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1.
Sara M. Nilson;Joan M. Burke;Brenda M. Murdoch;James L. M. Morgan;Ronald M. Lewis; 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2024,141(3):304-316
The Katahdin hair breed gained popularity in the United States as low input and prolific, with a propensity to exhibit parasite resistance. With the introduction of genomically enhanced estimated breeding values (GEBV) to the Katahdin genetic evaluation, defining the diversity present in the breed is pertinent. Utilizing pedigree records (n = 92,030) from 1984 to 2019 from the National Sheep Improvement Program, our objectives were to (i) estimate the completeness and quality of the pedigree, (ii) calculate diversity statistics for the whole pedigree and relevant reference subpopulations and (iii) assess the impact of current diversity on genomic selection. Reference 1 was Katahdins born from 2017 to 2019 (n = 23,494), while reference 2 was a subset with at least three generations of Katahdin ancestry (n = 9327). The completeness of the whole pedigree, and the pedigrees of reference 1 and reference 2, were above 50% through the fourth, fifth and seventh generation of ancestors, respectively. Effective population size (Ne) averaged 111 animals with a range from 42.2 to 451.0. The average generation interval was 2.9 years for the whole pedigree and reference 1, and 2.8 years for reference 2. The mean individual inbreeding and average relatedness coefficients were 1.62% and 0.91%, 1.74% and 0.90% and 2.94% and 1.46% for the whole pedigree, reference 1, and reference 2, respectively. There were over 300 effective founders in the whole pedigree and reference 1, with 169 in reference 2. Effective number of ancestors were over 150 for the whole pedigree and reference 1, while there were 67 for reference 2. Prediction accuracies increased as the reference population grew from 1k to 7.5k and plateaued at 15k animals. Given the large number of founders and ancestors contributing to the base genetic variation in the breed, the Ne is sufficient to maintain diversity while achieving progress with selection. Stable low rates of inbreeding and relatedness suggest that incorporating genetic conservation in breeding decisions is currently not of high priority. Current Ne suggests that with limited genotyping, high levels of accuracy for genomic prediction can be achieved. However, intense selection on GEBV may cause loss of genetic diversity long term. 相似文献
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Population Structure Among Progeny-tested Bulls of the Red Dairy Breeds in Finland,Norway and Sweden
Anne Guro Larsgard Jukka Pösö Kjell Johansson Gunnar Klemetsdal 《Acta Agriculturae Scandinavica, Section A - Animal Sciences》2013,63(4):203-212
Abstract The Icelandic cattle breed is believed to have been brought to Iceland from Norway around 1100 years ago. Since then it is thought to have been almost completely isolated and to have gone through large fluctuations in population size. Here molecular markers were used to assess the breed's genetic diversity and the current within-population genetic structure using a randomly selected unbiased sample from the population as verified by calculations of the coefficient of relationship (R). Measures of genetic diversity suggest that there is considerable diversity within the breed despite long-term isolation and the effective population size is high considering the isolation and the breeding system used in recent years. No evidence of recent bottlenecks was found and analysis of population structure suggests that the population is uniform in structure. 相似文献
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Yoshinobu Uemoto Keiichi Suzuki Jumpei Yasuda Sanggun Roh Masahiro Satoh 《Animal Science Journal》2021,92(1):e13643
The Japanese Shorthorn is a Japanese Wagyu breed maintained at a small population size. We assessed the degree of inbreeding and genetic diversity among Japanese Shorthorn cattle using pedigree analysis. We analyzed the pedigree records of registered Japanese Shorthorn born between 1980 and 2018, after evaluating the pedigree completeness. The average of the actual inbreeding coefficients increased at the same rates annually from approximately 1.5% in 1980 to 4.2% in 2018 and was higher than the expected inbreeding coefficients over time. The effective population size based on the individual coancestry rate largely decreased from 127.8 in 1980 to 82.6 in 1999, and then remained almost constant at approximately 90. Three effective numbers of ancestors decreased over time until 1995, then remained almost constant. In particular, the effective number of founder genomes (Nge) decreased from 43.8 in 1980 to 11.9 in 2018. The index of genetic diversity based on Nge decreased from 0.99 in 1980 to 0.96 in 2018 due to genetic drift in non-founder generations. Changes in inbreeding and genetic diversity parameters were similar between Japanese Shorthorn and other Japanese Wagyu breeds, but the magnitude of the changes was lower in the Japanese Shorthorn. 相似文献
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F.J.C. Faria A.E.V. Filho F.E. Madalena & L.A. Josahkian 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2009,126(2):148-153
Zebu breeds play an important role in cattle production systems in Brazil. To assess the genetic variability from animals in the Herd Books of Nelore, Gir and Guzerat breeds, generation intervals, inbreeding, effective population size and parameters of gene origin (effective number of founders, ancestors and founder genomes) were calculated using pedigree records from 1938 to 1998. Breed subdivision was quantified by Wright's F -statistics. Calculations were separately carried out for consecutive 4-year intervals in the period 1979–98. Generation interval was around 8 years for the three breeds. Total inbreeding increased in all the breeds reaching values of 2.13%, 2.28% and 1.75%. Effective population size decreased from 85 to 68 in Nelore, from 70 to 45 in Gir and remained nearly constant around 104 in Guzerat. The quantities assessing the number of contributing ancestors decreased with time in all the breeds, and in the last analysed period the most important ancestor accounted for 14%, 3.1% and 4.1% in Nelore, Gir and Guzerat, respectively. Results indicate that the studied breeds are suffering from a loss of genetic variability which can result in negative effects on breeding and conservation purposes. 相似文献
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K. Wijnrocx L. François A. Stinckens S. Janssens N. Buys 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2016,133(5):375-383
The genetic diversity in 23 dog breeds raised in Belgium was investigated using both genealogical analysis and microsatellite markers. Some of these breeds are native breeds, with only small populations maintained. Pedigree and molecular data, obtained from the Belgian kennel club, were used to calculate the inbreeding coefficients, realised effective population size as well as probabilities of gene origin and average observed heterozygosity. Inbreeding coefficients ranged from 0.8 to 44.7% and realised effective population size varied between 3.2 and 829.1, according to the used method and breed. Mean observed heterozygosity ranged from 0.47 to 0.73. Both pedigree and molecular methods reveal low genetic diversity and presence of bottlenecks, especially in native Belgian breeds with small population sizes. Furthermore, principal component analysis on the set of investigated diversity parameters revealed no groups of breeds that could be identified in which similar breeding strategies could be applied to maintain genetic diversity. 相似文献
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旨在调查恩施黑猪基因组群体遗传学参数与选择信号。本研究利用Porcine 80K SNP芯片,通过计算亲缘系数、近交系数、连锁不平衡程度与有效群体大小等群体遗传学层面的参数评估恩施黑猪种群结构关系,运用CLR和iHS方法检测恩施黑猪基因组选择信号,并通过生物信息学分析揭示其潜在受选择基因。亲缘系数计算发现,咸丰县恩施黑猪个体间平均亲缘系数为0.12;近交系数计算表明, 16%的样本近交系数大于0.125,存在明显近交累积。此外,本研究构建了恩施黑猪全基因组连锁不平衡图谱;利用连锁不平衡信息,恩施黑猪估计历史有效群体大小呈现逐代下降趋势,其中5世代前有效群体大小约为25头。基于CLR方法共检测到126个显著选择信号候选区域,总长约为51.6 Mb,占基因组总长的2.1%。利用iHS方法,共发现248个显著选择信号候选区域,长度约为78.78 Mb,约占基因组总长的3.2%。富集分析表明,与选择信号区域重叠的LPAR2、NDUFA13、MEF2B、AHR基因分别与胴体长度(滴水损失)、精子形成、骨骼肌分化和总产仔数相关。研究表明,现存恩施黑猪群体血统较窄,近交累积严重,有效群体大小较小,并呈现继续缩小的趋势。选择信号分析揭示的一系列潜在受选择基因能够为未来恩施黑猪的遗传改良提供一定的参考依据。 相似文献
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Miguel A. Toro Beatriz Villanueva Jesús Fernández 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2020,137(4):345-355
Effective population size is a key parameter in conservation genetics. In the management of conservation programs using pedigree information, there is a consensus that the optimal method for maximizing effective population size is to calculate the contribution of each potential parent (the number of offspring that each individual leaves to the next generation) by minimizing the global pedigree-based coancestry between potential parents weighted by their contributions. When using molecular data, the optimal method for managing genetic diversity will remain the same but now the molecular coancestry calculated from markers will replace the pedigree-based coancestry. However, in this situation, the concept of effective population size loses its meaning because with optimal molecular management, genetic diversity increases in early generations and therefore effective population size takes negative values. Furthermore, in the long term, the molecular effective population size does not attain an asymptotic value but it shows an unpredictable behaviour. 相似文献
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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. 相似文献
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P. Berg L.F. Groeneveld C. Brekke D.I. Våge K.M. Sørheim L. Grøva 《Acta Agriculturae Scandinavica, Section A - Animal Sciences》2020,69(1-2):47-52
ABSTRACTThe Norwegian coastal goat is a national and endangered breed. Coastal goat populations are mainly divided with a large mainland and two small island populations. The objective of this study is to describe genetic diversity in the feral Skorpa island population and its relationship to the mainland coastal goat population (Selje) using the Norwegian milk goat population as a reference. Analyses were based on 96 samples genotyped by the CaprineSNP50 Beadchip from three populations; 7 Skorpa (SK), 37 Selje (SE) and 52 Norwegian milk goats (MG). The SK population had significantly less genetic variation and higher levels of inbreeding than the two other populations. It was more distant from the two mainland populations than they were from each other. The marginal contribution of the SK population to genetic diversity was small. Means of introducing genetic diversity into the SK population should be considered if the population is prioritized for conservation. 相似文献
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I Cervantes F Goyache A Molina M Valera J P Gutiérrez 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2008,125(5):301-310
The objective of this study was to test the performance of a recently proposed methodology for the estimation of realized effective size (N(e)) based on individual increase in inbreeding (DeltaF(i)) on several real pedigrees: (a) an experimental mice population; (b) a closed pedigree of fighting bulls; (c) the Spanish Purebred (SPB, Andalusian) horse pedigree; (d) the Carthusian strain of SPB pedigree; (e) the Spanish Arab horse pedigree; and (f) the Spanish Anglo-Arab horse pedigree. Several reference subpopulations were defined on the basis of generation length in order to consider only animals in the last generation, to assess the influence of the pedigree content on the estimates of N(e). The estimates of realized N(e) computed from DeltaF(i) (Ne) tended to be higher than those obtained from regression on equivalent generations. The new parameter Ne remained approximately stable when pedigree depth achieved about five equivalent generations. Estimates of take into account the genetic history of the populations, the size of their founder population, and the mating policy or bottlenecks caused by poor use of reproducing individuals. The usefulness of the realized N(e) computed from individual increase in inbreeding in real pedigrees is also discussed. 相似文献
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阐述了良种牛保种的重要意义．基因的随机漂移、选择与杂交、近交是特定基因从群体中消失的主要原因,群体及其有效含量和系统选育的科学组织是保种的重要内容。最后介绍我国良种牛的保种方法及其存在的问题,并提出解决的办法。 相似文献
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Livestock guard dog (LGD) breeds from the Western Balkans are a good example of how complex genetic diversity pattern observed in dog breeds has been shaped by transition in dog breeding practices. Despite their common geographical origin and relatively recent formal recognition as separate breeds, the Karst Shepherd, Sarplaninac and Tornjak show distinct population dynamics, assessed by pedigree, microsatellite and mtDNA data. We genotyped 493 dogs belonging to five dog breeds using a set of 18 microsatellite markers and sequenced mtDNA from 94 dogs from these breeds. Different demographic histories of the Karst Shepherd and Tornjak breeds are reflected in the pedigree data with the former breed having more unbalanced contributions of major ancestors and a realized effective population size of less than 20 animals. The highest allelic richness was found in Sarplaninac (5.94), followed by Tornjak (5.72), whereas Karst Shepherd dogs exhibited the lowest allelic richness (3.33). Similarly, the highest mtDNA haplotype diversity was found in Sarplaninac, followed by Tornjak and Karst Shepherd, where only one haplotype was found. Based on FST differentiation values and high percentages of animals correctly assigned, all breeds can be considered genetically distinct. However, using microsatellite data, common ancestry between the Karst Shepherd and Sarplaninac could not be reconstructed, despite pedigree and mtDNA evidence of their historical admixture. Using neighbour‐joining, STRUCTURE or DAPC methods, Sarplaninac and Caucasian Shepherd breeds could not be separated and additionally showed close proximity in the NeighborNet tree. STRUCTURE analysis of the Tornjak breed demonstrated substructuring, which needs further investigation. Altogether, results of this study show that the official separation of these dog breeds strongly affected the resolution of genetic differentiation and thus suggest that the relationships between breeds are not only determined by breed relatedness, but in small populations even more importantly by stochastic effects. 相似文献
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M. Ragab J.P. Sánchez M. Baselga 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2015,132(1):68-73
The purpose of this study is to use demographic and litter size data on four Spanish maternal lines of rabbits (A, V, H and LP), as a case study, in order to: (i) estimate the effective population size of the lines, as a measure of the rate of increase of inbreeding, and (ii) study whether the inbreeding effect on litter size traits depends on the pattern of its accumulation over time. The lines are being selected for litter size at weaning and are kept closed at the same selection nucleus under the same selection and management programme. The study considered 47 794 l and a pedigree of 14 622 animals. Some practices in mating and selection management allow an increase of the inbreeding coefficient lower than 0.01 per generation in these lines of around 25 males and 125 females. Their effective population size (Ne) was around 57.3, showing that the effect of selection, increasing the inbreeding, was counterbalanced by the management practices, intended to reduce the rate of inbreeding increase. The inbreeding of each individual was broken down into three components: old, intermediate and new inbreeding. The coefficients of regression of the old, intermediate and new inbreeding on total born (TB), number born alive (NBA) and number weaned (NW) per litter showed a decreasing trend from positive to negative values. Regression coefficients significantly different from zero were those for the old inbreeding on TB (6.79 ± 2.37) and NBA (5.92 ± 2.37). The contrast between the coefficients of regression between the old and new inbreeding were significant for the three litter size traits: 7.57 ± 1.72 for TB; 6.66 ± 1.73 for NBA and 5.13 ± 1.67 for NW. These results have been interpreted as the combined action of purging unfavourable genes and artificial selection favoured by the inbreeding throughout the generations of selection. 相似文献
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M.G. Melka K. Stachowicz F. Miglior F.S. Schenkel 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2013,130(6):476-486
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. 相似文献
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Salina wildrye (Leymus salinus [M.E. Jones] Á. Löve) is a perennial cool-season grass that potentially could become an important restoration species in the Colorado Plateau. However, its seed production has never been commercially viable due to sparse heading. We compared a 4x ssp. salmonis population, Lakeside C3, to an 8x ssp. salinus population, 9043501, for seed production ? related traits and measured the response of 9043501 to 2 cycles of selection for increased spike number over a 4-yr period at Millville, Utah. Seed yield of Lakeside and 9043501 was similar (P > 0.10) in 2013, but seed yield of 9043501 was 81% greater (P < 0.10) than Lakeside in 2014 and 191% greater (P < 0.01) in 2015. Lakeside spike number was 99% greater (P < 0.0001) than 9043501 in 2013, but they were similar (P > 0.10) in 2014 and 2015. Seeds per spike of 9043501 were 71% (P < 0.05), 80% (P < 0.05), and 209% (P < 0.01) greater than Lakeside in 2013, 2014, and 2015, respectively. Selection in 9043501 increased (P < 0.05) spike number by 4.3 spikes per plant (19.8%) per cycle of selection in the first seed-production yr (2013), but no change was seen in 2014 or 2015 (P > 0.10). Selection did not change (P > 0.10) seeds per spike or individual seed mass. Consequently, seed yield increased (P < 0.05) 0.32 g per plant per cycle (36.8%) in 2013, with no increase (P > 0.10) in 2014 or 2015. Dry matter per plant across the 4 yr increased (P < 0.01) 10.3 g per plant per cycle (9.3%), and canopy height increased (P < 0.01) 3.9 cm per cycle (6.6%) in 2013. AFLP DNA primers detected a 1.7% loss of genetic variation per cycle, presumably due to a combination of selection and genetic drift, but no plant traits were diminished as a result. 相似文献