Evaluation of inbreeding and genetic diversity in Japanese Shorthorn cattle by pedigree analysis

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 (N_ge) decreased from 43.8 in 1980 to 11.9 in 2018. The index of genetic diversity based on N_ge 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.     

Monitoring of genetic diversity in the Japanese Black cattle population by the use of pedigree information

The gene pool of the Japanese Black cattle has been completely closed to foreign breeds during the last 100 years. Genetic diversity of the Japanese Black cattle from 1960 to 2000 was monitored with three estimates of effective number of ancestors. Founder genome equivalent (N_ge) accounts for all the causes of reduction of diversity. Effective number of founders (N_ef) and non‐founders (N_enf) explain reduced diversity because of unequal genetic contributions of founders and random genetic drift in non‐founders, respectively. Further examination using gene dropping simulation was conducted to obtain information on survival of founder alleles. Unique founder alleles were dropped down along the actual pedigree with Monte Carlo procedure following Mendelian segregation rules, and generated genotypes of all the current live animals (612 959 heads). Pedigree records consisted of 2 075 188 animals was used for these analysis. The estimates of three effective numbers (N_ef, N_ge, and N_enf) decreased from 418.6 to 50.3, 86.6 to 7.3, and 109.2 to 8.5, respectively, during the period 1960–2000. The increasing differences between two kinds of genetic diversity indices derived from N_ge and N_ef showed that large part of the reduced diversity from 1980 was attributed to genetic drift caused by the intensive use of particular limited number of sires. In gene dropping analysis, probabilities of extinction of founder alleles were derived from their distributions of frequency in the current animals. Several founders showed low probabilities of allele extinction, irrespective of their relatively low genetic contributions. This suggests that these founders have lineages through which their alleles are surely transmitted to the current breed. The use of these founders as a strategy for recovering the genetic diversity was discussed.     

Estimates of genetic diversity in the brown cattle population of Switzerland obtained from pedigree information

The study investigates the genetic diversity present as well as its development in the Brown Cattle population of Switzerland from pedigree information. The population consisted of three subpopulations, the Braunvieh (BV), the original Braunvieh (OB) and the US‐Brown Swiss (BS). The BV is a cross of OB with BS where crossing still continues. The OB is without any genetic influence of BS. The diversity measures effective population size, effective number of ancestors (explaining 99% of reference genome) and founder genome equivalents were calculated for 11 reference populations of animals born in a single year from 1992 onwards. The BS‐subpopulation consisted of animals and their known ancestors which were used in the crossing scheme and was, therefore, quite small. The youngest animals were born in 2002, the oldest ones in the 1920s. Average inbreeding was by far the highest in BS, in spite of the lowest quality of pedigrees, and lowest in OB. Effective population size obtained from the difference between average inbreeding of offspring and their parents was, mostly due to the heavy use of few highly inbred BS‐sires, strongly overestimated in some BV‐reference populations. If this parameter was calculated from the yearly rate of inbreeding and a generation interval of 5 years, no bias was observed and ranking of populations from high to low was OB – BV – BS, i.e. equal to the other diversity parameters. The high genetic diversity found in OB was a consequence of the use of many natural service sires. Rate of decrease of effective number of ancestors was steeper in BV than OB was, however, equal for founder genome equivalents. Founder genome equivalents were more stable than effective population sizes calculated from the difference between average inbreeding of offspring and parents. The five most important ancestors contributed one‐third of the 2002‐reference genomes of BV and OB, in BV all were BS‐sires. The relative amount of BS‐genes in the BV‐genome increased from 59.2% to 78.5% during the 11 years considered.     

Conservation of genetic diversity in the Japanese Black cattle population by the construction of partially isolated lines

In the Japanese Black cattle population, five genetically divergent subpopulations have played important roles as suppliers of breeding stocks to the entire breed. We supposed a situation where five lines were constructed from each of the five subpopulations, and applied to this set of lines a management plan to conserve genetic diversity. Assuming that the male migration pattern among the lines followed the island model, we assessed the optimum male migration rate and required male numbers in each line, satisfying the following three conditions simultaneously: (i) the rate of inbreeding in each line was below 0.01 per generation; (ii) at least 97% of the initial genetic diversity was preserved after 10 generations; and (iii) more than 50% of the genes in an initial line were retained in the line after 10 generations. We found that approximately one breeding male should be selected per year and one breeding male should be exchanged among the lines per generation in each line to satisfy these three conditions. Numerical analysis with the migration rates actually observed among the five subpopulations demonstrated that the initial genetic differentiation among the lines was rapidly decayed by an asymmetrical migration pattern. For a successful plan, migration among lines should be strictly managed.     

Pedigree analysis of genetic subdivision in a population of Japanese Black cattle

Twenty‐five subpopulations (i.e. populations of prefectures) of more than 2000 Japanese Black cows younger than or equal to 10 years of age were analyzed to evaluate the genetic relationships in the current population. The total number of cows analyzed was 392 346 and their pedigrees were traced back to 1944 or before. Using the pedigree records, the genetic relationships among the subpopulations were estimated by the two different measurements: (i) the average additive relationship coefficients and (ii) Nei's standard genetic distances. Principal component analysis (PCA) was performed to the matrix of the average additive relationship coefficients, and the factor loadings of subpopulations were plotted on the plane to visualize the genetic configuration of subpopulations. To understand the grouping process of the subpopulations, cluster analysis was applied to the matrix of the Nei's genetic distances, and a dendrogram was constructed. There was a high consistency between the results from PCA and cluster analysis. Eight subpopulations with relatively low migration rates showed their unique genetic compositions, and the other 17 subpopulations with high migration rates formed a single cluster. The major cause of the genetic similarity among the 17 subpopulations was inferred to be the strong genetic influence from one subpopulation (Hyogo prefecture) with prominent characteristics for meat quality.     

Evolution of the genetic variability of eight French dairy cattle breeds assessed by pedigree analysis

A pedigree analysis was performed on eight French dairy cattle breeds to assess their change in genetic variability since a first analysis completed in 1996. The Holstein, Normande and Montbéliarde breeds are selected internationally with over hundreds of thousands cows registered in the performance recording system. Three breeds are internationally selected but with limited numbers of cows in France (Brown Swiss, French Simmental and French Red Pied). The last two remaining breeds (Abondance and Tarentaise) are raised at regional level. The effective numbers of ancestors of cows born between 2004 and 2007 varied between 15 (Abondance and Tarentaise) and 51 (French Red Pied). The effective population sizes (classical approach) varied between 53 (Abondance) and 197 (French Red Pied). This article also compares the genetic variability of the ex situ (collections of the French National Cryobank) and in situ populations. The results were commented in regard to the recent history of gene flows in the different breeds as well as the existence of more or less stringent bottlenecks. Our results showed that whatever the size of the breeds, their genetic diversity impoverished quite rapidly since 1996 and they all could be considered as quite poor from a genetic diversity point of view. It shows the need for setting up cryobanks as gene reservoirs as well as sustainable breeding programmes that include loss of genetic diversity as an integrated control parameter.     

Assessment of genetic diversity and population structure of Vietnamese indigenous cattle populations by microsatellites

Cattle play a very important role in agriculture and food security in Vietnam. A high level of cattle diversity exists and serves different needs of Vietnamese cattle keepers but has not yet been molecularly characterized. This study evaluates the genetic diversity and structure of Vietnamese indigenous cattle populations, using microsatellite markers. A total of 410 individuals from six indigenous cattle populations and an exotic breed was characterized using 27 microsatellite markers A total of 362 alleles was detected and the number of alleles per locus ranged from 8 (INRA005 and ILSTS005) to 17 (ETH185). The level of gene diversity was high indicated by a mean expected heterozygosity (He) across populations and loci of 0.73. Level of inbreeding (mean F_IS=0.05) and genetic differentiation (mean F_ST=0.04) was moderate. The phylogenetic tree based on Reynolds genetic distance reflected geographic distances. Structure analysis indicated five homogeneous clusters. The Brahman, Lang Son, Ha Giang and U Dau Riu cattle were assigned to independent clusters while Nghe An, Thanh Hoa and Phu Yen cattle were grouped in a single cluster. We conclude that Vietnamese indigenous cattle have high levels of genetic diversity and distinct genetic structures. Based on these results, we recommend that for conservation homogenous populations (Nghe An, Thanh Hoa and Phu Yen) can be grouped to reduce costs and U Dau Riu, Lang Son and Ha Giang populations should be conserved separately to avoid loss of genetic diversity.     

Genetic diversity in Polish hounds estimated by pedigree analysis

Data from 247 litters of Polish hounds born at 105 kennels between 1960 and 2004 was analysed in order to evaluate the genetic variability of the breed. The breed originated from 19 founders and the founder genome equivalent ranged from 2.043 to 1.287 over the span of forty-four years of breeding. The high imbalance of founder contributions to the gene pool was noted, with the dominant contribution of four founders. The low number of the founders and the high disproportion of particular dogs in breeding use resulted in the increasing value of inbreeding coefficient which ranged from 0.0771 to 0.370. The poor gene pool seems to be strictly connected to the deteriorating health of the population which draws into question the future of the breed.     

Epidemiologic and genetic analysis of veterinary data of German Brown cattle]

In totally 3740 cows of the breed German Brown Swiss distributed over 115 herds risk factors for the occurrence of diseases were analysed using a threshold model. Disease data were recorded by ten practitioners in southern Bavaria. The most frequent diseases were fertility disorders, followed by metabolic, udder and calving disorders. The influence of the herds could demonstrated clearly for all diseases analysed. The effect of the lactation number contributed significantly to the frequency of milk fever, mastitis, retained placenta, endometritis/metritis and ovary cysts. Heritability estimates vary between h2 = 0.5% and h2 = 4.2% with exception of anestrus/acyclia (h2 = 8.8%). With higher milk yield of cows the disease frequencies increase, especially fertility diseases. However, increasing herd milk yield is associated with decreasing disease frequencies. A depression of A.I.-parameters and an increase of culling rate caused by diseases could be observed. In the case of the occurrence of uterus- and ovary disorders days open are elongated by 58 days in comparison to cows without diseases. Recording of disease data for use in electronic data processing seems necessary, in order to diminish production diseases by breeding and herd control programmes. An important prerequisite in organization of disease data recording is an efficient cooperation between the veterinary practitioner, farmer, inseminator and the official milk recording organisation.     

Estimates of genetic variance and variance of predicted genetic merits using pedigree or genomic relationship matrices in six Brown Swiss cattle populations for different traits

The amount of variance captured in genetic estimations may depend on whether a pedigree‐based or genomic relationship matrix is used. The purpose of this study was to investigate the genetic variance as well as the variance of predicted genetic merits (PGM) using pedigree‐based or genomic relationship matrices in Brown Swiss cattle. We examined a range of traits in six populations amounting to 173 population‐trait combinations. A main aim was to determine how using different relationship matrices affect variance estimation. We calculated ratios between different types of estimates and analysed the impact of trait heritability and population size. The genetic variances estimated by REML using a genomic relationship matrix were always smaller than the variances that were similarly estimated using a pedigree‐based relationship matrix. The variances from the genomic relationship matrix became closer to estimates from a pedigree relationship matrix as heritability and population size increased. In contrast, variances of predicted genetic merits obtained using a genomic relationship matrix were mostly larger than variances of genetic merit predicted using pedigree‐based relationship matrix. The ratio of the genomic to pedigree‐based PGM variances decreased as heritability and population size rose. The increased variance among predicted genetic merits is important for animal breeding because this is one of the factors influencing genetic progress.     

Comparison of genetic gains per year for carcass traits among breeding programs in the Japanese Brown and the Japanese Black cattle

The breeding program for beef cattle in Japan has changed dramatically over 4 decades. Visual judging was done initially, but progeny testing in test stations began in 1968. In the 1980s, the genetic evaluation program using field records, so-called on-farm progeny testing, was first adopted in Oita, Hyogo, and Kumamoto prefectures. In this study, genetic trends for carcass traits in these 3 Wagyu populations were estimated, and genetic gains per year were compared among the 3 different beef cattle breeding programs. The field carcass records used were collected between 1988 and 2003. The traits analyzed were carcass weight, LM area, rib thickness, s.c. fat thickness, and beef marbling standard number. The average breeding values of reproducing dams born the same year were used to estimate the genetic trends for the carcass traits. For comparison of the 3 breeding programs, birth years of the dams were divided into 3 periods reflecting each program. Positive genetic trends for beef marbling standard number were clearly shown in all populations. The genetic gains per year for all carcass traits were significantly enhanced by adopting the on-farm progeny testing program. These results indicate that the on-farm progeny testing program with BLUP is a very powerful approach for genetic improvement of carcass traits in Japanese Wagyu beef cattle.     

Clinical and pathological aspects of hemophilia a in Japanese Brown cattle

A coagulopathy with subcutaneous bleeding and muscular or peritracheal/periesophageal bleeding occurred in two male Japanese Brown calves of the same dam. One of the affected calves died three days after the onset of bleeding and the other survived normally until being slaughtered despite once suffering from subcutaneous hematoma. Hemostatic tests of the latter case showed prolonged activated partial thromboplastin time (APTT), and severely reduced factor VIII activity. In addition, von Willebrand factor activity, determined by the human platelet aggregation test, was within the normal range; therefore, the calf was diagnosed with hemophilia A. These are the first bovine cases of hemophilia A definitely diagnosed clinicopathologically.     

Gene dropping analysis of founder contributions in a closed Japanese black cattle population

Gene dropping simulation was applied to Japanese Black cattle population in Hyogo prefecture, to examine the survivals of alleles originated from founder animals. In the analysis, unique alleles were assigned to founders, and the genotypes of all descendants along the actual pedigree were generated through Monte Carlo simulation following Mendelian segregation rules. By replicating this process 10 000 times, the distribution of frequencies of alleles from each founder was estimated. From the distribution, several quantities useful for the management of genetic diversity, such as the probability of allele extinction and the probability of alleles surviving at a critically low frequency were derived. The materials used were 68 781 animals born in 1955–1998 and their pedigree records traced back to the population in 1937 or before. The expected number of alleles retained in the population drastically decreased during the analyzed period, and reached to 57.9 in the population of 1998, which was only 3.3% of the total number of alleles assigned to founders. Detailed analysis of major founders with relatively high genetic contributions to the current population revealed that alleles from most of the major founders are now at high risk of future extinction. These results strongly suggest that for the management of genetic diversity, the genetic contributions of founders are not fully informative, and emphasize the importance of the detection of live animals having founder alleles with high extinction possibilities.     

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.     

种群遗传变异及基因多样度分析

阐述了种群遗传学和生态遗传学研究的基本单位－种群的定义和意念含义,其一是种系变异含义,其二是生态适应含义,并概述了遗传变异的研究历史。从３个方面及质量性状变异,数量性状变异与基金变异,介绍了种群遗传变异的研究方法,重点介绍了基因变异的测量和亚种群基因多样度的测量,并且依据研究所得的遗传参数对中国苜蓿不同种群遗传结构和多样度进行了例证分析。     

牛微卫星标记PCR扩增方法的研究

试验综合利用微卫星多重PCR、DNA池、复合点样和快速银染技术对5个品种牛的群体遗传变异情况进行了分析，建立了一套快速分析家兔群体遗传变异的方法，大大提高了分析效率，缩短了试验时间。试验的各群体家兔遗传变异结果与实际育种事实相符。     

基于SSR标记的河南省狗牙根遗传多样性及群体遗传结构分析北大核心CSCD

应用SSR分子标记,对河南省15个居群共288份狗牙根材料进行遗传多样性及群体遗传结构分析,结果表明,10对引物共扩增出173条条带,其中163条为多态性条带,多态性条带百分率为94.29%,表明河南省狗牙根具有丰富的多态性。15个居群间的遗传分化系数为0.3857,即发生在居群间的遗传变异达到38.57%,大部分的遗传变异发生在居群内部,居群间基因流为0.7964,居群之间存在一定程度的基因交流。不同居群间遗传一致度的变化范围是0.746~0.964,平均为0.767。15个居群间的UPGMA聚类分析结果表明居群间没有完全按照地理来源进行聚类,遗传距离和地理距离矩阵之间的Mantel检验结果表明狗牙根居群间的遗传距离与地理距离之间无相关性。288份狗牙根材料之间的遗传距离为0.0173~0.5205,平均为0.3113,UPGMA聚类结果将所有材料分为3组。基于Structure软件的群体遗传结构分析结果表明,可将288份狗牙根材料分为2个亚群和一个混合型群体,与288份材料的UPGMA聚类结果基本一致,由此可判断两个亚群的遗传背景单一,混合型群体存在一定的种质基因渗透,遗传背景较为复杂。     

Population structure and genetic diversity in Colombian Simmental cattle

Tropical Animal Health and Production - A vital requirement to design and implement a breeding program is to know the structure and genetic diversity of a population. The aim of this study was to...     

Development of novel SNP system for individual and pedigree control in a Japanese Black cattle population using whole‐genome genotyping assay

Individual identification and parentage analysis using DNA markers are essential for assuring food identity and managing livestock population. The objective of this study was to develop a single nucleotide polymorphism (SNP) panel system for individual effective identification and parentage testing in a Japanese Black cattle population using BovineSNP50 BeadChip. On the basis of SNP frequencies, 60 unlinked informative SNPs were finally selected as candidate markers. The allelic frequencies for each SNP were estimated using additional individuals by PCR‐RFLP (restriction fragment length polymorphism). A total of 87 SNP markers added in conjunction with previously developed 27 SNPs were evaluated to assess the utility of the test. The estimated identity power was 2.01 × 10^?34. Parentage exclusion probabilities, when both suspected parents' genotypes were known and when only one suspected parent was genotyped, were estimated as 0.99999997 and 0.99998010, respectively. This developed SNP panel was quite powerful and could successfully exclude false sires with a probability of >0.9999 even if the dam's genotype information was not obtained. The SNP system would contribute to management of the beef industry in Japan.