长江三角洲白山羊扬州群体的遗传共适应特性

采用淀粉凝胶多座位电泳法检测长江三角洲白山羊扬州群体结构基因座遗传变异,并分析群体的遗传共适应特性。结果表明,在显隐性-共显性模式中未发现座位间的遗传共适应现象,而在共显性-共显性模式中Tf-Lap、Tf-X-p、Lap-Es-D和Lap-X-p组合都存在遗传共适应,表明在长江三角洲白山羊扬州群体结构基因座间存在遗传共适应性,可能对维持座位间的遗传平衡状态起主要作用。

Inferring Genome Ancestry and Estimating Molecular Relatedness Among 187 Chinese Maize Inbred Lines

The inference of genome ancestry and the estimation of molecular relatedness are of great importance for breeding efficiency and association studies. Seventy SSR loci, evenly distributed in 10 chromosomes, were assayed for polymorphism among 187 commonly used maize （Zea mays L.） inbreds which represent the genetic diversity in China. The identified 290 alleles served as raw data for estimating population structure using the coalescent linked loci, based on the ADMIXTURE model. Population number, K, has been inferred to be between five and seven. Specifying five subpopulations （K = 5） led to a distinct decrease and specifying K to be greater than six resulted in only minimal increases in the likelihood value. Therefore, population number, K, has been inferred into six subpopulations, which are PA, BSSS （includes Reid）, PB, Lan （Lancaster Sure Crop）, LRC （Luda Reb Cob, a Chinese landrace, and its derivatives）, and SPT （Si-ping-tou, a Chinese landrace and its derivatives）. The Kullback-Leibler distance of pairwise subpopulation was also inferred as n × p （187 ×6） Q matrices, which gave a detailed percentage of genetic composition of six subpopulations and molecular relatedness of each line. The genome-wide linkage disequilibrium （LD） indicated that the asso- ciation studies in QTLs and/or candidate genes might avoid nonfunctional and spurious associations, as most of the LD blocks were broken among diverse germplasm. The defined population structure has given us a clear genetic structure of these lines for breeding practice and established a good basis for association analysis.

SHEsis,a powerful software platform for analyses of linkage disequilibrium,haplotype construction,and genetic association at polymorphism loci

In multiloci-based genetic association studies of complex diseases, a powerful and high efficient tool for analyses oflinkage disequilibrium (LD) between markers, haplotype distributions and many chi-square/p values with a large numberof samples has been sought for long. In order to achieve the goal of obtaining meaningful results directly from raw data,we developed a robust and user-friendly software platform with a series of tools for analysis in association study withhigh efficiency. The platform has been well evaluated by several sets of real data.

Isolation and characterization of 45 polymorphic microsatellite loci of turbot(Scophthalmus maximus)and cross-species amplification

Turbot （Scophthalmus maximus） is a flatfish species commercially important for aquaculture. In this study, we generated a microsatellite-enriched genomic DNA library for Scophthalmus rnaxirnus, and then isolated and characterized 45 microsateIIite loci by genotyping 30 individuals. The observed number of alleles ranged from 2 to 19 with an average of 6.24, while the effective number of alleles ranged from 1.30 to 11.11 with an average of 3.66. The expected heterozygosities varied from 0.235 to 0.9254 and polymorphic information content ranged from 0.204 4 to 0.903 3, with an average of 0.622. Twelve loci deviated significantly from Hardy-Weinberg equilibrium, and no significant linkage disequilibrium was observed between any pair of loci after Bonferroni correction. In cross-species amplification, five flatfish species （Paralichthys lethostigma, Verasper rnoseri, platichthys stellatus, Hippoglossoides dubius and Cynoglossus semilaevis） showed at least one polymorphic locus. These polymorphic microsatellite loci should prove useful for population analysis of turbot and other related species.

Linkage Disequilibrium in Wild and Cultured Populations of Pacific Oyster(Crassostrea gigas)

Linkage disequilibrium(LD) can be applied for mapping the actual genes responsible for variation of economically important traits through association mapping.The feasibility and efficacy of association studies are strongly dependent on the extent of LD which determines the number and density of markers in the studied population,as well as the experimental design for an association analysis.In this study,we first characterized the extent of LD in a wild population and a cultured mass-selected line of Pacific oyster(Crassostrea gigas).A total of 88 wild and 96 cultured individuals were selected to assess the level of genome-wide LD with 53 microsatellites,respectively.For syntenic marker pairs,no significant association was observed in the wild population;however,three significant associations occurred in the cultured population,and the significant LD extended up to 12.7 c M,indicating that strong artificial selection is a key force for substantial increase of genome-wide LD in cultured population.The difference of LD between wild and cultured populations showed that association studies in Pacific oyster can be achieved with reasonable marker densities at a relatively low cost by choosing an association mapping population.Furthermore,the frequent occurrence of LD between non-syntenic loci and rare alleles encourages the joint application of linkage analysis and LD mapping when mapping genes in oyster.The information on the linkage disequilibrium in the cultured population is useful for future association mapping in oyster.

人类白细胞抗原A和DRB1基因与1型糖尿病的相关性研究

目的研究江苏地区人类白细胞抗原（HL4）-A和月出-DRBl基因频率及单倍型与1型糖尿病的相关性。方法于2008至2009年在江苏省江阴市和南京市选择自发酮症急性起病、依赖胰岛素治疗的1型糖尿病门诊或住院患者51例（1型糖尿病组），其中男27例，女24例，平均发病年龄（14±9）岁。另以2002至2006年登记加入中华骨髓库江苏分库的汉族无关骨髓捐献志愿者HLA分型资料20248份为对照。从受试者外周血中提取细胞基因组DNA，利用聚合酶链反应-寡核苷酸探针序列特异性引物技术进行HLA—A和月似-DRBl基因分型，应用Arlequin软件分析计算单倍型频率及连锁不平衡情况，通过卡方检验等比较组间基因频率、单倍型频率及疾病相关性分析。结果HLA-A点频率最高的为A＊02和A＊24，HLA-DRBl位点频率最高的为DRBl＊09。与对照组相比，1型糖尿病组HLA—A＊3[6．86％（7／102）比2．43％（984／40496），X^2=8．40，P〈0．01，比值比（OR）=3．00]、A＊24[27．45％（28／102）比16．79％（6799／40496），X^2=8．27，P〈0．01，OR=1．87]和DRBl＊09[32．35％（33／102）比16．15％（6540／40496），X^2=19．69，P〈0．01，OR=2．47]、DRBl＊03[15．69％（16／102）比4．76％（1927／40496），X^2=26．66，P〈0．01，OR=3．69]频率显著升高。A＊01-DRBl＊03在连锁不平衡分析中为1型糖尿病组所特有。结论检测出位点A＊03、A＊24及DR03、DR09对1型糖尿病的易患性，发现3个有易患作用的A—DR单倍型，观察到与1型糖尿病关联的祖先单倍型A01DR03。

The consequences of genomic architecture on ecological speciation in postglacial fishes

The quest for the origin of species has entered the genomics era. Despite decades of evidence confirming the role of the environment in ecological speciation, an understanding of the genomics of ecological speciation is still in its infancy. In this review, we explore the role of genomic architecture in ecological speciation in postglacial fishes. Growing evidence for the num- ber, location, effect size, and interactions among the genes underlying population persistence, adaptive trait divergence, and re- productive isolation in these fishes reinforces the importance of considering genomic architecture in studies of ecological speci- ation. Additionally, these populations likely adapt to new freshwater environments by selection on standing genetic variation, as de novo mutations are unlikely under such recent divergence times. We hypothesize that modular genomic architectures in post- glacial fish taxa may be associated with the probability of population persistence. Empirical studies have confirmed the genic na- ture of ecological speciation, implicating surprisingly extensive linkage disequilibrium across the genome. An understanding of these genomic mosaics and how they contribute to reproductive barriers remains unclear, but migration rates and the strength of selection at these loci is predicted to influence the likelihood of population divergence. Altogether, understanding the role of ge- nomic architecture is an important component of speciation research and postglacial fishes continue to provide excellent organ- isms to test these questions, both from the perspective of variation in architectures among taxa, and with respect to the distinct environments they have colonized. However, more empirical tests of ecological speciation predictions are needed [Current Zoo- logy 59 （1）： 53-71, 2013].

Bovine HSD17B8 gene and its relationship with growth and meat quality traits

17 β-Hydroxysteroid dehydrogenase type 8 （HSD17B8） is an important regulator of lipid and steroid metabolism. In the present study, we aimed to assess the effects of HSD17B8 on growth and meat quality traits in cattle. Transcription profile analysis showed that HSD17B8 was primarily expressed in the salpinx, liver, and testis. Meanwhile, we identified three SNPs （SNPI： intron 1-A91G; SNP2： exon 1-A90G; and SNP3： intron 8-A86G） of the bovine HSD17B8 gene and investigated its haplotype frequencies and linkage disequilibrium. The detected SNPs were found associated with growth traits （body weight, body length, height at withers, heart girth, hip width, and average daily gain） in native cattle populations （Nanyang and Jiaxian） as well as the meat quality traits （Warner- Bratzler shear force, rib area, dressing percentage, carcass weight, and backfat thickness） in commercial breeds （Angus, Hereford, Limousin, Luxi, Simmental, and Jinnan）. Our results provided evidence that polymorphisms in the HSD17B8 gene were associated with growth traits and meat quality traits. Moreover, our findings might be used for marker-assisted selection in beef cattle breeding program