Relationship between inbreeding and milk production traits in two Italian dairy sheep breeds

The effects of inbreeding in livestock species breeds have been well documented and they have a negative impact on profitability. The objective of this study was to evaluate the levels of inbreeding in Sarda (SAR, n = 785) and Valle del Belice (VdB, n = 473) dairy sheep breeds and their impact on milk production traits. Two inbreeding coefficients (F) were estimated: using pedigree (F_PED), or runs of homozygosity (ROH; F_ROH) at different minimum ROH lengths and different ROH classes. After the quality control, 38,779 single nucleotide polymorphisms remained for further analyses. A mixed-linear model was used to evaluate the impact of inbreeding coefficients on production traits within each breed. VdB showed higher inbreeding coefficients compared to SAR, with both breeds showing lower estimates as the minimum ROH length increased. Significant inbreeding depression was found only for milk yield, with a loss of around 7 g/day (for SAR) and 9 g/day (VdB) for a 1% increase of F_ROH. The present study confirms how the use of genomic information can be used to manage intra-breed diversity and to calculate the effects of inbreeding on phenotypic traits.     

Genome-wide identification of runs of homozygosity islands in the Gyr breed (Bos indicus)

Runs of homozygosity (ROH) are contiguous homozygous regions of the genome. These regions can be used to identify genes associated with traits of economic interest, as well as inbreeding levels. The aim of the present study was to analyse the length and distribution of ROH islands in Gyr cattle and to identify genes within these regions. A population of 173 animals selected for beef production and a population of 291 animals selected for dairy production were used. Differences in the number of short ROH (ROH_{1-2 Mb}) were observed between the two populations, while the number of long ROH (ROH_{>16 Mb}) was similar. ROH islands with the highest incidences (>0.50) overlapped in several segments of the genome in the two populations. The genes identified were associated with milk production, growth, reproduction, immune response and resistance traits. Our results contribute to the understanding of how selection can shape the distribution of ROH and ROH islands within the same breed when animals are selected for different purposes such as dairy or beef production.     

Estimates of autozygosity derived from runs of homozygosity: empirical evidence from selected cattle populations

Using genome‐wide SNP data, we calculated genomic inbreeding coefficients (F_ROH > _1 Mb, F_{ROH > 2 Mb}, F_{ROH > 8 Mb} and F_{ROH > 16 Mb}) derived from runs of homozygosity (ROH) of different lengths (>1, >2, >8 and > 16 Mb) as well as from levels of homozygosity (F_HOM). We compared these values of inbreeding coefficients with those calculated from pedigrees (F_PED) of 1422 bulls comprising Brown Swiss (304), Fleckvieh (502), Norwegian Red (499) and Tyrol Grey (117) cattle breeds. For all four breeds, population inbreeding levels estimated by the genomic inbreeding coefficients F_{ROH > 8 Mb} and F_{ROH > 16 Mb} were similar to the levels estimated from pedigrees. The lowest values were obtained for Fleckvieh (F_PED = 0.014, F_{ROH > 8 Mb} = 0.019 and F_{ROH > 16 Mb} = 0.008); the highest, for Brown Swiss (F_PED = 0.048, F_{ROH > 8 Mb} = 0.074 and F_{ROH > 16 Mb} = 0.037). In contrast, inbreeding estimates based on the genomic coefficients F_{ROH > 1 Mb} and F_{ROH > 2 Mb} were considerably higher than pedigree‐derived estimates. Standard deviations of genomic inbreeding coefficients were, on average, 1.3–1.7‐fold higher than those obtained from pedigrees. Pearson correlations between genomic and pedigree inbreeding coefficients ranged from 0.50 to 0.62 in Norwegian Red (lowest correlations) and from 0.64 to 0.72 in Tyrol Grey (highest correlations). We conclude that the proportion of the genome present in ROH provides a good indication of inbreeding levels and that analysis based on ROH length can indicate the relative amounts of autozygosity due to recent and remote ancestors.     

Detection of runs of homozygosity in conserved and commercial pig breeds in Poland

Runs of homozygosity (ROH) are continuous segments of the genome that arose as a result of inbreeding, resulting in the inheritance of identical haplotypes from both parents who shared a common ancestor. In the present study, we performed a detailed characterization and comparison of ROH in four pig breeds, including intensively selected Polish Landrace as well as native unselected animals of Puławska and two Złotnicka breeds (White and Spotted). We used a medium-density PorcineSNP60 BeadChip assay (Illumina) and cgaTOH software to detect ROH covering a minimum of 30 adjacent SNPs and maintaining a size over 1 Mb. By analysing ROH distribution and frequency across the genome, we also identified genomic regions with high ROH frequency (so-called “ROH hotspots”). The obtained results showed that the analysed conserved breeds were characterized by a higher ROH span and higher ROH-based inbreeding coefficients (F_ROH), which likely result from past population bottlenecks, increasing the overall inbreeding level within these populations. The analysis of ROH distribution across the genomes revealed the presence of both shared and breed-specific ROH hotspots. These hotspots, presumably representing genome regions under selection, overlapped with a variety of genes associated with processes connected with immune system functioning, reproduction, glucose homeostasis and metabolism. The genome regions with ROH hotspots overlapping in all analysed populations, located on SSC4 (51.9–55.9 Mb) and 13 (92.6–97.8 Mb), covered thirty-one different genes, including MMP16, SLC7A13, ATP6V0D2, CNGB3, WWiP1, RiMDN1 and CPNE3. These genes are primarily associated with biological regulation and metabolism, processes that could be responsible for the variety of the selected production and functional features.     

Genome-wide scan for runs of homozygosity in the composite Montana Tropical® beef cattle

The aim of this study was to assess the distribution of runs of homozygosity (ROH) and autozygosity islands in the composite Montana Tropical^® beef cattle to explore hotspot regions which could better characterize the different biological types within the composite breed. Montana animals (n = 1,436) were genotyped with the GGP-LD BeadChip (~30,000 markers). ROH was identified in every individual using the plink v1.90 software. Medium and long ROH prevailed in the genome, which accounted for approximately 74% of all ROH detected. On an average, 2.0% of the genome was within ROH, agreeing with the pedigree-based inbreeding coefficient. The Montana cattle with a higher proportion of productive breed types showed the highest number of autozygosity islands (n = 17), followed by those with a higher proportion of breeds adapted to tropical environments (n = 15). Enriched terms (p < .05) associated with the immune and inflammatory response, homeostasis, reproduction, mineral absorption, and lipid metabolism were described within the autozygosity islands. In this regard, over-represented GO terms and KEGG pathways described in this population may play a key role in providing information to explore the genetic and biological mechanisms together with the genomic regions underlying each biological type that favoured their optimal performance ability in tropical and subtropical regions.     

Estimation of inbreeding depression on female fertility in the Finnish Ayrshire population

Single nucleotide polymorphism (SNP) data enable the estimation of inbreeding at the genome level. In this study, we estimated inbreeding levels for 19,075 Finnish Ayrshire cows genotyped with a low‐density SNP panel (8K). The genotypes were imputed to 50K density, and after quality control, 39,144 SNPs remained for the analysis. Inbreeding coefficients were estimated for each animal based on the percentage of homozygous SNPs (F_PH), runs of homozygosity (F_ROH) and pedigree (F_PED). Phenotypic records were available for 13,712 animals including non‐return rate (NRR), number of inseminations (AIS) and interval from first to last insemination (IFL) for heifers and up to three parities for cows, as well as interval from calving to first insemination (ICF) for cows. Average F_PED was 0.02, F_ROH 0.06 and F_PH 0.63. A correlation of 0.71 was found between F_PED and F_ROH, 0.66 between F_PED and F_PH and 0.94 between F_ROH and F_PH. Pedigree‐based inbreeding coefficients did not show inbreeding depression in any of the traits. However, when F_ROH or F_PH was used as a covariate, significant inbreeding depression was observed; a 10% increase in F_ROH was associated with 5 days longer IFL0 and IFL1, 2 weeks longer IFL3 and 3 days longer ICF2 compared to non‐inbred cows.     

Genetic diversity and genomic inbreeding in Japanese Black cows in the islands of Okinawa Prefecture evaluated using single-nucleotide polymorphism array

Maintaining genetic diversity and inbreeding control are important in Japanese Black cattle production, especially in remote areas such as the islands of Okinawa Prefecture. Using a single-nucleotide polymorphism (SNP) array, we evaluated the genetic diversity and genomic inbreeding in Japanese Black cows from the islands of Okinawa Prefecture and compared them to those from other locations across Japan. Linkage disequilibrium decay was slower in cows in the islands of Okinawa Prefecture. The estimated effective population size declined over time in both populations. The genomic inbreeding coefficient (F_ROH) was estimated using long stretches of consecutive homozygous SNPs (runs of homozygosity; ROH). F_ROH was higher in the cows on the islands of Okinawa Prefecture than on other locations. In total, 818 ROH fragments, including those containing NCAPG and PLAG1, which are major quantitative trait loci for carcass weight in Japanese Black cattle, were present at significantly higher frequencies in cows in the islands of Okinawa Prefecture. This suggests that the ROH fragments are under strong selection and that cows in the islands of Okinawa Prefecture have low genetic diversity and high genomic inbreeding relative to those at other locations. SNP arrays are useful tools for evaluating genetic diversity and genomic inbreeding in cattle.     

Runs of homozygosity and analysis of inbreeding depression

Pedigree information was traditionally used to assess inbreeding. The availability of high-density marker panels provides an alternative to assess inbreeding, particularly in the presence of incomplete and error-prone pedigrees. Assessment of autozygosity across chromosomal segments using runs of homozygosity (ROH) has emerged as a valuable tool to estimate inbreeding due to its general flexibility and ability to quantify the chromosomal contribution to genome-wide inbreeding. Unfortunately, the identification of ROH segments is sensitive to the parameters used during the search process. These parameters are heuristically set, leading to significant variation in the results. The minimum length required to identify an ROH segment has major effects on the estimation of inbreeding and inbreeding depression, yet it is arbitrarily set. To overcome this limitation, a search algorithm to approximate mutation enrichment was developed to determine the minimum length of ROH segments. It consists of finding genome segments with significant effect differences in trait means between animals with high and low burdens of autozygous intervals with a specific length. The minimum length could be determined heuristically as the smallest interval at which a significant signal is detected. The proposed method was tested in an inbred Hereford cattle population genotyped for 30,220 SNPs. Phenotypes recorded for six traits were used for the approximation of mutation loads. The estimated minimum length was around 1 Mb for yearling weight (YW) and average daily gain (ADG) and 4 Mb for birth weight and weaning weight. These trait-specific thresholds estimated using the proposed method could be attributed to a trait-dependent effect of homozygosity. The detection of significant inbreeding effects was well aligned with the estimated thresholds, especially for YW and ADG. Although highly deleterious alleles are expected to be more frequent in recent inbreeding (long ROH), short ROH segments (<5 Mb) could contain a large number of less deleterious mutations with substantial joint effects on some traits (YW and ADG). Our results highlight the importance of accurate estimation of the ROH-based inbreeding and the necessity to consider a trait-specific minimum length threshold for the identification of ROH segments in inbreeding depression analyses. These thresholds could be determined using the proposed method provided the availability of phenotypic information.     

Is neutral genetic diversity related to quantitative variation in semen traits in bulls?

Conservation decisions based on neutral genetic diversity have been observed to promote retention of useful quantitative variation in biological populations. An experiment was undertaken to determine the association between microsatellite marker polymorphisms and phenotypic variation in semen production and cryosurvival traits in bulls. Thirty-five ejaculates were collected from ten bulls of two breeds and evaluated before and after cryopreservation for several semen traits. The bulls were also genotyped using a set of sixteen bovine-specific microsatellite marker loci. Fixation indices (F_ST), heterozygosity and Nei's genetic distance measures were computed from allele frequency data for each of the bulls. Molecular and phenotypic data were used to compute tri-distance matrices for the ten bulls and correlated using Mantel's test in GenAIEx 6.5. The study revealed extensive heterogeneity in semen traits, heterozygosity and F_ST values among the bulls. Large pairwise phenotypic and genetic distances were also observed. Correlation between pairwise genetic distances and phenotypic distances was significant and highly positive for sperm viability (r = .61, p < .001) and moderately positive for sperm motility (r = .40–42, p < .05) variables. For sperm morphology, ejaculate volume and sperm concentration, correlation with genetic distances was positive, low and not significantly different from zero (p > .05). A tendency for a triangular-shaped relationship between genetic and phenotypic distances for post-thaw motility and viability traits was also observed. Accordingly, association with neutral genetic diversity was absent for semen production traits and moderate to highly positive for sperm cryosurvival traits. Given these findings, conservation decisions based on neutral genetic diversity may capture variation in some adaptive traits, but not others.     

Inbreeding Depression on Semen Quality in Austrian Dual‐Purpose Simmental Bulls

Using pedigree data, the inbreeding coefficients of 715 Austrian dual‐purpose Simmental (Fleckvieh) bulls stationed in two artificial insemination (AI) centres in Upper and Lower Austria were calculated and incorporated in statistical models for the analysis of semen quality. Five semen quality parameters (volume, concentration, motility, number of spermatozoa per ejaculate and percentage of viable spermatozoa) of approximately 30 000 ejaculates, used in two separate data sets, were investigated. The mixed model included the fixed effects age class of the bull, bull handler, semen collector, month and year of collection, number of collection per bull and day, time interval since last collection, the linear continuous effect of the inbreeding coefficient of the bull, interactions between age class and month, and age class and interval since last collection, respectively, as well as the random effect of the bull and the random residual effect. Non‐linear effects of inbreeding were significant for motility only. Despite the quite low inbreeding coefficients (mean 1.3%), all semen quality traits showed inbreeding depression, in four of the five traits significantly in at least one of the data sets. The magnitude of inbreeding depression was small, which might partly be caused by the low inbreeding levels and a potential pre‐selection of the bulls in the AI centres. However, monitoring of inbreeding depression on fertility traits is recommended to avoid unrecognized deterioration of such traits.     

中国西门塔尔牛育种效果分析

采用6个国家级种畜场1980～2000年间的数据对中国西门塔尔牛21年来的育种效果进行分析。对主要性状的遗传力、遗传相关进行了估计．并计算出总性能指数。所有性状均采用动物模型并利用MT-DFREML(多性状非求导)软件进行分析。     

Estimation of inbreeding and effective population size of full‐blood wagyu cattle registered with the American Wagyu Cattle Association

The objective of this research was to examine the population structure of full‐blood (100%) Wagyu cattle registered in the United States with the American Wagyu Association, with the aim of estimating and comparing the levels of inbreeding from both pedigree and genotypic data. A total of 4132 full‐blood Wagyu cattle pedigrees were assessed and used to compute the inbreeding coefficients (F_IT and F_ST) and the effective population size (N_e) from pedigree data for the period 1994 to 2011. In addition to pedigree analysis, 47 full‐blood Wagyu cattle representing eight prominent sire lines in the American Wagyu cattle population were genotyped using the Illumina BovineSNP50 BeadChip. Genotypic data were then used to estimate genomic inbreeding coefficients (F_ROH) by calculating runs of homozygosity. The mean inbreeding coefficient based on the pedigree data was estimated at 4.80%. The effective population size averaged 17 between the years 1994 and 2011 with an increase of 42.9 in 2000 and a drop of 1.8 in 2011. Examination of the runs of homozygosity revealed that the 47 Wagyu cattle from the eight prominent sire lines had a mean genomic inbreeding coefficient (F_ROH) estimated at 9.08% compared to a mean inbreeding coefficient based on pedigree data of 4.8%. These data suggest that the mean genotype inbreeding coefficient of full‐blood Wagyu cattle exceeds the inbreeding coefficient identified by pedigree. Inbreeding has increased slowly at a rate of 0.03% per year over the past 17 years. Wagyu breeders should continue to utilize many sires from divergent lines and consider outcrossing to other breeds to enhance genetic diversity and minimize the adverse effects of inbreeding in Wagyu.     

Genetic and Environmental Influences on Semen Traits in A.I. Bulls

Contents: Repeatability and heritability coefficients were estimated for ejaculate volume, mass movement, individual motility, sperm concentration, first and second post-freezing control of motility, number of doses frozen, total number of spermatozoa and total number of motile spermatozoa per ejaculate in the first ten ejaculates of 175 Swiss Holstein and 673 Simmental young bulls (200 pure Simmental, 473 Simmental x Red Holstein crosses). Data were analysed using the univariate individual animal model with effects of interval between consecutive collections, age of bull at collection, season of collection, breed group of Simmental bulls according to percentage of Red Holstein genes, bull (within breed group) and permanent environment. Crossbred bulls had a better performance in all traits. Repeatability coefficients ranged from 0.28 to 0.46. They indicate that the prediction of semen quality in young bulls of the Swiss Holstein and the Simmental breed is possible to some extent. Heritabilities in Swiss Holstein bulls were generally very low and did usually not exceed 0.10, but standard errors of these estimates were high. Relatively high heritabilities (0.18–0.30) were found for Simmental bulls, Differences in heritabilities between these two breed groups were probably a consequence of the low number of Swiss Holstein bulls.     

An independent confirmation of a quantitative trait locus for milk yield and composition traits on bovine chromosome 26

Several reports have demonstrated that bovine chromosome 26 (BTA26) harbours significant or suggestive quantitative trait loci (QTL) for milk production and composition traits in dairy cattle. Our previous study showed that a C/T substitution in the bovine TCF7L2 gene on BTA26 was significantly linked to QTL for protein yield (PY) in a Canadian dairy cattle population. Actually, this polymorphism was one of the markers derived from a genome‐wide screening of QTL for milk PY using an amplified fragment length polymorphism technique combined with a DNA pooling strategy. In the present study, 990 Holstein bulls with complete genotype and phenotype data from 14 sire families were analysed to confirm, if the QTL effects exist in other populations. Statistical analysis revealed that this marker was significantly associated with PY, protein percentage, milk yield and fat yield (FY) (p < 0.001) in the US Holstein population. These results indicate that this QTL region has a pleiotrophic effect on different milk traits and is portable in different populations.     

Genetic parameters for carcass traits and their live animal indicators in Simmental cattle

The objective of this study was to estimate parameters required for genetic evaluation of Simmental carcass merit using carcass and live animal data. Carcass weight, fat thickness, longissimus muscle area, and marbling score were available from 5,750 steers and 1,504 heifers sired by Simmental bulls. Additionally, yearling ultrasound measurements of fat thickness, longissimus muscle area, and estimated percentage of intramuscular fat were available on Simmental bulls (n = 3,409) and heifers (n = 1,503). An extended pedigree was used to construct the relationship matrix (n = 23,968) linking bulls and heifers with ultrasound data to steers and heifers with carcass data. All data were obtained from the American Simmental Association. No animal had both ultrasound and carcass data. Using an animal model and treating corresponding ultrasound and carcass traits separately, genetic parameters were estimated using restricted maximum likelihood. Heritability estimates for carcass traits were 0.48 +/- 0.06, 0.35 +/- 0.05, 0.46 +/- 0.05, and 0.54 +/- 0.05 for carcass weight, fat thickness, longissimus muscle area, and marbling score, respectively. Heritability estimates for bull (heifer) ultrasound traits were 0.53 +/- 0.07 (0.69 +/- 0.09), 0.37 +/- 0.06 (0.51 +/- 0.09), and 0.47 +/- 0.06 (0.52 +/- 0.09) for fat thickness, longissimus muscle area, and intramuscular fat percentage, respectively. Heritability of weight at scan was 0.47 +/- 0.05. Using a bivariate weight model including scan weight of bulls and heifers with carcass weight of slaughter animals, a genetic correlation of 0.77 +/- 0.10 was obtained. Models for fat thickness, longissimus muscle area, and marbling score were each trivariate, including ultrasound measurements on yearling bulls and heifers, and corresponding carcass traits of slaughter animals. Genetic correlations of carcass fat thickness with bull and heifer ultrasound fat were 0.79 +/- 0.13 and 0.83 +/- 0.12, respectively. Genetic correlations of carcass longissimus muscle area with bull and heifer ultrasound longissimus muscle area were 0.80 +/- 0.11 and 0.54 +/- 0.12, respectively. Genetic correlations of carcass marbling score with bull and heifer ultrasound intramuscular fat percentage were 0.74 +/- 0.11 and 0.69 +/- 0.13, respectively. These results provide the parameter estimates necessary for genetic evaluation of Simmental carcass merit using both data from steer and heifer carcasses, and their ultrasound indicators on yearling bulls and heifers.     

西门塔尔牛与我国地方黄牛的杂种优势预测分析

旨在利用覆盖全基因组和与性状相关的SNPs标记分析西门塔尔牛和地方黄牛两个亲本群体的遗传结构,通过亲本种群之间的遗传距离预测不同杂交组合在生长、胴体和肉质性状上的杂种优势。本研究选择来自内蒙古锡林郭勒盟乌拉盖管理区牧场的1 222头西门塔尔牛和8个地方黄牛品种190头共组成8个杂交组合,对亲本群体进行遗传结构分析。利用牛770K SNP芯片对两个亲本群体进行基因型分型,通过牛QTL数据库筛选与目的性状对应的QTLs,对全基因组SNP位点进行映射分析得到与性状相关的SNP标记。利用两种SNP标记构建状态同源矩阵,计算各杂交组合亲本间的遗传距离。结果,所有亲本群体聚成3类,西门塔尔牛聚成一类,北方黄牛（蒙古牛、西藏牛和柴达木牛）聚成一类,南方黄牛（昭通牛、平武牛、南丹牛、文山牛和凉山牛）聚成一类。西门塔尔牛与北方黄牛在PCA图上的距离较近,说明两者之间亲缘关系相对较近,遗传背景差异较小。在各性状中,遗传距离最大的亲本组合都是西门塔尔牛与南丹牛杂交组合。除了大理石花纹评分性状是西门塔尔牛与昭通牛之间的遗传距离最小,其余性状遗传距离最小的亲本组合都是西门塔尔牛与平武牛杂交组合。据此推测,各性状杂种优势较优的可能组合是西门塔尔牛与南丹牛杂交组合。     

Birth weight,reproduction traits and effects of inbreeding in Nicaraguan Reyna Creole cattle

Reyna Creole cattle in Nicaragua comprise about 650 purebred animals, and the breed has been shown to have a high level of inbreeding. To characterize the breed, as basis for a conservation program, information from two herds on birth weight (BW, n = 1097), age at first calving (AFC, n = 449) and calving interval (CI, n = 1,347) was analysed. Overall averages were 27.8 kg for BW, 37.4 months for AFC and 424 days for CI. Large differences between the herds were observed for all traits. Thus, there would be opportunities for management interventions to improve reproduction results. The heritability for BW was 0.34. For CI, the heritability of 0.20 and the additive genetic standard deviation of 36 days were comparatively high values. No genetic variation was found in AFC. Estimated inbreeding effects were associated with large standard errors due to the small size of the data and incompleteness of pedigrees. Nevertheless, significant effects were shown of dam inbreeding level on all traits. For each percentage of increased inbreeding, BW decreased by 0.06 kg, AFC increased by 3.5 days and CI increased by 1.4 days. The effects of the inbreeding level of the individual itself were not significant. The relatively good reproduction traits of Reyna Creole cattle shown in this study, despite high inbreeding levels, will be supplemented with a characterization of milk production traits.     

Effects of models with finite loci, selection, dominance, epistasis and linkage on inbreeding coefficients based on pedigree and genotypic information

Considering the effects of selection, dominance, epistasis and linkage, a stochastic computer simulation was performed to study how well inbreeding coefficients calculated from pedigree (f_ped) and genotypic frequencies (f_het) correspond to the inbreeding coefficient that is defined as the proportion of autozygous loci in the modelled genome (i.e. the level of autozygosity, f_aut). Although in random mating populations all three inbreeding coefficients show almost (with slight deviations in models with two loci) the same expectation, they represent three separate variables. First, f_aut, f_ped and f_het responded differently to selection, dominance, epistasis and linkage. Second, they did not have the same standard deviations, which means that the effects of random drift, especially in models under selection, were not affecting all three coefficients in the same way. Finally, they were not always defined in the same domain. With selection as the most important factor responsible for the observed discrepancies, the bias (discrepancy) was present in both directions, thus leading to overestimation or underestimation of the observed level of autozygosity depending on the genetic model, linkage and initial gene frequency. Variation of the autozygosity level (between replicates) was increased notably in models with additive inheritance under selection and was an additional potential source of bias. Thus, when the trait is, to a large extent, controlled by a finite number of loci and when selection is present, the bias in the estimation of the autozygosity is likely to occur and caution is necessary whenever conclusions are based on inbreeding coefficients estimated from the pedigree or decrease in heterozygosity.     

基因芯片技术在晋南牛种公牛选育中的应用

为了更好的保护开发利用晋南牛,确保晋南牛的遗传多样性,本研究应用基因芯片技术,对晋南牛进行群体遗传特性的检测及后备种公牛的遗传评估,为晋南牛的分子辅助选育与保种提供理论与技术支持。采集18月龄健康、体重相近（（350±20）kg）的荷斯坦牛、和顺肉牛、西门塔尔牛、延边牛及利木赞牛血样各10份,及晋南牛后备公牛血样25份,根据不同牛品种分为6组,其中前5组每组10个重复,晋南牛后备公牛25个重复。应用Illumina SNP 50K高密度牛SNP芯片进行基因型检测,分析比较晋南牛的群体遗传特征,运用亲缘矩阵计算晋南牛后备公牛的亲缘系数,同时用BLUP进行遗传评估。结果表明,晋南牛在遗传结构上与荷斯坦牛、和顺肉牛、西门塔尔牛及利木赞牛关系较远,与延边牛较近,为中国地方品种群体;对晋南牛后备公牛进行遗传评估,得出了牛的基因组胴体重方差育种值排名,JN23的胴体重倍数性状标准差最大,从基因组水平可选作肉用种公牛;应用亲缘分析对晋南牛后备公牛家系进行分类,避免群体间的近交。本研究对晋南牛后备公牛进行了遗传评估、近交家系分析、传统表型选择及遗传疾病检测,最终选留的种公牛为JN07、JN23、JN05、JN08、JN02、JN13、JN19、JN14,通过多种选育方法结合提高了公牛的选择准确性,为晋南牛的群体选育提高奠定了基础。     

Effect of breed of sire,breed of dam,pasture program and of their interactions on preweaning performance of crossbred beef calves

Angus (A), Hereford (H), Jersey (J), Simmental (S) and Brahman (B) bulls (202), were mated to A and H cows (855 cow-years) to produce F₁ calves. Cows were randomly assigned within age and breed to two pasture programs. The two pasture programs were expected to differ in particular with respect to the energy level offered to the cows during winter (tall fescue hay versus corn silage). Effects of genotypes, pasture program and of their interactions on preweaning traits were studied. Differences (P< 0.05) between pasture programs were found only for frame and muscle scores. Marginal means for A dams were higher (P<0.05) than those for H cows for all traits, except birth weight. Calves sired by B bulls were heavier (P<0.01) at birth than those sired by S, A and H, and J bulls. For the other traits, S-sired calves tended to have the largest estimated means, followed by calves of B bulls, then by the average of calves sired by A and H bulls and finally by J-sired offspring. Significant (P< 0.05) breed of sire × breed of dam interactions involved only extreme sire breeds. All hypotheses involving pasture program × breed of sire interactions were not significant. Muscle score was the only trait affected (P< 0.05) by a pasture × breed of dam interaction. However, its effect was only magnitudinal. Birth weight was the only trait not affected at all by the pasture program × breed of sire × breed of dam interaction. In the other traits, significant interactions reflected changes in the magnitude of the response rather than in the ranking of genotypes across pasture programs.