率分布,获得群体遗传数据,探究其在法医学中的应用价值。方法使用Microreader^(TM)23HS Plex ID System试剂盒对中国...目的评价Microreader^(TM)23HS Plex ID System试剂盒中包含的23个常染色体STR基因座在中国北方汉族人群中等位基因频率分布,获得群体遗传数据,探究其在法医学中的应用价值。方法使用Microreader^(TM)23HS Plex ID System试剂盒对中国北方汉族人群548例无关样本DNA进行检测,收集分型数据,计算各基因座的等位基因频率、样本的杂合度(heterozygosity,H)、这些常染色体STR基因座的多态信息含量(polymorphism information content,PIC)、个体识别力(power of discrimination,DP)和非父排除率(probability of paternity exclusion,PE)并使用统计软件对各基因座是否符合Hardy-Weinberg平衡进行检验;同时对Microreader^(TM)23HS Plex ID System的累积个体识别能力(CDP)和累积非父排除率(CPE)进行计算。结果在548例无关样本中23个STR基因座共计检出260个等位基因,等位基因频率为0.0009~0.5902,H为0.611~0.885,PIC为0.577~0.864,DP为0.815~0.973(平均DP为0.922),PE为0.089~0.406,CDP=1-3.663×10^(-27),CPE=1-2.668×10^(-16),所有基因座等位基因的分布符合Hardy-Weinberg平衡。结论Microreader^(TM)23HS Plex ID System的23个基因座在中国北方汉族人群中具有良好的多态性,在法医学个人识别、群体遗传学研究、亲子鉴定,特别是复杂亲缘关系鉴定中应用价值较高。展开更多
The Chinese Bamboo Partridge(Bambusicola thoracica) is a gamebird endemic to China.Ten polymorphic microsatellite(simple sequence repeat) markers were obtained through cross-species amplification for this partridge fr...The Chinese Bamboo Partridge(Bambusicola thoracica) is a gamebird endemic to China.Ten polymorphic microsatellite(simple sequence repeat) markers were obtained through cross-species amplification for this partridge from its relative species Gallus gallus.The number of alleles per locus varied from 4 to 13.The observed heterozygosity ranged from 0.1220 to 1.0000 and the expected heterozygosity from 0.1183 to 0.8898.Four microsatellite loci showed significant differences from the Hardy-Weinberg equilibrium.These polymorphic loci provide a valuable tool for the investigation of the phylogeography and conservation genetics of this partridge.展开更多
Associations between ＂lipid-related＂ candidate genes,blood lipid concentrations and coronary artery disease（CHD） risk are not clear.We aimed to investigate the effect of three newly identified lipids loci from gen...Associations between ＂lipid-related＂ candidate genes,blood lipid concentrations and coronary artery disease（CHD） risk are not clear.We aimed to investigate the effect of three newly identified lipids loci from genome-wide association studies on CHD and blood lipid levels in Chinese Han population.The genotypes of SNPs at three newly identified lipid loci and blood lipids concentrations were examined in 1360 CHD patients and 1360 age-and sex-frequency matched controls from an unrelated Chinese Han population.Allele T of rs16996148 occurred less frequently in CHD patients with the odds ratio（OR） being 0.64（95% CI 0.50 to 0.81）,after adjusting for conventional risk factors and was associated with a 33% decreased CHD risk（P0.01） comparing with the major allele G.Individuals with GT genotype had the lowest CHD risk.No associations were found between the polymorphisms of other two loci with CHD risk and all three SNPs had no effect on lipid profile in this population.SNP rs16996148 on chromosome 19p13 is significantly associated with lower risk for CHD in Chinese Han population.However,it remains unresolved why these lipid-related loci had significantly less effects than the correspondingly expected effects on blood lipids levels in this population.展开更多
This paper presents a quick, easy to implement and versatile way of using stochastic simulations to investigate the power and design of using single nucleotide polymorphism (SNP) arrays for genome-wide association stu...This paper presents a quick, easy to implement and versatile way of using stochastic simulations to investigate the power and design of using single nucleotide polymorphism (SNP) arrays for genome-wide association studies in farm animals. It illustrates the methodology by discussing a small example where 6 experimental designs are considered to analyse the same resource consisting of 6006 animals with pedigree and phenotypic records: (1) genotyping the 30 most widely used sires in the population and all of their progeny (515 animals in total), (2) genotyping the 100 most widely used sires in the population and all of their progeny (1102 animals in total), genotyping respectively (3) 515 and (4) 1102 animals selected randomly or genotyping respectively (5) 515 and (6) 1102 animals from the tails of the phenotypic distribution. Given the resource at hand, designs where the extreme animals are genotyped perform the best, followed by designs selecting animals at random. Designs where sires and their progeny are genotyped perform the worst, as even genotyping the 100 most widely used sires and their progeny is not as powerful of genotyping 515 extreme animals.展开更多
The blood clam(Tegillarca granosa)is an economically important marine shellfish in the southeast coastal area of China.In T.granosa breeding practice,growth-related traits are most important phenotypic selection index...The blood clam(Tegillarca granosa)is an economically important marine shellfish in the southeast coastal area of China.In T.granosa breeding practice,growth-related traits are most important phenotypic selection index.In order to increase the breeding efficiency,we used a previously published genetic linkage map of T.granosa to map quantitative trait loci(QTL)for growth-related traits in a single full sibling F1 family.Eight growth-related traits including shell length(SL),shell height(SH),shell width(SW),shell weight(Swi),shell umbo width(SUW),as well as outer ligament length(OLL),meat weight(MW)and total weight(TW)of T.granosa were measured for QTL mapping.The estimated phenotypic correlations between any 2 of the 8 growth-related traits were significant(P<0.001).Twenty-nine QTL were identified for growth-related traits,including 13 QTL with the phenotypic variance of 4.20-15.63%in the female map and 16 QTL of 3.99%-14.58%in the male map.Thirteen amplification fragment length polymorphism(AFLP)markers were validated to closely link to seven QTL except the shell height.This is the first report of QTL mapping on growth-related traits in T.granosa.These QTL and their tightly linked markers present the initial step towards the goal of marker-assisted selection in T.granosa.展开更多
基金financially supported by the National Natural Science Foundation of China (30770316)
文摘Echinotriton chinhaiensis is a critically endangered salamander and its distribution is restricted to Ningbo, Zhejiang Province of China. In this study, we developed and characterized fifteen polymorphic microsatellite loci for E. ehinhaiensis from dinucleotide- and tetranucleotide- enriched library. The number of alleles ranges from 4 to 12 with an average of 7.27 alleles per locus. The observed and expected heterozygosities values were from 0.250 to 0.844 and 0.511 to 0.872 with an average value of 0.596 and 0.722; respectively. The polymorphic microsatellite loci described in this paper are useful in the further study on genetic diversity and gene flow, which would be helpful to formulate effective conservation strategies for the E. chinhaiensis.
文摘目的评价Microreader^(TM)23HS Plex ID System试剂盒中包含的23个常染色体STR基因座在中国北方汉族人群中等位基因频率分布,获得群体遗传数据,探究其在法医学中的应用价值。方法使用Microreader^(TM)23HS Plex ID System试剂盒对中国北方汉族人群548例无关样本DNA进行检测,收集分型数据,计算各基因座的等位基因频率、样本的杂合度(heterozygosity,H)、这些常染色体STR基因座的多态信息含量(polymorphism information content,PIC)、个体识别力(power of discrimination,DP)和非父排除率(probability of paternity exclusion,PE)并使用统计软件对各基因座是否符合Hardy-Weinberg平衡进行检验;同时对Microreader^(TM)23HS Plex ID System的累积个体识别能力(CDP)和累积非父排除率(CPE)进行计算。结果在548例无关样本中23个STR基因座共计检出260个等位基因,等位基因频率为0.0009~0.5902,H为0.611~0.885,PIC为0.577~0.864,DP为0.815~0.973(平均DP为0.922),PE为0.089~0.406,CDP=1-3.663×10^(-27),CPE=1-2.668×10^(-16),所有基因座等位基因的分布符合Hardy-Weinberg平衡。结论Microreader^(TM)23HS Plex ID System的23个基因座在中国北方汉族人群中具有良好的多态性,在法医学个人识别、群体遗传学研究、亲子鉴定,特别是复杂亲缘关系鉴定中应用价值较高。
基金supported by the National Natural Science Foundation of China (Grant No. 30760036,30960051)Young Scientists (Jinggang Star) Training Scheme of Jiangxi ProvinceNatural Science Foundation of Jiangxi Province (2009GZN0075)
文摘The Chinese Bamboo Partridge(Bambusicola thoracica) is a gamebird endemic to China.Ten polymorphic microsatellite(simple sequence repeat) markers were obtained through cross-species amplification for this partridge from its relative species Gallus gallus.The number of alleles per locus varied from 4 to 13.The observed heterozygosity ranged from 0.1220 to 1.0000 and the expected heterozygosity from 0.1183 to 0.8898.Four microsatellite loci showed significant differences from the Hardy-Weinberg equilibrium.These polymorphic loci provide a valuable tool for the investigation of the phylogeography and conservation genetics of this partridge.
基金supported by grants from the National Natural Sciences Foundation of China (No. 30525031 and No.30430590)
文摘Associations between ＂lipid-related＂ candidate genes,blood lipid concentrations and coronary artery disease（CHD） risk are not clear.We aimed to investigate the effect of three newly identified lipids loci from genome-wide association studies on CHD and blood lipid levels in Chinese Han population.The genotypes of SNPs at three newly identified lipid loci and blood lipids concentrations were examined in 1360 CHD patients and 1360 age-and sex-frequency matched controls from an unrelated Chinese Han population.Allele T of rs16996148 occurred less frequently in CHD patients with the odds ratio（OR） being 0.64（95% CI 0.50 to 0.81）,after adjusting for conventional risk factors and was associated with a 33% decreased CHD risk（P0.01） comparing with the major allele G.Individuals with GT genotype had the lowest CHD risk.No associations were found between the polymorphisms of other two loci with CHD risk and all three SNPs had no effect on lipid profile in this population.SNP rs16996148 on chromosome 19p13 is significantly associated with lower risk for CHD in Chinese Han population.However,it remains unresolved why these lipid-related loci had significantly less effects than the correspondingly expected effects on blood lipids levels in this population.
基金Project supported by Ovita Limited, Dunedin, New Zealand
文摘This paper presents a quick, easy to implement and versatile way of using stochastic simulations to investigate the power and design of using single nucleotide polymorphism (SNP) arrays for genome-wide association studies in farm animals. It illustrates the methodology by discussing a small example where 6 experimental designs are considered to analyse the same resource consisting of 6006 animals with pedigree and phenotypic records: (1) genotyping the 30 most widely used sires in the population and all of their progeny (515 animals in total), (2) genotyping the 100 most widely used sires in the population and all of their progeny (1102 animals in total), genotyping respectively (3) 515 and (4) 1102 animals selected randomly or genotyping respectively (5) 515 and (6) 1102 animals from the tails of the phenotypic distribution. Given the resource at hand, designs where the extreme animals are genotyped perform the best, followed by designs selecting animals at random. Designs where sires and their progeny are genotyped perform the worst, as even genotyping the 100 most widely used sires and their progeny is not as powerful of genotyping 515 extreme animals.
基金supported by the National Key R&D Program of China (2020YFD0900802)National Natural Science Foundation of China (Nos.31902358)+1 种基金the Natural Science Foundation of Shandong Province (ZR2020MC192)the“First class fishery discipline”programme in Shandong Province,China,programme in Shandong Province,China.
文摘The blood clam(Tegillarca granosa)is an economically important marine shellfish in the southeast coastal area of China.In T.granosa breeding practice,growth-related traits are most important phenotypic selection index.In order to increase the breeding efficiency,we used a previously published genetic linkage map of T.granosa to map quantitative trait loci(QTL)for growth-related traits in a single full sibling F1 family.Eight growth-related traits including shell length(SL),shell height(SH),shell width(SW),shell weight(Swi),shell umbo width(SUW),as well as outer ligament length(OLL),meat weight(MW)and total weight(TW)of T.granosa were measured for QTL mapping.The estimated phenotypic correlations between any 2 of the 8 growth-related traits were significant(P<0.001).Twenty-nine QTL were identified for growth-related traits,including 13 QTL with the phenotypic variance of 4.20-15.63%in the female map and 16 QTL of 3.99%-14.58%in the male map.Thirteen amplification fragment length polymorphism(AFLP)markers were validated to closely link to seven QTL except the shell height.This is the first report of QTL mapping on growth-related traits in T.granosa.These QTL and their tightly linked markers present the initial step towards the goal of marker-assisted selection in T.granosa.
