Whole genome sequence analysis to detect signatures of positive selection for high fecundity in sheep

Ovulation rate and prolificacy are the most important reproductive traits that have major impact on the efficiency of lamb meat production. Here, we compared the whole genomes of the Romanov sheep, known as one of the high prolific breeds, and four other sheep breeds namely Assaf, Awassi, Cambridge and British du cher, to identify genetic mechanisms underlying prolificacy in sheep. Selection signature analysis revealed 637 and 477 protein‐coding genes under positive selection from F_ST and nucleotide diversity (Pi) statistics, respectively. Further analysis showed that several candidate genes including LEPR, PDGFRL and KLF5 genes are involved in sheep prolificacy. The identified candidate genes in the selected regions are novel and provide new insights into the genetic mechanisms underlying prolificacy in sheep and can be useful in sheep breeding programmes to develop improved breeds for high reproductive efficiency.     

Genetic correlations between growth and reproductive traits in Zandi sheep

For the first time, the current study reports the genetic and phenotypic correlations between growth and reproductive traits in Zandi sheep. The data were comprised of 4,309 records of lamb growth traits from 1,378 dams and 273 sires plus 2,588 records of reproductive traits from 577 ewes. These data were extracted from available performance records at Khojir Breeding Station of Zandi sheep in Tehran, Iran, from 1993 to 2008. Correlations were estimated from two animal models in a bivariate analysis using restricted maximum likelihood procedure between lamb growth traits [birth weight (BW), weaning weight at 3 months of age (WW), as well as six-month weight (6 MW)] and ewe reproductive traits [litter size at birth (LSB), litter size at weaning (LSW), total litter weight at birth (TLWB), and total litter weight at weaning (TLWW)]. The genetic correlations between BW and reproductive traits varied from low to high ranges from 0.10 for BW–LSB to 0.86 for BW–TLWB. WW was moderately (0.37) to highly (0.96) correlated with all the reproductive traits. Moreover, the genetic correlations were observed between 6 MW and reproductive traits, varied from 0.19 to 0.95. Relationships between growth and reproductive traits ranged from 0.01 for BW–LSW to 0.28 for BW–TLWB in phenotypic effects. Results indicated that selection to improve WW would have high effect on genetic response in TLWW, and also, these results could be effective for all of the reproductive traits in Zandi sheep.     

绵羊经济性状相关基因研究进展及其应用

绵羊是重要的农业经济动物之一,不同绵羊品种具有各自独特的性状。利用性状存在变异的绵羊个体,对其进行基因组水平的分析,可以定位获得影响某种性状的基因区段或主效突变位点,鉴定得到的这些重要基因可为绵羊遗传育种提供分子标记,加快遗传选育进程。文章综述了在绵羊中鉴定得到的影响繁殖、生长、抗病及抗逆性状的主效基因发现过程及相应的调控机理,同时还综述了这些基因在绵羊分子育种方面的研究进展,有助于后续探索这些重要基因的具体分子机制,并为绵羊分子育种提供新思路。     

Genetic approaches to the improvement of fertility traits in the pig

One of the major determinants for litter size in pigs is prenatal mortality. It occurs most frequently during the first few weeks of gestation and can be attributed to abnormalities in developmental processes during embryogenesis including trophoblastic elongation and blastocyst implantation. Improvement of litter size has been attempted by means of phenotypic selection. However, another promising approach in pursuit of this aim has been the use of genotypic information. Reproductive traits in general are well-suited for application of marker-assisted selection (MAS). The possibility of exerting selection criteria at the molecular level shortens the generation interval as the selection decision can take place early in the life of an animal. Moreover, in consideration of the sex-limited nature of reproductive traits, genotypic information allows for selection in the gender in which the trait cannot be directly observed. Accordingly, there has been considerable interest in mapping and identifying genes involved in the regulation of reproductive traits and in elucidating their expression patterns. This review offers a comprehensive, if not exhaustive, account of the efforts being made and the approaches currently used in this field. One approach has been to choose candidate genes a priori because of the physiological importance of the proteins they encode and their role in the reproduction of other mammals. The usefulness of candidate genes is then examined by association studies between genetic polymorphisms identified in the respective candidate genes and the phenotypic reproductive traits. The other approach discussed uses pre-existing or designed families for linkage analyses in order to map the location of quantitative trait loci (QTL) for the reproductive trait of interest. The results reported were not consistent among different studies but the QTL regions detected may be useful for identification of positional candidate genes in further molecular genetic studies. However, a better understanding of porcine reproduction requires that these functional genomic approaches are merged and integrated with detailed analyses of the proteome to establish linkages between predisposition and physiology.     

国外部分高繁殖力绵羊主效基因简述

繁殖性状是绵羊的重要经济性状。作者就国外一些高繁殖力绵羊品种的繁殖特性以及相关主效基因的发现、遗传效应、定位等研究进展作一综述。      

Reproduction in farm animals in an era of rapid genetic change: will genetic change outpace our knowledge of physiology?

Compared with other domestic species, genetic nucleus selection has gradually increased both prolificacy and productivity of the breeding sow and the post-natal growth performance of commercial progeny. However, increasing variation in litter birth weight and foetal development may be indirect consequences of interactions among multiple genes controlling prolificacy and prenatal development. Phenotypic plasticity in the litter phenotype also results from effects of sow metabolic state on the developing embryo. New genomic tools may provide the opportunity to better balance the selection of genes controlling the component traits affecting the size and quality of litters born, particularly in multiparous sows.     

Genetic correlations for litter weight weaned with growth, prolificacy, and wool traits in Columbia, Polypay, Rambouillet, and Targhee sheep

Total litter weight weaned at 120 d postpartum per ewe lambing is often believed to be a measure of range ewe productivity. Genetic correlations for litter weight weaned at 120 d with prolificacy, growth, and wool traits for Columbia, Polypay, Rambouillet, and Targhee sheep were estimated using REML with animal models. Observations per breed ranged from 5,140 to 7,083 for litter weight weaned, from 5,140 to 7,095 for prolificacy traits, from 7,750 to 9,530 for growth traits, and from 4,603 to 18,443 for wool traits. Heritability estimates for litter weight weaned were low and ranged from 0.02 to 0.11. Fraction of variance due to permanent environmental effects averaged 0.05 and, due to effects of mates, averaged 0.01. Estimates of genetic correlations with litter weight weaned varied from breed to breed. The ranges were as follows: 0.42 to 0.65 with litter size born, 0.80 to 0.99 with litter size weaned, -0.22 to 0.28 with birth weight, -0.07 to 0.23 with average daily gain to weaning, -0.56 to 0.19 with fleece weight, -0.15 to 0.02 with fleece grade, and -0.11 to 0.08 with staple length. Results suggest that, if selection were practiced on litter weight weaned, the average correlated responses would be expected to be favorable or neutral for prolificacy, growth, and wool traits although responses might vary from breed to breed.     

影响梅山猪繁殖性能的生理结构及遗传因素研究进展

梅山猪是太湖猪的一个类群,以繁殖力高闻名于世.本文通过对梅山猪高产仔数性状的生理结构、遗传因素等加以综述,主要阐述了梅山猪的子宫、胎盘对高产的作用、影响多产仔性能QTL的精细定位、主效基因的多态性与高产仔数之间的关系及早期胚胎特有的发育机能对高产的影响.探讨了如何从基因组水平研究梅山猪高产的成因,以期为深入地解析梅山猪高产的分子遗传机制提供一些参考.     

6个绵羊群体BMP15、GDF9基因多态性分析

本研究旨在检测新吉细毛羊、中国美利奴羊（无角型）、东北细毛羊、杜×寒杂交羊（F1）、杜×寒杂交羊（F3）、白头杜泊羊6个绵羊群体骨形态发生蛋白15（bone morphogenetic protein 15,BMP15）、生长分化因子9（growth differentiation factor 9,GDF9）基因的多态性,为绵羊繁殖力的标记辅助选择和育种提供理论依据。以6个绵羊群体共378只个体为研究对象,利用PCR-SSCP技术检测BMP15、GDF9基因多态性;用DNAStar软件与I-TASSER软件预测蛋白质二级结构和三级结构;计算基因频率、基因型频率、Hardy-Weinberg平衡、杂合度（He）、纯合度（Ho）、有效等位基因数（Ne）和多态信息含量（PIC）。运用GraphPad Prism 6软件对新吉细毛羊群体BMP15基因多态性与产羔数进行相关性分析。结果显示,BMP15基因P1引物扩增片段存在多态性,6个群体共呈现3种基因型：AA、AC、CC,该突变为BMP15基因外显子1上58-60 bp 3个碱基（CTT）缺失,新吉细毛羊、杜×寒杂交羊（F3）、白头杜泊羊的χ²值均达到显著水平,处于Hardy-Weinberg不平衡状态,不同基因型间新吉细毛羊平均产羔数差异均不显著（P>0.05）;GDF9基因P2引物扩增片段存在多态性,6个群体共呈现3种基因型：DD、DE、EE,其中新吉细毛羊仅有1种基因型：DD,该突变为GDF9基因外显子2上477 bp处T→C的转换,该突变未导致氨基酸的改变,除新吉细毛羊外其余5个群体χ²值均未达到显著水平,处于Hardy-Weinberg平衡状态,说明GDF9基因T477C突变不能作为新吉细毛羊多胎性状遗传标记位点。     

绵羊TSHR基因多态性及其与繁殖性状关联分析

为探讨TSHR基因多态性与绵羊季节性繁殖和产羔数的关系,本实验采用Sequenom Mass-ARRAY?SNP分型技术检测常年发情的小尾寒羊(407只)、湖羊(101只)、策勒黑羊(48只)和季节性发情的苏尼特羊(21只)、滩羊(22只)、草原型藏羊(161只)TSHR基因的单核苷酸多态性(SNP)位点,并进行群体遗传学分析及其与小尾寒羊产羔数的关联分析。结果表明:TSHR基因g.89430525G>A、g.89363881T>C和g.89431097C>G的基因型频率和等位基因频率在常年发情绵羊品种和季节性发情绵羊品种间差异极显著(P<0.01);这3个SNP位点在大多数绵羊品种中表现为中度多态,且在各个绵羊品种中处于哈代温伯格平衡状态(P>0.05);TSHR基因g.89431097C>G位点的多态性与小尾寒羊第1～3胎的产羔数显著相关(P<0.05),其中CC型母羊的产羔数显著低于CG和GG型母羊(P<0.05)。本研究表明,TSHR基因与绵羊季节性繁殖性状具有较强的相关性,同时参与绵羊季节性繁殖和多羔性状的调控。     

Genetic parameters among weight, prolificacy, and wool traits of Columbia, Polypay, Rambouillet, and Targhee sheep

Genetic parameters for Columbia, Polypay, Rambouillet, and Targhee sheep were estimated using REML with animal models for prolificacy, weight, and wool traits. All bivariate analyses included a covariance between additive genetic effects for the two traits plus appropriate additional covariances. Number of observations by breed ranged from 5,140 to 7,095 for prolificacy traits, from 7,750 to 9,530 for weight traits, and from 4,603 to 34,746 for wool traits. Heritability estimates ranged from .03 to .11 for prolificacy traits (litter size at birth and litter size at weaning), from .09 to .26 for weight traits (birth weight and average daily gain), and from .25 to .53 for wool traits (fleece weight, fleece grade and staple length). Estimates of direct genetic correlations among prolificacy and among weight traits were positive and ranged from .58 to 1.00 and .18 to 1.00, respectively. Estimates of direct genetic correlation between fleece weight and staple length were positive (.50 to .70) but were negative between fleece weight and fleece grade (-.60 to -.34) and between staple length and fleece grade (-.72 and -.40). Prolificacy and wool traits were essentially uncorrelated. Weight and prolificacy traits were slightly positively correlated. Weight traits had a moderate positive direct genetic correlation with fleece weight and staple length, but were uncorrelated with fleece grade. These estimates of genetic parameters between prolificacy, weight, and wool traits can be used to construct multiple-trait selection indexes for dual-purpose sheep.     

Increased litter size in Rambouillet sheep: II. Expected responses from alternative selection criteria.

The variance and covariance components estimated from an experimental flock of Rambouillet sheep were used to predict response in litter size to direct and indirect selection. Indirect traits considered were ovulation rate and scrotal circumference. Ovulation rate was the most useful indirect selection criterion for genetic improvement of litter size. Expected response in litter size to indirect selection on ovulation rate was 93% as large as the expected response to direct selection on litter size. Selection based on an index of litter size and ovulation rate was estimated to produce 123% as much response in litter size as selection on litter size alone, and selection on an index of litter size, ovulation rate, and scrotal circumference resulted in 133% as much response in litter size as direct selection on litter size.     

Estimation of additive and non-additive genetic parameters for reproduction, growth and survival traits in crosses between the Moroccan D'man and Timahdite sheep breeds

Genetic breed differences, heterosis, recombination loss, and heritability for reproduction traits, lamb survival and growth traits to 90 days of age were estimated from crossing D'man and Timahdite Moroccan breeds. The crossbreeding parameters were fitted as covariates in the model of analysis. The REML method was used to estimate (co)variance components using an animal model. The first estimation of crossbreeding effects for Timahdite and D'man breeds shows that breed differences in litter traits are mainly of maternal genetic origin: +1.04 lambs, +1.88 kg, +0.60 lambs, and +2.23 kg in favour of D'man breed for litter size at lambing, litter weight at lambing, litter size at weaning, and litter weight at 90 days, respectively. The breed differences in lamb growth and survival are also of maternal genetic origin for the majority of traits studied, but in favour of the Timahdite breed: +3.48 kg, +45 g day⁻¹ and +0.19 lambs for weight at 90 days, for average daily gain between 30 and 90 days of age, and for lamb survival to 90 days, respectively. The D'man direct genetic effect was low and negative for survival and birth weight of lambs during the first month of life. All traits studied showed positive heterosis effects. Recombination loss effects were not significant. Therefore, crossbreeding of Timahdite with D'man breeds of sheep can result in an improved efficiency of production of saleable lambs. Heritability estimates were medium for litter size but low for the other reproduction traits. Direct heritabilities were low for body weights and lamb survival at 90 days and the corresponding maternal heritabilities showed, however, low to moderate estimates. For litter traits, the estimates of genetic and phenotypic correlations were positive and particularly high for genetic correlations.     

Productivity of crosses based on prolific breeds of sheep

The results of main and short papers on the productivity of crosses between domestic and prolific breeds presented in Zürich in 1976 have been summarized according to the important reproduction and production traits. Fertility, prolificacy, mortality rate, litter size born and weaned, ovulation rate, accelerated and out-of-season lambing, milk production, growth and carcass traits were analysed. More attention has been paid to the reproduction traits, because of their importance in crossbreeding with prolific breeds. For all analysed traits the amount of heterosis has been estimated from various information sources: midparent value, F₁, F₂, B₁ (backcrosses), one of the parent breeds. The use of prolific breeds mostly leads to an improvement in the reproductive characters. The breed differences are decisive for all traits. The reproduction traits generally show higher heterosis effects than the production traits, but this statement cannot be held as a rule. For international comparisons in future the traits must be standardized.     

运用贝叶斯方法估计中国美利奴羊(新疆型)毛用性状及繁殖性状的遗传参数

为了解中国美利奴羊（新疆型）近年来遗传结构的变化趋势以及探讨毛用性状与繁殖性状的遗传关系,需要进一步研究这些性状的遗传力以及它们之间的关系。本研究收集额敏县聚鑫细毛羊养殖专业合作社1985-2018年中国美利奴羊（新疆型）共计9 428只羊毛生产记录和1987-2018共计5 887只年繁殖记录,运用BLUPF90软件结合Gibbs抽样方法,利用单性状模型对中国美利奴（新疆型）毛用性状（细度支数、等级、总评分、毛长、污毛重和鉴定时体重）和繁殖性状（配种次数、妊娠天数、胎产羔数和总产羔数）进行方差组分和遗传力估计,利用双性状模型分析毛用性状与繁殖性状之间的遗传相关与表型相关。结果显示,中国美利奴羊（新疆型）毛用性状细度支数、等级、总评分、毛长、污毛重、鉴定时体重的遗传力估计值分别为0.471±0.020、0.088±0.030、0.114±0.018、0.426±0.025、0.328±0.041、0.317±0.046;繁殖性状配种次数、妊娠天数、胎产羔数及总产羔数的遗传力估计值分别为0.056±0.009、0.022±0.010、0.120±0.018、0.163±0.016;毛用性状与胎产羔数、总产羔数之间的遗传相关范围为-0.031~0.286,鉴定时体重与胎产羔数（0.286）、总产羔数（0.204）遗传相关最高,细度支数与胎产羔数（-0.143）、总产羔数（-0.048）呈负的遗传相关;毛用性状与胎产羔数、总产羔数之间的表型相关范围为-0.210~0.216,毛长与总产羔数（0.216）表型相关最高,细度支数与胎产羔数（-0.137）、总产羔数（-0.210）呈显著负表型相关。本研究结果发现,毛用性状与繁殖性状之间存在一定的关系,这一结果可为今后制定中国美利奴羊育种规划提供数据基础,为选育优质高产、繁殖性能好的细毛羊提供理论依据,从而进一步提高细毛羊产业经济效益。     

几个中国地方猪群体遗传结构和产仔数性状选择信号分析

旨在对几个中国地方猪品种进行群体遗传结构分析,并筛选与中国地方猪产仔数相关的基因组选择信号及候选基因.本研究下载了6个中国地方品种猪共计102头个体的Illumina PorcineSNP60芯片数据,构建了包括19头迪庆藏猪、16头明光小耳猪、16头五指山猪在内的低产仔数组和包括11头姜曲海猪、20头蓝塘猪、20头梅...     

Phenotypic and genetic parameter estimates for reproductive traits in Zandi sheep

This study reports on the phenotypic and genetic (co)variance components for reproductive traits in Zandi sheep, using between 1,859 and 2,588 records obtained from 577 ewes. The data were collected from the Khojir Breeding Station of Zandi sheep in Tehran, Iran from 1994 to 2008. The basic traits were litter size at birth (LSB), litter size at weaning (LSW), litter mean weight per lamb born (LMWLB), and litter mean weight per lamb weaned (LMWLW), and the composite traits were total litter weight at birth (TLWB) and total litter weight at weaning (TLWW). Genetic analyses were carried out using the restricted maximum likelihood method that was explored by fitting the additive direct genetic effects and permanent environmental effects of the ewes as random effects and the ewe age at lambing and lambing year as fixed effects for all of the investigated traits. Akaike’s information criterion was used to choose the most appropriate model. LSB, LSW, LMWLB, LMWLW, TLWB, and TLWW direct heritability estimates were 0.07, 0.05, 0.12, 0.10, 0.08, and 0.14, respectively. The estimated fractions of variance due to the permanent environmental effects of the ewe ranged from 0.03 for LMWLB to 0.08 for LMWLW and TLWW. Corresponding repeatability estimates ranged from 0.10 for LSW to 0.22 for TLWW. Direct genetic correlations varied from ?0.61 for LSB–LMWLB to 0.88 for LSB–LSW and LSB–TLWB. Results indicate that genetic change depends not only on the heritability of traits, but also on the observed phenotypic variation; therefore, improvement of non-genetic factors should be included in the breeding programs.     

绵羊FecB基因遗传多样性及其产羔数的关联分析

FecB是19世纪80年代在布鲁拉美利奴（Booroola Merino）绵羊中发现的能增加排卵数和产羔数的一个常染色体突变基因,是在绵羊中识别出的第一个高繁殖力主效基因。本研究利用PCR-SSCP以及PCR-RFLP方法对湖羊、小尾寒羊、阿勒泰羊、洼地绵羊共470只的FecB基因进行单核苷酸多态性分析,验证FecB基因为绵羊的高繁殖力的主效基因,并以洼地绵羊为研究对象,检验FecB基因是否为洼地绵羊高繁殖力的主效基因。实验结果表明上述两种方法均能准确判型,稳定可靠性良好,并且判断的结果一致。研究结果显示：上述4个绵羊品种均携带FecB突变,且能证明FecB基因为洼地绵羊高繁殖力的主效基因。     

Functional infertility in sheep

Most studies on reproductive efficiency in sheep have concerned the prolificacy of the ewe and the lambing rate of the flock. Some work has been done on reproductive failure but this has seldom separated fertilisation rate from embryonic and fetal loss. Inadequate attention has been given to the level of barrenness in working flocks and to the effect of the ram on conception rate and litter size.     

BMPR-IB基因多态性与河北肉用绵羊产羔数及羔羊生长发育的相关性研究

为了研究BMPR-IB基因单核苷酸多态性及其对绵羊产羔数和羔羊生长发育的影响,试验采用PCR-RFLP方法对小尾寒羊、杜泊、德克赛尔及河北肉用绵羊的BMPR-IB基因单核苷酸多态性进行了测定,并对BMPR-IB基因多态性与河北肉用绵羊产羔数和生长发育的关系进行了研究。结果表明:基因型频率在各品种间分布极不平衡,BB基因型河北肉用绵羊群体的总体平均产羔数显著高于B+基因型(P<0.05),极显著高于++基因型群体(P<0.01);90日龄时,++基因型河北肉用绵羊的胸宽和腰角宽显著高于B+基因型群体(P<0.05)。说明BMPR-IB基因的基因型对河北肉用绵羊羔羊的生长发育有一定影响。