Comparison of casein haplotypes between two geographically distant European dairy goat breeds.

The aim of this paper was to characterize the diversity among haplotypes based on 22 single nucleotide polymorphisms (SNPs) and one deletion within four casein genes in two geographically distant goat populations, the Sicilian Girgentana breed and the Norwegian goat breed. Forty Girgentana goats were genotyped for the aforementioned polymorphisms and the resulting data set was compared with 436 goats from the Norwegian population previously genotyped for these markers. Several casein gene polymorphisms were not in Hardy-Weinberg equilibrium either in Girgentana, or in the Norwegian breed. The SNP haplotype frequencies for the four casein genes were calculated and despite the large geographical distance and phenotypic divergence between these breeds, a proportion of casein loci haplotypes were found to be identical between both Norwegian and Girgentana goats. However, for the CSN2 gene there were no common haplotypes between the two populations. The level of linkage disequilibrium between the casein genes was less in the Girgentana population than in the Norwegian population.     

Segment-based coancestry,additive relationship and genetic variance within and between the Norwegian and the Swedish Fjord horse populations

ABSTRACT

The Fjord horse originates from Norway but forms a global population due to several small populations in foreign countries. There exists no information about the additive relationship and the genetic variance between these subpopulations. By collecting blood samples from Norwegian and Swedish Fjord horses, a sample of 311 Norwegian and 102 Swedish horses gave 485,918 SNPs available for analysis. Their inbreeding coefficients were calculated and compared to the pairwise coancestry and the shared genomic segments. The effective population size was almost similar with the two methods in the Norwegian Fjord horse population (63 and 71), but very different in the Swedish population (269 and 1136) and unprecise due to a much smaller number of observations. The study showed that coancestry from shared genomic segments can be used to estimate additive genetic relationship and genetic variation within and between the global populations of the Fjord horse.     

Genetic diversity of Chinese indigenous goat breeds based on microsatellite markers

Eighteen microsatellites were used to investigate the genetic diversity and differentiation of eight Chinese indigenous goat breeds. The results indicated that there is a significant difference of genetic diversity between different loci. Chinese indigenous goat breeds have similar genetic diversity to other Asian goats, but with lower Fst. The clustering of individuals and populations showed that Chinese indigenous goat breeds might have originated from two ancestral populations. The genetic differentiation between populations is consistent with the results of archaeology, mtDNA and RAPD.     

Geographical variation of skull size and shape in various populations in the black giant squirrel

We osteometrically examined the skulls of the black giant squirrel (Ratufa bicolor) from three mainland populations (M. Malayan Peninsula, V. South Vietnam, and B. Burma, India and North Thailand) and from two island populations (T. Tioman, and S. Sumatra Islands). The skull in the Malayan peninsula population was significantly smaller than that of the two other mainland populations. It is consistent with Bergmann's rule as shown in the gray-bellied squirrel. The two island populations did not show obvious differences in comparison with the Malayan population in many measurements. In the proportion analysis eliminating the size factor, the differences among populations were not easily confirmed and we concluded that the osteological characters peculiar to each population could not be shown in this species. The first and second principal component scores of M, S, and T populations were intermingled, whereas the V and B populations of V and B were not separated in the chart. We pointed out that the morphological differences were demonstrated between northern and southern groups of the Isthmus of Kra in the mainland populations, and that the two island populations did not show the island-isolation effect in comparison with the M population. The adaptational variation related to feeding and locomotion could not be confirmed among populations of the black giant squirrel as shown in the proportion analysis.     

Genetic diversity in Egyptian and Italian goat breeds measured with microsatellite polymorphism.

Seven microsatellite markers were used to study genetic diversity of three Egyptian (Egyptian Baladi, Barki and Zaraibi) and two Italian (Maltese and Montefalcone) goat breeds. The microsatellites showed a high polymorphic information content (PIC) of more than 0.5 in most of the locus-breed combinations and indicated that the loci were useful in assessing within- and between-breed variability of domestic goat (Capra hircus). The expected heterozygosity of the breeds varied from 0.670 to 0.792. In the geographically wider distributed Egyptian Baladi breed there were indications for deviations from random breeding. Analysis of genetic distances and population structure grouped the three Egyptian goat breeds together, and separated them from the two Italian breeds. The studied Mediterranean breeds sampled from African and European populations seem to have differentiated from each other with only little genetic exchange between the geographically isolated populations.     

Factors affecting the breeding success of the African Black Oystercatcher (Haematopus moquini): a perspective on protection and food availability

Breeding success (fledglings pair^?1 y^?1) of the Red-listed African Black Oystercatcher (Haematopus moquini) is highly variable, both spatially and temporally. Despite a diversity of natural factors causing this variability, there is evidence that two anthropogenic factors, i.e. disturbance and an introduced mussel (Mytilus galloprovincialis), are having an impact on the local breeding success of this species. Using a data set comprising 87 site-years of nest-monitoring data across most of the species’ breeding range, we analysed the extent and causes of variability in breeding success. Breeding success differed across three population categories defined by varying levels of human disturbance: island populations, protected mainland populations, and unprotected mainland populations. Differences in breeding success between island populations and protected mainland populations were likely due to differing exposure to predators; however, differences between protected and unprotected mainland populations were unlikely caused by this as both experience equivalent predation levels (although from different predators). Protection only improved the breeding success of oystercatchers in very high-quality habitats (with a high biomass of alien mussels), and where populations were ‘released’ from high levels of human disturbance. In unprotected mainland areas, human activity impacted on the breeding success of local populations primarily through predation of small chicks by uncontrolled dogs, and by rising tides drowning chicks that were hiding from human disturbance. The findings of this study note the potential conservation dilemma resulting from an invasive species improving the conservation status of a Red-listed species, and encourage the implementation of restricted sites in high-quality habitats with high breeding pair densities.     

Microsatellite diversity of the Nordic type of goats in relation to breed conservation: how relevant is pure ancestry?

In the last decades, several endangered breeds of livestock species have been re‐established effectively. However, the successful revival of the Dutch and Danish Landrace goats involved crossing with exotic breeds and the ancestry of the current populations is therefore not clear. We have generated genotypes for 27 FAO‐recommended microsatellites of these landraces and three phenotypically similar Nordic‐type landraces and compared these breeds with central European, Mediterranean and south‐west Asian goats. We found decreasing levels of genetic diversity with increasing distance from the south‐west Asian domestication site with a south‐east‐to‐north‐west cline that is clearly steeper than the Mediterranean east‐to‐west cline. In terms of genetic diversity, the Dutch Landrace comes next to the isolated Icelandic breed, which has an extremely low diversity. The Norwegian coastal goat and the Finnish and Icelandic landraces are clearly related. It appears that by a combination of mixed origin and a population bottleneck, the Dutch and Danish Land‐races are separated from the other breeds. However, the current Dutch and Danish populations with the multicoloured and long‐horned appearance effectively substitute for the original breed, illustrating that for conservation of cultural heritage, the phenotype of a breed is more relevant than pure ancestry and the genetic diversity of the original breed. More in general, we propose that for conservation, the retention of genetic diversity of an original breed and of the visual phenotype by which the breed is recognized and defined needs to be considered separately.     

世界及我国奶山羊产业发展现状及趋势分析

近年来,世界山羊养殖数量持续增长,据联合国粮农组织(FAO)统计显示,2018年全球山羊养殖数量已超10.4亿只,其中奶山羊养殖数量超2.16亿只,约有90%以上的奶山羊和山羊奶产自亚洲和非洲。欧洲的奶山羊存栏和产奶量均在亚洲和非洲之后,但其单产水平远高于其他各大洲,在世界奶山羊每只平均年产奶量100 kg以上的国家中,前十位均为欧洲国家。我国奶山羊产业发展迅速,2018年我国奶山羊实际存栏约518万只,年产羊奶量约100万t,约占全国鲜奶产量的3.3%。本文对全球及我国奶山羊产业进行了纵向和横向比较,客观分析我国奶山羊产业的地位、发展现状以及未来发展趋势,旨在为我国奶山羊产业的发展提供参考。     

长江中下游以及东南沿海的7个山羊群体的遗传多样性分析

利用23个微卫星标记对宜昌白山羊、马头山羊、湘东黑山羊、福清山羊、戴云山羊、黄淮山羊、长江三角洲白山羊等7个山羊群体进行了遗传多样性检测,结果显示:23个基因座中21个座位在所有群体中都具有多态性,基因座BM0203在各个群体中分别为纯合基因座,但存在群体间变异,基因座BM6444在湘东黑山羊、宜昌白山羊群体中为单态,但在其他群体都存在多个等位基因。总群体基因杂合度为0.819 0,7个群体PIC平均值在0.630 5~0.691 9之间。根据Nei氏遗传距离用UPGMA方法对7个群体进行亲缘关系聚类,马头山羊和湘东黑山羊首先聚为一类,福清山羊、戴云山羊、长江三角洲白山羊、黄淮山羊再和前者依次聚类,最后,宜昌白山羊和它们整个聚为一类。     

江苏地方山羊品种H-FABP基因的SNPs检测及群体遗传学分析

采用PCR-SSCP和DNA测序技术对2个江苏地方山羊品种的心脏型脂肪酸结合蛋白(heart fatty acid binding protein,H-FABP)基因进行单核苷酸多态性(SNP)检测和群体遗传学分析。结果表明,在所扩增的片段中,仅在H-FABP基因外显子2的第132位检测到G/C碱基突变,形成GG和GC基因型,2个山羊群体均是纯合GG基因型占主导优势,且该位点处于Hardy-Weinberg平衡状态;黄淮山羊群体的杂合度、有效等位基因数和多态信息含量指标均高于长江三角洲白山羊群体,表明其群体内的遗传变异程度相对较大、遗传多样性也更为丰富。     

Genomic differentiation with isolation by distance along a latitudinal gradient in the spotted-leg treefrog Polypedates megacephalus

The patterns of isolation by distance (IBD) entailing increased genetic differentiation among populations have aroused extensive concerns for evolutionary biologists. Although the IBD may act on spatial processes contributing to the genetic differentiation among populations in anuran species, the factors shaping the IBD of frogs among populations in natural systems are largely unknown. Here, we studied the genetic differentiation among six populations with 24 individuals of the spotted-leg treefrog along a latitudinal gradient (1860.31 km) based on 1020 single nucleotide polymorphisms from restriction site-associated DNA sequencing. The results showed that the genetic diversity differed significantly among populations and that the insular populations had higher genetic diversity than the mainland populations. Furthermore, we also found a significant genetic differentiation among populations (F_ST = 0.277) and no sign of inbreeding (F_UNI = −0.145). The IBD was detected for all populations, and a higher degree of the IBD was indicated when controlling for the effects of the isolation between Hainan and mainland populations caused by the Qiongzhou Strait. Our findings suggest that the form of the Qiongzhou Strait plays a key role in shaping the genetic diversity and population differentiation in treefrogs.     

攀西黑山羊群体的AFLP遗传多样性研究

 研究采用随机片段长度多态性分析了攀西地区的5个黑山羊品种（类群）的遗传多样性。结果表明：15对引物共扩增出1003条多态条带,多态频率平均为99.01%,5个黑山羊群体的遗传多样性指数变异范围为0.0136~0.2131,其中建昌黑山羊平均遗传多样性指数最高（0.1346）,攀枝花黑山羊次之（0.1329）,乐至黑山羊最低（0.1101）。5个群体遗传距离范围为0.0062~0.0281,攀枝花黑山羊与建昌黑山羊之间的遗传距离最小（DR=0.0062）,云岭黑山羊与攀枝花黑山羊之间的遗传距离次之（DR=0.0128）,乐至黑山羊与金堂黑山羊间遗传距离最大（DR=0.0281）,金堂黑山羊与其它4个类群遗传距离较大（DR=0.0173-0.0281）,说明攀枝花黑山羊与建昌黑山羊的亲缘关系最近,与云岭黑山羊的亲缘关系较近,乐至黑山羊与金堂黑山羊的亲缘关系最远,金堂黑山羊与其它4个类群遗传距离均比较远。聚类结果与群体地理分布、生态条件差异情况基本一致。     

山羊乳中上皮黏蛋白MUC1遗传多态性与产羔数的相关性研究

采用SDS-PAGE法分析9个山羊群体乳中上皮黏蛋白MUC1遗传多态性,并通过构建的线性模型,采用最小二乘法分析乳MUC1位点遗传多态性与产羔数的相关性。结果表明:(1)9个山羊群体中,乳MUC1在SDS-PAGE上均呈现出了丰富的遗传多态性,表现为1条或2条迁移率不同的区带,317个个体共检测到7个不同分子质量的MUC1区带,分别代表A、B、C、D、E、F、G7个等位基因,共有17种基因型。(2)乳MUC1位点对山羊产羔数的影响达到显著水平(P<0.05);基因型为CC、EE和FF的个体产羔数的最小二乘均值显著大于基因型为BB、BD和CF的个体最小二乘均值(P<0.05)。因此,说明山羊乳MUC1遗传多态性有望作为产羔数的有效遗传标记。     

Improvement in the national genetic evaluation of warmblood riding horses by including information from related studbooks

Abstract

Young horse performance test data from two warmblood riding horse populations, Norwegian warmblood (NWB) and Swedish warmblood (SWB), were analysed to examine whether including information from a related studbook would increase the accuracy of the genetic evaluations within a population. Ten conformation and performance traits from 31,588 horses, 774 NWB and 30,814 SWB were analysed separately and jointly using single trait animal models. Heritabilities were moderate to high, and varied from 0.15 (conformation, joint data) to 0.74 (jumping technique, NWB data). The genetic similarity (GS) between populations was 31%, with the SWB, as expected given the size of the populations, contributing most to the GS (98%). Genetic correlations between the same traits in the two populations were 0.43–0.90 but with large standard errors (0.2–0.3). Including information from the other population increased the average accuracy of estimated breeding values for common stallions, on average 4% for SWB and 110% for NWB.     

Population genomics provides insights into the evolution and adaptation of tree shrews (Tupaia belangeri) in China

Physiological adaptation of tree shrews (Tupaia belangeri) to changing environmental temperature has been reported in detail. However, the T. belangeri origin (mainland or island), population history, and adaptation to historical climate change remain largely unknown or controversial. Here, for the first time, we sequenced the simplified genome of 134 T. belangeri individuals from 12 populations in China and further resequenced one individual from each population. Using population genomic approaches, we first observed considerable genetic variation in T. belangeri. Moreover, T. belangeri populations formed obvious genetic structure and reflected different demographic histories; they generally exhibited high genetic diversity, although the isolated populations had relatively low genetic diversity. The results presented in this study indicate that T. b. modesta and T. b. tonquinia were separated recently and with a similar population dynamics. Second, physical barriers rather than distance were the driving factors of divergence, and environmental heterogeneity may play an important role in genetic differentiation in T. belangeri. Moreover, our analyses highlight the role of historical global climates in the T. belangeri population dynamics and indicate that the decrease of the T. belangeri population size may be due to the low temperature. Finally, we identified the olfaction-associated adaptive genes between different altitude populations and found that olfactory-related genes of high-altitude populations were selectively eliminated. Our study provides demographic history knowledge of T. belangeri; their adaption history offers new insights into their evolution and adaptation, and provides valuable baseline information for conservation measures.     

中国假俭草居群遗传多样性研究Ⅱ:三种等位酶证据

选择产自我国不同地域的6个假俭草(Eremochloa ophiuroides (Munro) Hack)居群,利用垂直平板丙烯酰胺凝胶电泳技术分析了过氧化物同工酶(POD)、酯酶同工酶(EST)和苹果酸脱氢酶同工酶(MDH)酶谱的9个等位酶位点.结果表明:中国假俭草的基因多样性为0.336,其中居群内为0.176,占总变异的52.4%,居群间为0.16,占总变异的47.6%;居群间遗传一致度为0.945～1.000,其中连云港和贵州2个居群间的遗传一致度明显低于其余4个;中国假俭草居群内的遗传多样性大于居群间遗传多样性,种内遗传差异很小.     

Genetic diversity and structure in Asian native goat analyzed by newly developed SNP markers

In the current study, a total of 65 single nucleotide polymorphisms (SNPs) within the intron region were developed in goat (Capra hircus) by utilizing genomic information of cattle and sheep due to poor available genomic information on goat. Using these markers, we carried out genetic diversity and structure analyses for 10 Asian goat populations. The phylogenetic tree and principal components analysis showed good correspondence between clustered populations and their geographic locations. The STRUCTURE software analysis illustrated six divergent genetic structures among 10 populations. Myanmar and Cambodia populations showed high admixture patterns with different ancestry, suggesting genetic introgression into native goat populations. We also investigated the correlation between genetic diversity and geographic distance from a domestication center. This result showed a decreasing trend of genetic diversity according to the distance (P = 0.014). This result supported common consensus that western Asia is one of the centers of origin for modern Asian domestic goat.     

Assessing the genetic diversity conserved in the Norwegian live poultry genebank

ABSTRACT

The aim of this study was to evaluate genetic diversity within and between lines at the Norwegian live poultry gene bank as well as assessing the conservation value in an international context. Eight lines including the national breed, Jærhøns, were genotyped with the 600K Affymetrix^® Axiom^® Chicken Genotyping Array. The white egg layers were generally more inbred than the brown layers. Comparative analyses were carried out with 72 international populations of different origins. The lines that were last bred for commercial production in Norway, Norbrid, are clearly separated from the rest of the international set and more closely related to the current commercial lines. The brown egg layer Norbrid 7 has the highest relative contribution to genetic diversity. The Norwegian genebank lines are of conservation value in a national and international perspective, as they all add genetic diversity to the global set.     

Genetic diversity of Chinese domestic goat based on the mitochondrial DNA sequence variation

The aim of this study was to characterize the genetic diversity of domestic goat in China. For this purpose, we determined the sequence of the mitochondrial DNA (mtDNA) control region in 72 individuals of the Yangtze River delta white goat, and reanalysed 723 published samples from 31 breeds/populations across China. All goat haplotypes were classified into four haplogroups (A–D) previously described. The phylogenetic pattern that emerged from the mtDNA control region sequence was confirmed by the analysis of the entire cytochrome b sequence of eight goats representative of the four haplogroups. It appeared that in Chinese domestic goat, haplogroups A and B were dominant and distributed in nearly all breeds/populations, while haplogroups C and D were only found in seven breeds/populations. Four breeds/populations contained all four haplogroups. When grouping the breeds/populations into five geographic groups based on their geographic distributions and ecological conditions, the southern pasturing area had the highest diversity whereas the northern farming area had the lowest diversity. 84.29% and 11.37% of the genetic variation were distributed within breeds and among breeds within the ecologically geographical areas, respectively; only 4% of genetic variation was observed among the five geographic areas. We speculate that the traditional seasonal pastoralism, the annual long-distance migrations that occurred in the past, and the commercial trade would account for the observed pattern by having favoured gene flows.     

我国主要地方山羊品种随机扩增多态DNA研究

利用随机扩增多态DNA技术研究了我国主要地方山呼吸主部分国外品种共计23个山羊品种251个山羊个体的随机扩增多态DNA。结果表明：（1）总群体平均遗传多样性指数（Hsp)为0.7084,群体遗传分化指数为0.8583,山羊品种间平均遗传距离指数（AIGD）（0.0810－0.2044）明显大于品种内的AIGD（0.0444－0.1112),不同山羊品种的遗传多样性指数（Ho)除安哥拉山羊和承德无角山羊大于50％外,其它各品种均低于50％,上述结果说明所研究山羊群体不仅具有较为丰富的遗传多样性,而且山羊核基因组遗传变异主要存在于品种间,我国地方山羊品种间遗传分化比较明显。（2）中卫山羊（0.3410)和辽宁绒山羊（0.2589）的Ho值明显低于各品种的平均值（0.3881）;雷州山羊（0.0566）、中卫山羊（0.0564）和辽宁绒山羊（0.0444)的AIGD值也明显低于各群体的平均值（0.0749),说明辽宁绒山羊、中卫山羊和雷州山羊核基因组的遗传多样性相对其它品种来说较为贫乏,应作为重点保护对象。