Efecto de dos estrategias de agrupación de padres fantasmas en la evaluación genética de rasgos de crecimiento en el ganado Braunvieh mexicano

The study aimed to compare two grouping strategies for unknown parents or phantom parent groups (PPG) on the genetic evaluation of growth traits for Mexican Braunvieh cattle. Phenotypic data included birth (BW), weaning (WW) and yearling (YW) weights. Pedigree included 57,341 animals. The first strategy involved 12 PPG (G12) based on the birth year of the unknown parent’s progeny and the sex of the unknown parent, while the second involved 24 PPG (G24) based on the birth year of the unknown parent’s progeny and 4-selection pathways. The animal models included fixed effects and the random direct additive genetic effect; WW also included random maternal genetic and maternal permanent environmental effects. Product-moment correlations between EBV from G0 (no PPG) and G12 were 0.96, 0.77 and 0.69 for BW, WW and YW, respectively, and between EBV from G0 and G24 were 0.91, 0.54, and 0.53, respectively. Corresponding rank correlations between G0 and G12 were 0.94, 0.77, and 0.72, and between G0 and G24 were 0.89, 0.61, and 0.60. Genetic trends showed a base deviation from the genetic trend of G0, except for BW of G12. The results did not support the use of the two grouping strategies on the studied population and traits, and further research is required. Introducing PPG to the model, enough phenotype contribution from descendants to PPG, and avoiding collinearity between PPG and fixed effects are important. Genetic groups should reflect changes in the genetic structure of the population to the unknown parents, including different sources of genetic materials, and changes made by selection over time.

FACTORS OF EVALUATION OF BREEDING BULLS AND MANAGEMENT OF BREEDING POPULATIONS

В статье рассмотрены цифровой формат оценки племенной ценности инбредных быков-производителей по качеству потомства и ее влияние на последующие поколения животных. Выявление инбредного гетерозиса у производителей помогает сделать оценку быков по качеству потомства более информативной за счет определения глубины изменения параметров генетической структуры популяции и степени увеличения частоты рецессивных генов в подконтрольных популяциях. Одной из причин значительной разницы в удое, МДЖ и МДБ российских и американских коров голштинской породы являлась их удаленность от родоначальника. Другой причиной считается стремление селекционеров к инбридингу на выдающихся предков, однако в случае инбредного гетерозиса высокие показатели родителей быстро затухают в последующих поколениях потомков. Исследования были проведены в хозяйствах Московской области малой и средней производственной мощности. Для сравнения проанализированы результаты оценки быков-производителей из США и других стран с высокоразвитым молочным скотоводством. Методами изучения были имитационный и регрессионный анализ данных первичного зоотехнического учета и собственных исследований. Эксперимент показал, что быки-производители с высокими степенями родства уменьшали изменчивость признаков молочности среди дочерей: по удою — на 77,9%; по МДЖ — на 33,4%; по МДБ — на 36,0%, по сравнению с отцами, имеющими низкие степени родства. При этом в их поголовье в первом поколении повышается генетический тренд по удою на 14,3—21,4%, а племенная ценность — на 10,8—26,8%. В настоящее время в зарубежных популяциях голштинской породы широко применяют геномный метод оценки племенной ценности, при котором не требуется информация о родословных животных и не учитывается степень их родства, что отрицательно влияет на получение высококачественного потомства. Повышение племенной ценности по признакам в популяции сыновей и внуков быков-лидеров породы угасает, если в генофонде родителей имел место инбредный гетерозис. The article considers of the inbred breeding bulls breeding value by offspring quality and its impact on subsequent generations of animals’ digital format assessing. Identification of inbred heterosis helps to make the bulls’ assessment by the offspring quality more informative, by determining the depth of changes in the genetic structure of the population parameters and the recessive genes at populations frequency degree increase controlling. One of the reasons for the significant difference in milk yield, MJ and MDB of Russian and American Holstein cows was their distance from the ancestor. Another reason is considered to be of the breeders to inbreeding for outstanding ancestors’ desire, but in the case of inbred heterosis, high rates of parents quickly fade in descendants in subsequent generations. The research was carried out in the farms of the Moscow region of small and medium production capacity. For comparison, the results of the evaluation of breeding bulls in the United States and other countries with highly developed dairy cattle breeding were analyzed. The research methods were simulation and regression analysis of primary zootechnical accounting data and authors’ own research. Experimental data showed that breeding bulls with high degrees of relation reduced the variability of milk production among daughters by milk yield in 77.9%: for MJ in 33.4%; for MDB in 36.0% in compared with fathers with relation’s low degrees. At the same time, in livestock’s first generation, the genetic trend in milk yield increases in 14.3—21.4%, and the breeding value in 10.8—26.8%. Currently, the genomic method of assessing the breeding value is widely used in foreign populations of the Holstein breed, which does not require information about the pedigrees of animals, and does not take into account the degree of their kinship, which negatively affects the production of high-quality offspring. The breeding qualities of the sons of the bull leaders of the breed are quickly disabled the surge of increased breeding value by signs in the population of sons and grandchildren of bulls-leaders of the breed is fading if inbred heterosis took place in the parents' gene pool.

Dissecting genetic trends to understand breeding practices in livestock: a maternal pig line example

Background Understanding whether genomic selection has been effective in livestock and when the results of genomic selection became visible are essential questions which we have addressed in this paper. Three criteria were used to identify practices of breeding programs over time: (1) the point of divergence of estimated genetic trends based on pedigree-based best linear unbiased prediction (BLUP) versus single-step genomic BLUP (ssGBLUP), (2) the point of divergence of realized Mendelian sampling (RMS) trends based on BLUP and ssGBLUP, and (3) the partition of genetic trends into that contributed by genotyped and non-genotyped individuals and by males and females. Methods We used data on 282,035 animals from a commercial maternal line of pigs, of which 32,856 were genotyped for 36,612 single nucleotide polymorphisms (SNPs) after quality control. Phenotypic data included 228,427, 101,225, and 11,444 records for birth weight, average daily gain in the nursery, and feed intake, respectively. Breeding values were predicted in a multiple-trait framework using BLUP and ssGBLUP. Results The points of divergence of the genetic and RMS trends estimated by BLUP and ssGBLUP indicated that genomic selection effectively started in 2019. Partitioning the overall genetic trends into that for genotyped and non-genotyped individuals revealed that the contribution of genotyped animals to the overall genetic trend increased rapidly from ~ 74% in 2016 to 90% in 2019. The contribution of the female pathway to the genetic trend also increased since genomic selection was implemented in this pig population, which reflects the changes in the genotyping strategy in recent years. Conclusions Our results show that an assessment of breeding program practices can be done based on the point of divergence of genetic and RMS trends between BLUP and ssGBLUP and based on the partitioning of the genetic trend into contributions from different selection pathways. However, it should be noted that genetic trends can diverge before the onset of genomic selection if superior animals are genotyped retroactively. For the pig population example, the results showed that genomic selection was effective in this population.

Relationship between direct and maternal genetic effects on weaning weight of Limousin and crossbred beef calves

Population genetic parameters, direct and maternal breeding value, the genetic trend in the weaning weight of Limousin beef cattle calves were estimated in the period 1992–2019. Data of 19 764 calves (15 437 purebred Limousin and 4 327 crossbred) were computed. Crossbred calves were sired by Limousin breeding bulls from Simmental dams. Calves in question came from 37 herds and from 240 sires in Hungary. DFREML and MTDFREML software was used for the estimation of population genetic parameters, BLUP animal model for breeding value estimation. Weighted linear regression model was used for describing genetic trends. The maternal heritability (h²_m ± SE = 0.29 ± 0.03; 0.32 ± 0.10) was approximately half of the direct heritability (h²_d ± SE = 0.63 ± 0.05; 0.68 ± 0.12). The direct maternal covariance is negative, the direct maternal genetic correlation coefficients (r_dm ± SE = –0.80 ± 0.03 and –0.96 ± 0.07) are strong negative. The Spearman rank correlation between direct and maternal breeding value in purebred population is moderate and negative (r_rank = –0.33; P < 0.01), in crossbred population it is strong and negative (r_rank = –0.99; P < 0.01). According to direct and maternal breeding values of sires, the genetic trend of the weaning weight of purebred and crossbred Limousin calves appeared stagnant during the examined period (b = +0.01 kg/year to +0.19 kg/year). Keywords: d

Genetic parameters and trends for reproductive traits in Blanco Orejinegro cattle from Colombia

The Colombian creole cattle breed Blanco Orejinegro (BON) is an important zoogenetic resource, but there is little knowledge about the genetic parameters and trends of its reproductive traits. Therefore, the aim of this study was to estimate parameters for the reproductive traits calving interval (CI), age at first calving (AFC), gestation duration (GD) and genetic trends for CI in the BON breed. Genealogy information from 7,799 animals was used, and employing the MTDFREML program, the components of the variance, heritability (h2), repeatability (rep), and estimated breeding values (EBV) for CI (n=3308), AFC (n=729), and GD (n=306) were estimated, in addition to the inbreeding coefficient (F) of the population. Genetic trends were established through linear regression using R software. Finally, the animals were classified as inbred (F > 0) and noninbred (F=0), and the effect of inbreeding on reproductive performance was established through a generalized linear model using the R program. An average F value of 4.41%±0.06 was observed. The h2 for CI was 0.11±0.03 with a rep of 0.15±0.04; for AFC, h2 was 0.00±0.05; and for GD, h2 was 0.00±0.08. The genetic trend for CI was -0.01 days/year. Finally, for CI, inbreeding depression was evident; this trait increased when inbreeding increased. These results indicate an important environmental influence on reproductive traits. The heritability estimate for CI suggests that little genetic progress could be achieved through selection. The evidence of inbreeding depression raises the need to control inbreeding to conserve this genetic resource.

Performance Evaluation, Genetic Parameter and Genetic Trend Estimation of Production and Reproduction Traits of Sahiwal Cattle in Chhattisgarh

Background: Performance evaluation is necessary for formulation of suitable breeding plans for genetic improvement in a population. Therefore, this study aimed to assess the production, reproduction performances and estimate the genetic parameter and genetic trend on 649 lactation records of 238 Sahiwal cows at an organized farm in Chhattisgarh. Methods: The analysis was performed by using fixed model in LSML. Genetic trend for traits was estimated through linear regression of breeding values over the years.Result: Least-squares means for total lactation milk yield (TLMY), 305day or less milk yield (305DMY), lactation length (LL), dry period (DP) and peak yield (PY) were 1385.1±26.7 kg, 1331.4±23.6 kg, 291.0±3.7 days, 214.8±6.0 days, 7.5±0.1 kg, while for reproduction traits; age at first calving (AFC), service period (SP) and calving interval (CI), the means were 1522.8±19.1 days, 212.4±5.9 days and 498.3±6.0 days, respectively. All the traits were significantly influenced by period of calving/birth whereas season had significant effect only on PY. The highest heritability (0.29 ± 0.05) was estimated for 305DMY and lowest (0.11 ± 0.07) for SP in Sahiwal cows. Very high and positive genetic correlations was found among production traits. The first lactation 305DMY showed positive genetic trend, while LL, DP, SP and CI showed a negative genetic trend.

AlphaPart—R implementation of the method for partitioning genetic trends

Background In this paper, we present the AlphaPart R package, an open-source implementation of a method for partitioning breeding values and genetic trends to identify the contribution of selection pathways to genetic gain. Breeding programmes improve populations for a set of traits, which can be measured with a genetic trend calculated from estimated breeding values averaged by year of birth. While sources of the overall genetic gain are generally known, their realised contributions are hard to quantify in complex breeding programmes. The aim of this paper is to present the AlphaPart R package and demonstrate it with a simulated stylized multi-tier breeding programme mimicking a pig or poultry breeding programme. Results The package includes the main partitioning function AlphaPart, that partitions the breeding values and genetic trends by pre-defined selection paths, and a set of functions for handling data and results. The package is freely available from the CRAN repository at http://CRAN.R-project.org/package=AlphaPart. We demonstrate the use of the package by partitioning the nucleus and multiplier genetic gain of the stylized breeding programme by tier-gender paths. For traits measured and selected in the multiplier, the multiplier selection generated additional genetic gain. By using AlphaPart, we show that the additional genetic gain depends on accuracy and intensity of selection in the multiplier and the extent of gene flow from the nucleus. We have proven that AlphaPart is a valuable tool for understanding the sources of genetic gain in the nucleus and especially the multiplier, and the relationship between the sources and parameters that affect them. Conclusions AlphaPart implements the method for partitioning breeding values and genetic trends and provides a useful tool for quantifying the sources of genetic gain in breeding programmes. The use of AlphaPart will help breeders to improve genetic gain through a better understanding of the key selection points that are driving gains in each trait.

The level of milk production jersey cows depending on genealogy

The purpose of the research. Was to study the milk productivity and reproductive abilities of Jersey cows in the context of bulls and their fathers. Object of research. Cows, bulls-fathers of the Jersey breed in the breeding reproducer, data from the “Selex” program. Results and practical significance. The results of evaluating the use of Jersey bulls by a set of characteristics are shown. Indicators of daughters of some bulls-producers are given; milk productivity and reproductive qualities. A wide range of characteristics was evaluated – from milk productivity and reproductive qualities, to health indicators (milk yield coefficient, milk yield rate, and animal body weight (exterior). It is shown that there is a sufficient spread of productivity values in the herd for some indicators, the best are the daughters of some bulls, and for others, the daughters of others. The best bulls of VJ Lutz, VJ Hihl and DJ Hulk with productivity of daughters more than 6000 kg, as well as the worst bulls of Q Hirse and VJ Lurak with yields below 6000 kg were identified. The percentage of fat in milk (more than 6.0 %) was higher in the daughters of Q Hirse, VJ Lutz. The coefficient of dairy cows depending on the bulls-producers ranged from 1267 (father VJ Zdzhorup) to 1575 kg (father VJ Herodot). The conducted research will allow selection and selection of bulls and cows taking into account the genetic trend in generations, and regulate the level of intensity of the selection process in the population. Scientific novelty. Breeding work in cattle breeding Kaluga region is to increase breeding value and enhance the productive qualities of Jersey cattle. For the first time in the region, a comprehensive assessment of imported Jersey cows on productive, reproductive and technological characteristics was given.