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PubMed2006

Benefits of cooperation between breeding programs in the presence of genotype by environment interaction.

Dairy cattle breeding programs and dairy farmers are selecting sires and dams across environments. Genotype x environment interaction (G x E) limits the possibilities for cooperation between breeding programs operating in different environments. The objectives of this study were 2-fold: 1) to investigate the effects of heritability, selection intensity, number of progeny per bull, and size of breeding programs on possibilities for cooperation between dairy cattle breeding programs in the short and long term in the presence of G x E, and 2) to quantify the effect of such cooperation on genetic gain. A dairy cattle situation with 2 breeding programs operating in 2 environments was simulated using a deterministic pseudo-BLUP selection index model. Long-term cooperation between the 2 breeding programs was possible in the presence of G x E, when the genetic correlation was higher than 0.80 to 0.90, resulting in up to 15% extra genetic gain. In addition, in the initial generations of selection, the breeding programs could benefit from mutually selecting sires and dams from each other when the genetic correlation was as low as 0.40 to 0.60. With more intense selection, breeding programs were less likely to benefit from cooperation with breeding programs in other environments. Heritability and number of progeny per bull had little effect on possibilities for cooperation, unless the heritabilities and the number of progeny per bull were extremely different in the 2 environments. Small breeding programs benefited more from cooperation than did large breeding programs, and benefits were possible even at lower values (i.e., <0.80) of the genetic correlation. Possibilities for cooperation across environments would affect the optimal design of dairy cattle breeding programs considering genetic gain, inbreeding, and costs.

Animals↗
PubMed2005

Genetic structure and differentiation of 12 African Bos indicus and Bos taurus cattle breeds, inferred from protein and microsatellite polymorphisms.

Level of genetic differentiation, gene flow and genetic structuring of nine Bos indicus and three Bos taurus cattle breeds in Cameroon and Nigeria were estimated using the genetic information from 16 microsatellite, five blood protein and seven milk protein markers. The global heterozygote deficit across all populations (Fit) amounted to 11.7% (p < 0.001). The overall significant (p < 0.001) deficit of heterozygotes because of inbreeding within breeds (Fis) amounted to 6.1%. The breeds were moderately differentiated (Fst = 6%, p < 0.001) with all loci except CSN1S2 contributing significantly to the Fst value. The 12 populations belong to two genetic clusters, a zebu and a taurine cluster. While inferred sub-clusters within the taurine group corresponded extremely well to predefined breed categorizations, no real sub-clusters, corresponding to predefined breeds, existed within the zebu cluster. With the application of prior population information, cluster analysis achieved posterior probabilities from 0.962 to 0.994 of correctly assigning individuals to their rightful populations. High gene flow was evident between the zebu populations. Positive and negative implications of the observed genetic structure of the breeds on their development, improvement and conservation are discussed. The study shows that the breeds are threatened by uncontrolled breeding and therefore are at risk to become genetically uniform in the future. This situation can be avoided by putting in place effective breeding and management measures aimed at limiting uncontrolled mating between the breeds and to preserve special characteristics, genetic as well as breed biodiversity. The first step towards realizing these goals might be to geographically demarcate the breeds.

Animals↗
PubMedDate not supplied

Genetic diversity measures of local European beef cattle breeds for conservation purposes.

This study was undertaken to determine the genetic structure, evolutionary relationships, and the genetic diversity among 18 local cattle breeds from Spain, Portugal, and France using 16 microsatellites. Heterozygosities, estimates of Fst, genetic distances, multivariate and diversity analyses, and assignment tests were performed. Heterozygosities ranged from 0.54 in the Pirenaica breed to 0.72 in the Barrosã breed. Seven percent of the total genetic variability can be attributed to differences among breeds (mean F(st) = 0.07; P<0.01). Five different genetic distances were computed and compared with no correlation found to be significantly different from 0 between distances based on the effective size of the population and those which use the size of the alleles. The Weitzman recursive approach and a multivariate analysis were used to measure the contribution of the breeds diversity. The Weitzman approach suggests that the most important breeds to be preserved are those grouped into two clusters: the cluster formed by the Mirandesa and Alistana breeds and that of the Sayaguesa and Tudanca breeds. The hypothetical extinction of one of those clusters represents a 17% loss of diversity. A correspondence analysis not only distinguished four breed groups but also confirmed results of previous studies classifying the important breeds contributing to diversity. In addition, the variation between breeds was sufficiently high so as to allow individuals to be assigned to their breed of origin with a probability of 99% for simulated samples.

Algorithms↗
PubMedDate not supplied

Pedigree analysis of eight Spanish beef cattle breeds.

The genetic structure of eight Spanish autochthonous populations (breeds) of beef cattle were studied from pedigree records. The populations studied were: Alistana and Sayaguesa (minority breeds), Avileña - Negra Ibérica and Morucha ("dehesa" breeds, with a scarce incidence of artificial insemination), and mountain breeds, including Asturiana de los Valles, Asturiana de la Montaña and Pirenaica, with extensive use of AI. The Bruna dels Pirineus breed possesses characteristics which make its classification into one of the former groups difficult. There was a large variation between breeds both in the census and the number of herds. Generation intervals ranged from 3.7 to 5.5 years, tending to be longer as the population size was larger. The effective numbers of herds suggest that a small number of herds behaves as a selection nucleus for the rest of the breed. The complete generation equivalent has also been greatly variable, although in general scarce, with the exception of the Pirenaica breed, with a mean of 3.8. Inbreeding effective population sizes were actually small (21 to 127), especially in the mountain-type breeds. However, the average relatedness computed for these breeds suggests that a slight exchange of animals between herds will lead to a much more favourable evolution of inbreeding. The effective number of founders and ancestors were also variable among breeds, although in general the breeds behaved as if they were founded by a small number of animals (25 to 163).

Animals↗
PubMed2000

Effects of dietary fat and sire breed on puberty, weight, and reproductive traits of F1 beef heifers.

Prepubertal F1 heifers (n = 246; from crossbred dams bred to either Hereford [H], Limousin [L], or Piedmontese [P] sires) were fed 1.9% (LF) or 4.4% (HF) dietary fat from 254+/-4 d of age until they reached puberty or the breeding season started. Safflower seeds (37% oil with 79% linoleic acid) were the added fat source. Blood samples and backfat thickness measurements were obtained from 60 randomly selected heifers representing the sire breeds and diets studied. In addition, five H-sired heifers from both diets were serially bled at 28-d intervals. Total gain, ADG, body condition score, and backfat thickness were affected by sire breed (P < 0.001) but not diet. Backfat thickness was affected (P < 0.01) by the diet x time on feed interaction. Diet did not affect pubertal age (P > 0.10) but tended (P = 0.08) to affect the percentage of heifers pubertal by the beginning of breeding (June 4). Sire breed effects on puberty age at beginning of breeding, percentage pubertal at the beginning of breeding, and puberty age during the entire study were all highly significant. The effect of the diet x sire breed interaction on percentage of heifers pubertal at beginning of breeding (P < 0.05) was 74.4 vs 76.3% in H-sired, 69.8 vs 60.5% in L-sired, and 76.2 vs 97.6% in P-sired heifers (LF vs HF, respectively). Number of AI services per pregnancy and final pregnancy percentage were not affected by diet or the diet x sire breed interaction. Diet affected progesterone (P < 0.05) and cholesterol (P < 0.001) concentrations, and sire breed tended to affect (P = 0.06) cholesterol concentrations. The effect of the diet x time on feed interaction on cholesterol concentrations was highly significant. There were no effects of diet or sample period on insulin or growth hormone concentrations in serially collected blood samples. We conclude that effects of supplemental dietary fat may be breed-dependent and hypothesize that a feeding period of approximately 60 d duration may be more appropriate than the 162 d used in this study.

Animal Feed↗
PubMed1991

[Studies of the blood-group of chicken. X. Analysis of blood-group and plasma protein polymorphism in eleven Chinese native fowl breeds].

This paper reports the results of blood-group and plasma protein polymorphism of eleven Chinese native fowl breeds. 1. The distribution frequencies of the blood-group genes (3 loci 12 alleles) in eleven Chinese native fowl breeds were significantly different in A and C loci, but not significant in B locus. The coefficients of homozygosity of blood-group gene in all breeds were almost similar, except in Gushi and Chonren pitted chickens. The distribution of blood-group factors in all breeds was extensive, and this means that the selection potential in these local breeds was very large. 2. The gene frequencies of alkaline phosphatase (Akp and Akp-2) transferrin (Tf) in some breeds were more different, while that of esterase (Es-1) was less different. Among Chinese Japanese and American-European native breeds, the difference of gene frequencies of esterase was greater, while that of alkaline phosphatase and transferrin was smaller. It showed the identity or diversity in breed origin and evolution in these Chinese local breeds and Japanese or American-European native breeds. 3. The cluster analysis of the eleven Chinese native fowl breeds showed that these breeds could be divided into four groups: White ear-lobe- Shouguang- Luyuan chickens; Xiaoshan-Xianju- Pudong chickens; Langshan- Taihe Silky- Beijing Youkei chickens and Gushi-Chonren pitted chickens.

Alkaline Phosphatase↗
PubMed1989

Hormonal patterns in breeding and nonbreeding kestrels, Falco tinnunculus: field and laboratory studies.

Plasma levels of luteinizing hormone (LH), androgens, and corticosterone (B) were measured in breeding and nonbreeding kestrels, both in the field and in captivity under different food conditions. LH levels in breeding males were elevated from courtship through incubation and androgen concentration peaked during courtship and laying. Seasonal changes in LH and androgens were similar in breeding and nonbreeding males, although androgens declined sharply after laying in breeding males. Egg laying was characterized by marked increases in both female body mass and plasma concentrations of LH and B. In both breeding and nonbreeding females LH and B increased during pair formation and courtship (March-April), although maximum levels were lower in nonbreeders. Two marked differences were found between free-living and captive (paired) birds. First, during winter plasma levels of LH were basal in free-living birds, while significantly elevated in both captive males and females. Second, during courtship androgen levels in breeding males were three-fold higher in the field than in captivity, probably as a result of intermale aggression under natural conditions. Females breeding early, late, or not at all had similar LH concentrations on arrival and during early courtship. Before breeding there were also no differences in LH (males and females) or in androgen levels (males) between pairs fed ad libitum and pairs temporary food rationed. However, captive females with experimentally reduced food intake showed low levels of B until their rations were increased. Nonbreeders showed hormonal changes similar to breeders, except for those changes in females that were associated with laying. These results suggest that at the start of the breeding season both nonbreeding and breeding kestrels have functional reproductive systems. That some breed early, late, or not at all is primarily an effect of food availability and is not due to hormonal modulation of the reproductive cycle.

Androgens↗
PubMed2004

Cumulus-oocyte communications in the horse: role of the breeding season and of the maturation medium.

Horse is a seasonal breeder and information on oocyte quality outside the breeding season is very limited. Ovaries obtained at the slaughterhouse are a convenient but often limited source of oocytes in this species. As the low quantity of ovaries leads to an intensive use of all available material, it would be useful to know whether ovaries collected during the non-breeding season are suitable for in vitro maturation (IVM). In an attempt to characterize the effect of season on oocyte quality, we investigated the permeability of the gap junctions (GJ) present between cumulus cells and oocytes because of their important role in oocyte growth and maturation. We also compared the effect of supplementing the maturation medium with bovine serum albumin (BSA) or oestrus mare serum (EMS). A total of 645 oocytes isolated from 158 and 154 ovaries collected during the breeding and the non-breeding season, respectively, were used in this study. Oocytes were matured for 30 h in TCM 199 supplemented either with 10% EMS or with 4 mg/ml BSA. The presence of permeable GJs between cumulus cells and oocytes was investigated with the injection of a 3% solution of the fluorescent dye Lucifer yellow into the ooplasm. No differences in efficiency of oocyte retrieval or oocyte meiotic competence were detected between oocytes collected during the breeding and non-breeding season. The vast majority (90%) of the oocytes collected during the breeding season had fully functional communications with their surrounding cumulus cells but such communications were completely interrupted in 55.3% of the oocytes collected during the non-breeding season. During the non-breeding season, the proportion of oocytes whose communications with cumulus cells were classified as closed or intermediate at the end of maturation was lower in the group matured with BSA than with EMS (71.4 vs 97.7, p < 0.05). The same trend, although not statistically significant, was observed during the breeding season also. The presence of BSA caused an incomplete cumulus expansion during both seasons. Our data indicate that oocytes collected during the non-breeding season do not show any meiotic deficiency but lack active communication with the surrounding cumulus cells at the time of their isolation from the ovary. No data are available at present for determining the consequences on the developmental competence even if data from other species suggest that this is likely.

Animals↗
PubMed2004

Public perceptions of reproductive biotechnologies: the case of farm animal breeding and reproduction in France and the United Kingdom.

Results of previous qualitative and quantitative stages of the research project demonstrated that, although consumers had poor knowledge about breeding and reproduction procedures, they were concerned about the impact of breeding practices on their food items. They acknowledged breeding and reproduction to be at the very core of animal-based food chain process. Since however modern breeding programmers beg so much for genetics, their practices increasingly raised consumer concerns. This paper presents results of a research addressing this issue and based on interviews of livestock breeders and specialized scientists. This research was undertaken within the frame of an EU funded project (Sustainable Farm Animal Breeding and Reproduction Project, 2000-2003). Interviews were performed according to the methodology of focus groups and results were used to prepare a discussion guide, including definitions of breeding techniques such as artificial insemination, embryo transfer, in vitro fertilization, and molecular genetics. Farm animal breeding and reproduction methods raised high level of concerns in conventional terms like safety, healthiness and quality of food, factory farming and related consequences on environment, international issues, and cost. Several propositions were presented that deal with modern farm animal breeding and reproduction, EU regulation of breeding procedures, education of consumers on breeding methods, and labelling of products on breeding and reproduction grounds.

Animals↗
PubMed2004

Breeding German sheep for resistance to scrapie.

Susceptibility to clinical scrapie is associated with polymorphisms in the prion protein (PrP) gene. The ARR allele reduces susceptibility to clinical disease caused by all known strains of the transmissible spongiform encephalopathy (TSE) agents. For the economically important German breeds of sheep the PrP allele frequencies are well known, but this paper presents representative genotyping results for 1526 sheep from two smaller milk sheep breeds and 2446 sheep from 14 mostly indigenous land sheep breeds. The ARR allele was detected in each breed but the breed-specific ARR frequencies varied between 1 and 63 per cent. In small populations with a very low ARR frequency the ARR allele could be lost by genetic drift. A simulation study was therefore made to examine the effects of different breeding schemes in populations of different sizes on attempts to select for the ARR allele in an endangered population. In breeds in which no homozygous rams are available the breeding strategy would depend on the number of heterozygous rams, and the genotyping and selection of suitable breeding ewes would reduce the time required to achieve a highly resistant population. In general, in all the breeds a selection programme to achieve 99 per cent ARR homozygous genotypes would be feasible in six to nine generations, depending on the initial allele frequencies. In small populations the inbreeding rate may increase if no specific mating plans are developed by the breeding organisations.

Alleles↗
PubMed2003

Genetic divergence in cellular resistance to heat shock in cattle: differences between breeds developed in temperate versus hot climates in responses of preimplantation embryos, reproductive tract tissues and lymphocytes to increased culture temperatures.

The detrimental effects of heat stress on fertility in cattle are less pronounced in heat-tolerant breeds. Although these genetic differences reflect differences in thermoregulation, cells from heat-tolerant breeds are less adversely compromised by increased temperature (that is, heat shock) than cells from heat-sensitive breeds. Experiments were performed to test the hypothesis that cells and tissues from two thermotolerant breeds (Brahman and Senepol) are better able to survive and function after exposure to increased temperature than cells and tissues from two thermosensitive breeds (Holstein and Angus). Exposure of embryos at>eight-cell stage at day 5 after insemination to heat shock of 41.0 degrees C for 6 h decreased development to the blastocyst stage and the number of cells per embryo. However, the deleterious effect of heat shock on blastocyst formation and the number of cells per embryo was less pronounced for Brahman than for Holstein and Angus breeds. Embryos from Senepol cows had very low development and it was not possible to determine heat shock effects in this breed. In contrast to the sensitivity of embryos to heat shock, there was no effect of a 41.0 degrees C heat shock on [(3)H]leucine incorporation into proteins secreted by oviductal or endometrial explants. Lymphocytes from Brahman and Senepol cows were more resistant to heat-induced apoptosis than lymphocytes from other breeds. Heat shock reduced lymphocyte glutathione content but the magnitude of the decrease was not affected by breed. In conclusion, embryos from Brahman cows are more resistant to heat shock than embryos from Holstein or Angus cows. Genetic differences are also present in thermotolerance for apoptosis response in lymphocytes, with Brahman and Senepol cattle being more resistant to heat shock than Angus and Holstein breeds. It is likely that the evolutionary forces that led to the Brahman and Senepol breeds being adapted to hot climates resulted in the selection of genes controlling resistance to cellular heat shock.

Analysis of Variance↗
PubMed1992

Estimated breeding values for meat characteristics of crossbred cattle with an animal model.

Longissimus muscle area, shear force measure, and sensory panel scores for flavor, juiciness, and tenderness, and marbling score were obtained from 682 steer carcasses, resulting from crosses among five Bos taurus and Bos indicus breeds. The single-trait model used included birth year and as covariates breed fractions, weaning age, and days on feed. The numerator relationship matrix was for 1,350 animals (682 steers, 74 pure breed and 52 F1-cross sires and 542 dams). The coefficient matrix was inverted to examine standard errors of prediction. Estimated breeding value is the sum of the estimate of genetic deviation and the weighted (fractions) sum of estimates of breed effects. Heritabilities used in estimating breeding values were .62, .06, .05, .11, .05, and .43 for longissimus muscle area, shear force, flavor, juiciness, tenderness, and marbling score. Sires within a breed or crossbred group tended to rank similarly due to large differences among breed effects (e.g., the six Sahiwal sires ranked in the highest six places for shear force). These results illustrate that for traits with large breed differences, selection of the proper breed should be done before selection within that breed.

Animals↗
PubMed1995

Individual multilocus genotypes using microsatellite polymorphisms to permit the analysis of the genetic variability within and between Italian beef cattle breeds.

We investigated the genetic variability within and between cattle breeds. The polymorphisms of 17 microsatellites were studied in 220 unrelated animals belonging to four Italian beef cattle breeds (Chianina, Marchigiana, Romagnola, and Piemontese). Variations of allelic frequencies were examined to characterize the breeds and their relationships. Wahlund coefficients, Polymorphism Information Content values, and Haldane exact test for Hardy-Weinberg proportions were calculated. The results show that the Hardy-Weinberg equilibrium is not always maintained. Moreover, in addition to the classical genetic distances, a new method, based on the consideration of a multilocus genotype of each animal, was set up to measure the genetic similarity between animals or within groups of animals. All the results showed that, whereas Chianina occupies an intermediate position and Piemontese is the most distinct of all four breeds, Marchigiana and Romagnola display the strongest similarity. The new method also provides evidence that average similarities are always higher within breeds than between breeds. By comparing pairwise the multilocus genotypes, it was also possible to discriminate the individuals with higher or lower genetic similarities so that each breed could be subdivided into two groups of animals in relation to their similarity to the average breed multilocus genotype. High similarities between breeds were detected, somewhat surprisingly, when the most homogeneous groups of each breed were compared. The microsatellite multilocus genotype is particularly efficient in evaluating the between- and within-breeds genetic similarities and for subgrouping genetically more homogeneous animals.

Alleles↗
PubMed1998

Sex effects on breed of sire differences for birth, weaning, and yearling weights.

Weights of males and females can be considered to be correlated traits with different averages and variances. This study attempted to determine whether defining traits as expressed in males or in females would change estimates of breed of sire differences needed to calculate across-breed factors for adjustment of within-breed EPD to across-breed EPD. Records from the US Meat Animal Research Center of progeny of Hereford, Angus, and MARC III composite dams mated to 12 sire breeds that had been used to calculate breed of sire adjustments in 1996 were used. Breeds of sire were Hereford, Angus, Shorthorn, Brahman, Simmental, Limousin, Charolais, Maine-Anjou, Gelbvieh, Pinzgauer, Tarentaise, and Salers. Female and male records for birth (BWT), weaning (WWT), and yearling (YWT) weights were considered to be separate although correlated traits. Heritability estimates for expression as females and males were as follows: .44 and .47 for BWT, .25 and .19 for WWT, and .55 and .49 for YWT. Corresponding genetic correlations between expression in males and females were .85, 1.00, and .92. Phenotypic standard deviations were slightly larger and coefficients of variation slightly smaller for males than for females; the largest differences were for YWT. Breeds ranked similarly for female and male weights; the major exception was Brahman for BWT. Averages of breed of sire contrasts for expression in females and males were almost identical to contrasts from analyses of combined male and female records. Largest differences between averaged and combined breed of sire contrasts were approximately 1 kg for BWT and WWT and approximately 2 kg for YWT. The results show that considering male and female weights as separate traits is not needed in calculation of across-breed adjustment factors from US Meat Animal Research Center records.

Animals↗
PubMed1998

Effect of ignoring random sire and dam effects on estimates and standard errors of breed comparisons.

Data were weights of F1 calves and weaning weights of top-cross progeny from sires and maternal grandsires of 13 breeds. Three analyses were performed on each trait to obtain estimates and standard errors of breed effects needed to calculate across-breed EPD and accuracies. Model (R) for records of F1 progeny contained fixed effects for birth year and date of birth, sex, age and breed of dam, and breed of sire, and a random residual effect. The second analysis included random effects for sires (RS), and the third analysis included random effects for sires and dams (RSD). In maternal analysis of top-cross progeny, model (Rm) contained fixed effects for cycle of experiment, age of dam, year of birth, sex, breeds of maternal grandam and grandsire, and breed of sire, and a random residual effect. In addition, the second and third analyses fit random effects for maternal grandsires (RSm) and for maternal grandsires and daughters of maternal grandsires (RSDm). Estimates of breed of sire effects changed only slightly for different models. Total variance increased in RSD and RS relative to R. Standard errors of breed of sire comparisons were underestimated with Model R, compared to Models RS and RSD. Standard errors of other contrasts were generally not affected. Variance components, breed effects, and standard errors followed patterns for Rm, RSm, and RSDm similar to those for R, RS, and RSD. Ignoring random variation due to sires and dams underestimated standard errors of breed of sire comparisons.

Animals↗
PubMed2002

Genetic diversity and assignment tests among seven French cattle breeds based on microsatellite DNA analysis.

Genetic variability and relationships among six native French cattle breeds (Abondance, Tarentaise, Villard de Lans, Montbéliarde, Limousin, and Charolais) and one foreign breed (Holstein) were investigated using 23 microsatellite markers. These breeds were also compared with four Swiss breeds genotyped in a previously published study. Interestingly, the French alpine breeds have smaller population sizes but showed higher genetic variability than the larger Holstein breed. Neighbor-joining trees and PCA (principal components analysis) showed that alpine breeds tend to cluster together. Abondance and Tarentaise breeds were closely related, whereas the Holstein was highly differentiated from all breeds analyzed. Two different assignment tests for determining the breed of origin of individuals were compared: "direct" and "exclusion-simulation" approaches. The exclusion-simulation significance test correctly assigns fewer individuals than the direct approach but provides a confidence level (e.g., P < 0.01) for each individual being assigned. Accurate assignment with high statistical confidence is required for animal traceability. Unfortunately, the accuracy of assignment greatly decreases as the threshold level of confidence of assignment increases (e.g., from P < 0.05 to P < 0.001). Assignment accuracy also greatly declines as the level of population differentiation decreases below the level often found between related breeds (e.g., F(ST) < 0.1).

Animals↗
PubMed2026

Genome-Wide SNP Characterisation of Three Kazakh Sheep Breeds: Kazakh Fat-Tailed Coarse-Wool, Degeres, and Etti Merino.

Kazakhstan's sheep portfolio underpins much of the country's mutton and wool production, yet several of its principal breeds remain genomically uncharacterised. The aim of this study was to characterise the genomic diversity, population structure, and global phylogenetic placement of three economically important Kazakh breeds and to determine whether they constitute separate gene pools requiring independent management. We present the first genome-wide SNP characterisation to include the Degeres (DE), the Etti Merino (EM), and the Kazakh fat-tailed coarse-wool (KKG) breeds simultaneously. A total of 1497 animals (DE = 354, EM = 642, KKG = 501) sampled across seven production households were genotyped and, after quality control, analysed at 42,279 SNPs, of which 22,766 LD-pruned markers were used for principal component analysis and AMOVA. We applied principal component analysis (PCA), pairwise FST, analysis of molecular variance (AMOVA), neighbour-joining phylogenetics, model-based ancestry estimation (ADMIXTURE), and Hill-number diversity profiling, and projected the breeds against the global Ovine SNP50 HapMap panel (74 reference breeds, 2819 animals; 37,685 shared SNPs). All three breeds retained uniformly high within-breed diversity (expected heterozygosity 0.413-0.417) with fixation indices at or near zero. AMOVA partitioned 94.03% of variance within breeds (&#x3a6;ST = 0.060, p < 0.001). PCA, phylogeny, and ADMIXTURE concordantly resolved three breed-specific clusters at K = 3, with a maximum interbreed FST of 0.038 within the study dataset. Against the global panel, EM was genetically closest to Merino and Merino-derived reference breeds (pooled FST = 0.017) and substantially more distant from Southwest Asian sheep (FST = 0.045), whereas DE and KKG showed the reciprocal pattern (FST = 0.027 and 0.020 to Southwest Asia, 0.052 to the Merino group). DE additionally displayed the heterozygote excess and partial admixture expected of an incompletely consolidated composite. These results delineate three distinct gene pools and carry direct implications for breed management and the conservation of genomic diversity in Kazakhstani sheep.

ADMIXTURE↗
PubMed2003

[Microsatellite analysis of genetic diversity and phylogenetic relationship of eight sheep breeds in Xinjiang].

To reveal the genetic diversity and syseighttemic relationship of main sheep breeds in north Xingjiang, the genetic polymorphisms of 10 microsatellites in 8 sheep breeds and one first filial generation (F1) in north Xinjiang were studied by means of PCR, polyacrylamide gel electrophoresis and silver staining. Number of alleles, average effective number of alleles (E) and average rates of homozygote of each breeds were counted. According to allele frequencies of ten microsatellites, polymorphism information content (PIC), mean heterozygosity (h) and genetic distances were calculated for each breeds. By using the Neighbor-joining method of Molecular Evolutionary Genetics Analysis software, a dendrogram was obtained based on genetic distances. Another dendrogram was obtained by Maximum Likelihood method in PHYLIP (3.6) software. The bootstrap values were evaluated for each crunode of the dendrogram by means of bootstrap test. The systemic relationship was analyzed as well. The results showed that 8 of 10 microsatellite loci were highly polymorphic, but BM1824 and MAF65 were low and medium polymorphic respectively, so the 8 microsatellite loci were effective markers for analysis of genetic relationship among sheep breeds. The average PIC (0.5631), h (0.5721) and E(2.9) of the whole population was all lower than those of other sheep breeds reported in the documents, which showed the gene polymorphisms and genetic diversity in these sheep breeds are relative rare. The genetic distances of native Aletai, Kazak and Bashibai sheeps in Xingjiang from foreign sheep breeds and cultivated breeds bearing foreign bloodline are relatively large. Consequently, they clustered in two groups. The phylogenetic relationship between different sheep breeds was in accordance with their resource, breeding history, differentiation and localities.

Algorithms↗