五指山猪小群体遗传学检测

本研究利用26个微卫星基因座对中国热带农业科学院热带作物品种资源研究所保种场的五指山猪小群体58个样本进行了遗传学检测,用非变性(中性)聚丙烯酰胺凝胶电泳检测微卫星的PCR扩增产物,统计了群体平均基因纯合率、等位基因数,利用等位基因频率计算出各群体的平均遗传杂合度(H)、多态信息含量(PIC)。统计结果:全群平均基因纯合率为66.5%;平均多态信息含量、平均观测杂合度为、平均期望杂合度分别为0.807、0.338、0.835;每个位点平均等位基因数为11.92,此结果说明该群体虽然近交程度较高,但仍具有丰富的遗传多样性,遗传变异较大。     

Genome-wide detection of selective signatures in a Jinhua pig population

The aim of this study was to detect evidence for signatures of recent selection in the Jinhua pig genome. These results can be useful to better understand the regions under selection in Jinhua pigs and might shed some lights on groups of genes that control production traits. In the present study, we performed extended haplotype homozygosity(EHH) tests to identify significant core regions in 202 Jinhua pigs. A total of 26 161 core regions spanning 636.42 Mb were identified, which occupied approximately 28% of the genome across all autosomes, and 1 158 significant(P0.01) core haplotypes were selected. Genes in these regions were related to several economically important traits, including meat quality, reproduction, immune responses and exterior traits. A panel of genes including ssc-mir-365-2, KDM8, RABEP2, GSG1L, RHEB, RPH3AL and a signal pathway of PI3K-Akt were detected with the most extreme P-values. The findings in our study could draw a comparatively genome-wide map of selection signature in the pig genome, and also help to detect functional candidate genes under positive selection for further genetic and breeding research in Jinhua and other pigs.     

牙鲆连续两代减数分裂雌核发育家系的遗传特征

对牙鲆(Paralichthys olivaceus)减数分裂雌核发育二倍体(Meio-G1)再次诱导减数分裂雌核发育,获得连续两代雌核发育二倍体家系(Meio-G2),以Meio-G1亲本与1尾普通牙鲆雄鱼人工授精获得的家系作为对照组(control)。利用15个微卫星标记对3个家系进行遗传特征分析。结果显示,15个微卫星位点在Meio-G1、Meio-G2和对照组3个家系中,分别扩增到30、28、50个等位基因,平均等位基因数为2.0、1.9、3.3,平均观测杂合度(Ho)分别为0.875 3、0.774 2、0.908 3,平均纯合度分别为0.124 7、0.221 5、0.091 7。3个家系个体间的平均遗传相似系数分别为0.891 7、0.923 8、0.520 2,亲代与子代之间的平均相似系数分别为0.916 6、0.930 4、0.560 3。高重组率的Poli9-8tuf、Poli18tuf、Poli107tuf 3个位点在Meio-G1和Meio-G2中观测杂合度均为1.0,低重组率的Poli33tuf、Poli24MHFS两个位点在Meio-G1和Meio-G2中均全部纯合,观测杂合度为0。结果表明,Meio-G2的纯合度、个体间平均相似系数以及亲子之间的平均相似度均略高于Meio-G1,显著高于对照组家系,证明连续两代诱导减数分裂雌核发育,能提高鱼类纯合度和遗传相似度,具有固定母本遗传性状的作用。     

近交陆川猪的遗传稳定性研究

旨在探讨高度近交陆川猪的遗传稳定性。本试验采集20头近交和6头非近交陆川猪的耳组织样品进行个体基因组重测序,通过扫描全基因组SNPs分析近交陆川猪群体的遗传多样性,并基于基因组纯合度挖掘近交陆川猪群体中特异的纯合区域（region of homozygosity,ROHs）及相关基因。结果表明,近交陆川猪群体的观察杂合度（0.373）小于期望杂合度（0.491）,推测其发生了选择或者近交;系统进化树和群体遗传结构分析发现,近交陆川猪群体在近交过程中分化成为两个近交家系,且230、236、239、132、130及126号个体亲缘关系最近;在近交群体中,基因组纯合度和基因组长纯合片段比例的均值分别为59.64%和0.12,都极显著高于非近交群体53.18%和0.05（P<0.01）,说明该近交陆川猪群体已达到高度近交;近交群体和非近交群体中分别有1 250和633个ROHs,重叠分析结果显示,特异存在于近交群体中的阳性纯合区域（positive region of homozygosity,pROHs）有224个,其中由于近交产生的纯合突变可能影响参与激素合成过程、胰液分泌、膜脂代谢过程、IgA产生的肠道免疫网络及纹肌细胞分化等相关的1 322个基因。结果提示,近交陆川猪群体的遗传多样性低、基因组纯合度高且已达到高度近交,说明该群体的遗传稳定性高。此外,近交陆川猪群体在近交过程中产生的纯合突变可能与机体的免疫、生长等生产性状相关。     

Relationship between inbreeding and milk production traits in two Italian dairy sheep breeds

The effects of inbreeding in livestock species breeds have been well documented and they have a negative impact on profitability. The objective of this study was to evaluate the levels of inbreeding in Sarda (SAR, n = 785) and Valle del Belice (VdB, n = 473) dairy sheep breeds and their impact on milk production traits. Two inbreeding coefficients (F) were estimated: using pedigree (F_PED), or runs of homozygosity (ROH; F_ROH) at different minimum ROH lengths and different ROH classes. After the quality control, 38,779 single nucleotide polymorphisms remained for further analyses. A mixed-linear model was used to evaluate the impact of inbreeding coefficients on production traits within each breed. VdB showed higher inbreeding coefficients compared to SAR, with both breeds showing lower estimates as the minimum ROH length increased. Significant inbreeding depression was found only for milk yield, with a loss of around 7 g/day (for SAR) and 9 g/day (VdB) for a 1% increase of F_ROH. The present study confirms how the use of genomic information can be used to manage intra-breed diversity and to calculate the effects of inbreeding on phenotypic traits.     

微卫星评价栉孔扇贝雌核发育二倍体纯合性

采用筛选获得的5对多态性微卫星引物对栉孔扇贝（Chlamys farreri）减数分裂雌核发育家系A和家系B、有丝分裂雌核发育家系A和家系B各30个个体、双亲及对照组40个个体进行了遗传变异分析,并对减数分裂和有丝分裂雌核发育后代的纯合性进行了比较。电泳结果表明,5对微卫星引物在减数分裂雌核发育和有丝分裂雌核发育个体中均能稳定重复地扩增出相应的序列;各雌核发育家系中均有部分个体出现父本基因,表明精子遗传物质失活不彻底,雌核发育组中存在正常受精个体;有丝分裂雌核发育二倍体在所有检测位点全部纯合,减数分裂雌核发育二倍体在部分位点纯合,但未发现在所有位点全部纯合的个体,在CFMSP007、CFMSP075、CFMSM009、CFMSM014和CFMSM020位点,杂合子比例分别为0．3400、0．3611、0．4884、0．4750和0．7500,平均杂合子比例为0．4829。研究结果显示,栉孔扇贝有丝分裂雌核发育二倍体均为纯合子,如精子的灭活率达到100％,有丝分裂雌核发育二倍体一代即可实现纯合,如再进行一次减数雌核发育即可建立纯系;减数分裂雌核发育二倍体由于具有较高的重组率,其与母本的遗传同质性较高。     

翘嘴鲌连续两代减数分裂雌核发育群体的遗传特征分析

通过异源精子冷休克技术获得翘嘴鲌减数分裂雌核发育一代(meio-G1)、减数分裂雌核发育二代(meio-G2),以太湖野生翘嘴鲌(Culter alburnus Basilewsky)为对照群体,采用微卫星(SSR)标记和随机扩增多态性DNA(RAPD)标记分析了3个群体的遗传特征。SSR结果显示,12个微卫星位点在meio-G1、meio-G2和对照组3个群体中,分别扩增到38、16和47个等位基因,平均等位基因数为3.166 7、1.333 3和3.916 7,平均观测杂合度(Ho)分别为0.430 6、0.333 3和0.675 0,平均纯合度分别为0.569 4、0.666 7和0.325 0。3个群体内个体间的平均遗传相似系数分别为0.543 0、1.000 0和0.571 9;聚类分析结果表明,meio-G1和对照组聚为一支,meio-G2单独聚为另一支。RAPD结果显示,14个引物在3个群体中检测到的位点数分别为74、61和64,3个群体的多态位点比例分别为63.51%、0和51.56%,按照Nei’s指数统计的3个群体的遗传相似度分别为0.801 8、1和0.846 0,meio-G2的基因组DNA同质性远高于meio-G1和对照组。两种分子标记结果均表明,meio-G2的纯合度、个体间的遗传相似系数均高于meio-G1和对照组,且个体间的基因型完全一致,是良好的育种材料。     

Fast development of genetically uniform strains by gynogenesis in Japanese flounder (Paralichthys olivaceus)

The Japanese flounder is a major species in both aquaculture and research. Inbred strains of Japanese flounder were developed efficiently in our laboratory by meiotic and mitotic gynogenetic reproduction techniques. To determine the induction efficiency of gynogenesis and the rate at which full homozygosity is produced, six meiotic gynogenetic females (G1–G6) that had experienced meiotic gynogenesis once and three common females (C1–C3) were selected for production of mitotic gynogenesis in our experiments. Of the nine adult females, all six gynogenetic fish successfully produced viable offspring. However, only one of the three common fish did. Using microsatellite markers, we estimated the homozygosity of gynogenetic fish induced by mitotic gynogenesis. We found that the homozygosity of seven lines (C1, G1–G6) increased quickly, individually from 43%, 72%, 69%, 71%, 78%, 69% and 58% to 100%, 100%, 100%, 90%, 100%, 100% and 90% offspring complete homozygosity. Under mitotic gynogenesis, individuals with higher homozygosity had a higher induction rate. The G4 line showed the highest induction rate, achieving 44.59% convert hatching rate and 29.28% convert normality rate. We conclude that meiotic gynogenesis may be a feasible method to produce DH genetic material in Japanese flounder.     

A proposed mechanism for loss of heterozygosity in rice hybrids

A phenomenon, loss of heterozygosity (LOH), was discovered in hybrid plants involving a selected plant (named AMR) of the Chinese rice cultivar ‘ZhongxinNo. 1’ as one parent. In these hybrids and some of their progenies, somatic variations were manifested by molecular genotypes and/or morphological phenotypes in vegetative parts of the same plant. Random amplified polymorphic DNA (RAPD) markers for the parents have been followed through the F₃ generation. RAPD markers were uniformly present or absent in all plants within some or all F₂ panicle rows derived from F₁ hybrids involving AMR. In contrast, RAPD markers segregated in the Mendelian manner for dominant markers in panicle rows derived from control hybrids. Certain F₂ panicle rows from F₁hybrids involving the special rice became fixed for all assayed RAPD markers. Genotype fixation was confirmed by molecular assays and field observations of the F₃ progenies. We propose a new biological mechanism, called ‘assortment mitosis,’ as being responsible for the observed phenomenon. The use of this mechanism in plant hybrids allows the development of uniform progenies as early as the F₂ generation. Therefore, the time required to obtain fixed non-parental type progenies for subsequent performance trials can be drastically shortened. Utilizing this mechanism in plant breeding represents a new approach and requires the modification of conventional plant breeding procedures. This revised version was published online in July 2006 with corrections to the Cover Date.     

Significance of allelic diversity and 2n gametes for approaching maximum heterozygosity in 4 x ppotatoes

Summary High level of heterozygosity is directly related to heterosis for yield in polysomic polyploids. Modern breeding schemes in potato (2n=4×=48) involve utilization of wild or cultivated 2 x relatives that provide a source of allelic diversity, and 2n gametes that transfer diversity to the 4 x level. Different levels of allelic diversity and different modes of 2 n egg formation were considered theoretically to determine their significance for the recovery of heterotic 4 x progeny from 2××4× crosses. The support from the experimental data is provided.Decline in parental allelic diversity in 2××4× crosses or 4××4× crosses resulted in significant yield reduction. The average level of homozygosity and loss of intra-locus interactions are equally adequate to predict the trend in yield changes in 4 x potatoes derived from parents of variable allelic diversity utilizing different modes of 2 n egg formation.The differences between the modes of 2 n gamete formation increase when the genetic diversity decreases. The more genetically diverse parents the less pronounced differences between 2 n gametes. Breeding of 4 x cultivars for polygenic traits where nonadditive effects are important should be oriented towards maximizing heterozygosity in terms of allelic diversity. Utilization of 2 n gametes to generate 4 x progeny following 2×–× or 2×–2× crosses upgrades the level of heterozygosity depending on diversity present in parents.