Association mapping identifies markers related to major early‐maturating traits in upland cotton (Gossypium hirsutum L.)

Association mapping is a promising tool to identify genes for quantitative traits. A total of 172 upland cotton (Gossypium hirsutum L.) accessions were assessed. The panel was phenotyped for four major early‐maturating traits across multiple environments and genotyped using 331 polymorphic simple sequence repeat (SSR) markers. The gene diversity of the 331 markers averaged 0.40 (range: 0.04–0.78), and the polymorphism information content (PIC) averaged 0.34 (range: 0.04–0.75). Thirty‐nine significant markers related to early‐maturating traits were simultaneously detected in at least two environments. Among the 39 markers, 11 for seed period (SP), seven for bud period (BP), six for flower and boll period (FBP), and 15 for growth period (GP). These markers were stable and could be used for marker‐assisted selection (MAS). Favourable alleles for SP, BP, FBP and GP were explored. These alleles can be directly used in MAS to improve cotton early maturity. This study lays the foundation for analysing the genetic mechanisms underlying early maturity, as well as the use of MAS to target traits in cotton.     

AQP7基因内含子4多态性与郏县红牛生长性状的关联分析

本试验旨在研究郏县红牛AQP7基因内含子4的遗传变异,分析其遗传多态性对生长性状的影响。采用PCR-SSCP、DNA序列分析及生物信息学技术探讨郏县红牛AQP7基因内含子4的多态性及其与生长性状的关联情况。结果发现,郏县红牛AQP7基因内含子4存在A、B、C 3个等位基因,其基因频率依次为0.838、0.076、0.086;郏县红牛AQP7基因4种不同基因型与其体重和胸围有显著相关(P< 0.05),与其他指标不存在相关性(P> 0.05),且BC基因型个体的体重和胸围均显著大于其他3种基因型(P< 0.05)。暗示BC基因型是提高郏县红牛生长性状的有利基因型,AQP7基因内含子4的遗传多态性与郏县红牛的生长性状存在相关,因此可作为该品种生长性状分子标记辅助选择的候选基因。     

瓦氏雅罗鱼耐碱性状相关分子标记的筛选

本研究以来自达里湖(碱水)和松花江(淡水)的瓦氏雅罗鱼(Leuciscus waleckii)杂交F2为实验材料,通过碱度耐受实验进行性状测定,以39对多态的EST-SSR和SSR为标记,对77个F2个体进行基因分型,根据Fisher确切概率法对F2基因型和耐碱性状进行关联分析。结果发现,有2个标记与耐碱性状显著相关(P0.05),其中1个标记为EST-SSR,从瓦氏雅罗鱼转录组数据库中调取该EST序列,基因注释结果显示该序列与团头鲂(Megalobrama amblycephala)低氧诱导因子HIF-3?基因、草鱼的低氧诱导因子HIF-4?基因具有很高的同源性。该基因的主要功能是参与鱼类的耐低氧反应过程,加强鱼类的耐低氧能力。本研究对于今后深入研究此功能基因的作用机制及培育适于盐碱水域养殖的鱼类新品种具有重要的意义。     

苏皖交界河网区后生浮游动物群落结构及其影响因子分析

鉴于长江中下游河网水流条件复杂,河流生境变化导致的浮游动物群落结构特异性,于2012年10月(平水期)和12月(枯水期)在长江下游江苏和安徽交界处的河网区布设6个采样点,进行轮虫和甲壳动物采样调查,并检测NH+4-N、NO-2-N、TN、TP、CODMn和Chl.a含量等水环境指标。结果表明,河网区共检出轮虫31种,优势种包括螺旋龟甲轮虫(Keratella cochlearis)和疣毛轮虫(Synchaeta sp.)等;枝角类14种,优势种为象鼻溞(Bosmina sp.);桡足类20种,优势种为跨立小剑水蚤(Microcyclops varicans)、中华窄腹剑水蚤(Limnoithona sinensis)和温剑水蚤(Thermocyclops sp.)。轮虫密度最高,平均为350.69个/L,其次为桡足类3.44个/L,枝角类最少,仅0.15个/L。轮虫和甲壳动物的季节变化规律不同,平水期的轮虫种类多于枯水期,枝角类和桡足类则相反,浮游动物的密度变化规律也类似。CCA分析表明,氮、磷、CODMn和Chl.a共同影响了浮游动物的群落结构与分布,枯水期轮虫密度与枝角类和桡足类密度均显著正相关(P0.01),叶绿素a与3类浮游动物密度也显著正相关(P0.05)。受长江汛后水文条件的影响,河网区浮游动物群落组成及优势种变化有其特定规律,轮虫与甲壳动物的种间关系也对其种类和密度的季节变化造成影响,而食物限制则是枯水期种群竞争的重要因素。     

全基因组关联分析鉴别白色杜洛克×二花脸F2资源家系中猪阴囊疝易感基因位点的鉴定

【目的】通过基于单倍型的病例-对照全基因组关联分析(GWAS)鉴别白色杜洛克×二花脸F2资源家系中影响猪阴囊疝的易感位点及位置功能候选基因,并在远缘纯种猪阴囊疝三联体核心家系（Trio）群体中进行重复验证。【方法】利用Illumina porcine 60K SNP芯片对1 020头白色杜洛克×二花脸F2资源家系阴囊疝群体(包含19个阴囊疝患病个体)进行扫描获取基因型。通过Plink v1.07软件对基因型数据进行质量控制;剔除个体基因型检出率< 90%的个体,剔除SNP位点检出率< 90%、哈迪温伯格平衡卡方检验P≤10-3和最小等位基因频率< 0.05及性染色体上和无法定位的SNP位点。质控合格的SNP位点用PHASEBOOK构建出F2资源家系中每个个体的单倍型,并采用隐马尔可夫模型将其归类到数目预先定义的祖先单倍型中。使用基于广义线性混合模型的GLASCOW软件进行利用祖先单倍型的病例-对照全基因组关联分析。采用保守的Bonferroni校正方法得到基因组显著水平和染色体显著水平的阈值。对F2资源家系中达到染色体显著水平的易感SNP位点在包含237个患病个体的远缘纯种猪阴囊疝三联体核心家系(Trio)群体中进行同样的质控,并利用Haploview软件对质控合格的SNP位点分别展开基于单点和基于单倍型的传递不平衡分析(TDT),进行重复验证。【结果】白色杜洛克×二花脸F2资源家系中全部个体的38 033个SNP标记通过质控。在GWAS分析中,共发现108个达染色体显著水平(P<2.63×10-5)的猪阴囊疝关联SNP位点,分别位于染色体2、8和17上,最强相关的SNP位点位于17号染色体上。在远缘三联体核心家系群中,724个个体的96个SNP位点通过质控。对质控合格的SNP位点进行基于单点的TDT分析,结果发现5个显著相关的SNP位点得到重复验证(P<0.05),其中2号染色体上有1个SNP位点和17号染色体上有4个SNP位点,分别位于IQGAP2,CHMP4B,SERINC3,ZNF334 等4个基因内或其上下游。基于单倍型的TDT验证分析发现两个易感单倍型框,其中与基于单点TDT验证分析有重合的仅有SSC17上CHMP4B内及下游的两个易感位点。结合疝气发生机制及TDT分析结果,推测IQGAP2和CHMP4B可能是影响猪阴囊疝发生的两个重要的位置功能候选基因。【结论】本研究利用基于小样本的GWAS分析和较大样本群验证分析,在SSC2和SSC17上分别鉴别1个和4个阴囊疝易感位点,在SSC17上鉴别到两个易感单倍型。易感位点附近的2个基因IQGAP2和CHMP4B可能是影响猪阴囊疝发生的位置功能候选基因,值得进一步研究。     

利用高密度SNP对猪血糖和糖基化血清蛋白性状的全基因组关联分析

【目的】测定苏太猪和白色杜洛克×二花脸F₂资源家系240 d血糖（glucose,GLU）和糖基化血清蛋白（glycosylated serum proteins,GSP）浓度,采用全基因组关联分析定位影响GLU和GSP的染色体位点,为最终鉴别影响该性状的因果基因奠定基础,同时为人类低血糖症和糖尿病的遗传学研究提供参考。【方法】分别将435头苏太猪和760头白色杜洛克×二花脸F2资源家系F₂个体在相同条件下饲养至240日龄进行统一屠宰,收集血液后分离血清,利用全自动生化分析仪测定GLU和GSP浓度。采集猪只耳组织提取DNA并测定DNA浓度。将质检合格的DNA样品利用Illumina porcine 60K SNP芯片判定基因型。运用PLINK软件对SNP判型结果进行质控,将合格的SNP标记用于后续的关联性分析,利用广义混合线性模型及R语言GenABEL软件包进行全基因组关联分析,定位影响苏太猪和白色杜洛克×二花脸F₂资源家系240 d血清GLU和GSP含量的染色体位点。根据全基因组关联分析结果从Ensembl或NCBI网站上分析可能的位置候选基因。【结果】全基因组关联分析共检测到5个与血清GLU和GSP达染色体显著水平相关的SNP位点。其中白色杜洛克×二花脸F₂资源群体在10号染色体（SSC10）24.67Mb处定位到与血清GSP含量显著相关的SNP（ALGA0057739,P=1.58×10^-5）,解释表型变异为3.72%。苏太猪群体共检测到2个与血清GSP显著相关的SNP（ALGA0108699和DRGA0017552,P=1.45×10^-5）,解释表型变异均为3.72%。使用猪参考基因组序列（10.2版本）,无法定位到具体的染色体位置。通过人、猪比较基因组分析,这两个SNP都位于SSC8,距STPG2基因3’端约180.0-193.0 kb。将两个群体进行Meta分析,未发现新的与GSP显著相关的SNP;在1号染色体250.32Mb处（DRGA0002016,P=2.48×10^-5）和14号染色体43.97Mb处（ASGA0062984,P=1.29×10^-5）,定位到与血清GLU显著相关的SNP。通过搜寻显著相关SNP所在染色体区域内的注释基因,发现ASPM、TRPM3和KCTD10 等基因是影响血清GSP和GLU的重要候选基因。【结论】检测到5个显著影响猪血清GLU和GSP的SNP位点。这些SNP位点所处染色体区域内的ASPM、TRPM3、STPG2和KCTD10基因是影响血清GSP和GLU的重要候选基因。     

Novel SNP in 5' flanking region of EDG1 associated with marbling in Japanese Black beef cattle

Marbling, defined by the amount and distribution of intramuscular fat, is an economically important trait of beef cattle in Japan. The endothelial differentiation , sphingolipid G-protein-coupled receptor , 1 ( EDG1 ) gene has been considered as a positional functional candidate for the gene responsible for marbling. We have recently reported that 2 single nucleotide polymorphisms (SNPs), c.-312A > G in the 5' untranslated region (UTR) and c.*446G > A in the 3' UTR in EDG1 were associated with marbling in Japanese Black beef cattle, but this was not functional and a causal mutation for marbling. In the present study, we detected 2 novel SNPs, referred to as g.1475435G > A and g.1471620G > T , in the 5' flanking region of the EDG1 between low-marbled and high-marbled steer groups, which were previously shown to have EDG1 expression differences in musculus longissimus muscle. The g.1475435G > A SNP seemed not to segregate in Japanese Black beef cattle. The g.1471620G > T SNP was associated with the predicted breeding value for beef marbling standard number by the analyses using Japanese Black beef cattle population. Based on these findings, we hypothesized that the g.1471620G > T SNP might have an impact on EDG1 expression and also marbling.     

Estimation of phenotypic divergence in a collection of <Emphasis Type="Italic">Capsicum</Emphasis> species for yield-related traits

Phenotypic divergence among the 24 accessions belonging to a collection of six species of Capsicum from different geoclimatic regions available in field gene bank of CIMAP, Lucknow, India, was quantified by multivariate analysis for 12 quantitative and qualitative traits. Based on their values, all 24 accessions were grouped into six clusters such that the genetic stocks within cluster had smaller D ² values among themselves than those belonging to different clusters. The accessions of Capsicum annuum were distributed in different clusters in morphotyping representing different species, suggesting that taxonomic characteristics are not always related to agronomic traits. No parallelism/association was found between geographical and phenotypic diversity. Accessions 15 and 23 (clusters V and VI, respectively) had distinct identity. The three characteristics that played the greatest role in differentiation were fruit diameter, number of fruits per plant, and leaf diameter, which can be utilized as conventional/morphological markers for the improvement of chilli yield and obtaining good segregants in chilli breeding programs.     

Linking temperate demersal fish species to habitat: scales,patterns and future directions

Adoption of the ecosystem approach to fisheries management relies on recognition of the link between fish and other components of the ecosystem, namely their physical and biological habitat. However, identifying the habitat requirements of marine fishes and hence determining their distribution in space and time is scientifically complex. We analysed the methodologies and findings of research on temperate, demersal fish habitat requirements to highlight the main developments in this field and to identify potential shortfalls. Many studies were undertaken over large spatial scales (≥100s km²) and these generally correlated abundances of fish to abiotic variables. Biological variables were accounted for less often. Small spatial scale (≤m²), experimental studies were comparatively sparse and commonly focused on biotic variables. Whilst the number of studies focusing on abiotic variables increased with increasing spatial scale, the proportion of studies finding significant relationships between habitat and fish distribution remained constant. This mismatch indicates there is no justification for the tendency to analyse abiotic habitat variables at large spatial scales. Innovative modelling techniques and habitat mapping technologies are developing rapidly, providing new insights at the larger spatial scales. However, there is a clear need for a reduction in study scale, or increase in resolution additional to the integration of biotic variables. We argue that development of sound predictive science in the field of demersal fish habitat determination is reliant on a change in focus along these lines. This is especially important if spatial management strategies, such as Marine Protected Areas (MPA) or No Take Zones (NTZ), are to be used in future ecosystem‐based approaches to fisheries management.     

河南省农产品地理标志保护研究——以原阳大米为例

以原阳大米为例,分析了河南省农产品地理标志保护中面临的困境,提出了提高产品质量,加大宣传和执法力度,完善行会建设,创新管理模式等建议。