EFFICIENCY OF USING BULLS EVALUATED BY THE QUALITY OF OFFSPRING AND GENOME IN FARMS OF THE LENINGRAD REGION

Показана эффективность использования быков, оцененных по качеству потомства и геному, в хозяйствах Ленинградской области. В среднем повышение молочной продуктивности в условиях региона от использования импортной спермы 84 проверенных по качеству потомства быков составило +19 кг молока (10138 кг молока, 3,83% жира, 3,20% белка), 68 геномно оцененных быков — +24 кг молока (10568 кг молока, 3,85% жира, 3,23% белка). Наилучшие результаты при оценке по качеству потомства в хозяйствах Ленинградской области получены от импортных производителей с племенной ценностью более +600 кг молока (+218 кг молока по быкам, оцененным по качеству потомства, +120 кг молока по геномно оцененным быкам). Уровень племенной ценности по удою улучшателя Дэвиса 138027041 варьирует от +297 до +615 кг молока. В высокопродуктивных (10000 кг и выше) стадах превышение удоя над сверстницами было больше, чем в стадах с продуктивностью 8000 кг молока при коэффициенте повторяемости 0,85. Быки с высокой геномной оценкой (от +719 кг до +1137 кг молока) повысили удой дочерей, по сравнению со сверстницами, в хозяйствах Ленинградской области от +274 кг (Стерлинг 69701759) до +1063 кг (Салун 70358061). С увеличением геномной племенной ценности производителей наблюдается рост продуктивности дочерей в хозяйствах области на 1469 кг молока. Между оценками племенной ценности быков разными методами (в США метод BLUP, в Ленинградской области — «дочери—сверстницы») выявлена положительная связь по удою для быков, проверенных по качеству потомства, +0,54, имеющих геномную оценку — +0,52; по содержанию жира в молоке — +0,48 и +0,57, белка — +0,66 и +0,61, соответственно. Применение современных методов оценки быков (как по качеству потомства, так и по геному) и использование ценных генотипов быков позволят повысить генетический потенциал скота. This article shows the effectiveness of using bulls evaluated by the quality of offspring and genome in the farms of the Leningrad region. On average, the increase in milk productivity in the region from the use of imported sperm of 84 bulls tested for the quality of offspring was +19 kg of milk (10138 kg of milk, 3.83% fat, 3.20% protein), 68 genomically evaluated bulls — +24 kg of milk (10568 kg of milk, 3.85% fat, 3.23% protein). The best results in assessing the quality of offspring in the farms of the Leningrad region were obtained from imported producers with a breeding value of more than +600 kg of milk (+218 kg of milk for bulls evaluated for the quality of offspring, +120 kg of milk for genomically evaluated bulls). The level of breeding value for the milk yield of the improver Davis 138027041 varies from +297 to +615 kg of milk. In highly productive (10,000 kg and higher) herds, the excess of milk yield over peers was greater than in herds with a productivity of 8000 kg of milk with a repeatability coefficient of 0.85. Bulls with a high genomic rating (from +719 kg to +1137 kg of milk) increased the milk yield of their daughters compared to their peers in the farms of the Leningrad region from +274 kg (Sterling 69701759) to +1063 kg (Saloon 70358061). With the increase in the genomic breeding value of producers, there is an increase in the productivity of daughters in the farms of the region by 1469 kg of milk. A positive relationship was found between the estimates of the breeding value of bulls by different methods (in the United States, the BLUP method, in the Leningrad region — «daughters—peers» method) for bulls tested for the quality of offspring +0.54, with a genomic score of +0.52; in terms of fat content in milk — +0.48 and +0.57, protein — +0.66 and +0.61, respectively. The use of modern methods for evaluating bulls (both by the quality of offspring and by genome) and the use of valuable genotypes of bulls will increase the genetic potential of livestock.

Important effect of the X chromosome in genomic evaluations of reproductive traits in beef cattle

The aim of this study was to evaluate the efficiency of inclusion and the prediction ability of the X chromosome for reproductive (occurrence of early pregnancy – P16 and age at first calving - AFC) and andrological traits (scrotal circumference -SC) in a herd of Nellore beef cattle herd. 3,263 genotypes of females and males were used. Genomic prediction for SC, AFC and P16 was carried out considering two scenarios: 1) only autosomal markers or 2) autosomal + X chromosome markers. To evaluate the effect of inclusion of the X chromosome on selection, the responses to the selection performed were compared including or not the X chromosome in the evaluation of the traits. Higher heritability estimates were obtained for SC (0.40 and 0.31), AFC (0.11 and 0.09) and P16 (0.43 and 0.38) for the analyses including the X chromosome compared to those without. The percent reduction on mean genomic breeding values when selection was based on the results of analysis that did not include the X chromosome to 1, 5 and 10% of the top males, was for SC slightly more than 7% of the mean genomic breeding value of the selected animals. For P16, the loss can reach more than 4%, while this loss does not seem to be as important for AFC. Average predictive correlation of 0.79, 0.98 and 0.84 for SC, AFC and P16 was obtained, respectively. These estimates demonstrate that inclusion of the X chromosome in the analysis can improve the prediction of genomic breeding values, especially for SC.

ПЛЕМЕННАЯ ЦЕННОСТЬ БЫКОВ, ОЦЕНЕННЫХ ПО ГЕНОМУ И КАЧЕСТВУ ПОТОМСТВА

The purpose of this article was to compare the results of evaluating the breeding value of bulls, evaluated by the genome and the quality of the offspring. For analysis, we used data on the genetic value of bulls belonging to foreign companies (n17), domestic breeding enterprises of the Central Federal District (n15) and the NorthWest Federal District (n6). It was revealed that as the time for checking the bulls on the quality of the offspring increases, the effectiveness of their initial genomic estimate for milk production decreases to 74.4 on average for sires owned by foreign companies, to 52.2 and 59.3 for bulls belonging to domestic breeding enterprises. The best results when evaluating the quality of the offspring (183 kg of milk) were obtained from sires with a high genomic score (699 kg of milk) belonging to foreign companies. The correlation coefficients between the estimates by genome and by quality of the offspring ranged from 0.66 (P0.01) for bulls belonging to the breeding enterprise of the NorthWestern Federal District, to 0.49 (P0.01) for sires belonging to the breeding enterprise of the Central federal district. High statistically significant correlations have bulls estimated by their fat content r0.720.83 (P0.001) and milk protein r0.800.84 (P0.001). The distribution of bulls by the level of genomic breeding value showed that the genomic score is overestimated in comparison with the offspring quality scoring. Bulls with a genomic score for milk yield less than 500 kg of milk received a negative rating for the quality of offspring (253 kg) in conditions of the US farms and 325 kg in conditions of farms in the Leningrad Region. On average, bulls with a genomic breeding value of 501600 kg in the conditions of the Leningrad Region demonstrated a superiority in the breeding value indicator by 23.6, with a genomic breeding value of 9011100 kg by 40.9. Under the US farm conditions, the same genomically evaluated bulls maintained their breeding value by 46.7 and 91.2, respectively. Therefore, to reduce the risk when using genomically evaluated bulls, it is necessary to select sires with high scores by productivity traits.Целью настоящей статьи было сопоставление результатов оценки племенной ценности быков, оцененных по геному и по качеству потомства. Для анализа использованы данные генетической ценности быков, принадлежащих импортным компаниям (n17), отечественным племпредприятиям Центрального федерального округа (n15) и СевероЗападного федерального округа (n6). Выявлено, что по мере увеличения времени проверки быков по качеству потомства результативность их первоначальной геномной оценки по удою снижается до 74,4 в среднем по производителям, принадлежащим импортным компаниям, до 52,2 и 59,3 по быкам, принадлежащим отечественным племпредприятиям. Наилучшие результаты при оценке по качеству потомства (183 кг молока) получены от производителей, имеющих высокую геномную оценку (699 кг молока), принадлежащих импортным компаниям. Коэффициенты корреляции между оценками по геному и по качеству потомства варьировали от 0,66 (P0,01) по быкам, принадлежащим племпредприятию СевероЗападного федерального округа, до 0,49 (P0,01) по производителям, принадлежащим племпредприятию Центрального федерального округа. Высокие, статистически достоверные корреляции имеют быки, оцененные по содержанию жира r0,720,83 (P0,001) и белка r0,800,84 (P0,001) в молоке. Распределение быков по уровню геномной племенной ценности показало, что геномная оценка завышена по сравнению с оценкой по качеству потомства. Быки, имеющие геномную оценку по удою менее 500 кг молока, получили отрицательную оценку по качеству потомства (253 кг) в условиях ферм США и 325 кг в условиях хозяйств Ленинградской области.В среднем быки с геномной племенной ценностью 501600 кг в условиях Ленинградской области сохранили превосходство показателя племенной ценности на 23,6, с геномной племенной ценностью 9011100 кг на 40,9. В условиях ферм США эти же геномно оцененные быки сохранили показатель племенной ценности, соответственно, на 46,7 и 91,2. Следовательно, для снижения риска при использовании геномно оцененных быков, необходимо отбирать для воспроизводства производителей с высокой оценкой по признакам продуктивности.

The effects of training population design on genomic prediction accuracy in wheat

Genomic selection offers several routes for increasing genetic gain or efficiency of plant breeding programs. In various species of livestock there is empirical evidence of increased rates of genetic gain from the use of genomic selection to target different aspects of the breeder’s equation. Accurate predictions of genomic breeding value are central to this and the design of training sets is in turn central to achieving sufficient levels of accuracy. In summary, small numbers of close relatives and very large numbers of distant relatives are expected to enable accurate predictions.To quantify the effect of some of the properties of training sets on the accuracy of genomic selection in crops we performed an extensive field-based winter wheat trial. In summary, this trial involved the construction of 44 F2:4 bi- and triparental populations, from which 2992 lines were grown on four field locations and yield was measured. For each line, genotype data were generated for 25,000 segregating single nucleotide polymorphism markers. The overall heritability of yield was estimated to 0.65, and estimates within individual families ranged between 0.10 and 0.85. Within cross genomic prediction accuracies of yield BLUEs were 0.125 – 0.127 using two different cross-validation approaches, and generally increased with training set size. Using related crosses in training and validation sets generally resulted in higher prediction accuracies than using unrelated crosses. The results of this study emphasize the importance of the training set design in relation to the genetic material to which the resulting prediction model is to be applied.

Influence of population structure on the compilation of the Bonsmara genomic reference population

The most popular beef breed in South Africa is the Bonsmara, a locally developed composite breed adapted to sub-tropical conditions. The establishment of a genomic reference population is currently ongoing for the application of genomic selection. To date, 583 Bonsmara cattle (388 bulls and 195 cows) have been genotyped with the GeneSeek® Genomic Profiler Bovine HD™ Chip (GGP-HD) 80 K chip, and the population structure of the reference population was studied. The average minor allele frequency for the Bonsmara was 0.280 across 56 248 autosomal single-nucleotide polymorphisms (SNPs), whereas the observed and expected heterozygosity values were 0.361 and 0.365, respectively. After pruning the data set for SNPs in linkage disequilibrium, 19 119 SNPs were retained, averaging 659 SNPs per autosomal chromosome. This generated an average SNP density of 1 SNP per 90 kb. Structure analysis revealed a non-homogenous population with a high level of genetic admixture, which may negatively influence genomic breeding value prediction accuracy. Genotyping of a further 990 Bonsmara cattle are pending, using the GeneSeek® GGP-HD 150 K chip. As more animals will be added to the reference population, the profile of the reference population are expected to change in such a way to ensure improved genomic estimated breeding value accuracies.