Genetic diversity of mtDNA D-loop sequences in four native Chinese chicken breeds

1. To explore the genetic diversity of Chinese indigenous chicken breeds, a 585 bp fragment of the mitochondrial DNA (mtDNA) region was sequenced in 102 birds from the Xichuan black-bone chicken, Yunyang black-bone chicken and Lushi chicken. In addition, 30 mtDNA D-loop sequences of Silkie fowls were downloaded from NCBI. The mtDNA D-loop sequence polymorphism and maternal origin of 4 chicken breeds were analysed in this study.

2. The results showed that a total of 33 mutation sites and 28 haplotypes were detected in the 4 chicken breeds. The haplotype diversity and nucleotide diversity of these 4 native breeds were 0.916 ± 0.014 and 0.012 ± 0.002, respectively. Three clusters were formed in 4 Chinese native chickens and 12 reference breeds. Both the Xichuan black-bone chicken and Yunyang black-bone chicken were grouped into one cluster. Four haplogroups (A, B, C and E) emerged in the median-joining network in these breeds.

3. It was concluded that these 4 Chinese chicken breeds had high genetic diversity. The phylogenetic tree and median network profiles showed that Chinese native chickens and its neighbouring countries had at least two maternal origins, one from Yunnan, China and another from Southeast Asia or its surrounding area.     

5个新疆绵羊群体线粒体DNA的遗传多样性研究

为了探讨5个新疆绵羊群体的群体内和群体间的遗传变异,试验采用PCR-SSCP和克隆测序技术利用3对引物对5个新疆绵羊群体的线粒体DNA做了系统的分析研究.结果表明:5个新疆绵羊品种中都存在A、B、C 3种单倍型,且以A单倍型为主,而欧洲绵羊以B单倍型为主.     

Evaluation of genetic richness among Vietnamese native pig breeds using microsatellite markers

We have elucidated genetic relationships of Vietnamese native pigs (VNP) using preliminarily collected samples by a single‐nucleotide polymorphism (SNP) array. In order to confirm our previous results and compare with the results of a previous study using microsatellite (MS) markers, we aimed to characterize genetic diversity and population structure in wider varieties (24 breeds from 21 Provinces) of VNP across the country using 20 polymorphic MS markers recommended by ISAG/FAO (International Society for Animal Genetics/Food and Agriculture Organization) for diversity study. In this study, we collected 1,136 DNA samples of the VNPs and three exotic breeds. Our results revealed that the average number of alleles and allelic richness across the loci in VNPs were 10.0 and 7.6, which were higher than those of exotic breeds. Genomic components among VNPs were subjected to the sampling locations. Interestingly, Co Binh Thuan showed remarkable genetic feature compared to the other VNPs, because the habitation of Co Binh Thuan was relatively far from the other breeds. The results of this study provided useful information for exploitation, conservation, and development trends of the VNP breeds. More recently, African swine fever caused significant damage to most of the VNP populations. Therefore, our findings will help a reconstruction scheme of the VNP genetic resources.     

Investigation of an outbreak of sheeppox among native sheep breeds in the Western Himalayas of India

Veterinary Research Communications - An outbreak of sheeppox was investigated in a cluster of villages situated in Western Himalayan ranges of a Northern Indian state. Non-migratory sheep...     

Microsatellite-based diversity analysis and genetic relationships of three Indian sheep breeds

The genetic structure of three Indian sheep breeds from two different geographical locations (Nali, Chokla from north‐western arid and semi‐arid region; Garole from eastern saline marshy region) of India was investigated by means of 11 ovine‐specific microsatellite markers as proposed in FAOs MoDAD programme. Microsatellite analysis revealed high allelic and gene diversity in all the three breeds. Nali sheep showed higher mean number of alleles and gene diversity (6.27 and 0.65) than Chokla (5.63 and 0.64) and Garole (5.63 and 0.59). High within population inbreeding estimates observed in the three breeds (F_IS, Chokla = 0.286, Nali = 0.284, Garole = 0.227) reflected deficit of heterozygotes. The overall estimates for F‐statistics were significantly (p < 0.05) different from zero. High values of F_ST (0.183) across all the loci revealed substantial degree of breed differentiation. Based on pair wise F_ST and N_m between different breeds, Nali and Chokla (F_ST = 6.62% and N_m = 4.80) were observed to be the closest followed by Garole and Nali (F_ST = 20.9% and N_m = 1.80), and Garole and Chokla (F_ST = 21.4% and N_m = 1.71). In addition, genetic distance estimates, phylogeny analysis and individual assignment test used to evaluate interbreed genetic proximity and population structure also revealed substantial genetic differentiation between Garole and the other two Rajasthani (Nali and Chokla) sheep. This divergent status of Garole sheep indicated genetic uniqueness of this breed suggesting higher priority for its conservation.     

Prion protein genetic polymorphisms and breeding strategies in Portuguese breeds of sheep

Polymorphisms at the prion protein locus were studied in 965 animals, representative of 13 native and 3 exotic sheep breeds in Portugal. In general, ARQ was the predominant allele in most breeds, but the desirable ARR allele was present in all breeds studied. A different pattern was found in Ile de France, where ARR was predominant and VRQ had the highest frequency among the breeds analysed. In most of the breeds, especially in those of the coarse-wool type, the major hurdle in selecting for genetic resistance to clinical scrapie was the elimination of ARQ rather than VRQ alleles. Breeding schemes aiming at the creation of ARR-homozygous selection nuclei were simulated for representative breeds, and results indicate that, with intense selection, it would take between 4 years in Ile de France and 11 years in Mondegueira to obtain homozygosity in the nucleus, and the length of time needed for fixation was not affected by the type of mating (random or assortative) used. Nevertheless, intense selection for the PrP genotype alone would have undesirable consequences in terms of inbreeding, and correlated responses in production and adaptation traits should be evaluated before such a scheme is adopted.     

Genetic variation among native chicken breeds of Iran based on biochemical polymorphisms

(1) Genetic distances and heterozygosity were determined in 5 Iranian native chickens: Dashtyary, Lary, Marandy, Naked neck and Common breed, using three blood group systems (A, B and D) and 4 serum protein loci (albumin, transferrin, alkaline phosphatase and esterase). (2) The highest D(A) and D(S) were obtained between Dashtyary and Lary breeds. (3) The average heterozygosity for each breed in all loci ranged from 0.330 for Dashtyary to 0.370 for Common breed. (4) Dendrograms based on an unweighted pair-group method using an arithmetic average (UPGMA) showed two distinct clusters. One cluster included Dashtyary and the other contained the remaining 4 breeds.     

利用微卫星标记对四个绵羊品种遗传多样性的初步研究

采用3个微卫星标记，对4个中国地方绵羊品种进行遗传多样性检测。利用POPGENE软件分析了受试羊等位基因频率、等位基因数、有效等位基因数、遗传杂合度。     

Analysis of genetic diversity and the determination of relationships among western Mediterranean horse breeds using microsatellite markers

The distribution of genetic diversity and the genetic relationships among western Mediterranean horse breeds were investigated using microsatellite markers. The examined sample included seven Spanish and three Italian local horse breeds and populations, plus a Spanish Thoroughbred outgroup. The total number of animals examined was 682 (on average 62 animals per breed; range 20–122). The microsatellite marker set analysed provided 128 alleles (10.7 alleles per locus). Within‐breed genetic diversity was always high (>0.70), with breeds contributing about 8% of the total genetic variability. The mean molecular coancestry of the entire population examined was 0.205, Losino being the breed that contributed most. In addition to Nei's standard and Reynolds’ genetic distances, pair‐wise kinship distance and molecular coancestry were estimated. Remarkably similar breed rankings were obtained with all methods. Clustering analysis provided an accurate representation of the current genetic relationships among the breeds. Determining coancestry is useful for analysing genetic diversity distribution between and within breeds and provides a good framework for jointly analysing molecular markers and pedigree information. An integrated analysis was undertaken to obtain information on the population dynamics in western Mediterranean native horse populations, and to better determine conservation priorities.     

The genetic diversity and structure of 18 sheep breeds exposed to isolation and selection

The phylogenetic layout of the genotyped (30 microsatellite) 18 sheep breeds in this study demands and provides the opportunity to evaluate both neutral and adaptive components of genetic diversity in a naturally and artificially selected and subdivided sheep population. Seven Pramenka strains from Bosnia and Herzegovina and Croatia characterized by a very low intensity of artificial selection, preserved the highest neutral genetic variability. Eight central and north‐western European breeds under considerable artificial isolation and selection preserved the lowest genetic variability. Only combinations of various phylogenetic parameters offer a reasonable explanation for underlying evolutionary forces working in the investigated island and mainland sheep breeds under variable natural and artificial selection. More than 60% of total genetic, diversity was allocated to virtually unselected Pramenka strains, and an additional 25% to native moderately selected Graue Gehoernte Heidschnucke and intensively selected Ostfriesische Milchschafe. Some economically very important breeds and strains did not contribute to a pool with maximal genetic diversity, while they play an important role in the cultural heritage of respective countries.     

Analyses of genetic diversity in five Canadian dairy breeds using pedigree data

The issue of loss of animal genetic diversity, worldwide in general and in Canada in particular, has become noteworthy. The objective of this study was to analyze the trend in within‐breed genetic diversity and identify the major causes of loss of genetic diversity in five Canadian dairy breeds. Pedigrees were analyzed using the software EVA (evolutionary algorithm) and CFC (contribution, inbreeding, coancestry), and a FORTRAN package for pedigree analysis suited for large populations (PEDIG). The average rate of inbreeding in the last generation analyzed (2003 to 2007) was 0.93, 1.07, 1.26, 1.09 and 0.80% for Ayrshire, Brown Swiss, Canadienne, Guernsey and Milking Shorthorn, respectively, and the corresponding estimated effective population sizes were 54, 47, 40, 46 and 66, respectively. Based on coancestry coefficients, the estimated effective population sizes in the last generation were 62, 76, 43, 61 and 76, respectively. The estimated percentage of genetic diversity lost within each breed over the last four decades was 6, 7, 11, 8 and 5%, respectively. The relative proportion of genetic diversity lost due to random genetic drift in the five breeds ranged between 59.3% and 89.7%. The results indicate that each breed has lost genetic diversity over time and that the loss is gaining momentum due to increasing rates of inbreeding and reduced effective population sizes. Therefore, strategies to decrease rate of inbreeding and increase the effective population size are advised.     

猪品种遗传多样性的研究进展

从猪品种的体型外貌、染色体带型、血型和蛋白质以及DNA分子水平等几个方面对猪的遗传多样性进行论述 ,并对遗传多样性的度量参数作了分析。认为猪种遗传多样性的研究是保种和利用的理论基础 ,从形态到DNA分子水平对猪品种遗传多样性的研究在遗传资源大量流失的今天具有重要意义。     

山羊品种遗传多样性的分析

利用6个微卫星标记对中西部7个山羊品种(陕南白山羊、陕北白绒山羊、西农萨能羊、关中奶山羊、太行山羊、黄淮山羊、伏牛山羊)共计322个个体进行了遗传多样性检测,并根据Nei氏遗传距离进行了聚类分析。结果表明:6个微卫星标记在这7个品种中存在高度多态性;陕北白绒山羊的遗传变异程度最大,平均杂合度和平均多态信息含量分别为:0.8401和0.8244;而关中奶山羊的遗传变异程度相对较小,平均杂合度和平均多态信息含量分别为:0.7990和0.7784。UPGMA聚类分析表明,黄淮山羊和伏牛山羊聚为一类,陕南白山羊,太行山羊,陕北白绒山羊依次加入,西农萨能羊和关中奶山羊作为一类最后加入。     

Dental configuration among different breeds of sheep

Three breeds of sheep, Southdown, Suffolk and Romney, and two mixed breeds, Border Leicester over Romney and Coopworth over Romney, managed identically on a research station, where they were free from culling and allowed to live their natural life, had their dental configuration examined. The sheep were divided into age groups with 10 sheep in each. The least variation was found in the relation of the upper dental pad to the lower jaw. The most statistically significant differences were found in the first age group: one year six months. The Suffolk breed was noticeably different from the others. Deepened gingival sulci, as well as the inconsistency of bleeding after probing associated with labial gingivitis highlighted the problems of using these latter criteria as indicators of health or disease among sheep on the basis of a single examination.     

Genetic structure and diversity among sheep breeds in the United States: identification of the major gene pools

Understanding existing levels of genetic diversity of sheep breeds facilitates in situ and ex situ conservation activities. A comprehensive evaluation of US sheep breeds has not been previously performed; therefore, we evaluated the genetic diversity among and within 28 US sheep breeds. Both major and minor breeds were included in the analysis and consisted of 666 animals from 222 producers located in 38 states. The level of within-breed genetic diversity was variable and not dependent upon status of a breed as a major or minor breed. Bayesian cluster analysis indicated the breeds were grouped more by physiological differences (meat vs. wool production) rather than geographic origin. Results suggest several actionable items to improve in situ and ex situ conservation. The results clearly identify breeds in need of increased in situ and ex situ management (e.g., Hog Island and Karakul) and allow several suggestions for in situ management of flocks. Conversely, several of the breeds appear genetically similar and therefore require less emphasis on collecting germplasm samples for the gene bank. Commercially important breeds (e.g., Rambouillet and Suffolk) were found to have substantial variation, which should enable breeders to proceed, unencumbered by genetic diversity concerns, with selection strategies that maximize profit.     

The biodiversity and genetic structure of Balearic sheep breeds

The Balearic sheep breeds, Mallorquina, Menorquina, Roja Mallorquina, Ibicenca and one possible new genetic group, Formentera, constitute a unique genetic resource in the Mediterranean farming landscape, displaying high genetic diversity levels and being well differentiated among themselves and with respect to the continental sheep breeds. We used a microsatellite panel of markers to study genetic diversity and relationships with other Spanish breeds. The results reported in this study have important implications for the use, conservation and breeding of Balearic sheep stocks. A mean number of 7.59 alleles was found among the Balearic sheep breeds for the microsatellites scored. The whole mean value of observed heterozygosity amounted to 0.62, whereas the expected heterozygosity value was 0.69, suggesting the presence of a great degree of genetic variability, although a significant deficit of heterozygotes was detected for some markers. Genetic distance estimates showed that Balearic sheep are differentiated from the other Spanish breeds and in particular, from the Merino type. The Ibicenca breed showed the highest distance value from other breeds. The neighbour‐net method of analysis clustered the Roja Mallorquina, Menorquina and Mallorquina breeds. The Structure results clearly demonstrated the genetic differentiation among the four Balearic sheep breeds, with the Ibicenca and Formentera races joined, with slight migration among them. Few external genetic influences from the Spanish mainland breeds were detected.     

优质猪肉生产和地方猪种利用

1　开展优质猪肉生产我国的养猪生产目前已经发展到一个新的阶段。在 90年代之前 ,我国人均猪肉占有量在 2 0ｋｇ以下 ,总量供应不足 ,这是第 1阶段。从 1991年至 1999年 ,人均猪肉占有量从 2 0ｋｇ猛增到 3 0ｋｇ左右 ;1997年达 2 9ｋｇ ;1998年达 3 1 1ｋｇ ;1999年 (估计 )达 3 1 7ｋｇ。供求矛盾基本解决 ,部分大、中城市出现猪肉相对过剩 ,这是第 2阶段。目前 ,人们对猪肉品质提出了新的要求 ,安全猪肉或优质猪肉的生产应运而生。这是我国养猪生产发展的第 3阶段。优质猪肉的基本概念有 2个 :一是猪肉的品质要好 ,特别是肌肉的颜色、肌…