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1.
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.  相似文献   
2.
【目的】分析危害棕榈科Palmae植物的一种重要入侵食叶害虫椰子织蛾Opisina arenosella单倍型在原产地和入侵地的分布特点,揭示椰子织蛾入侵我国的虫源信息。【方法】利用线粒体COI基因分析16个地理种群共计172个样本,比较椰子织蛾印度种群和入侵地(中国、马来西亚和泰国)种群的遗传关系。【结果】片段长度为625 bp的172条序列共鉴定出12个单倍型,包含15个变异位点,构成2个明显的单倍型分支,其中一个分支由11个单倍型(IN1~IN11)组成,均来自印度种群,单倍型IN1是6个印度种群的共享单倍型,IN2~IN11为独享单倍型;另一个分支为单倍型HAP,由来自中国、马来西亚和泰国的种群共享;HAP与11个来自印度的单倍型IN1~IN11均存在4个变异位点。【结论】入侵地区的椰子织蛾种群来自同一基因型或者具有相同的入侵源;椰子织蛾种群入侵后受环境选择压力,在新栖息地产生新的突变或杂交。  相似文献   
3.
基于叶绿体DNA分析的楸子种质遗传多样性研究   总被引:1,自引:0,他引:1  
利用4对叶绿体DNA引物扩增49份楸子[Malus prunifolia(Willd.)Borkh.]种质资源的4个叶绿体DNA基因间区trnH-psbA、trnS-trnG spacer + intron、trnT-5′trnL和5′trnL-trnF序列,基于4个叶绿体DNA基因间区的序列变异,从母系遗传的角度评价楸子的遗传多样性水平。结果显示:4个叶绿体DNA基因间区序列经测序、拼接、比对和合并之后的片段长度为3 790 bp,共有173个多态性变异位点,其中包含2个单一突变位点、20个简约信息位点和151个插入/缺失位点。在49份楸子种质中,trnH-psbA、trnS-trnG spacer + intron、trnT-5′trnL和5′trnL-trnF区域的变异位点的数量分别为26个、25个、120个和2个,单倍型数量分别为9个、7个、8个和3个,合并之后的叶绿体DNA片段的单倍型有14个。核苷酸多样性和单倍型多样性最高的区域均为trnH-psbA(Hd = 0.775,Pi = 0.02143),最低的为5′trnL-trnF(Hd = 0.481,Pi = 0.00072)。49份楸子种质4个叶绿体DNA区域合并后的遗传多样性较高(Hd = 0.854,Pi = 0.00949)。Tajima’s D检验中,4个叶绿体DNA区域在P > 0.10水平上均不显著,楸子的4个叶绿体DNA区域在进化上遵循中性进化模型。楸子的遗传变异主要存在于群体内部,不同居群间基因交流频繁,多数居群间遗传分化较少,与地理距离不完全相关。  相似文献   
4.
试验旨在探究晋汾白猪载脂蛋白A5(apolipoprotein A5,ApoA5)基因的单倍型与体重和肉质性状的相关性。选取180头晋汾白猪为研究群体,利用PCR技术检测ApoA5基因的单核苷酸多态性(single nucleotide polymorphism,SNP),并采用Haploview软件分析这些SNP位点的连锁不平衡程度;筛选非完全连锁的SNP位点,构建不同的ApoA5基因单倍型,统计不同单倍型的基因频率,并通过SPSS软件分析不同ApoA5基因单倍型与晋汾白猪体重和肉质性状的相关性,鉴定优良性状的ApoA5基因单倍型。结果显示,晋汾白猪ApoA5基因共检测到21个SNPs位点,其中5个完全连锁单倍型块,分别包含5、2、3、4和2个SNPs位点;另外10个非完全连锁的标签SNP组合成不同的ApoA5基因单倍型,其中Hap 1的基因频率最高,达到46.7%,远高于其他单倍型;ApoA5基因单倍型与晋汾白猪的初生重、断奶重、6月龄体重、肌内脂肪含量、剪切力和滴水损失均具有明显的相关性,而与pH24 h没有明显的相关性;ApoA5基因Hap 11晋汾白猪的初生重、断奶重、6月龄体重和肌内脂肪含量均最高,且剪切力最低,滴水损失也相对较低;Hap 6的初生重最低;Hap 2的断奶重和6月龄体重均最低;Hap 3的肌内脂肪含量最低,剪切力最高;Hap 10的滴水损失最高。晋汾白猪ApoA5基因Hap 11属于优良性状单倍型,是一个具有优良性状的分子标记,可以用于晋汾白猪的分子育种,提高选种效率。  相似文献   
5.
偏分离(TRD)是生物中普遍存在的现象,本研究拟在高密度基因芯片判断基因型的大规模群体中挖掘猪基因组标记位点的偏分离位点并探究其潜在的遗传机制。本研究用60K Illumina Porcine SNP芯片对1 020头F2资源家系(杜洛克与二花脸杂交F0-F2群体)进行基因型分型,用偏分离分析软件TRDscan (BF>100)和TDT (P<0.01)方法在单个位点上检测偏分离信号,并对二者共有的显著信号位点附近100 kb窗口的基因进行功能分析。此外,本研究还利用单倍型分型的软件包PHASEBOOK采用多位点连锁分析的策略分析了父源和母源配子中的偏分离区域,并在该区域内搜寻潜在的QTLs。结果表明:1)在单位点的偏分离分析中共鉴定到44个显著的偏分离位点,筛选到23个相关基因;对父本和母本特异性偏分离效应进行分析时,分别鉴定到27和35个显著偏分离位点,其中,分别有11和25个位点的100 kb附近有已注释的功能基因。2)基于单倍型多位点连锁的偏分离结果显示,父本显著偏分离位点位于5和13号染色体上,在该偏分离区域内搜寻功能相关的QTL,共搜寻到3个与繁殖性状(木乃伊数、产活仔数、黄体数)有关的QTLs;分析母本偏分离位点时,在4、6和12号染色体上定位到显著偏分离区域,结合已知的猪QTL数据库,共找到了5个与繁殖性状相关的QTLs。本研究利用大规模猪家系数据系统地鉴别了猪基因组的偏分离位点,为解析猪中的偏分离现象和进一步探究其生物学机制提供了一定的参考作用。  相似文献   
6.
【目的】谷子抽穗时间的适应性表现是广适性新品种选育的基础,分析抽穗时间关键基因的遗传变异和单倍型效应,为品种适应性改良提供基础信息。【方法】通过全基因组关联分析(genome-wide association study,GWAS),定位谷子抽穗时间关键基因SiTOC1,利用多组学数据库(multi-omics database for Setaria italica,MDSi)提供的SiTOC1数字表达量,分析SiTOC1的组织时空表达特性,并利用原生质体对SiTOC1蛋白进行亚细胞定位。采用qRT-PCR在短日(10 h光照/14 h黑暗)条件下进行SiTOC1 24 h节律表达模式分析。利用有代表性的99份谷子品种,分析SiTOC1编码区和启动子区的遗传多态性、单倍型以及转录水平,并对单倍型与抽穗时间的关系进行鉴定。【结果】在第1染色体物理位置31 456 761 bp处鉴定到了一个显著的关联信号,与抽穗时间紧密相关,该位点附近存在一个拟南芥抽穗期TOC1的同源基因SiTOC1SiTOC1在光周期响应组织(根、茎、叶等)中高表达,亚细胞定位于细胞核,在傍晚表达量上调,呈现出24 h节律性表达模式。SiTOC1在不同谷子品种中存在丰富的多态性,但REC和CCT结构域高度保守。SiTOC1编码区2种主要单倍型H-2和H-6分别与启动子单倍型Hp-591C和Hp-591A共分离,其中,启动子单倍型Hp-591C较Hp-591A的相对表达量显著上调了约2.5倍(P=0.014),并且该单倍型在三亚市、长治市和乌鲁木齐市3个环境下的抽穗时间分别平均延迟9、11和12 d。【结论】SiTOC1启动子区第591 bp处的SNP是引起抽穗时间差异的主效位点,单倍型Hp-591A较Hp-591C早熟,可作为主效单倍型用于分子育种选择。  相似文献   
7.
Bacterial canker of kiwifruit, caused by Pseudomonas syringae pv. actinidiae (Psa), is a disease that is spreading rapidly in several kiwifruit‐producing countries, causing significant economic losses. In 2011, it was detected for the first time in Spain, in the south of Galicia (northwest Spain). Kiwifruit orchards were therefore inspected and sampled in 2011 and 2012 to determine the pathogen distribution, and the isolates obtained were characterized by morphology, fatty acids profile, biochemical tests and molecular techniques. Isolates were obtained from Actinidia deliciosa ‘Hayward’ (from leaves, canes, flower buds, fruits and roots), from A. deliciosa ‘Summer’, from Actinidia chinensis ‘Jin Tao’ (from canes and leaves) and from A. chinensis pollinator ‘Belén’ (from canes). Results of the analysis of the cfl gene (phytotoxin production‐related), the tox–argK gene cluster and phylogenetic analysis of the cts gene demonstrated that all Psa isolates from northwest Spain correspond to the Psa3 population, which includes strains of haplotype 2. This is the first record of Psa3 and haplotype 2 in Spain.  相似文献   
8.
Bacterial wilt caused by Ralstonia solanacearum is a destructive disease for many crops. The aim of this study was to investigate the phylogenetic relationships and genetic structure of an R. solanacearum population from diverse origins in Taiwan. All 58 tested isolates belonged to phylotype I, except the two biovar 2 isolates from potato. These belonged to phylotype IIB sequevar 1 and were identical to known potato brown rot strains, which were probably introduced. Phylotype I isolates were grouped into 10 sequevars. Sequevar 15 was predominant (34 out of 56 isolates). Its distribution covered the whole island and it was largely associated with solanaceous crops such as tomato, and with tomato field soil. A total of 14 haplotypes were identified based on a partial endoglucanase gene sequence. Parsimony network analysis revealed that haplotype A was the oldest haplotype in the local population. It encompassed all but one of the sequevar 15 isolates. Large variation in virulence on tomato was observed among the 58 isolates, and seven pathotypes were identified. Significant genetic differentiation was detected among pathotypes. Moreover, genetic differentiation was detected between biovar 3 and biovar 4 subgroups and between the strains associated with solanaceous and non‐solanaceous species, but none was detected between strains from different geographic origins. The results suggest that the phylotype I population in Taiwan is homogeneous, while mutation and local adaptation to specific ecological niches keep shaping the population.  相似文献   
9.
  1. The Atlantic salmon shows strong population structure with reduced gene flow, owing to homing behaviour. Supportive breeding with allochtonous parr or fish‐farm escapees could affect native population genetic structure by the introgression of foreign genes. Mature male parr are potentially powerful vehicles for promoting introgression: they can fertilize eggs in competition with anadromous males. As a consequence, foreign males contribute more to introgression than foreign females. This effect must be taken into account for the correct development of conservation programmes. Foreign males constitute an inadvertent way to disrupt the genetic structure, as the allochtonous parr or fish‐farm escapees can survive in the river during the parr stage.
  2. A short polymorphic fragment of the sex‐determining gene (sdY) was used as a marker to assess introgression via males into south European salmon populations. In order to find haplotype variants for the intronic sequence of sdY, samples were investigated from 16 different rivers across the distribution range of the salmon, together with historical samples (1950–1960) from three Spanish rivers.
  3. Two novel haplotypes, in addition to the three already described in Atlantic salmon, were found for this locus. Most samples, including historical ones, displayed the common haplotype (D) previously found in salmon all over Europe; however, north European haplotype variants were also detected in salmon inhabiting the southern European rivers that were systematically supplemented with foreign stocks between 1981 and 1994.
  4. Analysis of haplotype variation in the sdY intron constitutes a powerful and inexpensive tool, not only to specifically assess male‐mediated introgression into natural populations of Atlantic salmon, but also for monitoring salmon escapees.
  相似文献   
10.
为筛选多态性丰富的羊草叶绿体非编码区片段,本研究以9个不同地理位置的羊草居群为材料,通过对12个叶绿体非编码区DNA片段测序及其序列间变异分析试图从中找出有遗传差异的叶绿体DNA(cpDNA)片段,并利用有多态性的cpDNA片段进行遗传多样性分析。结果表明,序列ndhF-rpl32、trnL-trnF、trnC-ycf6、aptI-aptH具有比较丰富的变异,可作为下一步研究野生羊草群体遗传学和谱系地理学较为理想的分子标记。在37个羊草个体4条非编码区片段的合并序列中,共检测到15种单倍型,单倍型多态性(Hd)为0.928,核苷酸多态性(Pi)为0.00101;遗传分化指数(Fst)为0.58884,基因流(Nm)为0.17,基因流较小;中性检验Tajima’s D(-1.08542)和Fu’s Fs(-5.301)均为负值,且差异不显著(P>0.10),推测羊草遵循中性进化理论,可能经历过种群扩张;AMOVA结果显示,65%的分子变异出现在居群间,35%出现在居群内;Mantel检验得到,遗传距离与地理距离具有显著相关性(r=0.449,P<0.05);居群分化值Nst 0.386(0.1865)大于Gst 0.234(0.1506),差异显著(P<0.05),表明羊草居群存在分子谱系地理结构。通过系统发育树分析得到,羊草15个单倍型分为两大分支,H2和H10聚为一支,它们与别的居群个体亲缘关系较远,其余单倍型聚为另一支;单倍型网络图显示,H2和H12、H10和H12亲缘关系较远,与系统发育树分析结果基本一致。本研究为羊草的种质资源保护、谱系地理学研究等工作奠定了基础。  相似文献   
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