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恩施黑猪基因组群体遗传学参数的估计与选择信号研究 总被引：1，自引：1，他引：0
旨在调查恩施黑猪基因组群体遗传学参数与选择信号。本研究利用Porcine 80K SNP芯片,通过计算亲缘系数、近交系数、连锁不平衡程度与有效群体大小等群体遗传学层面的参数评估恩施黑猪种群结构关系,运用CLR和iHS方法检测恩施黑猪基因组选择信号,并通过生物信息学分析揭示其潜在受选择基因。亲缘系数计算发现,咸丰县恩施黑猪个体间平均亲缘系数为0.12;近交系数计算表明, 16%的样本近交系数大于0.125,存在明显近交累积。此外,本研究构建了恩施黑猪全基因组连锁不平衡图谱;利用连锁不平衡信息,恩施黑猪估计历史有效群体大小呈现逐代下降趋势,其中5世代前有效群体大小约为25头。基于CLR方法共检测到126个显著选择信号候选区域,总长约为51.6 Mb,占基因组总长的2.1%。利用iHS方法,共发现248个显著选择信号候选区域,长度约为78.78 Mb,约占基因组总长的3.2%。富集分析表明,与选择信号区域重叠的LPAR2、NDUFA13、MEF2B、AHR基因分别与胴体长度(滴水损失)、精子形成、骨骼肌分化和总产仔数相关。研究表明,现存恩施黑猪群体血统较窄,近交累积严重,有效群体大小较小,并呈现继续缩小的趋势。选择信号分析揭示的一系列潜在受选择基因能够为未来恩施黑猪的遗传改良提供一定的参考依据。 相似文献
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旨在探究提高杜洛克猪胴体性状基因组选择准确性的方法，为提高种猪胴体性状的基因组选择准确性提供理论基础。本研究以2 796头杜洛克公猪和3 149头杜长大商品猪的校正115 kg体重日龄(AGE115)、校正115 kg背膘厚(BF115)和校正115 kg眼肌面积(LEA115)为研究对象。构建加性动物模型和加显动物模型验证显性效应对杜洛克猪基因组选择准确性的影响；探究在参考群中对杜洛克猪与杜长大猪进行不同的组合对于杜洛克猪基因组选择准确性的影响。参考群分组如下：组1,杜洛克猪作为参考群；组2,杜长大猪作为参考群；组3,杜洛克和杜长大猪合并作为参考群。研究结果表明：加入显性效应后，AGE115基因组选择的准确性在组1、组2、组3中提高了2.84%～4.87%,杜洛克猪BF115和LEA115的基因组选择准确性在组1、组3中提高了1.37%～16.18%;组3相对于组1,在加性动物模型中BF115和LEA115的基因组选择准确性提高了6.19%～7.35%,在加显动物模型中BF115的基因组选择准确性提高了6.52%。综上，显性效应能够提升猪胴体性状的基因组选择准确性，合并杜洛克猪与杜长... 相似文献
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为了分析盆周山地猪群体的选择信号，本研究利用猪50K基因芯片，运用Tajima’s D方法分析盆周山地猪群体基因组上受选择的信号区域，并通过生物信息学分析筛选受选择的候选基因。结果表明，盆周山地猪群体基因组上受选择的区域有252个，这些区域共包含267个候选基因，其中，在猪上已注释的基因184个，如免疫性状相关基因MYO1G、CD86、IKF2，肉质性状相关基因PRKAG3、PRDM16、SND1，繁殖性状相关基因FSHR、LTF、AP3B1和生长性状相关基因SREBF2、SDC3、SLIT3。候选基因GO功能富集表明，这些基因参与了机体的免疫、行为、心管发育等生物学进程。KEGG信号通路分析发现，部分基因可能与催产素信号通路相关。本研究首次构建了盆周山地猪全基因组水平上的选择信号图谱，筛选了受选择的重要经济性状候选基因，研究结果为更好地保护、开发和利用盆周山地猪奠定了理论基础。 相似文献
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【目的】利用选择信号分析方法在伊犁鹅和霍尔多巴吉鹅中筛选与产蛋性状相关的候选基因。【方法】选取健康状况良好、饲养管理水平一致的2岁伊犁鹅母鹅和霍尔多巴吉鹅母鹅各24只,采集血液样本,提取基因组DNA,利用全基因组重测序技术进行选择信号检测分析,筛选出受到选择的候选区域,针对注释基因进行GO功能和KEGG通路富集分析,进一步筛选出与鹅产蛋性状相关的候选基因。【结果】全基因组重测序的平均测序深度为15.28×,与参考基因组比对率在97.31%以上。通过群体分化指数(Fst)对伊犁鹅和霍尔多巴吉鹅2个群体进行分析,共筛选到1 231个候选区域。与核苷酸多样性(Pi)进行联合分析后,伊犁鹅群体共筛选出10个候选区域,得到5个注释基因;霍尔多巴吉鹅群体中共筛选出353个候选区域,得到263个注释基因。GO功能和KEGG通路富集分析发现,初步筛选出6个可能与鹅产蛋性状相关的候选基因(BMP2、BMP6、MIS、ENO1、LIF、EP300),还发现了IL-18基因可能与禽类的免疫有关。【结论】本研究筛选出6个可能与鹅产蛋性状相关的候选基因,为揭示鹅产蛋性状的分子调控机制提供了参考。 相似文献
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【目的】阐明晋南牛的遗传结构特征，通过选择信号检测挖掘与晋南牛经济性状相关的候选基因，探究其在进化过程中的受选择情况。【方法】对晋南牛和红安格斯牛全基因组测序数据进行分析，鉴定2个群体的单核苷酸多态性(single nucleotide polymorphism, SNP)标记，分析其在基因组的位置及其结构特征，基于SNP信息进行主成分分析(PCA)、构建状态同源矩阵(IBS);采用群体遗传分化指数(Fst)和核苷酸多样性比值(θπ)方法联合筛选晋南牛基因组受到强烈选择的区域，并对筛选到的受选择基因进行数量性状基因座(QTL)定位、GO功能和KEGG通路富集分析。【结果】晋南牛群体SNPs位点主要分布于基因间区域，其次位于内含子区域。PCA和IBS分析结果表明，晋南牛和红安格斯牛2个群体间不存在杂交现象，且晋南牛群体中个体间遗传距离较远。通过Fst和θπ联合分析共筛选到188个潜在受选择区域。QTL分析结果表明晋南牛的选择信号多与生长、肉质及抗病性状相关。GO功能和KEGG通路富集分析显示，筛选到晋南牛强受选择的与经济性状相关的候选基因11个... 相似文献
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【目的】皮山红羊是分布于新疆和田地区的新发现多羔性地方绵羊品种。本研究基于全基因组重测序技术从基因组水平上了解皮山红羊的群体遗传结构及产羔性状受选择信号区域,并对候选基因进行验证。【方法】选择30只连续产2～3羔的经产皮山红羊母羊为高繁组(high fertility, HF),30只连续产单羔的经产皮山红羊母羊为低繁组(low fertility, LF),对这两个群体进行全基因组重测序。应用主成分分析(PCA)、系统进化树、群体遗传结构及全基因组扫描(Fst&θπ)等综合分析法确定候选区域,进一步筛选皮山红羊产羔性状候选基因。采用飞行质谱分型技术对候选基因进行分型验证。【结果】皮山红羊高、低繁殖组群体连锁不平衡(LD)分析衰减曲线相似,系统进化树显示两组群体分化程度不明显。PCA结果显示,两个群体明显聚成一簇,个别个体离群,其位置及相互关系符合进化树结构以及群体结构结果。设置同时达到Top 1%Z(Fst)值和θπ值的窗口为候选区域,共注释229个强选择信号,HF和LF组注释基因分别为86和143个,其中筛选到42个可能与繁殖性状相关的候选基因,如MARF1、CHGA、BM... 相似文献
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RBP4基因在五个猪种中的群体遗传特性分析 总被引：2，自引：0，他引：2
李娜 《江西畜牧兽医杂志》2009,(4):11-12
RBP4基因是近年来在猪繁殖性状上发现的一个候选基因。利用PCR-RFLP方法,以大白猪、长白猪、杜洛克猪、山西瘦肉型猪新品系(SD-III系)、大汉梅猪为试验动物,分析RBP4基因在各群体中的遗传特性。结果发现各群体都存在AA、AB和BB3种基因型,均处于中度多态,除杜洛克猪外,其余各群体都处于Hardy-Weinberg遗传平衡状态。 相似文献
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旨在解析太湖流域地方猪品种内部遗传结构,鉴定梅山猪亚群间、二花脸群体间和米猪群体间体重体尺性状差异的候选基因。试验采集440头猪样本(代表太湖流域地方猪最全面血统)进行基因芯片分型,并使用该基因分型数据集进行多种群体遗传学分析,明确太湖流域地方猪品种内部的遗传结构,并鉴定梅山猪亚群间、以及二花脸和米猪群体间体重体尺性状差异的候选SNP位点和候选基因。结果显示:在太湖流域地方猪种内部,二花脸猪与米猪间的亲缘关系最接近,其遗传距离小于梅山猪两个亚群间的遗传距离,并且拥有最为一致的进化路线。太湖流域地方猪各品种及梅山猪品种内两个亚群间都达到高度分化水平,Fst值均大于0.25,ADMIXTURE分析表明,包括梅山猪两个亚群在内的8个群体的群体结构不完全一致,在K=8时,各自展现出完全不同的祖先血统组成。通过梅山猪亚群间Fst分析、以及米猪和二花脸猪间Fst分析,在猪1、3和6号等染色体上,共鉴定到24个位点在两个分析中都表现出受选择状态,并在这些位点上下游50 kb范围注释到20个基因,其中有8个基因被报道与体重体尺性状相关。此外,受选择位点形成的选择区域与多个猪体重体尺相关QTLs重叠。试验确定了太湖流域地方猪种内部遗传结构,初步解析了这些猪种体重体尺性状差异的遗传基础,为进一步保护和利用这些种群奠定了良好的理论基础。 相似文献
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Francisco Joel Jahuey‐Martínez Gaspar Manuel Parra‐Bracamonte Ana María Sifuentes‐Rincn Victor Ricardo Moreno‐Medina 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2019,136(5):378-389
Charolais cattle are one of the most important breeds for meat production worldwide; in México, its selection is mainly made by live weight traits. One strategy for mapping important genomic regions that might influence productive traits is the identification of signatures of selection. This type of genomic features contains loci with extended linkage disequilibrium (LD) and homozygosity patterns that are commonly associated with sites of quantitative trait locus (QTL). Therefore, the objective of this study was to identify the signatures of selection in Charolais cattle genotyped with the GeneSeek Genomic Profiler Bovine HD panel consisting of 77 K single nucleotide polymorphisms (SNPs). A total 61,311 SNPs and 819 samples were used for the analysis. Identification of signatures of selection was carried out using the integrated haplotype score (iHS) methodology implemented in the rehh R package. The top ten SNPs with the highest piHS values were located on BTA 4, 5, 6 and 14. By identifying markers in LD with top ten SNPs, the candidate regions defined were mapped to 52.8–59.3 Mb on BTA 4; 67.5–69.3 on BTA 5; 39.5–41.0 Mb on BTA 6; and 26.4–29.6 Mb on BTA 14. The comparison of these candidate regions with the bovine QTLdb effectively confirmed the association (p < 0.05) with QTL related to growth traits and other important productive traits. The genomic regions identified in this study indicated selection for growth traits on the Charolais population via the conservation of haplotypes on various chromosomes. These genomic regions and their associated genes could serve as the basis for haplotype association studies and for the identification of causal genes related to growth traits. 相似文献
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【目的】探究品种、公猪出生胎次、公猪同窝仔猪数、公猪乳头数、采精季节、采精月龄和采精间隔对猪精液品质的影响,以及不同品种对精液质量稳定性的影响。【方法】选取909头杜洛克、长白、大白种公猪为试验群体,收集2021年4月至2022年4月27 408条精液测定记录,采用混合线性分析模型和方差分析探究品种、公猪出生胎次、公猪同窝仔猪数、公猪乳头数、采精季节、采精月龄和采精间隔对精液体积、精液密度、精子活力、直线前进运动精子比例、精子畸形率、总精子数及各精液性状稳定性的影响。【结果】从不同品种对精液品质的影响来看,长白猪精液体积和总精子数均显著高于大白猪、杜洛克猪(P＜0.05),杜洛克猪精液密度显著高于大白猪和长白猪(P＜0.05),杜洛克猪、大白猪精子活力均显著高于长白猪(P＜0.05),大白猪直线前进运动精子比例显著高于长白猪和杜洛克猪(P＜0.05),长白猪和大白猪精子畸形率均显著低于杜洛克猪(P＜0.05);从不同公猪出生胎次对精液品质的影响来看,1~3胎出生的公猪具有较高的精液品质;从不同采精季节对精液品质的影响来看,精液密度、精子活力和总精子数秋、冬季显著高于春、夏季(P＜0.05);从不同采精月龄对精液品质的影响来看,16~25月龄公猪具有较高的精液品质;从不同采精间隔对精液品质的影响来看,4~5 d为最佳采精间隔,采精间隔过长会导致精子畸形率上升;从不同公猪总乳头数来看,乳头数13~16个时,各精液性状品质都处于中等水平,有利于公猪生产应用。3个品种各精液性状间稳定性趋势不一,杜洛克猪和大白猪精液体积和精子活力的稳定性均显著高于长白猪(P＜0.05),杜洛克猪精液密度、精子畸形率和总精子数的稳定性均显著高于大白猪和长白猪(P＜0.05),大白猪直线前进运动精子比例的稳定性显著高于长白猪和杜洛克猪(P＜0.05)。各品种中,长白猪稳定性较差;各精液性状中,精子活力稳定性最好。【结论】品种、公猪出生胎次、采精季节、采精月龄和采精间隔均会影响公猪精液品质,可根据不同品种公猪制定更完善的选择方案,提高精液质量,加速公猪遗传改良。 相似文献
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Soma Y Uemoto Y Sato S Shibata T Kadowaki H Kobayashi E Suzuki K 《Journal of animal science》2011,89(3):601-608
Most QTL detection studies in pigs have been carried out in experimental F(2) populations. However, segregation of a QTL must be confirmed within a purebred population for successful implementation of marker-assisted selection. Previously, QTL for meat quality and carcass traits were detected on SSC 7 in a Duroc purebred population. The objectives of the present study were to carry out a whole-genome QTL analysis (except for SSC 7) for meat production, meat quality, and carcass traits and to confirm the presence of segregating QTL in a Duroc purebred population. One thousand and four Duroc pigs were studied from base to seventh generation; the pigs comprised 1 closed population of a complex multigenerational pedigree such that all individuals were related. The pigs were evaluated for 6 growth traits, 7 body size traits, 8 carcass traits, 2 physiological traits, and 11 meat quality traits, and the number of pigs with phenotypes ranged from 421 to 953. A total of 119 markers were genotyped and then used for QTL analysis. We utilized a pedigree-based, multipoint variance components approach to test for linkage between QTL and the phenotypic values using a maximum likelihood method; the logarithm of odds score and QTL genotypic heritability were estimated. A total of 42 QTL with suggestive linkages and 3 QTL with significant linkages for 26 traits were detected. These included selection traits such as daily BW gain, backfat thickness, loin eye muscle area, and intramuscular fat content as well as correlated traits such as body size and meat quality traits. The present study disclosed QTL affecting growth, body size, and carcass, physiological, and meat quality traits in a Duroc purebred population. 相似文献
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Crossbred progeny sired by either Duroc or Pietrain boars, normal for the ryanodine receptor gene, were evaluated for carcass composition and meat quality. Boars from each breed were mated to Yorkshire or F1 Yorkshire-Landrace females. A total of 162 off-spring was evaluated for carcass and meat quality traits at a common age (approximately 26 wk of age). Duroc-sired progeny had heavier (108.0 vs. 103.0 kg, P < 0.001) and longer carcasses (86.9 vs. 84.8 cm, P < 0.01), whereas Pietrain-sired pigs had less backfat at the first rib (44.6 vs. 47.7 mm, P < 0.01), last lumbar vertebrae (20.9 vs. 23.0 mm, P < 0.05), and 10th rib (23.0 vs. 25.5 mm, P < 0.01). No difference between Pietrain and Duroc progeny was detected for fat depth at the last rib (27.8 vs. 28.8 mm, respectively). Pietrain progeny had a higher percentage of lean at slaughter (52.6 vs. 50.7, P < 0.05) and higher dressing percentage (74.0 vs. 73.1, P < 0.01). Primal cut weights were collected with Pietrain progeny having a greater percentage of carcass as ham (23.0 vs. 22.4, P < 0.01) and loin (21.6 vs. 21.2, P < 0.05), whereas Duroc progeny had a higher percentage of belly weight (12.0 vs. 11.7, P < 0.05). Percentages of Boston butt (8.8 vs. 9.0) and picnic shoulder (9.9 vs. 9.9) were similar for Duroc vs. Pietrain progeny. Total weight of these five primal cuts, as a percentage of carcass weight, was higher for Pietrain progeny (75.2 vs. 74.3, P < 0.01). With heavier carcass weight, Duroc progeny had greater primal cut weights as a function of age. Subjective meat quality scores for color, marbling, and firmness (1 to 5 scale) were more favorable for Duroc-sired progeny. Furthermore, chops from Duroc progeny had higher 24-h pH (5.53 vs. 5.48, P < 0.001) and Minolta a* (17.33 vs. 17.04, P < 0.05) with less percentage drip loss (2.88 vs. 3.80, P < 0.001). No differences were detected between Duroc- and Pietrain-sired progeny for Minolta L* (54.77 vs. 55.37) or b* (7.58 vs. 7.58) objective color scores, percentage cooking loss (28.63 vs. 29.23), or Warner-Bratzler shear force (6.94 vs. 7.11 kg). Both sire breeds have beneficial traits that can be utilized in commercial pork production and merit further study. 相似文献
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【目的】估计杜洛克猪(Duroc,DD)、长白猪(Landrace,LL)、大白猪(Yorkshire,YY)繁殖性状和生长性状的遗传参数,分析不同年份育种值变化的遗传趋势,为制定合理的育种方案提供理论依据。【方法】以杜洛克猪、长白猪、大白猪繁殖性状和生长性状的性能测定数据为研究材料,其中繁殖性状数据10 963条,包括总产仔数(total number born,TNB)、产活仔数(number born alive,NBA)、出生窝重(litter born weight,LBW)和21日龄窝重(litter weight at 21 days,LW21);生长性状数据25 257条,包括达100 kg体重日龄(age at 100 kg live weight,AGE)和达100 kg体重背膘厚(backfat adjusted to 100 kg,BF)。采用基于动物模型的最佳线性无偏预测(best linear unbiased prediction,BLUP)方法,使用ASReml统计分析软件进行遗传力、遗传相关和育种值估计。【结果】TNB、NBA和LBW的遗传力在0.08~0.20之间,LW21的遗传力在0.02~0.05之间;AGE和BF的遗传力在0.22~0.37之间。繁殖性状TNB、NBA、LBW、LW21的遗传相关系数总体分布在0.20~0.97之间,呈中等偏上正相关;生长性状AGE和BF的遗传相关系数分布在-0.07~-0.03之间,呈微弱的负相关。杜洛克猪繁殖性状的遗传趋势上升幅度较大,长白猪、大白猪繁殖性状的遗传趋势上升幅度较小;生长性状中AGE的遗传趋势均呈下降趋势,且下降幅度较大,BF的遗传趋势变化幅度较小。【结论】本研究对杜洛克猪、长白猪、大白猪繁殖性状和生长性状的遗传参数和遗产趋势进行了准确的评估,结果可为该育种场的育种工作提供参考。 相似文献
18.
E Kanis G J Nieuwhof K H de Greef W van der Hel M W Verstegen J Huisman P van der Wal 《Journal of animal science》1990,68(5):1193-1200
Effects of recombinant porcine somatotropin (rpST) on growth, lean tissue growth, feed intake, feed conversion, lean tissue feed conversion, backfat thickness and lean percentage were examined in 96 growing pigs. The experiment used barrows and gilts from the genotypes Duroc, F1 (Dutch Yorkshire x Dutch Landrace) and Pietrain. Half the pigs received 14 mg rpST i.m. twice each week starting at 60 kg; others received a placebo. Pigs had ad libitum access to a diet containing 2,162 kcal net energy and 182 g crude protein per kilogram and were slaughtered at either 100 or 140 kg live weight. From 60 to 100 and from 100 to 140 kg, live weight responses to rpST averaged as follows: daily gain, +4.5 and +19.9%; feed intake, -4.4 and +3.5%; feed conversion, -8.4 and -13.9%; backfat thickness, -13.8 and -22.8%; lean percentage, +4.4 and +8.7%; lean tissue growth rate, +8.6 and +35.8%; and lean tissue feed conversion, -13.1 and -24.9%. No gender x rpST interaction was detected. However, a genotype x treatment interaction was significant for backfat thickness at both slaughter weights, showing a higher response to rpST in Duroc than in Pietrain and F1. Growth performance was improved more by rpST in F1 and Pietrain than in Duroc, especially at higher weights, but carcass traits were improved more by rpST in Duroc. The response to rpST in lean tissue growth rate from 60 to 100 kg was highest in fatter animals (Duroc, barrows), whereas from 100 to 140 kg, response in lean tissue growth rate to rpST was highest in leaner animals (Pietrain, F1, gilts). 相似文献
19.
为评价宁乡猪和杜洛克猪的杂交效果,本实验分别测定了91头宁乡猪和76头杜宁二元杂种猪的胴体性状和肉质性状指标,并对不同性状指标进行相关性分析。结果表明:在胴体性状方面,与宁乡猪相比,杜宁二元杂种猪的体直长、体斜长、胴体重、肋骨数和眼肌面积极显著提高,背膘厚和皮厚极显著降低;在肉质性状方面,杜宁二元杂种猪的肉色红度(a*)、pH45min和熟肉率极显著高于宁乡猪,pH24h显著低于宁乡猪。相关性分析显示,宁乡猪体斜长和胴体重存在极显著正相关(r=0.71),a*值与黄度(b*)值之间存在高度正相关(r=0.58);杜宁二元杂种猪体直长与体斜长存在极显著正相关(r=0.64),亮度(L*)值与b值极显著相关(r=0.54)。说明杜宁二元杂种猪在导入杜洛克血缘后,其胴体性状较宁乡猪得到较大改善,但肉质性状改善效果不明显。 相似文献