Genome-wide association studies of female reproduction in tropically adapted beef cattle

The genetics of reproduction is poorly understood because the heritabilities of traits currently recorded are low. To elucidate the genetics underlying reproduction in beef cattle, we performed a genome-wide association study using the bovine SNP50 chip in 2 tropically adapted beef cattle breeds, Brahman and Tropical Composite. Here we present the results for 3 female reproduction traits: 1) age at puberty, defined as age in days at first observed corpus luteum (CL) after frequent ovarian ultrasound scans (AGECL); 2) the postpartum anestrous interval, measured as the number of days from calving to first ovulation postpartum (first rebreeding interval, PPAI); and 3) the occurrence of the first postpartum ovulation before weaning in the first rebreeding period (PW), defined from PPAI. In addition, correlated traits such as BW, height, serum IGF1 concentration, condition score, and fatness were also examined. In the Brahman and Tropical Composite cattle, 169 [false positive rate (FPR) = 0.262] and 84 (FPR = 0.581) SNP, respectively, were significant (P < 0.001) for AGECL. In Brahman, 41% of these significant markers mapped to a single chromosomal region on BTA14. In Tropical Composites, 16% of these significant markers were located on BTA5. For PPAI, 66 (FPR = 0.67) and 113 (FPR = 0.432) SNP were significant (P < 0.001) in Brahman and Tropical Composite, respectively, whereas for PW, 68 (FPR = 0.64) and 113 (FPR = 0.432) SNP were significant (P < 0.01). In Tropical Composites, the largest concentration of PPAI markers were located on BTA5 [19% (PPAI) and 23% (PW)], and BTA16 [17% (PPAI) and 18% (PW)]. In Brahman cattle, the largest concentration of markers for postpartum anestrus was located on BTA3 (14% for PPAI and PW) and BTA14 (17% PPAI). Very few of the significant markers for female reproduction traits for the Brahman and Tropical Composite breeds were located in the same chromosomal regions. However, fatness and BW traits as well as serum IGF1 concentration were found to be associated with similar genome regions within and between breeds. Clusters of SNP associated with multiple traits were located on BTA14 in Brahman and BTA5 in Tropical Composites.     

Genetic effects on beef heifer puberty and subsequent reproduction.

Significant genetic variation exists within and between breeds of beef cattle for age at puberty (AP). In general, faster-gaining breed groups of larger mature size reach puberty at a later age than do slower-gaining breed groups of smaller mature size; breeds selected for milk production reach puberty at younger ages than do those breeds not selected for milk production. Heterosis, independent of heterosis effects on weight, influences most measures of puberty in females and scrotal circumference (SC) in males. Crossbred heifers reach puberty at younger ages and heavier weights than their straightbred counterparts. Scrotal circumference has been shown to be an excellent indicator of AP in yearling bulls. Furthermore, a favorable genetic relationship exists between SC in bulls and AP of female offspring. Beef cattle breeders may take a direct approach to breeding for AP and subsequent reproduction by directly selecting for measures of fertility such as SC. However, an indirect approach, involving selection for an array of traits that provide an appropriate "genetic environment" for the expression of fertility (i.e., size, milk production, calving ease) may be preferred. Although seedstock producers are limited to making change through within-breed selection, commercial producers can take advantage of both within- and between-breed selection as well as crossbreeding to achieve the same goal.     

Breed effects and heterosis in advanced generations of composite populations for puberty and scrotal traits of beef cattle

Heterosis effects were evaluated in F1, F2, and F3 generations of females and in the F1, F2, and combined F3 and F4 generations of males in three composite populations of beef cattle. Traits included weight, height, and condition scores at different ages, percentage of females reaching puberty at 368, 410, and 452 d, adjusted age, and adjusted weight of females at puberty and scrotal circumference and paired testicular volume of males. Breed effects were evaluated for the nine parental breeds (Red Poll [R], Hereford [H], Angus [A], Limousin [L], Braunvieh [B], Pinzgauer [P], Gelbvieh [G], Simmental [S], and Charolais [C]) that contributed to the three composite populations (MARC I = 1/4 C, 1/4 B, 1/4 L, 1/8 H, 1/8 A; MARC II = 1/4 G, 1/4 S, 1/4 H, 1/4 A; and MARC III = 1/4 R, 1/4 P, 1/4 H, 1/4 A). Breed effects were significant for all traits evaluated. Heterosis was significant for weight, height, and condition score at all ages and for most measures of puberty in each generation of each composite and for the mean of the three composite populations. Heterosis for age at puberty was largely independent of heterosis effects on 368-d weight. Heterosis was significant for scrotal circumference and paired testicular volume in each generation of each composite and for the mean of the three composite populations. Heterosis effects on scrotal measurements are mediated both through heterosis effects on growth rate and through factors that are independent of growth rate. Correlation coefficients among breed group means and correlations of breed rank for scrotal measurements with puberty traits of females were greater than or equal to .88 (P less than .01) for all puberty traits except weight at puberty, which was not associated with scrotal measurements. There was close agreement in heterosis observed for most traits and expectation based on retained heterozygosity. These results support the hypothesis that heterosis in cattle for size, puberty, and scrotal measurement traits is due to dominance effects of genes.     

中国不同牛种DGAT1基因遗传多样性及经济性状关联分析研究进展

乙酰辅酯A∶二酰甘油酰基转移酶(DGAT1)是甘油三脂合成过程中唯一的关键酶,对动物机体脂肪代谢、沉积起重要作用,已成为研究奶牛泌乳性状和肉牛主要经济性状的重要候选基因之一。近年来,随着相关研究的不断深入,研究者普遍认为DGAT1基因对奶牛的产奶量、乳脂率、乳蛋白率、乳糖率、乳脂肪酸及空怀天数、输精次数、初配年龄等繁殖性状均有显著影响,且与肉牛体脂也存在相关性。作者主要介绍了DGAT1基因的遗传多态性及其与经济性状关联分析在中国各地区不同品种奶牛、肉牛、水牛和牦牛上的研究进展,指出该基因对奶牛的产奶性能及肉牛的肉质性状、生长性状具有重要的调控作用。但由于环境条件、品种及选育背景等因素影响,DGAT1基因遗传多态性对不同地区不同牛群体的经济性状影响不尽相同。因此,要将DGAT1基因实际应用在品种选育工作中还需明确该基因对研究群体的具体遗传效应,并结合其他候选基因进行综合分析。     

Identification of differential selection traces in two Polish cattle breeds

Genetic improvement of animals based on artificial selection is leading to changes in the frequency of genes related to desirable production traits. The changes are reflected by the neutral, intergenic single nucleotide polymorphims (SNPs) being in long‐range linkage disequilibrium with functional polymorphisms. Genome‐wide SNP analysis tools designed for cattle, allow for scanning divergences in allelic frequencies between distinct breeds and thus for identification of genomic regions which were divergently selected in breeds' histories. In this study, by using Bovine SNP50 assay, we attempted to identify genomic regions showing the highest differences in allele frequencies between two distinct cattle breeds – preserved, unselected Polish Red breed and highly selected Holstein cattle. Our study revealed 19 genomic regions encompassing 55 protein‐coding genes and numerous quantitative trait loci which potentially may underlie some of the phenotypic traits distinguishing the breeds.     

深县猪mtDNA CytB基因的遗传多样性与母系起源研究

 研究过氧化物酶体增殖激活受体α (PPARα) 基因第7外显子SNP位点与牛的部分胴体、肉质性状的相关性。以6个牛品种(秦川牛、南阳牛、郏县红牛、鲁西牛、安格斯、夏南牛) 共计717个个体为研究对象,采用PCR SSCP结合DNA测序方法对PPARα基因第7外显子进行SNP检测,并该SNP位点与108头秦川牛的部分胴体、肉质性状的相关性进行分析。结果发现在PPARα基因第7外显子的184位检测到C→T突变,在南阳牛、秦川牛、郏县红牛、安格斯、鲁西牛、夏南牛这6个群体中等位基因E/F的频率分别是0.225/0.775,0.151/0.849,0.125/0.875,0.123/0.877,0.070/0.930, 0.157/0.783;遗传学指标结果显示：秦川牛、郏县红牛、安格斯、鲁西牛和夏南牛这5个群体属于低度多态(PIC<0.25),南阳牛为中度多态（PIC=0.288）;相关分析结果显示：该位点与秦川牛的背膘厚和胴体长两个性状显著相关,表现为FF基因型个体在背膘厚性状方面显著高于EE和EF基因型个体(P<0.05),FF基因型个体的胴体长显著高于EE基因型个体(P<0.05)。这一位点可能是影响牛背膘厚和胴体长的主效QTN或与之紧密连锁,可做为肉牛选育的候选分子标记。     

Allelic and Genotypic Frequencies of the Leptin Gene Sau3AI-Restriction Fragment Length Polymorphism and Evaluation of Its Association with Age at Puberty in Cattle in the Southwestern United States and Northern Mexico

Leptin is a hormone secreted by adipose tissue that influences appetite, growth, and reproduction. In cattle, the leptin gene contains a Sau3A-restriction fragment length polymorphism (RFLP) within intron II and exon III. This RFLP yields two alleles (A and B) and three genotypes (AA, AB, and BB). Because level of adiposity is important to numerous performance traits, two studies were conducted to assess the potential use of the leptin Sau3AI-RFLP as a selection tool in cattle in the Southwestern United States and Northern Mexico. The objective of the first study was to survey allelic and genotypic frequencies of the Sau3AI-RFLP in breed groups of cattle selected for beef production. High frequencies (≥0.76) of the A allele were observed in cattle that were Bos taurus (Angus and Criollo), Bos indicus-influenced (Brangus, Brahman, F₁-Hereford x Brahman, Santa Cruz, and Santa Gertrudis), and of historic lineage of Bos taurus x Bos indicus (African Mashona). Genotypic frequencies in these breed groups were 0.82 (AA), 0.16 (AB), and 0.02 (BB). The objective of the second study was to evaluate the relationship of the leptin RFLP to age at puberty in heifers. No relationship was detected (P < 0.38) between genotype and age at puberty. The A allele existed in the breed groups evaluated with high frequency, thus negating the ability to assess the relationship of the B allele to age at puberty. Findings do not support use of the leptin Sau3AI-RFLP as a marker in selection strategies for cattle in the Southwestern United States and Northern Mexico.     

Growth and pubertal development in Brahman-, Boran-, Tuli-, Belgian Blue-, Hereford- and Angus-sired F1 bulls

Growth and testicular development between 7 and 15 mo of age were evaluated in bulls produced by mating sires of six breeds (Hereford, Angus, Belgian Blue, Brahman, Boran, and Tuli) to Angus, Hereford, and MARC III (four-breed composite) cows. At 12 mo of age, Angus- and Hereford-sired bulls had the heaviest body weight (P < 0.08 to 0.001), whereas Brahman- and Belgian Blue-sired bulls were intermediate, and Boran- and Tuli-sired bulls weighed the least. Bulls sired by European breeds grew more rapidly after weaning (P < 0.01) than did Brahman-, Boran-, and Tuli-sired bulls, and these differences in growth rate were maintained through 15 mo of age, indicating that offspring of heat-adapted sire breeds (Brahman, Boran, and Tuli) have lower postweaning rates of gain, particularly during winter months, than do offspring of nonheat adapted sire breeds. Testis size was smaller initially (P < 0.01) and remained smaller in offspring of heat-adapted sire breeds through yearling age. By 15 mo of age, testis size was largest (P < 0.06 to 0.001) in Angus-sired bulls and had become similar among Hereford-, Brahman-, Boran- and Belgian Blue-sired bulls but remained smaller (P < 0.02 to 0.001) in Tuli-sired bulls. Thus, offspring of heat-adapted sire breeds had delayed testicular development compared with that of nonheat adapted sire breeds, particularly through yearling age. At puberty, Angus-sired bulls were 23 to 82 d younger (P < 0.05 to 0.001) than all other sire breeds except Hereford, and Brahman-sired bulls were older at puberty (P < 0.05 to 0.001) than were bulls of all other sire breeds except Boran. Testis size at puberty was quite similar among breeds of bulls (scrotal circumference = 27.9 +/- 0.1 cm) despite large breed differences in age, body weight, and hip height. Thus, measurement of yearling testis size was a reliable indicator of age at puberty among widely divergent breeds of bulls. In addition, the lower postweaning rates of gain and the smaller and slower testicular development in offspring of heat-adapted sire breeds should be noted by cattle producers considering use of such breeds in crossbreeding and breed improvement programs.     

Animal genetic resource trade flows: The utilization of newly imported breeds and the gene flow of imported animals in the United States of America

Animal germplasm exchange has recently received attention as a product of the FAO's State of the World's Animal Genetic Resources effort. Some have advocated a need to explore policies and regulations on the exchange of germplasm (e.g., Hiemstra, S.J., Drucker, A., Tvedt, M., Louwaars, N., Oldenbroek, J., Awgichew, K., Kebede, S., Bhat, P., da Silva Mariante, A. 2006. Exchange, use and conservation of animal genetic resources: policies and regulatory options. Centre for Genetic Resources. Wageningen Univ., the Netherlands, pp. 1­43). However, there has been little comprehensive assessment of either the economic or genetic impact of introduced germplasm into national populations. As a result, much of the discussion of gene flows has been based on assumptions and generalizations. The objective of this paper is to evaluate the genetic impact of germplasm imported into the United States during the last 25 to 50 years. The paper considers both new breeds (Meishan pigs, Tuli cattle, and Boer goats) and new animals within existing breeds (Limousin and Jersey cattle). Of the new breeds recently imported only one had an impact on US animal agriculture. Neither the Tuli nor the Meishan has impacted the US livestock industry. It appears that these breeds were initially viewed as attractive because of single traits, but producers did not find it attractive to adopt the new breeds based on these specific traits. In the end, these breeds did not prove competitive in the US under the current set of market conditions. This result would indicate that importation of new genetic resources due to a single trait of interest is not a viable importation strategy. By contrast, the Boer goat exhibited a number of production characteristics which made it desirable to US producers and thereby allowed the breed to become well established. A second portion of the study evaluated the importation and parentage pattern of Limousin cattle as they became established in the U. S. and the gene flow of imported Jersey cattle since the 1950′s. In both cases, the study relied on pedigree analysis. Over the past fifty years, Jersey cattle have been sporadically imported from various countries, but no imported animal has had an overpowering effect on the population. It appears that by the great-grand progeny level, the genes from imported animals are diminishing rather than increasing in the population. In evaluating the predicted transmitting abilities for imported cattle relative to high and moderately ranked domestically bred cattle, there were significant differences between these groups for milk production. This would be sufficient to explain why the impact of the imported cattle diminished. The results of our analysis at both the breed and individual level underscore the speculative nature of germplasm importation — even within breeds where there is a great deal of information available about production characteristics. From this analysis, we conclude that successful importation of new breeds into the US must be based on a large number of production characteristics; importation for a single characteristic (e.g., high prolificacy) while the breed is deficient in other areas does not lead to the breed's adoption. While not fully explored in this work, it appears that initial interest and acceptance from the private sector is crucial for breed acceptance, as the Boer goat demonstrates. Within an existing breed, importation of individual animals still appears to have a relatively high degree of risk and is dependent upon the importer's ability to pick viable candidates. However, once animals are imported their progeny must effectively compete with the domestic population, or else their genetic contribution will rapidly diminish.     

High incidence of single nucleotide polymorphisms in the prion protein gene of native Brazilian Caracu cattle

Different alleles of the human and ovine prion protein gene correlate with a varying susceptibility to transmissible spongiform encephalopathies. However, the pathogenic implications of specific polymorphisms in the bovine prion protein gene (PRNP) are only poorly understood. Previous studies on the bovine PRNP gene investigated common European and North American cattle breeds. As a consequence of decades of intensive breeding for specific traits, these modern breeds represent only a small fraction of the bovine gene pool. In this study, we analysed PRNP polymorphisms in the native Brazilian Caracu breed, which developed in geographical isolation since the 16th century. A total of 10 single nucleotide polymorphisms (SNPs) were discovered in the coding region of the Caracu PRNP gene. Eight of the SNPs occurred at high frequencies in Caracu cattle (variant allele frequencies = 0.10–0.76), but were absent or only rarely observed in European and North American breeds. One of the Caracu SNPs was associated with an amino acid exchange from serine to asparagine (f = 0.17). This SNP was not detected in Holstein–Friesian, Simmental and German Gelbvieh and was only rarely detected in beef cattle (f = 0.01). We found 17 haplotypes for PRNP in the Caracu breed.     

The contribution of migrant breeds to the genetic gain of beef traits of German Vorderwald and Hinterwald cattle

During the past decades, migrant contributions have accumulated in many local breeds. Cross‐breeding was carried out to mitigate the risk of inbreeding depression and to improve the performance of local breeds. However, breeding activities for local breeds were not as intensive and target oriented as for popular high‐yielding breeds. Therefore, even if performance improved, the gap between the performance of local and popular breeds increased for many traits. Furthermore, the genetic originality of local breeds declined due to the increasing contributions of migrant breeds. This study examined the importance of migrant breed influences for the realization of breeding progress of beef traits of German Vorderwald and Hinterwald cattle. The results show that there is a high amount of migrant contributions and their effects on performance are substantial for most traits. The effect of the French cattle breed Montbéliard (p‐value 0.014) on daily gain of Vorderwald bulls at test station was positive. The effects of Vorderwald ancestors (p‐value for daily gain 0.007 and p‐value for net gain 0.004) were positive for both traits under consideration in the population of Hinterwald cattle. Additionally, the effect of remaining breeds (p‐value 0.030) on net gain of Hinterwald cattle in the field was also positive. The estimated effect of Fleckvieh ancestors on net gain of Hinterwald cattle was even larger but not significant. Breeding values adjusted for the effects of the migrant breeds showed little genetic trend.     

Managing genomes of conserved livestock breeds with historical introgression to decrease genetic overlap with other breeds

Recovering the native genetic background of a breed and increasing the founder genome equivalent (FGE) that is contributed by a breed to the gene pool of the species can increase its value for conservation. The suitability of several strategies was compared, whereby a hypothetical multi‐breed population, the core set, was used to approximate the genetic diversity of the species. Twenty‐five generations of management were simulated based on genotypes of German Angler cattle. The scenarios were compared when the kinship reached 0.10. The native contribution (NC) increased in a population with 400 births per generation from 0.317 to 0.706, whereas 1,000 births enabled to reach 0.894. This scenario maximized the NC, constrained the native kinship, and the kinship of the core set so that its genetic diversity could not decrease. It increased the proportions of mainstream breeds because their genes were removed from the target breed. A substantial increase of the FGE was achieved in some other scenarios, which arose from reduced genetic overlap and from increased diversity within the breed. The latter factor is especially important for breeds with high contributions to the core set.     

Detection of selection signatures for agonistic behaviour in cattle

The identification of genomic regions including signatures of selection produced by domestication and its subsequent artificial selection processes allows the understanding of the evolution of bovine breeds. Although several studies describe the genomic variability among meat or milk production cattle breeds, there are limited studies orientated towards bovine behavioural features. This study is focused on mapping genomic signatures of selection which may provide insights of differentiation between neutral and selected polymorphisms. Their effects are studied in the Lidia cattle traditionally selected for agonistic behaviour compared with Spanish breeds showing tamed behaviour. Two different approaches, BayeScan and SelEstim, were applied using genotypic 50K SNP BeadChip data. Both procedures detected two genomic regions bearing genes previously related to behavioural traits. The frequencies of the selected allele in these two regions in Lidia breed were opposite to those found in the tamed breeds. In these genomic regions, several putative genes associated with enriched metabolic pathways related to the behavioural development were identified, as neurochondrin gene (NCDN) or glutamate ionotropic receptor kainate type subunit 3 (GRIK3) both located at BTA3 or leucine‐rich repeat and Ig domain containing 2 (LINGO2) and phospholipase A2‐activating protein (PLAA) at BTA8.     

秦川牛分子标记研究进展

秦川牛作为中国地方良种黄牛之一,具有独特的遗传性能.本文从秦川牛的分子群体遗传特征及起源、进化、经济性状、分子遗传标记及相关功能基因多态性等方面对其研究进展进行了综述,同时指出了秦川牛分子育种的前景及目前存在问题.     

Identification of genomic regions that exhibit sexual dimorphism for size and muscularity in cattle

Sexual dimorphism, the phenomenon whereby males and females of the same species are distinctive in some aspect of appearance or size, has previously been documented in cattle for traits such as growth rate and carcass merit using a quantitative genetics approach. No previous study in cattle has attempted to document sexual dimorphism at a genome level; therefore, the objective of the present study was to determine whether genomic regions associated with size and muscularity in cattle exhibited signs of sexual dimorphism. Analyses were undertaken on 10 linear-type traits that describe the muscular and skeletal characteristics of both males and females of five beef cattle breeds: 1,444 Angus (AA), 6,433 Charolais (CH), 1,129 Hereford, 8,745 Limousin (LM), and 1,698 Simmental. Genome-wide association analyses were undertaken using imputed whole-genome sequence data for each sex separately by breed. For each single-nucleotide polymorphism (SNP) that was segregating in both sexes, the difference between the allele substitution effect sizes for each sex, in each breed separately, was calculated. Suggestively (P ≤ 1 × 10⁻⁵) sexually dimorphic SNPs that were segregating in both males and females were detected for all traits in all breeds, although the location of these SNPs differed by both trait and breed. Significantly (P ≤ 1 × 10⁻⁸) dimorphic SNPs were detected in just three traits in the AA, seven traits in the CH, and three traits in the LM. The vast majority of all segregating autosomal SNPs (86% in AA to 94% in LM) had the same minor allele in both males and females. Differences (P ≤ 0.05) in allele frequencies between the sexes were observed for between 36% (LM) and 66% (AA) of the total autosomal SNPs that were segregating in both sexes. Dimorphic SNPs were located within a number of genes related to muscularity and/or size including the NAB1, COL5A2, and IWS1 genes on BTA2 that are located close to, and thought to be co-inherited with, the MSTN gene. Overall, sexual dimorphism exists in cattle at the genome level, but it is not consistent by either trait or breed.     

南阳牛经济性状的分子标记研究进展

南阳牛作为中国地方良种黄牛之一,具有独特的遗传特性.本文从南阳牛的经济性状分子遗传标记及相关功能基因多态性等方面对其研究进展成就作了综述,同时指出了南阳牛分子育种的前景和存在问题.     

Analysis of factors affecting the electric conductivity of cow's milk--breed, locale, season

The problem was studied in a set of 678 mammary glands of 212 cows - crossbreds between the Holstein-Friesian breed with the Slovak Spotted cattle, crossbreds of the Black-Pied Lowland and Bohemian Spotted breed, and three-way crossbreds of the Black-Pied Lowland, Swedish White and Bohemian Spotted cattle. The confrontation of the confidence intervals of milk conductivity (MC) in healthy mammary glands at alpha = 0.05 showed that in the crossbreds of the Black-Pied Lowland cattle the MC was statistically significantly higher than in the breed types of the Holstein-Friesian cattle. The MC values decrease when there is a larger proportion of the blood of beef-and-dairy cattle (Slovak Spotted and Bohemian Spotted breeds). The locality where the stock was kept was found to act as an important factor underlying MC only in cases when both the geographical conditions and breed proportions were different. In a set homogenized with respect to the breeds, statistically significant differences in MC were demonstrated between the spring and summer season, spring and autumn, summer and autumn, and autumn and winter season.     

Effects of breed proportion and components of heterosis for semen traits in a composite cattle breed

The aim of this study was to estimate the non‐additive genetic effects of the dominance component of heterosis as well as epistatic loss on semen traits in admixed Swiss Fleckvieh, a composite of Simmental (SI) and Red Holstein Friesian (RHF) cattle. Heterosis is the additional gain in productivity or fitness of cross‐bred progeny over the mid‐purebred parental populations. Intralocus gene interaction usually has a positive effect, while epistatic loss generally reduces productivity or fitness due to lack of evolutionarily established interactions of genes from different breeds. Genotypic data on 38,205 SNP of 818 admixed, as well as 148 RHF and 213 SI bulls as the parental breeds were used to predict breed origin of alleles. The genomewide locus‐specific breed ancestries of individuals were used to calculate effects of breed difference as well as the dominance component of heterosis, while proxies for two definitions of epistatic loss were derived from 100,000 random pairs of loci. The average Holstein Friesian ancestry in admixed bulls was estimated 0.82. Results of fitting different linear mixed models showed including the dominance component of heterosis considerably improved the model adequacy for three of the four traits. Inclusion of epistatic loss increased the accuracy of the models only for our new definition of the epistatic effect for two traits, while the other definition was so highly correlated with the dominance component that statistical separation was impossible.