Prediction of inbreeding in commercial females maintained by rotational mating with partially isolated sire lines

The solution to the inbreeding problem for livestock breeds in commercial use is often complicated by hierarchical population structure, in which favourable genes are accumulated in the upper level of the hierarchy (breeding population) by artificial selection and the genetic progress achieved is transferred to the lower level through migration of males. When the breeding population is subdivided into several isolated lines, rotational mating with the lines has been shown to be quite an effective system to reduce the short‐ and long‐term inbreeding of commercial females in the lower level. In practice, however, some amount of migration should be allowed among the lines to reduce the rate of inbreeding in each line. In this study, we developed the recurrence equation for the inbreeding coefficient of the commercial females maintained by the rotational mating with partially isolated lines. Numerical computations were carried out to evaluate the effect of the migration on the efficiency of the rotational mating. It was shown that even with a small amount of migration among the lines, the inbreeding of commercial females is substantially inflated. However, when four or five lines are available, the inbreeding coefficient of commercial females can be suppressed to an acceptable level, irrespective of the effective size of line and the migration rate. Application of the mating system to the population of Japanese Black cattle was also examined.     

Two generations of selection on restricted best linear unbiased prediction breeding values for income minus feed cost in laying hens.

Two generations of selection on restricted BLUP breeding values were applied in an experiment with laying hens. Selection had been on phenotype of income minus feed cost (IFC) between 21 and 40 wk of age in the previous five generations. The restriction of no genetic change in egg weight was included in the EBV for power-transformed IFC (i.e., IFCt, with t-values of 3.7 and 3.6 in the two generations, respectively). The experiment consisted of two selection lines plus a randomly bred control of 20 male and 80 female breeders each. Observations on 8,844 survivors to 40 wk were available. Relative to the base population average, the restriction reduced genetic gain in IFC from 4.1 and 3.9% to 2.0 and 2.2% per generation in the two selection lines, respectively. Average EBV for egg weight remained nearly constant after a strong increase in the previous five generations. Rates of genetic gain for egg number, body weight, and feed conversion (feed/egg mass) were not affected significantly. In the seventh generation, a genetic gain in feed conversion of 10.3% relative to the phenotypic mean of the base population was obtained.     

四川常羽乌骨鸡群体遗传多样性分析

利用选自家禽基因组的10个微卫星标记,对四川常羽乌骨鸡5个群体(四川山地乌骨鸡白羽系、黑羽系;黄忠山地乌骨鸡;黄忠山地乌骨鸡绿壳蛋系;草科乌骨鸡)的遗传多样性进行了检测,计算了各群体的群体杂合度、群体间遗传距离,并根据遗传距离进行了聚类分析。结果表明所选择的微卫星标记在各群体中表现出较高的多态性;四川5个乌骨鸡群体遗传多样性比较丰富,群体平均杂合度为0.5383到0.6659;各群体间的遗传距离有一定的差异;聚类分析将5个群体聚为三类。     

Pedigree analysis in the Austrian Noriker draught horse: genetic diversity and the impact of breeding for coat colour on population structure

The pedigree of the current Austrian Noriker draught horse population comprising 2808 horses was traced back to the animals considered as founders of this breed. In total, the number of founders was 1991, the maximum pedigree length was 31 generations, with an average of 12.3 complete generations. Population structure in this autochthonous Austrian draught horse breed is defined by seven breeding regions (Carinthia, Lower Austria, Salzburg, Styria, Tyrol, Upper Austria and Vorarlberg) or through six coat colour groups (Bay, Black, Chestnut, Roan, Leopard, Tobiano). Average inbreeding coefficients within the breeding regions ranged from 4.5% to 5.5%; for the colour groups, the coefficients varied from 3.5% to 5.9%. Other measures of genetic variability like the effective number of founders, ancestors and founder genomes revealed a slightly different genetic background of the subpopulations. Average coancestries between and within breeding areas showed that the Salzburg population may be considered as the nucleus or original stock whereas all other subpopulations showed high relationship to horses from Salzburg. The target of draught horse breeding in the 21st century does not meet the breeding concept of maximizing genetic gains any more. Stabilizing selection takes place. In this study, we show that demographic factors as well as structure given by different coat colours helped to maintain genetic diversity in this endangered horse breed.     

The assessment of genetic diversity within and among the eight subpopulations of Japanese Black cattle using 52 microsatellite markers

Japanese Black cattle are at risk for genetic homogeneity due to intensive use of a few sires. Therefore, assessment of the actual genetic diversity of this breed is important for future breeding plans. In the present study, we investigated the genetic diversity within and among eight subpopulations of Japanese Black cattle using 52 microsatellite markers. The parameters for genetic diversity of Japanese Black cattle were comparable to those of other cattle breeds, suggesting that the relatively high genetic diversity of the breed. However, upon comparison among the eight subpopulations, the Hyogo subpopulation showed markedly low genetic diversity. The results of the pairwise F_ST values, phylogenetic network and structure analysis indicated that the Hyogo population has remarkably high level of genetic differentiation from other populations, while Yamagata, Niigata, Hiroshima and Kagawa populations have low levels of genetic differentiation. Furthermore, multidimensional scaling plots indicated that individuals in some subpopulations were separated from individuals in the other subpopulations. We conclude that while the overall genetic diversity of Japanese Black cattle is still maintained at a relatively high level, that of a particular subpopulation is significantly reduced, and therefore the effective population size of the breed needs to be controlled by correct mating strategies.     

Selection within and across populations in livestock improvement

Genetic evaluations within and across populations (countries, breeds, herds) allow ranking on estimated genetic merit and selecting breeding individuals across populations. Selection within and across populations (combined selection) should by definition always be as good as, or better than, within-population selection, the limiting case. The advantage depends on the sizes of the populations, the number of populations, the initial genetic means, and the correspondence of the breeding objectives in the different populations, as measured by the genetic correlation for economic merit. The advantages of combined selection are evaluated deterministically for a simple case of selecting the best males for use across populations by using a common truncation line over the distributions of EBV for the different populations. Combined selection increases overall response rates in the cooperating populations. Where the initial genetic means are the same, small populations (100 males tested) benefit greatly from combined selection. Large populations (500 to 1,000 males tested) also benefit, but less. The results depend on the increased selection response to scale, response being approximately linear with the logarithm of the number tested. When the initial means differ, the genetically poorer population can catch up in three to five generations and then contribute to the increased responses with combined selection. When breeding objectives differ, selection usually gradually pulls the populations apart and they make less and less contribution to each other and finally become separate. These results have implications for breeding strategies. Their application would affect structures of populations and rates of genetic change possible by selection.     

Genetic description of a divergent selection experiment in Angora rabbits with overlapping generations

The chief aims of this paper were the following: (i) to describe the demography and genetic structure in two divergent selected lines for total fleece weight (TFW) of French Angora rabbits with overlapping generations; (ii) to describe the effects of inbreeding during an experiment of divergent selection. A study of longevity with the survival kit showed that there was no significant difference in the risk of death or culling between the low line (LL) and high line (HL). A significant effect of inbreeding (p < 0.05) was observed with a 30% higher risk factor in the highest class of inbreeding coefficient compared with the other classes. The means of generation interval were 562 and 601 days in LL and HL, respectively. The numbers of generations for LL and HL were 3.90 and 3.64, respectively. Generation intervals decreased significantly from 1995 to 2000 (p < 0.05). The number of daughters in HL was very variable. The number of animals per generation was higher in HL than in LL. Each buck left nearly three daughters to the next generation (2.52 in LL, 3.24 in HL). In both lines, the effective number of ancestor genomes still present in the genetic pool of the generation was around eight from the reference population of 1995 to that of 2001. Inbreeding in HL was always higher than in LL. The effect of inbreeding was also significant (p < 0.05) on TFW and live weight. The animals with the lowest inbreeding category produced a higher TFW (p < 0.05) than the others. The observed selection differentials were lower than that expected owing to the breeding animal management rules in order to control inbreeding increase.     

The effects of stage-specific selection on the development of benzimidazole resistance in Haemonchus contortus in sheep

Resistance to the benzimidazole (BDZ) class of anthelmintics in nematodes of sheep has become a common and global phenomenon. The rate at which the selection process and development of resistance occurs is influenced by a number of factors. Of these, the effects of stage-specific exposures to anthelmintic were investigated with a BDZ-resistant strain of Haemonchus contortus (HCR) over five parasite generations. Sheep were infected at each generation with the HCR strain and were treated with thiabendazole (TBZ), either 5 days post-infection (p.i.) (larval line), 21 days p.i. (adult line), or left untreated (no selection line). Additionally eggs from each generation were exposed to TBZ (egg line). Geometric worm burdens were calculated from post-mortem worm counts, both at the start of the study, and after the final selection studies for each of the selection lines. Egg hatch assays (EHAs) were also conducted throughout the study. All data relating to worm burdens and EHAs for each generation were analysed by linear regression to produce dose titration curves and lethal dose(50) (LD(50)) values for each of the selection lines. Over the five generations, LD(50) values on dose-response were increased and worm survival occurred at higher dose rates of TBZ irrespective of the parasite stage exposed to treatment. A similar picture was seen with ED(50) values, which showed a fluctuating but generally upward trend for each of the three selection lines. In contrast, LD(50) and ED(50) values were decreased in the no selection line, indicating some degree of reversion albeit to levels still considered to be BDZ-resistant.     

Selection for immune response in goats: the antibody response to diphtheria toxoid after 12 years of selection.

A herd of Norwegian dairy goats was subject to selection for high and low antibody response to diphtheria toxoid for 12 yr, or approximately 5.5 generations because sires were used for one mating season, whereas dams were used several years. The herd comprised approximately 100 milking goats. Only sires were tested and selected, five to seven sires were used in each line each year, and the percentage of male kids used for breeding varied between 15 and 50%. The mean phenotypic values of the lines diverged until the 4th yr, but the lines did not diverge any further. The means of both lines decreased during the experimental period. The restricted maximum likelihood (REML) estimate of the heritability of the trait in the base population was .19, whereas the realized heritability approached zero in the last six cycles of selection. Using the REML-estimate of heritability in an individual animal model, the mean breeding values (BLUP) of the lines were significantly different. The difference in mean BLUP values between the lines increased throughout the study. Yet, this increase was only 40% from the 2nd to the 12th yr. No effect of a major gene was observed in a test based on individual BLUP.     

四川地方乌骨鸡种群遗传变异的微卫星DNA分析

利用10个微卫星标记，对四川不同地区5个乌骨鸡种群的等位基因频率、各群体的遗传杂合度、群体间的遗传距离等进行了分析，并根据遗传距离对这几个乌骨鸡种群进行了聚类分析。结果表明，各乌骨鸡群体的遗传多样性较为丰富，并具有较高的选择潜力。各乌骨鸡种群间有一定的遗传距离，UPGMA聚类分析表明，四川山地乌骨鸡黑羽系与川南山地乌骨鸡被聚为一类，草科鸡与旧院黑鸡被聚为一类。     

Wright’s shifting balance theory of evolution in artificial breeding programmes: empirical testing using the model organism Tribolium castaneum

A subdivide/merge breeding system, based on Sewall Wright’s Shifting Balance Theory of Evolution, was modelled using Tribolium castaneum (the red flour beetle). Our objective was to determine the effects of population structure on selection response for increased offspring number, a fitness trait with large nonadditive gene effects. Two different population structures were established: a subdivided population that underwent periodic merging and an undivided control population. The experiment consisted of (1) 150 beetle pairs divided into 10 lines of 15 pairs each, and (2) an undivided control population of 150 beetle pairs. Selection of the subdivided population was performed within lines each generation and in generations 4, 8 and 12, poorer performing lines were eliminated with the remaining lines merged. After merging, selected individuals were randomly paired and re‐subdivided into 10 lines of 15 pairs each. The undivided population was mass selected for increased offspring number each generation using the same selection intensity as the subdivided lines. After 14 generations, selection response in the subdivide/merge system was not significantly different from the control population; however, within each generation, there were lines in the subdivided population that had average larva numbers exceeding those of the undivided population. These results indicate that subdivide/merge systems could be advantageous for shorter‐term breeding objectives. If superior lines are isolated, they can be full‐sib mated or selfed to produce highly inbred lines which can then be crossed – a standard plant breeding practice.     

基于SNP芯片分析青峪猪保种群体的遗传结构

为了更好地了解青峪猪在世代更替过程中遗传结构的变化,更好的保护和利用青峪猪遗传资源,本研究利用50K SNP芯片,对青峪猪保种群内141头（26头公猪,115头母猪）健康成年个体进行SNP测定,通过多种分析软件对青峪猪保种群体和各个世代进行系谱校正,进而实施群体遗传多样性、遗传距离以及遗传结构变化等分析。结果显示,该封闭保种群由3个重叠世代构成,群体有效含量为12头,且整个群体可以分为6个含有公猪的家系和1个不含公猪的家系。其中,第3世代的有效群体含量最少,仅为3头,多态性标记比例随着世代的增加不断下降;141头青峪猪的平均遗传距离为（0.260 4±0.025 2）,26头种公猪的遗传距离为（0.263 3±0.023 7）。随着繁殖世代的增加,各世代群体的遗传距离有轻微的上升趋势,部分种猪之间的亲缘关系和遗传距离较近;在141头青峪猪群体中共检测到1 481个基因组上长纯合片段（runs of hemozygosity,ROH）,78.01%的长度在200 Mb以内,基于ROH值计算的近交系数表明整个群体的平均近交系数为0.055,且各世代的近交系数在不断上升,到第3世代时已经达到了0.075。综上所述,通过对青峪猪分子水平的群体遗传结构研究表明,该保种群体在闭锁的继代繁育过程中存在群体遗传多样性损失,需要加强选配或导入外血以确保青峪猪遗传资源的长期保存。     

Estimation of genetic gains in populations with overlapping generations

A technique for estimating genetic improvement from an “internal genetic control” was developed for populations which fulfil the following requirements: (1) The population can be divided into distinct subpopulations (e.g. sire families or inbred lines) with several sets of offspring such as hatches or litters produced during the life‐span of each subpopulation. (2) The replacement of subpopulations or breeders in the selection programme takes place more or less continuously to provide overlapping generations. (3) The effect of ageing of the parents on progeny performance can be measured.

The genetic change in such populations independent of environmental time trends can be estimated directly from the breeding data without any need for a separate control population.

The technique was applied to a practical meat‐type poultry breeding operation to yield an estimated annual genetic improvement of 100 g body weight for each bird at 9 weeks of age.     

京海黄鸡连续3个世代类胰岛素样生长因子-Ⅰ外显子3的多态性研究

以7、8、9世代京海黄鸡母鸡为试验材料,采用PCR-SSCP技术对IGF-Ⅰ基因外显子3多态位点进行研究,并计算基因型、基因频率、卡方值和部分遗传多态性指标。结果表明,A等位基因随着世代数的增加不断减少;3个世代之间基因型分布达到显著(P＜0.05)或极显著(P＜0.01)差异;遗传杂合度随世代数的增加而升高;该位点3个世代均为中度多态。初步推断选留的确对IGF-Ⅰ基因31位点造成了影响,该位点可应用于育种实践中。     

东阿黑驴育种规划优化的研究

东阿黑驴是以德州驴为基础群向皮肉兼用型方向选育的新品种,本研究拟在其现有育种方案的基础上,探讨不同育种措施的最优化组合方案,为建立优质、高效的东阿黑驴育种体系奠定基础,为中国驴育种实践提供参考。本研究根据东阿黑驴的生产和育种现状,以选择指数法和基因流动法为基本方法,应用育种规划程序ZPLAN分析东阿黑驴现行育种方案的育种成效,对影响育种成效的各个因素进行优化分析,最终确定优化后的育种方案。结果表明,现行方案在投资规划期内可完成的遗传进展和育种效益分别为271.78和1 123.70元/（头·年）,世代间隔为5.24年,每年每个性状遗传进展分别为断奶重提高1.50 kg,18月龄体重提高0.09 kg,初产年龄缩短0.02 d,产犊间隔缩短0.17 d,皮产量增加1.04 kg。对影响育种的因素进行不同水平的组合分析,当群体规模理想状态为30 000头,主动育种群比例为0.5,育种群中种子公驴、测验公驴和种用母驴使用年限为1年,种子母驴使用年限为2年,生产群中公、母驴使用年限为1年时,可获得最大的育种遗传进展和育种效益,分别为320.40和2 945.00元/（头·年）,比现行育种方案分别高出17.9%和162.0%。东阿黑驴目前的育种方案没有达到理想育种状态,有较大的改进空间。研究通过对育种主要影响因素的不同水平优化组合,得到了最优的育种方案,使遗传进展和育种效益达到了最大化。     

Correlated changes in fertility and fitness traits in lines of oMt1a‐oGH transgenic mice selected for increased 8‐week body weight*

Correlated responses in fitness and fertility traits were compared in transgenic and nontransgenic lines of mice selected for increased 8‐week body weight. Two replicates of lines which either carried or did not carry the sheep metallothionein‐1a sheep growth hormone transgene (oMt1a‐oGH) were established. Host lines had been previously selected for rapid growth or selected randomly. Within‐litter selection was carried out for 13 generations, and a randomly selected control line was kept for each set of replicate lines. Mice were genotyped every generation for the presence of the transgene, but this information was not used in selection decisions. The oMt1a‐oGH construct was activated by adding 25 mm ZnSO₄ to the drinking water from 3 weeks (weaning) until 8 weeks of age. Zinc stimulation of the transgene was not carried out during mating, gestation and lactation. Correlated responses in fitness traits were measured by regression of least‐squares means (as deviations from the control lines) on generation number. Two fitness indexes were defined to combine the information on individual fitness traits. The proportion of infertile matings was higher in generations 7 to 13 than in generations 0 to 6. Correlated responses to selection showed an increase in the cohabitation to littering interval in nontransgenic lines and an increase in litter sizes in lines from the selected background. Preweaning pup survival did not change over generations. Overall fitness increased in the transgenic line from the selection background whereas no changes were observed in the transgenic line from the control background. The initial frequency of 0.5 of the transgene was reduced to less than 0.10 in the selected background, but increased to an average of 0.62 in the control lines. The comparison of specific mating groups involving transgenic and nontransgenic mates revealed that the only consistent disadvantage in having a transgenic parent was the increase in the length of the cohabitation to littering interval. Major fitness problems were not associated with the oMt1a‐oGH transgene, which makes this construct a potential choice for use in livestock breeding programmes.     

The identification of common haplotypes on bovine chromosome 5 within commercial lines of Bos taurus and their associations with growth traits

The cosegregation between a genetic marker and the QTL in a well-designed mapping population is the basis for successful QTL mapping. Linkage disequilibria are, however, also expected among individuals that descended from the same breeding line, and some common haplotypes should carry on and segregate among individuals of the line. These identical by descent haplotypes make it possible to identify and locate the QTL segregating in the line. We report the identification of common haplotypes within commercial lines of Bos taurus and their associations with growth traits. One hundred and seventy six male calves and their 12 sires (9 to 30 male calves of each sire) of the Beefbooster, Inc., M1 line selected for maternal traits over 30 yr were genotyped using 16 microsatellite markers chosen from bovine chromosome 5 for the initial haplotype and growth association analysis. In order to verify the results from the M1 line, another 170 male calves and their 14 sires from the Beefbooster M3 line were genotyped using nine microsatellite markers chosen from bovine chromosome 5. The alleles of each male calf contributed by the sire and by the dam were identified, and haplotypes in the M1 line were established along 93% of bovine chromosome 5. The haplotypes in the M3 line were established along the chosen regions of bovine chromosome 5. Regression analysis detected 10 haplotypes in three chromosomal regions (0 to 30 cM, 55 to 70 cM, and 70 to 80 cM) that showed significant associations with birth weight, preweaning average daily gain, and average daily gain on feed in M1 line and 9 haplotypes associated with the growth traits in the same chromosomal regions in the M3 line at the comparisonwise threshold level. On average, the 19 haplotypes have an effect of 0.68 SD on the growth traits, ranging from 0.41 SD to 1.02 SD The results provide a useful reference for further positional candidate gene research and marker-assisted selection.     

北京鸭群体遗传多样性及遗传资源分析

为研究北京鸭群体的遗传结构及遗传多样性,实验分别采集北京鸭F_0(120只)、F_1(100只)和F_2世代(100只)的血液样本,采用荧光标记毛细管电泳方法对北京鸭11个微卫星座位进行分析。结果表明:11个微卫星座位在北京鸭F_0、F_1和F_2世代的平均等位基因/有效等位基因数量分别为4.6/2.5、3.5/1.9和4.5/2.2个;平均多态信息含量分别为0.441 3、0.303 8和0.415 0;平均期望杂合度分别为0.487 7、0.363 3和0.454 2;北京鸭3个世代间的遗传变异指标差异不显著。近交系数及基因流分析结果表明,北京鸭群体3个世代近交系数较低,群体内近交系数为0.086 9,微卫星位点的平均基因流为0.934 1。总体来看,北京鸭群体遗传分化程度低,保持了北京鸭群体遗传多样性。     

山西白猪高产仔母系繁殖性能测定

以马身猪、太湖猪（二花脸类群）和长白猪为育种素材,采用标记辅助选择技术结合群体继代选育法,经7年6个世代育成山西白猪高产仔母系。对7个世代母猪繁殖性能分析结果表明,4世代母猪的繁殖性能最好,母猪初产窝产仔10.64头,产活仔数9.85头,断奶头数9.36头,哺育率达95.03%,初生个体均重1.42 kg,28日龄断奶窝重62.36 kg。除产活仔数外,均极显著高于0世代（P<0.01）。初生和断奶时仔猪均匀度随选育逐代提高,一致性增强。该品系已具有良好的繁殖性能,是一个优良的母本品系。