鸡8个功能基因5′-侧翼区与内含子的SNP多样性比较

本研究旨在探讨鸡功能基因5′-侧翼区的单核苷酸多态性(SNP)水平。作者以白来航鸡、隐性白洛克鸡、杏花鸡、丝羽乌骨鸡、固始鸡、红色原鸡为材料,扩增了GH、DDBC1、RIKEN、RASGRP3、IGF1、THRSP、VIP及PRL共8个基因的5′-侧翼区DNA序列。扩增序列全长为8,399bp,SNP的总数为161个,平均每52bp出现一个SNP。8个功能基因5′-侧翼区核苷酸多样性的θ均值和π均值分别为0.00620±0.00110和0.00559±0.00100。比较检验表明,5′-侧翼区的SNP多样性显著低于内含子区域。5′-侧翼区是基因表达的一个重要调控区域,在分子进化和系统发生过程中承受着比内含子区域更大的选择压,其较低的SNP多样性是适应性较好的表现。Tajima检验与Fu和Li检验表明,与鸡繁殖性状显著关联的VIP基因和PRL基因很可能是人工选择或自然选择的目的基因。     

鸡8个功能基因5'-侧翼区与内含子的 SNP多样性比较

本研究旨在探讨鸡功能基因5'-侧翼区的单核苷酸多态性(SNP)水平.作者以自来航鸡、隐性白洛克鸡、杏花鸡、丝羽乌骨鸡、固始鸡、红色原鸡为材料,扩增了GH、DDBC1、RIKEN、RASGRP3、IGF1、THRSP、VIP及PRL共8个基因的5'-侧翼区DNA序列.扩增序列全长为8,399 bp,SNP的总数为161个,平均每52 bp出现一个SNP.8个功能基因5'-侧翼区核苷酸多样性的θ均值和π均值分别为0.00620±0.00110和0.00559±0.00100.比较检验表明,5'-侧翼区的SNP多样性显著低于内含子区域.5'-侧翼区是基因表达的一个重要调控区域,在分子进化和系统发生过程中承受着比内含子区域更大的选择压,其较低的SNP多样性是适应性较好的表现.Tajima检验与Fu和Li检验表明,与鸡繁殖性状显著关联的VIP基因和PRL基因很可能是人工选择或自然选择的目的基因.     

家鸡腺苷琥珀酸裂解酶基因多态性与肌苷酸含量的关联及其与红原鸡的亲缘关系

根据腺苷琥珀酸裂解酶(adenylosuccinate lyase, ADSL)基因外显子2的序列设计引物, 用PCR-SSCP的方法对隐性白羽鸡、丝羽乌骨鸡、白耳鸡、藏鸡以及红色原鸡两个亚种进行了单核苷酸多态性分析, 并检测到了多态性, 表现为3种基因型, 对两种纯合子进行直接测序, 结果发现3484位碱基处发生C→T突变。对3种基因型的肌肉肌苷酸含量的最小二乘分析结果显示TT型(突变型)个体的肌肉肌苷酸含量极显著地高于CT型、显著地高于CC型个体, CT型个体也稍高于CC型, 但差异不显著, 初步推测该位点可能与肌肉肌苷酸含量有关。根据该多态位点的基因频率, 基于Nei氏的遗传距离运用NJ聚类法构建系统发生树, 进行家鸡与原鸡的亲缘关系分析, 结果发现, 丝羽乌骨鸡与白耳鸡的亲缘关系最近, 藏鸡和中国红原鸡亚种的亲缘关系也较近, 中国地方家鸡品种与中国红原鸡亚种的亲缘关系较近,而与泰国红色原鸡的亲缘关系较远,隐性白羽鸡与原鸡亲缘关系最远, 初步得出中国家鸡有自己独自的血缘来源的结论。     

利用DNA池和测序技术快速筛查SNPs及估算基因频率

选取产蛋性能具有明显差异的4个鸡品种(莱航鸡、阳山鸡、丝羽乌骨鸡和隐性白洛克鸡)构建品种DNA池,采用测序的方法研究鸡催乳素基因5′侧翼调控区远端序列(1028bp)的多态性,快速筛查到8个可能与产蛋性能相关的SNPs(C-2402T、T-2192C、C-2161G、C-2134G、C-2062G、G-2040A、A-1944G和C-1884A)。进一步利用测序图中SNP等位基因峰高的比值估算各鸡品种等位基因的频率,其中C-2402T、C-2161G、C-1884A和C-2062G、G-2040A位点等位基因频率的估算结果分别被PCR-RFLP、PCR-SSCP所验证,说明测序峰高比值估算等位基因频率的方法具有一定的可行性。     

华东地区地方鸡品种mtDNA控制区遗传多样性

为了探明我国华东地区地方鸡品种的遗传多样性和群体遗传结构,追溯其母系起源和进化过程,利用PCR技术扩增了11个地方鸡品种的线粒体DNA(mtDNA)控制区(D-loop)序列,并结合NCBI数据库中已发表的红色原鸡(Gallus gallus)D-loop区全序列,分析了它们的遗传多样性与亲缘关系,构建了11个品种与红色原鸡系统发生邻接树。结果表明:11个地方品种mtDNA D-loop区全长为1,231或1,232 bp,其中1,231 bp的序列有196条,1,232 bp的序列有123条,经过比对发现,两者在859 bp处存在单碱基缺失。11个地方品种319个个体共计检测到变异位点37个,总体单倍型多样度核苷酸多样度和平均核苷酸差异分别为0.901±0.009、0.00573±0.000001和6.833。按照鸡mtDNA单倍型分类通用标准,共包含35种单倍型,可以分为A、B、C和E共4个分支(单倍型群),分别包括11、10、9和5个单倍型。中介网络图中11个鸡品种也很明显地分成了4个支系,分别含有100、118、47和54条序列。系统发育树分为4个大枝,海南亚种(G.gallus jabouillei)自成一枝;C单倍型群与4个亚种的红色原鸡聚为一枝;E单倍型群与2个亚种红色原鸡聚为一枝;A和B单倍型群只与滇南亚种(G.gallus spadiceus)聚为一枝。11个品种中,除了狼山和丝羽乌骨鸡2个标准化品种外,都有很高的遗传多样性,可开发选择潜力很大。没有发现线粒体品种特异性DNA序列。华东地区地方品种至少有4个母系起源,部分品种可能受到了欧美高产品系的渗入。     

红色原鸡和中国家鸡遗传多样性及亲缘关系

对红色原鸡（Gallus gallus）和中国家鸡（Gallus domesticus）之间的遗传多样性和亲缘关系进行系统分析,可以为中国家鸡的起源进化、种质资源保护以及科学开发利用等研究提供理论依据,但迄今尚未见用微卫星标记进行分析比较的公开报道．本研究利用29对微卫星引物对红色原鸡Gallus gallus spadiceus亚种和Gallus gallus gallus亚种以及14个中国家鸡品种的568只个体进行扫描,共检测到286个等位基因,平均值为9．86±6．36;所有群体的期望杂合度为0．6708±0．0251,皖南三黄鸡的期望杂合度最高（0．6442）,固始鸡的最低（0．4532）．单个位点偏离Hardy-Weinberg平衡的群体数从0-7不等．整个群体平均遗传分化为17．9％（P〈0．001）,约有16．7％的遗传变异源自群体间的差异,所有的位点都极显著地贡献于这一结果（P〈0．001）;杂合子缺失的水平很高,为0．015（P〈0．01）,有8个位点显示显著的杂合子缺失．群体间的Reynolds’遗传距离从0．036（萧山鸡-鹿苑鸡）～0．371（泰国红色原鸡-河南斗鸡）不等,而Nm值变异范围为从0．583（泰国红色原鸡-河南斗鸡）～5．833（萧山鸡鹿苑鸡）．NJ系统发生树中,鹿苑鸡、萧山鸡、北京油鸡、河南斗鸡、淮南麻黄鸡、狼山鸡等重体型的鸡种首先形成一大类;鹿苑鸡与萧山鸡以及茶花鸡与藏鸡有着较近的遗传关系;茶花鸡和藏鸡与两个红色原鸡亚种亲缘关系较近,中国红色原鸡Gallus gallus spadiceus亚种与所有中国家鸡品种的亲缘关系比泰国红色原鸡Gallus gallus gallus亚种要近．结果表明：29个微卫星位点均具有较高的多态性,红色原鸡和中国家鸡群体间存在着极显著的遗传分化;中国家鸡和红色原鸡两个亚种的亲缘关系从近到远的排序是：进化型品种-原始型品种（茶花鸡与藏鸡）-中国红色原鸡亚种（Gallus gallus spadiceus）-     

中国地方品种鸡白细胞介素2基因的克隆及遗传进化分析(英)

鸡白细胞介素 2 (chIL 2 )是近年来新发现的一类细胞因子 .根据Sundick等发表的鸡IL 2基因序列设计一对特异性引物 ,从ConA体外激活的脾淋巴细胞中提取mRNA ,通过RT PCR方法分别扩增和克隆了我国仙居鸡、丝羽乌骨鸡两个地方品种和艾维茵商品肉鸡IL 2cDNA .仙居鸡、丝羽乌骨鸡和艾维茵商品肉鸡IL 2基因的编码区均由 42 9nt组成 ,编码一个由 143个氨基酸组成的前体蛋白 .基因 5′端含有 17个核苷酸 ,3′端含有 2 85个核苷酸组成的非编码区 ,3′ UTR中含有 5个重复的“ATTTA”序列 .编码蛋白氨基酸与来自GenBank的Kestrel、Obese和SC品系的来杭鸡比较 ,氨基酸的突变主要发生在 2 8～ 3 2位 .而这一区域仙居鸡和丝羽乌骨鸡的编码氨基酸序列与Kestrel来杭鸡相同 ,艾维茵商品肉鸡与Obese和SC来杭鸡相同 .基因系统进化树分析表明 ,仙居鸡、丝羽乌骨鸡和Kestrel来杭鸡具有很近的亲缘关系 ,艾维茵商品肉鸡与Obese和SC来杭鸡具有很近的亲缘关系 .中国的药用鸡品种———丝羽乌骨鸡在非常保守的 13 3位发生了氨基酸突变     

利用线粒体COI基因揭示中国乌骨鸡遗传多样性和群体遗传结构

全面了解中国乌骨鸡的遗传背景有利于保护和开发利用其种质资源。本研究测定了中国12个乌骨鸡品种线粒体细胞色素c氧化酶亚基I (cytochrome c oxidase subunit I, COI)基因, 比较分析其遗传多样性和群体遗传结构。255份乌骨鸡样品共检测到22个变异位点, 占分析位点的3.17%; 核苷酸多样性为0.00142-0.00339, 单倍型多样性为0.380-0.757, 其中略阳乌鸡核苷酸多样性最高, 德化黑鸡最低。检测到7个氨基酸变异位点, 来自6个品种共11个个体。定义了24种单倍型, 其中单倍型H1和H3为12个乌骨鸡品种共享, 出现频率分别为115次和64次; 盐津乌骨鸡单倍型数最多, 广西乌鸡最少。中性检验与错配分析显示实验种群未经历显著的群体扩张事件。分子变异分析显示81.06%的变异来自群体内; 品种间遗传距离为0.002-0.004, 品种间遗传分化系数F_st值为-0.035至0.594, 雪峰乌骨鸡与其他种群间的遗传分化程度最高。邻接树显示, 乌骨鸡未能独立形成分支, 不能从家鸡和红原鸡中有效区分开来。中国乌骨鸡中介网络图将24个单倍型分为3条进化主支, 呈现出一定的品种特异性, 由无量山乌骨鸡、云南盐津乌骨鸡和雪峰乌骨鸡组成单倍型H8、H9、H11、H12游离于这3条进化主支之外。增加其他家鸡和红原鸡COI基因的中介网络图主体结构与中国乌骨鸡的相同。结果表明中国乌骨鸡品种遗传多样性较低, 但品种间遗传分化显著, 可能是从当地家鸡中选育而来, 需要加强种质资源的保护。     

藏鸡和两种低地鸡线粒体全基因组序列 的测定和比对

藏鸡生活在青藏高原, 它对高原低氧具有一定的遗传适应能力. 丝羽乌骨鸡和寿光鸡都是低地鸡种, 缺乏对低氧环境的遗传适应能力. 鸡的线粒体基因组总长16785 bp, 共编码37个基因, 这些基因的编码产物均与线粒体的呼吸作用和氧化磷酸化相关, 它们的突变均有可能影响线粒体的功能, 因此均可被选为藏鸡低氧遗传适应的候选基因. 测定比较藏鸡和低地鸡的线粒体基因组, 可以为进一步研究藏鸡的低氧遗传适应机理提供线索. 本研究测定和比较了藏鸡、丝羽乌骨鸡和寿光鸡的线粒体全基因组序列, 发现藏鸡线粒体基因组总长为16784~16786 bp, 丝羽乌骨鸡为16785 bp, 寿光鸡为16784 bp; 比对后共发现突变(包括单核苷酸多态性(SNP)、单碱基缺失和插入)120个, 其中tRNA基因突变4个, rRNA基因突变10个, D-LOOP区突变39个, 基因间隔区突变1个, 编码蛋白质亚基的碱基突变66个(包括同义突变48个, 错义突变18个).     

藏鸡和两种低地鸡线粒体全基因组序列 的测定和比对

藏鸡生活在青藏高原, 它对高原低氧具有一定的遗传适应能力. 丝羽乌骨鸡和寿光鸡都是低地鸡种, 缺乏对低氧环境的遗传适应能力. 鸡的线粒体基因组总长16785 bp, 共编码37个基因, 这些基因的编码产物均与线粒体的呼吸作用和氧化磷酸化相关, 它们的突变均有可能影响线粒体的功能, 因此均可被选为藏鸡低氧遗传适应的候选基因. 测定比较藏鸡和低地鸡的线粒体基因组, 可以为进一步研究藏鸡的低氧遗传适应机理提供线索. 本研究测定和比较了藏鸡、丝羽乌骨鸡和寿光鸡的线粒体全基因组序列, 发现藏鸡线粒体基因组总长为16784~16786 bp, 丝羽乌骨鸡为16785 bp, 寿光鸡为16784 bp; 比对后共发现突变(包括单核苷酸多态性(SNP)、单碱基缺失和插入)120个, 其中tRNA基因突变4个, rRNA基因突变10个, D-LOOP区突变39个, 基因间隔区突变1个, 编码蛋白质亚基的碱基突变66个(包括同义突变48个, 错义突变18个).     

Genetic diversity of Vietnamese domestic chicken populations as decision‐making support for conservation strategies

The aims of this study were to assess the genetic diversity of 17 populations of Vietnamese local chickens (VNN) and one Red Jungle Fowl population, together with six chicken populations of Chinese origin (CNO), and to provide priorities supporting the conservation of genetic resources using 20 microsatellites. Consequently, the VNN populations exhibited a higher diversity than did CNO populations in terms of number of alleles but showed a slightly lower observed heterozygosity. The VNN populations showed in total seven private alleles, whereas no CNO private alleles were found. The expected heterozygosity of 0.576 in the VNN populations was higher than the observed heterozygosity of 0.490, leading to heterozygote deficiency within populations. This issue could be partly explained by the Wahlund effect due to fragmentation of several populations between chicken flocks. Molecular analysis of variance showed that most of genetic variation was found within VNN populations. The Bayesian clustering analysis showed that VNN and CNO chickens were separated into two distinct groups with little evidence for gene flow between them. Among the 24 populations, 13 were successfully assigned to their own cluster, whereas the structuring was not clear for the remaining 11 chicken populations. The contributions of 24 populations to the total genetic diversity were mostly consistent across two approaches, taking into account the within‐ and between‐populations genetic diversity and allelic richness. The black H'mong, Lien Minh, Luong Phuong and Red Jungle Fowl were ranked with the highest priorities for conservation according to Caballero and Toro's and Petit's approaches. In conclusion, a national strategy needs to be set up for Vietnamese chicken populations, with three main components: conservation of high‐priority breeds, within‐breed management with animal exchanges between flocks to avoid Wahlund effect and monitoring of inbreeding rate.     

红原鸡与家鸡的亲缘关系研究

对中国红原鸡滇地亚种和海南亚种与我国茶花鸡,泰和鸡和寿光鸡等地方鸡种以及芦花鸡,洛岛红等外国鸡种进行了血型（３个位点,１３个等位基因）,蛋白质（酶）多态（５个位点,１１个等位基因）和ＤＮＡ指纹分析,结果表明,红原鸡与茶花鸡（原始型品种）的亲缘关系较近;与泰和鸡,寿光鸡,芦花鸡,洛岛红（进化型品种）的亲缘关系较远,呈红原鸡－茶花鸡－泰和鸡,寿光鸡或芦花鸡,洛岛红这样一个进化阶梯,以上结果与国外资料（     

红色原鸡群体遗传多样性

为了阐明红色原鸡的群体遗传结构,以对其有效保护提供遗传学依据,采用33个微卫星标记对其群体中56个个体进行了PCR-聚丙烯酰胺多态性电泳检测。33个微卫星座位共检测到140个等位基因,所有座位都呈现出多态性,每个座位的等位基因数在2～8个之间,平均每个座位等位基因数4.24个,有效等位基因数3.30个。根据等位基因频率,计算出的群体表观杂合度、期望杂合度及多态信息含量分别为0.7980、0.6506和0.5948。结果表明,红色原鸡群体遗传多样性较丰富。     

Genetic diversity within chicken populations from different continents and management histories

Intra-population variation was assessed in 1970 chickens from 64 populations using 29 autosomal microsatellites. On average, 95% of the loci were polymorphic across populations. In 1456 ( c. 83%) of the 1763 combinations of populations and polymorphic loci, no departure from Hardy–Weinberg equilibrium was observed. On average, there were 11.4 alleles per locus and 3.6 alleles per population across loci. Within populations, the average observed heterozygote frequency was 0.46, with a range between 0.20 and 0.64. Dagu, a Chinese population, and the Red Jungle Fowl ( Gallus gallus gallus ) had the highest average heterozygote frequencies at 0.64 and 0.63 respectively. An inbred line used as a reference population for comparison showed the lowest average of observed heterozygote frequency (0.05), followed by the European population Hamburger Lackhuhn, whose average observed heterozygote frequency was 0.20. A total of 32 private alleles (alleles detected in only one population) for 20 loci were found in 18 populations. H'mong chickens, a Vietnamese population, carried the largest number of private alleles at five, followed by the Red Jungle Fowl with four private alleles. Genetic diversity within populations was low in the NW European fancy breeds and high in the non-commercial Asian populations, in agreement with population management history.     

Genetic characterization of biodiversity in highly inbred chicken lines by microsatellite markers

Forty-two microsatellite loci were analysed in 23 highly inbred chicken lines derived from Leghorn, Jungle Fowl, Fayoumi and Spanish breeds. Line-specific alleles among breeds and lines were detected. The band-sharing (BS) values were calculated and the proportion of shared alleles distances (Dps) were estimated. The BS values and Dps between sets of MHC-congenic lines ranged from 0.74 to 0.96, and 0.05-0.35, respectively. The BS values between each pair of noncongenic Leghorn lines were 0.32-0.97, and between Leghorn and exotic (Jungle Fowl, Fayoumi and Spanish) breeds were 0.03-0.55. The Dps between Fayoumi lines and other lines were much larger (0.66-1.34) than within Leghorns, and the Jungle Fowl breed had the largest distances with other lines (1.12-5.38). The phylogenetic consensus tree that was constructed grouped these 23 inbred chicken lines into four different clusters. These results are in accordance with the origin and breeding history of these inbred lines, which indicates that the use of microsatellites for the study of genetic biodiversity is accurate and reliable. In addition, the significance and value of inbred chicken lines in molecular genetic research is discussed.     

High genetic diversity and no inbreeding in the endangered copper redhorse, Moxostoma hubbsi (Catostomidae, Pisces): the positive sides of a long generation time

The evolutionary potential of a species is determined by its genetic diversity. Thus, management plans should integrate genetic concerns into active conservation efforts. The copper redhorse (Moxostoma hubbsi) is an endangered species, with an endemic distribution limited to the Richelieu River and a short section of the St Lawrence River in Quebec, Canada. The population, gradually fragmented since 1849, is characterized by a decline in population size and a lack of recruitment. A total of 269 samples were collected between 1984 and 2004 and genotyped using 22 microsatellite loci, which indicated that these fish comprise a single population, with a global F(ST) value of only 0.0038. Despite a small census size ( approximately 500), a high degree of genetic diversity was observed compared to common values for freshwater fishes (average number of 12.5 alleles/locus and average HO of 0.77 +/- 0.08). No difference was observed between expected and observed pairwise values of relatedness (r(xy): -0.00013 +/- 0.11737), suggesting an outbred population. Long-term Ne was estimated at 4476 whereas contemporary Ne values ranged from 107 to 568, suggesting a pronounced yet gradual demographic decline of the population, as no bottleneck could be detected for the recent past. By means of simulations, we estimated Ne would need to remain at more than approximately 400 to retain 90% of the genetic diversity over 100 years. Overall, these observations corroborate other recent empirical studies confirming that long generation times may act as a buffering effect contributing to a reduction in the pace of genetic diversity erosion in threatened species.     

The Effect of a Mutation in the Thyroid Stimulating Hormone Receptor (TSHR) on Development,Behaviour and TH Levels in Domesticated Chickens

The thyroid stimulating hormone receptor (TSHR) has been suggested to be a “domestication locus” in the chicken, due to a strong selective sweep over the gene found in domesticated chickens, differentiating them from their wild ancestor the Red Junglefowl (RJF). We investigated the effect of the mutation on development (incubation time), behaviour and thyroid hormone levels in intercross chickens homozygous for the mutation (d/d), wild type homozygotes (w/w) or heterozygotes (d/w). This allowed an assessment of the effect of genotype at this locus against a random mix of RJF and WL genotypes throughout the rest of the genome, controlling for family effects. The d/d genotype showed a longer incubation time, less fearful behaviours, lower number of aggressive behaviours and decreased levels of the thyroid hormone T4, in comparison to the w/w genotype. The difference between TSHR genotypes (d/d vs. w/w) in these respects mirrors the differences in development and behaviour between pure domesticated White Leghorns and pure RJF chickens. Higher individual T3 and T4 levels were associated with more aggression. Our study indicates that the TSHR mutation affects typical domestication traits, possibly through modifying plasma levels of thyroid hormones, and may therefore have been important during the evolution of the domestic chicken.     

藏鸡群体遗传多样性研究

藏鸡的体型外貌和生活习性与红色原鸡非常相似,是具有自己独特群体遗传特性的高原地方鸡种。为了有效保护并合理利用这一遗传资源,我们采用多重PCR与半自动荧光标记微卫星聚丙烯酰胺凝胶电泳相结合的方法检测了20个微卫星基因座的多态性,并随机抽取藏鸡群体中部分个体进行个体体形特征与生产性能的统计。结果表明藏鸡群体的20个微卫星基因座的多态等位基因数为4~10个,平均值为7.25个/基因座,多态信息含量（CPI）和杂合度（H）平均值分别为0.67、0.74。大染色体较小染色体的微卫星标记多态性程度要高。藏鸡群体的微卫星基因座多态性丰富,也解释了生产性能不均,外貌表现迥异的群体遗传特性。 Abstract: Morphological traits and living habit of Tibetan chicken, which is an aboriginal chicken breed on plateau with its own characteristic populational genetic features, are in great common with the Red Jungle Fowl, the assumed ancestry of domestic chicken. To fully exploit this chicken resource, Multiplex PCR with semi-automated polyacrilamide gel electrophoresis (PAGE) using fluorescently labeled microsatellite primers was used to detect the polymorphism at 20 microsatellite loci. At the same time, we randomly test the individual morphology and performance. It showed that numbers of polymorphic alleles were 4-10, with mean value 7.25 per locus. Polymorphism Information Content (CPI) and Heterozygosity (H) had mean values 0.67 and 0.74, respectively. Macrochromosomes had relatively higher polymorphism than microchromosomes(P>0.05). In all, high polymorphisms at microsatellite loci related to the uneven production performance and morphological discrepancy of population genetic characteristics in Tibetan chicken.     

Genetic Diversity and Population Structure Analysis Between Indian Red Jungle Fowl and Domestic Chicken Using Microsatellite Markers

The present study was conducted to assess the genetic diversity, population structure, and relatedness in Indian red jungle fowl (RJF, Gallus gallus murgi) from northern India and three domestic chicken populations (gallus gallus domesticus), maintained at the institute farms, namely White Leghorn (WL), Aseel (AS) and Red Cornish (RC) using 25 microsatellite markers. All the markers were polymorphic, the number of alleles at each locus ranged from five (MCW0111) to forty-three (LEI0212) with an average number of 19 alleles per locus. Across all loci, the mean expected heterozygosity and polymorphic information content were 0.883 and 0.872, respectively. Population-specific alleles were found in each population. A UPGMA dendrogram based on shared allele distances clearly revealed two major clusters among the four populations; cluster I had genotypes from RJF and WL whereas cluster II had AS and RC genotypes. Furthermore, the estimation of population structure was performed to understand how genetic variation is partitioned within and among populations. The maximum ?K value was observed for K = 4 with four identified clusters. Furthermore, factorial analysis clearly showed four clustering; each cluster represented the four types of population used in the study. These results clearly, demonstrate the potential of microsatellite markers in elucidating the genetic diversity, relationships, and population structure analysis in RJF and domestic chicken populations.