Whole genome SNPs among 8 chicken breeds enable identification of genetic signatures that underlie breed features

Many different chicken breeds are found around the world, their features vary among them, and they are valuable resources. Currently, there is a huge lack of knowledge of the genetic determinants responsible for phenotypic and biochemical properties of these breeds of chickens. Understanding the underlying genetic mechanisms that explain across-breed variation can help breeders develop improved chicken breeds. The whole-genomes of 140 chickens from 7 Shandong native breeds and 20 introduced recessive white chickens from China were re-sequenced. Comparative population genomics based on autosomal single nucleotide polymorphisms (SNPs) revealed geographically based clusters among the chickens. Through genome-wide scans for selective sweeps, we identified thyroid stimulating hormone receptor (TSHR, reproductive traits, circadian rhythm), erythrocyte membrane protein band 4.1 like 1 (EPB41L1, body size), and alkylglycerol monooxygenase (AGMO, aggressive behavior), as major candidate breed-specific determining genes in chickens. In addition, we used a machine learning classification model to predict chicken breeds based on the SNPs significantly associated with recourse characteristics, and the prediction accuracy was 92%, which can effectively achieve the breed identification of Laiwu Black chickens. We provide the first comprehensive genomic data of the Shandong indigenous chickens. Our analyses revealed phylogeographic patterns among the Shandong indigenous chickens and candidate genes that potentially contribute to breed-specific traits of the chickens. In addition, we developed a machine learning-based prediction model using SNP data to identify chicken breeds. The genetic basis of indigenous chicken breeds revealed in this study is useful to better understand the mechanisms underlying the resource characteristics of chicken.     

Genetic structure of the purebred domestic dog

We used molecular markers to study genetic relationships in a diverse collection of 85 domestic dog breeds. Differences among breeds accounted for approximately 30% of genetic variation. Microsatellite genotypes were used to correctly assign 99% of individual dogs to breeds. Phylogenetic analysis separated several breeds with ancient origins from the remaining breeds with modern European origins. We identified four genetic clusters, which predominantly contained breeds with similar geographic origin, morphology, or role in human activities. These results provide a genetic classification of dog breeds and will aid studies of the genetics of phenotypic breed differences.     

中国地方鸡种资源不同保种方法的分子检测

采用13对高度多态的微卫星标记对我国7个受国家重点保护的地方鸡种的原地保护和异地保存两种活体保种方法的保种效果进行了检测，计算了各品种的遗传杂合度和多态信息含量，比较了各品种在不同保种方法之间的遗传参数。结果表明：7个品种在两种保种方法中都有高度多态性，但异地保存的品种的多态性较原地保护的品种的多态性要多；虽然两种方法的保种效果较好，但是原地保护和异地保存之间在同一品种内的遗传变异并不相同。     

中国地方鸡种资源不同保种方法的分子检测*

 采用13对高度多态的微卫星标记对我国7个受国家重点保护的地方鸡种的原地保护和异地保存两种活体保种方法的保种效果进行了检测,计算了各品种的遗传杂合度和多态信息含量,比较了各品种在不同保种方法之间的遗传参数。结果表明:7个品种在两种保种方法中都有高度多态性,但异地保存的品种的多态性较原地保护的品种的多态性要多;虽然两种方法的保种效果较好,但是原地保护和异地保存之间在同一品种内的遗传变异并不相同。     

Analysis of genetic distribution and population genetic structure of the MyoD gene in 10 pig breeds

Restriction fragment length polymorphism (RFLP) data was applied to analyze the distribution of the MyoD gene in 10 pig breeds and pig breed crosses. The population genetic information about genetic distribution, variation, and heterozygosity of the MyoD gene in different breed populations were analyzed. Based on the allele frequency, genetic distance and evolution distance among each breed populations were calculated and Unweighted Pair Group Method with Arithmetic mean (UPGMA) phylogenetic tree was gained based on the evolution distances between populations. The results indicated that the distribution of the MyoD genotype kept in Hardy-Weinberg equilibrium in most tested groups but not in Duroc (D) and Duroc6(Landrance × Yorkshire) (DLY) population. Generally, the genetic diversity of the MyoD gene was abundant and these tested breed populations had high genetic variations. The evolution of the MyoD gene was under natural selection pressure. On the phylogenetic tree, 10 pig breeds were divided into 4 clusters. The first cluster consisted of four breeds developed from Landrace. The second cluster was two indigenous Chinese pig breeds. The third cluster was three breeds developed from Duroc. The fourth cluster was a Tibetan pig breed. The constitution of the topology of the phylogenetic tree was consistent with the breeding history of each pig breed. From this experiment, we can conclude that some RFLP data obtained from functional gene can be used in the genetic deviation research between some closely related species or between different populations in certain species. __________ Translated from Acta Veterinaria et Zootechnica Sinica, 2007, 38(1): 1–7 [译自: 畜牧兽医学报]     

用20个微卫星标记研究鲁西黄牛和渤海黑牛的遗传多样性

用20个微卫星座位分析了鲁西黄牛、渤海黑牛及用作参照的秦川牛品种的遗传多样性。3个中国黄牛品种在20个座位的等位基因数为4~25个,平均等位基因数接近9个。各座位等位基因长度与欧洲普通牛相似,但平均等位基因数高于报道的欧洲普通牛和部分中国其它黄牛品种。3个品种在不同座位均发现部分特有基因,以渤海黑牛居多,在3个座位检测到7个特有基因。平均有效等位基因数达到6个以上,平均杂合度接近0.8,平均多态信息含量约为0.85,这几项变异参数在3个品种间没有明显差异,但高于欧洲普通牛群体和报道的中国部分黄牛群体的相应值。结果表明,3个品种在当地生态条件下,经数千年的选育积累了丰富的遗传变异,属宝贵的遗传资源。遗传相似度分析结果显示,渤海黑牛先与秦川牛聚为1类,再与鲁西黄牛聚在一起,引证了鲁西黄牛受瘤牛血统影响较大的结论。     

基于线粒体DNA D-loop区的肉鸡品种遗传多样性和起源分析

【目的】探讨不同生长速度鸡品种（配套系）线粒体DNA D-loop区全序列遗传多样性和起源特性,为肉鸡品种选育和溯源提供理论依据。【方法】以不同生长速度的8个黄羽肉鸡配套系（中快速型5个、慢速型3个）、2个地方鸡种（固始鸡、藏鸡）、2个引进鸡种（隐性白羽鸡、安卡鸡）、1个白羽肉鸡（罗斯308）、817杂交肉鸡以及1个高产蛋鸡配套系（大午褐壳蛋鸡）共计15个鸡种为研究对象,采集血液提取DNA后进行PCR扩增,对15个鸡种共683个个体mtDNA D-loop区全序列进行测序,使用DnaSP 5.10软件分析各个鸡种遗传多样性和单倍型特点,使用MEGA 4.0软件计算种间遗传距离,构建不同单倍型与红色原鸡之间NJ系统发育树,分析起源和亲缘关系。【结果】15个鸡种线粒体D-loop区全序列大小为1 231—1 232bp,序列长度为1 231 bp的个体在859 bp处存在C碱基缺失。683个个体共检测到45个变异位点,组合为53个单倍型,可以分为A、B、C和E共4个单倍型群,其中中快速型肉鸡、817杂交肉鸡以及高产蛋鸡均是E单倍型为优势单倍型（≥48.89%）;慢速型黄羽肉鸡中鸿光黑鸡优势单倍型为B单倍型,京海黄鸡优势单倍型为A单倍型,雪山鸡4种单倍型相对均衡,3个慢速型黄羽肉鸡配套系E单倍型比例≤38.46%;地方鸡种中固始鸡的单倍型为A和C型,藏鸡的单倍型为A和B型。15个鸡种单倍型多样度（Hd）分布在0.496—0.853,核苷酸多样度（Pi）分布在0.00146—0.00673,遗传多样性相对丰富的品种（配套系）是新兴矮脚黄鸡、雪山鸡、京海黄鸡和罗斯308;遗传多样性程度相对较低的品种（配套系）是藏鸡、高产蛋鸡、安卡鸡、新兴麻鸡4号和墟岗黄鸡1号。15个鸡种Kiumura双参数距离范围为0.0016—0.0113,其中罗斯308种内遗传距离最大,而817杂交肉鸡和高产蛋鸡的种内遗传距离最小;种间遗传距离最大为高产蛋鸡与藏鸡之间,最小为高产蛋鸡与817杂交肉鸡之间;中快速型黄羽肉鸡配套系相互之间遗传距离相对较小,而与慢速型黄羽肉鸡配套系以及地方鸡种之间遗传距离相对较大;京海黄鸡和鸿光黑鸡均是与藏鸡遗传距离最小。聚类分析显示,A、B单倍型群与红色原鸡滇南亚种交叉聚为一枝;E单倍型与红色原鸡印度亚种交叉聚为一枝;C单倍型群与红色原鸡印度亚种、滇南亚种、指名亚种以及印尼亚种交叉聚为一枝。【结论】不同生长速度鸡种之间线粒体D-loop区遗传多样性程度差异较大;E单倍型与肉鸡生长速度具有较强的相关性,中快速型群体均以E单倍型为优势单倍型,而慢速型群体E单倍型比例均低于40%;我国家鸡群体具有多个红色原鸡母系起源,显示其在中性选择下被驯化。研究结果为肉鸡品种选育和溯源以及资源化开发利用提供了理论依据。     

部分地方鸡品种体量及生态特征的多元统计分析*

 利用主成分分析和聚类分析对我国11个地方鸡品种的体尺、体重和生态特征的资料进行了多元统计分析。单独对6项体量指标进行聚类的结果表明：我国11个地方鸡种大致可以分为大型鸡、中型鸡和小型鸡3类；多元统计分析12项指标的结果表明，主成分分析选取前3个特征值作为3个主成分（占总信息量的88.659%），根据各品种的前3个主成分值计算相似系数，并用最短距离法进行聚类分析，结果表明11个地方鸡品种可划分为高海拔型和低海拔型两类，这说明了生态因子亦是品种分类中的一个重要方面。     

IGF1-PI3K-Akt信号通路相关基因在黄羽肉鸡肌肉和肝脏中的表达

【目的】IGF1-PI3K-Akt信号通路是调控生长发育的关键通路,选择慢速型的广西麻鸡和中速型的花山麻鸡作为研究对象,探究IGF1-PI3K-AKT信号通路相关基因胰岛素样生长因子1( Insulin-like growth factors, IGF1)、胰岛素样生长因子1受体( Insulin- like growth factor receptor, IGF1R)和胰岛素受体底物1 (Insulin receptor substrate1, IRS1)在骨骼肌和肝脏中的发育性表达规律,为阐明黄羽肉鸡生长发育调控机理提供参考。【方法】采用SPSS20.0比较广西麻鸡和花山麻鸡在胚胎期至出生后早期的生长发育差异,采用实时荧光定量PCR方法检测上述3个基因在两个品种鸡胚胎期（9、12、16胚龄）和出生后（0、7、21、35、49和63日龄）胸肌、腿肌和肝脏中的表达差异,并将其与体重和组织重进行相关性分析。【结果】鸡生长发育早期体重、骨骼肌重和肝脏重变化呈现显著的品种和时间特异性,经过选育的花山麻鸡体重和组织重的增长在胚胎发育后期已经远远超过广西麻鸡。IGF1、IGF1R和IRS1基因表达存在显著的品种、组织和发育时段特异性,总体上,在胚胎期肌肉中的表达量高于肝脏组织,出生后则为肝脏中的表达量高于肌肉组织,广西麻鸡肌肉中的表达量高于花山麻鸡,而花山麻鸡肝脏中的表达量要高于广西麻鸡。IGF1基因在两个品种胸腿肌中均在9胚龄即可检测到表达,腿肌中表达量均是9胚龄时最高,除与12胚龄差异不显著外,与其他各阶段差异显著,表达量最低点出现在出雏0日龄时;胸肌中则是12胚龄时表达量最高,63日龄时最低;肝脏中则出现品种差异,广西麻鸡胚胎期未检测到表达,从出雏0日龄开始表达,表达高峰出现在21日龄时,而在花山麻鸡中虽然胚胎期检测到表达但表达量极低,49日龄时达到表达高峰。两品种鸡肌肉和肝脏各个阶段均检测到IGF1R mRNA的表达,在胸肌和腿肌中的表达量均表现为9胚龄最高,广西麻鸡9胚龄与其他各阶段差异显著,花山麻鸡9胚龄除与12胚龄差异不显著外,与其他各阶段均差异显著;肝脏中,广西麻鸡表达高峰出现在21日龄,且与9、12、16胚龄和0日龄差异显著,花山麻鸡则是63日龄时最高,与其他各阶段差异显著。两品种鸡肌肉和肝脏各个阶段均能检测到IRS1 mRNA的表达,在两品种肌肉中的表达量均表现为9胚龄或者12胚龄最高,与其他各阶段差异显著,随后下降,并在出雏后维持在较低水平;肝脏中IRS1的表达模式与IGF1R一致。IGF1、IGF1R和IRS1基因的表达两两之间均表现出显著或极显著的正相关关系,同时,肌肉中3个基因的表达与体重、胸（腿）肌重存在显著的负相关,而肝脏中3个基因的表达与体重、胸（腿）肌重、肝脏重均存在显著的正相关。【结论】IGF1-PI3K-AKT信号通路相关基因之间存在一致性趋势,品种间和组织间表达量的差异可能正是不同类型黄羽肉鸡生长发育差异的主要原因之一。     

四个山西地方山羊品种Pit-1基因多态性的研究

垂体释放因子1基因(Pit-1)是动物经济性状的重要候选基因之一。采用PCR-RFLP和PCR-SSCP技术对4个山西地方山羊品种的Pit-1基因进行多态性检测和分析,以了解该基因在这些品种中的遗传变异。结果表明:该基因座存在HinfⅠ限制性酶切多态性,表现AA和BB两种基因型,频率分别为0.01和0.99。洪洞奶山羊和吕梁黑山羊因突变而显著偏离Hardy-Weinberg平衡(P0.05)。利用PCR-SSCP检测出5种基因型。优势等位基因均为B,基因型频率的品种间差异明显。吕梁黑山羊和黎城大青羊显著偏离平衡状态(P0.05)。中性检验表明,4个品种处于中性突变或遗传漂变过程中。各群体的期望杂合度和观察杂合度较为接近。基于两种技术的Fst值分别为0.0102和0.0197,说明总群体中大约只有1%～2%的变异来自群体间,群体间的遗传分化较弱。     

利用微卫星DNA标记分析贵州3个地方猪种的遗传多样性

1材料与方法 1．1材料 采集3个地方猪种血液样品,共90份（表1）。采集个体品种特征明显,公母各半。     

运用荧光标记微卫星分析6个肉山羊品种遗传多样性

为了研究安徽白山羊、贵州白山羊、陕南白山羊、宜昌白山羊、马头山羊和波尔山羊6个肉山羊品种DNA分子水平上的遗传多样性,利用10个微卫星引物,分析6个肉山羊品种分子水平上的遗传变异和群体关系。10个微卫星位点均呈现高度多态,其多态信息含量(PIC)在0.531～0.812之间。F统计结果显示群体间存在极显著的遗传分化,遗传分化系数(Fst)为0.082。系统进化树NJ图把中国5个肉山羊和波尔山羊分为2支;中国肉山羊又被分成2个分支。系统进化树UPGMA图和主成分的二维坐标图进一步证实上述聚类结果的可靠性。此研究结果显示6个肉山羊品种遗传多样性丰富,具有很大的选育潜力,特别是中国地方品种,是将来开发利用的宝贵原始材料。     

不同品种肉兔断奶后生长性状的比较

【目的】比较不同肉兔品种断奶后的生长性能,并进行种质评估。【方法】分别分析了弗朗德巨兔、新西兰白兔、加利福尼亚兔、青紫蓝兔和福建黄兔的5、6、7、8、9和10周龄体重,平均日增重和上市日龄。断奶后生长数据来自上述5个品种的173窝肉兔,共计909只。模型中的固定效应包括品种类型、出生月份、母兔胎次、性别。窝效应作为随机效应,断奶数量和称重时间作为线性协变量。【结果】①5、6、7、8、9和10周龄体重,平均日增重及上市日龄的总平均数分别为619.46、791.57、941.51、1 107.51、1 309.51和1 445.52 g,23.64 g•d-1及103.14 d;②品种和断奶数量对个体断奶后生长性状影响显著（P＜0.05）;弗朗德巨兔的各周体重显著高于其它品种,福建黄兔的各周体重显著低于其它品种（P＜0.05）;③窝方差能解释生长性状大部分的总表型方差,为0.48-0.74。【结论】由于弗朗德巨兔具有生长速度快的特点,可将其作为杂交的终端父本;在肉兔选育时,选择指数应当同时兼顾断奶数量和生长性状。     

The Study on Correlation Analysis of Single Nucleotide Polymorphism of IGF2 Gene and Body Fatness Traits in Chicken

Insulin-like growth factor Ⅱ has profound effects on the growth and differentiation of animal embryo. Some researches indicated that it affects the fat metabolism of poultry.This study was designed to investigate the effect of IGF2 on chicken fatness traits.Broiler, Hyline Brown layer and three native breeds (Shiqiza, Beijing You, Baier) were used in this research. Body weight and body composition traits were measured in broiler line at the age of 7 weeks. Primers for exon2 in IGF2 were designed from database of chicken genomic sequence. Polymorphisms were detected by PCR-SSCP and DNA sequencing.The total χ2 test results showed that there was a significant difference (P＜ 0.01) in the frequency of genotype among breeds. A C/G mutation at base position 139 was found among individuals in broiler line and the least square analysis showed that BB genotype birds had significant lower (P＜ 0.05) abdominal fat weight and percentage of abdominal fat than AA or AB genotype birds. From the results we can conclude putatively that IGF2 gene is the major gene affecting the fatness traits of chicken or it links with the major gene,and the mutation could be used as the molecular genetic marker to select the chicken for low abdominal fat.     

利用三倍体胚乳遗传模型定位爆裂玉米膨爆特性QTL

 【目的】探讨爆裂玉米膨爆特性的分子遗传基础，为遗传改良和分子标记辅助选择提供有益信息。【方法】以普通玉米自交系丹232和爆裂玉米自交系N04为亲本构建259个F2﹕3家系群体，利用SSR标记构建分子标记遗传图谱，利用三倍体胚乳遗传模型和区间作图法对F2﹕3群体在两种环境条件下的膨爆特性进行了QTL定位和效应分析。【结果】构建的爆裂玉米SSR遗传连锁图谱包含183个标记，覆盖玉米基因组1762.2 cM，标记间平均距离为9.63 cM。爆裂玉米的膨爆特性是由效应不等的多基因控制的数量性状，同时受环境条件的影响。两种环境条件下共检测到18个爆花率QTL，17个膨化体积QTL和21个膨化倍数QTL。单个QTL可解释的表型变异介于4.4%～28.0%，可解释的表型总变异为65.8%～96.6%，基因的作用方式为加性、部分显性、显性和超显性的QTL数目分别为2、1、4、20和1、5、1、22，超显性在膨爆特性的遗传中起着最重要的作用。【结论】与以往膨爆特性以加性效应遗传为主的研究结果不一致的主要原因在于三倍体胚乳模型对显性效应的细分和对显性效应较小QTL的显性效应的高估。     

Signatures of positive selection for local adaptation of African native cattle populations: A review

Cattle are central to the lives and diverse cultures of African people. It has played a crucial role in providing valuable protein for billions of households and sources of income and employment for producers and other actors in the livestock value chains. The long-term natural selection of African cattle typically signals signatures in the genome, contributes to high genetic differentiations across breeds. This has enabled them to develop unique adaptive traits to cope with inadequate feed supply, high temperatures, high internal and external parasites, and diseases. However, these unique cattle genetic resources are threatened by indiscriminate cross-breeding, breed replacements with exotic cosmopolitan breeds, and climate change pressures. Although there are no functional genomics studies, recent advancements in genotyping and sequencing technologies have identified and annotated limited functional genes and causal variants associated with unique adaptive and economical traits of African cattle populations. These genome-wide variants serve as candidates for breed improvement and support conservation efforts for endangered cattle breeds against future climate changes. Therefore, this review plans to collate comprehensive information on the identified selection footprints to support genomic studies in African cattle to confirm the validity of the results and provide a framework for further genetic association and QTL fine mapping studies.     

中国鹅5个品种遗传多样性的随机扩增多态DNA分析

用４０个１０－寡核苷酸随机引物对中国鹅的５个品种－狮头鹅,皖西白鹅,太湖鹅,浙东白鹅和四川白鹅进行了随机扩增多态ＤＮＡ（ＲＡＰＤ）分析。结果表明,用筛选出的１４个引物共扩增出１７４个ＤＮＡ片段,其中的４８个（占２８．２％）在５个品种间表现为多态性。根据扩增ＤＮＡ片段的异同,计算了各品种和个体间的遗传多样性指数和遗传距离指数。同时,用分子进化遗传分析软件（ＭＥＧＡ）以ＵＰＧＭＡ法和ＮＪ法对遗传距离指     

山东省猪种mtDNA CytB基因遗传多样性及系统进化研究

 【目的】利用mtDNA CytB基因为标记,从分子水平探讨12个猪种166个样本（8个山东省猪种,3个引进猪种和梅山猪种）的遗传多样性和各猪种间的亲缘关系,为山东省猪种合理利用以及生物多样性保护提供基础资料。【方法】对各猪种样本mtDNA CytB基因进行PCR扩增和测序,采用现代生物信息学方法进行数据处理分析。【结果】山东8个猪种种内遗传变异和种间遗传距离均较小,有共享单倍型。山东各猪种和梅山猪与大约克的遗传距离也较小,但与引进猪种杜洛克和长白的遗传距离较大。利用分子系统进化树和CytB基因4个SNP位点的分类方法将上述样本分为2个独立的支系,第一支以中国猪种为主,将除鲁烟白猪的一种单倍型在内的所有山东猪种、梅山猪和大约克的两种单倍型聚为一类,第二支以引进猪种为主,将长白、杜洛克、大约克的一种单倍型和鲁烟白猪的一种单倍型聚为一类。【结论】山东猪种有共同的母系祖先,品种内母系遗传多样性较贫乏;外来猪种引入山东后主要是用作父本以提高生产速度和瘦肉率等,对本地猪种未有母系贡献;利用CytB基因4个SNP位点对欧洲单倍型和亚洲单倍型的分类方法,可以方便地估测利用中外猪种结合培育的猪新品种（配套系）的母系血统情况。     

中国沙皮犬种群遗传现状的初步分析

中国沙皮犬是原产于我国广东省佛山市南海区大沥镇的一种世界名犬。目前,原产地中国沙皮犬数量极少,且种质极为混乱。为了保护这种面临灭绝的珍贵品种资源,本研究首次从分子水平分析了原产地沙皮犬种群的遗传背景。提取了92只沙皮犬的血液DNA,进行了随机扩增多态DNA(RAPD)分析。筛选出12个重复性、多态性好的随机引物,共扩增出70个位点,分子量在250~2 000 bp之间,种群共享带数为6条,多态性高达91.42%,表明沙皮犬群体存在较丰富的遗传多样性。聚类分析结果表明:绝大部分骨嘴沙皮犬和肉嘴沙皮犬分别聚在一块,与其各自的外部形态特征基本相符。骨肉嘴沙皮犬和肉嘴沙皮犬的遗传距离比骨肉嘴沙皮犬和骨嘴沙皮犬的遗传距离相对近些,从分子水平为沙皮犬各类型的保种和繁育生产提供了新的指导。     

东北民猪和哈尔滨白猪胃底腺、空腸腸腺及腸絨毛、結腸腸腺的比较

胃底腺粘膜的总重量和总面积,两猪种间差异不显著。但在单位距离内,胃底腺的密度,初生和15公斤民猪都非常显著地大于哈白猪。其余各项差异都不显著。民猪的空肠肠腺密度和肠绒毛密度与哈白猪比较,差异都不显著。但在单位距离内,肠腺的高度和肠绒毛的高度,民猪各有一个阶段大于哈白猪。各猪种肠绒毛高度的年令变化,初生阶段两者都显著地大于15公斤和30公斤阶段。初生及30公斤的结肠肠腺的密度及高度,两猪种间的差异都不显著。但十五公斤阶段,在单位距离内,结肠肠腺的密度及高度,哈白猪优于民猪。