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。     

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（     

Biodiversity of 52 chicken populations assessed by microsatellite typing of DNA pools

In a project on the biodiversity of chickens funded by the European Commission (EC), eight laboratories collaborated to assess the genetic variation within and between 52 populations from a wide range of chicken types. Twenty-two di-nucleotide microsatellite markers were used to genotype DNA pools of 50 birds from each population. The polymorphism measures for the average, the least polymorphic population (inbred C line) and the most polymorphic population (Gallus gallus spadiceus) were, respectively, as follows: number of alleles per locus, per population: 3.5, 1.3 and 5.2; average gene diversity across markers: 0.47, 0.05 and 0.64; and proportion of polymorphic markers: 0.91, 0.25 and 1.0. These were in good agreement with the breeding history of the populations. For instance, unselected populations were found to be more polymorphic than selected breeds such as layers. Thus DNA pools are effective in the preliminary assessment of genetic variation of populations and markers. Mean genetic distance indicates the extent to which a given population shares its genetic diversity with that of the whole tested gene pool and is a useful criterion for conservation of diversity. The distribution of population-specific (private) alleles and the amount of genetic variation shared among populations supports the hypothesis that the red jungle fowl is the main progenitor of the domesticated chicken.     

Genetic structure of a wide-spectrum chicken gene pool

The genetic structure of 65 chicken populations was studied using 29 simple sequence repeat loci. Six main clusters which corresponded to geographical origins and histories were identified: Brown Egg Layers; predominantly Broilers; native Chinese breeds or breeds with recent Asian origin; predominantly breeds of European derivation; a small cluster containing populations with no common history and populations that had breeding history with White Leghorn. Another group of populations that shared their genome with several clusters was defined as 'Multi-clusters'. Gallus gallus gallus (Multi-clusters), one of the subspecies of the Red Jungle Fowl, which was previously suggested to be one of the ancestors of the domesticated chicken, has almost no shared loci with European and White Egg layer populations. In a further sub-clustering of the populations, discrimination between all the 65 populations was possible, and relationships between each were suggested. The genetic variation between populations was found to account for about 34% of the total genetic variation, 11% of the variation being between clusters and 23% being between populations within clusters. The suggested clusters may assist in future studies of genetic aspects of the chicken gene pool.     

Genetic characterization of Bhutanese native chickens based on an analysis of Red Junglefowl (Gallus gallus gallus and Gallus gallus spadecieus), domestic Southeast Asian and commercial chicken lines (Gallus gallus domesticus)

The genetic diversity of Bhutanese chickens needs to be understood in order to develop a suitable conservation strategy for these birds in Bhutan. In this, work, we used microsatellite markers to examine the genetic diversity of Bhutanese chickens. Four Bhutanese chicken varieties (Black plumage, Frizzle, Naked neck and Red Junglefowl-like, corresponding to Yuebjha Narp, Phulom, Khuilay and Seim, respectively), two subspecies of Red Junglefowl (Gallus gallus gallus and Gallus gallus spadecieus), two varieties of Thai native chickens (Pradhu Hang Dam and Chee; Gallus gallus domesticus) representing the Southeast Asian domestic chicken, and two commercial lines (Broiler and Single Comb White Leghorn) were genotyped with 18 microsatellites that included 16 loci recommended by the FAO/ISAG for investigations of genetic variability in chickens. All loci were polymorphic, with the number of alleles ranging from six (MCW0111) to 23 (MCW0183). Substantial genetic variation was observed in all populations, with the Bhutanese native chicken Yuebjha Narp (Black plumage chicken) showing the lowest genetic variability. Despite extensive intrapopulation variation, the genetic differentiation among 10 populations was moderate. A neighbor-joining tree revealed the genetic relationships involved while principal component analysis showed that Bhutanese native chickens should be given priority in conservation efforts because of their genetic distinctiveness. Chee chickens are especially valuable as a reservoir of predomestic diversity, as indicated by their greater genetic variation and their position in the phylogenetic tree.     

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.     

Genetic variation within and between populations of hermaphroditic <Emphasis Type="Italic">Bulinus truncatus</Emphasis> tetraploid freshwater snails of the Albertine Rift,East Africa

Genetic variability within and among Bulinus truncatus of the Albertine Rift freshwater bodies were assessed to investigate the degree of inbreeding and gene flow in the snail populations. The effect of ploidy on the genetic structuring of B. truncatus is also described. We characterized the genetic structure of seven B. truncatus populations from Lake Albert, Lake Kivu, and Katosho swamp in Tanzania using five polymorphic microsatellite loci. Genetic differentiation was quantified using pairwise FST values and Nei’s standard genetic distances. Different alleles were observed across all loci and genetic diversity was low although it varied greatly across populations; observed heterozygosity was, however, higher than the expected heterozygosity in three of the populations studied. Significant heterozygote deficiencies were observed coupled with significant linkage disequilibria in five populations for all the five loci examined in this study. We found significant genetic differentiation among the seven freshwater bodies; private alleles were observed across all loci indicating restricted or absence of gene flow between populations. Limited snail dispersal and the reproductive biology of B. truncatus are the major forces shaping the genetic variation observed. Low genetic variation within B. truncatus populations exposes them to a high parasite infection risk as predicted in the Red Queen hypothesis.     

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.     

Microsatellite loci in the house fly,Musca domestica L. (Diptera: Muscidae)

Genomic libraries from house flies enriched for (CA)₁₅ and (CAG)₁₀ repeats were constructed by using biotinylated probes. Twenty‐five loci were isolated and evaluated for polymorphisms in wild flies representing two geographically diverse populations. Fourteen of 19 dinucleotide loci, and one of six trinucleotide loci were polymorphic. One hundred and twenty‐seven alleles were detected, 39 of which were private. Average number of alleles per polymorphic locus was 8.4 ± 2.5 and average heterozygosity was 72 ± 4%. F_ST by the private allele method was 0.73. Three of 15 loci showed significant heterozygote deficiencies, attributed to null alleles. Five of 15 loci were amplified in the face fly, Musca autumnalis.     

菲律宾蛤仔EST-SSRs标记开发及不同地理群体遗传多样性

利用13对微卫星引物对大连、莆田、青岛3个地理群体蛤仔遗传多样性进行了检测。结果表明:13个基因座共检测到154个等位基因,每个座位检测到的等位基因数在2-7个之间,平均有效等位基因数为2.7657;3个群体平均观测杂合度分别为0.4387、0.4194、0.2383,平均期望杂合度分别为0.6488、0.6484、0.5526;群体间的遗传多样性差异不显著(P＞0.05)。NJ聚类结果显示大连和莆田群体的蛤仔亲缘关系较近,二者与青岛群体关系较远。3个群体均有不同程度的偏离Hardy-Weinberg平衡现象,表明各群体基因频率和基因型频率的稳定性相对较低。本研究所获得的微卫星标记的多态信息含量(PIC)>0.5,说明这些微卫星位点的多样性较高,可为下一步遗传图谱构建研究提供参考。     

原鸡海南亚种的巢址特征

选择适宜的巢址对降低巢捕食风险,提高繁殖成效有重要意义。2008年3—7月,在海南省大田国家级自然保护区,采用随机样线法结合访问法在各种生境类型中系统地寻找原鸡海南亚种(Gallus gallus jabouillei)的巢,并在野外追踪观察基础上用样方法对原鸡的巢址选择进行研究。共记录到原鸡的巢16个,以巢为中心选取样方并测量反映巢址的13个特征生境参数,同时分析16个对照样方以进行比较,并通过主成分分析探讨影响巢址选择的主导因子。结果表明:(1)原鸡的巢位于密集的丛生草本下或低矮的灌木丛基部。营巢背景多样,其中位于草本植物下10个(62.5%);灌草丛5个(31.3%);灌木下1个(6.25%)。(2)Mann–WhitneyU检验的结果显示,原鸡偏好于比较开阔、地面落叶稀少而靠近的小道和林缘的位置营巢。(3)主成分分析表明,植被盖度因子和空间位置因子贡献率最大,在降低巢捕食风险中有重要价值,是影响原鸡巢址选择的主要因素。     

原鸡海南亚种的巢址特征

选择适宜的巢址对降低巢捕食风险,提高繁殖成效有重要意义。2008年3—7月,在海南省大田国家级自然保护区,采用随机样线法结合访问法在各种生境类型中系统地寻找原鸡海南亚种(Gallus gallus jabouillei)的巢,并在野外追踪观察基础上用样方法对原鸡的巢址选择进行研究。共记录到原鸡的巢16个,以巢为中心选取样方并测量反映巢址的13个特征生境参数,同时分析16个对照样方以进行比较,并通过主成分分析探讨影响巢址选择的主导因子。结果表明：（1) 原鸡的巢位于密集的丛生草本下或低矮的灌木丛基部。营巢背景多样,其中位于草本植物下10个(62.5%);灌草丛5个(31.3%);灌木下1个(6.25%)。（2) Mann–Whitney U检验的结果显示,原鸡偏好于比较开阔、地面落叶稀少而靠近的小道和林缘的位置营巢。（3) 主成分分析表明,植被盖度因子和空间位置因子贡献率最大,在降低巢捕食风险中有重要价值,是影响原鸡巢址选择的主要因素。     

Isolation and characterization of microsatellite markers from the limpet Cellana grata

This note describes the development of nine polymorphic microsatellite loci in the limpet Cellana grata to investigate population structure and cohort variation in this species. The number of alleles ranged from seven to 22 and observed heterozygosity ranged from 0.62 to 0.95. Deviation from the Hardy-Weinberg equilibrium was detected in two loci, both as a result of heterozygote deficiency. Null alleles were detected in one of these loci. These genetic markers will be used to investigate the genetic structure of C. grata populations, as well as variation among cohorts of this common intertidal species.     

鸡SNP多样性的比较研究与群体有效规模的估算

以红色原鸡(Red Jungle Fowl, RJF)、丝羽乌骨鸡(Taihe silk Chicken, TS)、隐性白洛克鸡(White Recessive Rock, WRR)为资源群, 在鸡一号染色体的Contig.060226.1上选取了一个200 kb的区域, 比较研究了3个群体的SNP (single nucleotide polymorphism)多样性、估算了鸡的初始群体有效规模大小(effective size of population, Ne)。红色原鸡、丝羽乌骨鸡、隐性白洛克鸡3个群体的平均杂合度分别为0.28533±0.03475、0.32926±0.03919、0.30168±0.04038。显著性检验差异不显著(P=0.2368>0.05)。根据Latter 和Nei的方法对鸡的群体有效规模进行了估算, 鸡的初始群体有效规模大小为20 000～150 000。鸡在驯养的早期阶段经历过严厉的瓶颈效应, 但瓶颈效应对鸡各品种SNP的多样性并未产生显著影响。笔者认为, 鸡在驯养的早期阶段群体有效规模足够大, 品种分化过程中群体迅速扩张, 品种间的广泛杂交(特别是和红色原鸡之间)以及鸡基因组的高重组率等因素是导致家鸡和原鸡以及各家鸡品种间SNP多样性没有显著差别的重要原因。     

Temporal genetic variation in a population of the pocket gopher,Geomys bursarius

Genetic variation at eight polymorphic loci was examined in a population of a subterranean rodent, the plains pocket gopher (Geomys bursarius), sampled over a 10-yr period. Two loci exhibited relatively minor changes in gene frequencies, while the remaining loci demonstrated major shifts in predominant alleles, loss of minor alleles, and addition of alleles due to migration. Significant deviations from Hardy-Weinberg expectations, concomitant to heterozygote deficiencies, were observed for several loci. Temporal heterogeneity, as measured by F_ST, was high and comparable to that exhibited by local populations sampled over relatively short periods of time. The high degree of temporal genetic variation is consistent with observations that fossorial rodents occur in locally isolated populations with small effective population sizes that are subject to genetic drift, bottlenecking, and inbreeding.     

牙鲆微卫星标记的筛选及群体遗传结构分析

采用生物素-磁珠吸附微卫星与质粒二次检测相结合的方法克隆牙鲆微卫星,并利用所得到的引物分析野生群体遗传结构.共获得2805个阳性克隆,测序得到3120个含微卫星的序列.其中完美型、非完美型和混合型分别占57.97%、7.25%和34.78%.用Primer 3.0软件设计牙鲆微卫星引物,从中筛选出具稳定多态性的30对,分析中国黄海、渤海海域4个不同海区牙鲆野生群体(大连、北戴河、丹东、青岛)遗传结构.结果显示:有效等位基因数为3.93～9.94,平均为6.95;观测杂合度为0.532～0.895,平均为0.753;期望杂合度为0.635～0.902,平均为0.820;Hardy-Weinberg平衡指数(d)的变化范围为-0.247～0.512,其中7个位点表现为杂合子过剩(d>0),其余位点表现为杂合子缺失(d>0).聚类分析显示:4个群体聚为两类,大连与丹东聚为一类,北戴河与青岛聚为一类.     

Isolation and characterization of microsatellite loci from the endangered highlands scrub hypericum (Hypericum cumulicola)

We report the isolation of 19 primer pairs for amplification of polymorphic microsatellite loci for Hypericum cumulicola. These markers were evaluated in 24 individuals from one population; two to four alleles were detected per locus, and observed heterozygosity ranged from 0 to 0.5. Two loci demonstrated significant heterozygote deficiencies, possibly due to null alleles, and significant linkage disequilibrium was found between six pairs of loci. The remaining microsatellite loci will help determine if genetic differentiation is responsible for life‐history differences between natural and anthropogenically disturbed populations of H. cumulicola.     

Characterization of the genetic diversity, structure and admixture of British chicken breeds

The characterization of livestock genetic diversity can inform breed conservation initiatives. The genetic diversity and genetic structure were assessed in 685 individual genotypes sampled from 24 British chicken breeds. A total of 239 alleles were found across 30 microsatellite loci with a mean number of 7.97 alleles per locus. The breeds were highly differentiated, with an average F(ST) of 0.25, similar to that of European chicken breeds. The genetic diversity in British chicken breeds was comparable to that found in European chicken breeds, with an average number of alleles per locus of 3.59, ranging from 2.00 in Spanish to 4.40 in Maran, and an average expected heterozygosity of 0.49, ranging from 0.20 in Spanish to 0.62 in Araucana. However, the majority of breeds were not in Hardy-Weinberg Equilibrium, as indicated by heterozygote deficiency in the majority of breeds (average F(IS) of 0.20), with an average observed heterozygote frequency of 0.39, ranging from 0.15 in Spanish to 0.49 in Cochin. Individual-based clustering analyses revealed that most individuals clustered to breed origin. However, genetic subdivisions occurred in several breeds, and this was predominantly associated with flock supplier and occasionally by morphological type. The deficit of heterozygotes was likely owing to a Wahlund effect caused by sampling from different flocks, implying structure within breeds. It is proposed that gene flow amongst flocks within breeds should be enhanced to maintain the current levels of genetic diversity. Additionally, certain breeds had low levels of both genetic diversity and uniqueness. Consideration is required for the conservation and preservation of these potentially vulnerable breeds.