Comparative Study of the Genetic Diversity of Local Steppe Cattle Breeds from Russia, Kazakhstan and Kyrgyzstan by Microsatellite Analysis of Museum and Modern Samples

The comparative molecular genetic study of museum and modern representatives of cattle breeds can help to elucidate the origin and maintenance of historical genetic components in modern populations. We generated the consensus genotypes for 11 microsatellite loci for 24 museum samples of Kalmyk, Kyrgyz, and Kazakh cattle, dated from the first quarter of the 20th century, and compared them with those of modern Kalmyk, Kyrgyz, and Kazakh white-headed breeds. The level of genetic diversity of the modern Kalmyk and Kyrgyz cattle (uHe = 0.771–0.778) was similar to those observed in the museum samples (uHe = 0.772–0.776), while a visible decrease in genetic variability in the modern Kazakh white-headed breed compared to museum Kazakh cattle was detected (uHe = 0.726 and 0.767, respectively). The PCA plot, FST- and Jost’s D-based networks, and STRUCTURE clustering provided strong evidence of the maintenance of the historical genetic background in modern populations of Kalmyk and Kyrgyz cattle. In spite of the allele pool of Kazakh white-headed cattle having undergone great changes compared to the museum Kazakh cattle, several animals still carry the visible aspect of the historical genetic components. Our results can be used for the selection of individuals for the creation of gene banks and may significantly improve the efficiency of conservation programs aimed at preserving genetic diversity in the national genetic resources of cattle.

GENETIC VARIABILITY OF SIRE BULLS IN THE ARKHANGELSK POPULATION OF THE KHOLMOGORY BREED WHEN OBSERVED OVER GENERATIONS

Проблема и цель. Целью настоящего исследования являлось изучение и анализ генетической структуры потомства у быков-производителей по поколениям (периодам наблюдений). Мониторинг генетической структуры холмогорской породы крупного рогатого скота позволяет провести исследования, дающие информацию во временной шкале по частотам генотипов групп крови для холмогорской породы; осуществлено наблюдение для интервалов наблюдений. Методология. Проведены исследования частот аллелей ЕАВ-локуса. Для холмогорской породы по быкам-производителям определена динамика формирования современной генетической структуры архангельской популяции. Определены частотные характеристики аллелей и анализ динамики их изменения. Результаты. Исследования показали, что аллелофонд холмогорской породы сбалансирован, но отмечена динамика убыли и возрастания частот отдельных аллелей-маркеров, которые свойственны только холмогорской породе крупного рогатого скота. Наблюдалась также достаточно высокая чувствительность и специфичность тестирования. Отмечено, что степень гомозиготности в разрезе анализируемых поколений быков-производителей имеет тенденцию к снижению с 11,4 % (1-й интервал наблюдений) до 5,7 % (9-й интервал). С другой стороны, количество эффективных аллелей – к росту – с 8,8 до 17,6 %. Наибольшее генетическое расстояние имеют чистокровные быки-производители холмогорской породы первого-второго интервалов наблюдений с голштинизированными восьмого-девятого интервалов (расстояния 0,25 и 0,23; 0,27 и 0,47 соответственно). Продолжающееся дистанцирование современных быков-производителей от предыдущих поколений подтверждает проведение поглотительного скрещивания и смещение породы в сторону голштинской с течением времени и в перспективе развития. Заключение. В результате работы проведена оценка генетической структуры холмогорской породы КРС Архангельской популяции и установлено, что в процессе проводимых селекционных мероприятий у быков холмогорской породы отмечается устойчивое увеличение числа аллелей, а чистопородные быки генетически дистанцируются от быков, межпородно гибридизованных с голштинской породой, в ряду поколений с течением времени. Выявлено, что наиболее генетически отдаленными являются чистопородные и голштинизированные быки-производители. Kholmogorskaya breed, Holsteinized stud bulls, allele pool, alleles of the EAB locus blood groups, homozygosity, genetic similarity, genetic distance Problems and purpose of investigation. The purpose of this research was to study and analyze the genetic structure of the bulls ofspring of stud bulls by generations (observation periods). Monitoring of the genetic structure of Kholmogorskaya breed made it possible to carry out studies that provide information on the time scale on the frequencies of genotypes of blood groups for Kholmogorskaya breed. The checkup of the observation intervals was carried out. Methodology. The studies of the allele frequencies of the EAB-locus were carried out. For Kholmogorskaya breed stud bulls, the dynamics of formation of the modern genetic structure of the Arkhangelsk population was determined. The frequency characteristics of the alleles and the analysis of the dynamics of their change were determined. Results. Studies showed that the allele pool of Kholmogorskaya breed was balanced, but the dynamics of the decrease and increase in the frequencies of individual marker alleles, which were characteristic only of Kholmogorskaya breed of cattle, were noted, and a sufciently high sensitivity and specifcs of testing wereobserved. It was noted that the degree of homozygosity in the context of the analyzed generations of stud bulls tended to decrease from 11.4 % (1st observation interval) to 5.7 % (9th interval). On the other hand, the number of efective alleles increased from 8.8 to 17.6 %. The maximal genetic distance was in purebred stud bulls of Kholmogorskaya breed of the frst and second observation intervals with Holsteinized bulls of the eighth to ninth generation intervals (distances 0.25 and 0.23; 0.27 and 0.47, respectively). The continuing distancing of modern stud bulls from previous generations confrmed accumulation cross breeding and the shift of the breed towards Holstein over time and in the future. Conclusion. As a result of the work, the assessment of the genetic structure of Kholmogorskaya breed of the Arkhangelsk population was carried out and it was found that in the process of breeding activities in the bulls of Kholmogorskaya breed there was a steady increase in the number of alleles, and purebred bulls genetically distance themselves from bulls interbreed hybridized with Holstein breed in a number of generations over time. It was revealed that the most genetically distant animals were purebred and Holsteinized stud bulls.

RED-AND-WHITE COW SELECTING FOR MILKABILITY TRAITS AND MONITORING OF KAPPA-CASEIN FORMS AND OTHER GENETIC MARKERS

Изучена эффективность селекции при расширении круга ДНК-маркеров (κ-CN, bGH, PiT-1), а также целесообразность определения критериев оценки изменчивости (кроме генеалогических линий) и при использовании локусов, относимых к QTL-факторам, но с низким полиморфизмом. При существующих темпах быстрого нарастания гомозиготности генетическая изменчивость угрожающе снижается. Это характерно для популяций голштинской породы и крупного рогатого скота «улучшаемых» ею отечественных пород. Проведен поиск ассоциаций с наиболее значимыми признаками селекции в стаде племенного завода красно-пестрой породы. Коровы с гетерозиготным АВ генотипом κ-казеина превосходили сверстниц стада с АА генотипом по удою на 1077 кг молока (P<0,05) и высоте в крестце — на 3,3 см (P<0,01), по МДЖ и МДБ уступали, соответственно, на 0,14 и 0,02%. Выявлено превосходство коров с гетерозиготным генотипом по живой массе во все периоды выращивания телок, снижение возраста их плодотворного осеменения на 1,3 мес. При совершенствовании признаков с использованием генотипов κ-казеина и ряда других локусов обоснована целесообразность отбора и моделирование подбора, а также направленного выведения ремонтных быков. Подчеркнута необходимость дальнейшего изучения функций генов на пути сохранения полезного спектра аллелофонда племенных стад и продолжения эффективной селекции. The efficiency of breeding with the extended DNA marker resources (κ-CN, bGH, and PiT-1) and the effects of reasonable assessment criteria for variability (excluding genealogical lines) at low levels of polymorphism of loci assigned to the QTL factors have been studied. Genetic variability tends to reduce at the current rate of arising homozygosity. It is typical for the Holstein cattle populations and the domestic cattle breeds “improved” by Holsteins. Exploration of associations between selection traits of importance across the Red-and-White cattle in the herd at the breeding enterprise was performed. The milk yield and the sacral height of the cows with k-casein heterozygous AB genotypes were 1077 kg (P<0,05) and 3.3 cm (P<0,01) higher, respectively, than that in their herd peers with genotype AA. With respect to the mass fractions of fat (MFF) and the mass fractions of protein (MFP), their values were 0.14% and 0.02%, respectively, lower. The cows of heterzygous genotype were more efficient in the liveweight during all of the periods of rearing the heifers; reduction in age by 1.3 months at their first effective insemination was recorded. Selecting including target replacement bull selecting and selection modeling are proven reasonable to improve the traits with the use of genotypes at k-casein and other loci. The need of further studying the gene functions is amphasized to preserve the pedigree-cattle allele pool of rare variants important in selective breeding for efficient productivity.

Characteristics of allele pool of cattle of simmental breed in Kazakhstan

One of the key aspects of studying of new breeds, types and lines of farm animals is to evoluation the state of their allele pool by using DNA markers. At the same time, it should be noted that a significant contribution to the characteristic of allelic diversity of breeds is made by regional populations, the formation of which in most cases took place on the basis of local cattle, which are carriers of their own unique allele pool. It is known that studies on microsatellites make it possible to determine the genetic diversity within and between breeds, and the average number of alleles, observed and expected heterozygosity, allow us to calculate the genetic parameters of populations and evaluate their diversity. The purpose of the research was to study the features of the allele pool of a new intra-breed type Ertis of Red-and-White dairy cattle in the Simmental breed. The sampling of biological materials has been carried out according to generally accepted methods. Genotyping has been performed with a set of StockMarks Cattle at 12 loci. Identification of amplification products has been performed on the abi Prism 310 genetic analyzer (Applied Biosystems, USA) using capillary electrophoresis. Decoding of the obtained graphical results has been carried out in the program GeneMapper 4,0. The results of researches on the genetic structure of the studied population of cattle have been reflected in the article. It has been found that there are 65 alleles in 12 loci of the microsatellite, of which 7 alleles with a frequency of occurrence of ≤1 % have been identified. The most informative loci were TGLA227, TGLA122, ETH3, and TGLA53. The average level of expected heterozygosity was 0,68, with random inbreeding – 0,0488. Studies of the genetic profile of the new intra-breed type of dairy cattle Ertis allowed us to establish the wide variety of allele pool in it, and the small number of rare alleles allocated gives grounds for the possibility of determining this population as an independent structural unit in Simmental breed.

Immunogenetic indicators in Simmental cattle breeding

Immunogenic analysis allows to identify the genetic effect of individuals on the total gene pool of the herd and the formation of the allele pool in certain groups of animals. Of great importance is the use of data on blood types when breeding livestock along the lines, when significant genetic similarity is created within the entire population. Studies of Simmental cattle were conducted in 1995-2011. According to the results of the analyzes in the breeding herds of the “Combine” farm and the “Abodimovskiy” farm of the Saratov region, 15 of the most frequently encountered B-system alleles were identified. Comparative analysis of alleles showed that B-alleles B2G2KE'1O' (12.4%), O1I'Q' (15.2%), O3QA'2E1J2 (25.3%) are the most characteristic for the main lines and the herd as a whole. However, in the herd there are alleles that are not found in other zones - B2O1Y2D' - (2.3%), B2O3Y2A'2E2P'2Q' - (2.1%), I1E'2G"- (2.1%), Y2A'1D'E' - (1.0%). This indicates that the studied group represents a kind of population that can be attributed to the Volga zonal type. Genetic affinity between the lines, groups of bulls, families was determined on the basis of the genetic similarity index (r). An index of up to 0.5 is considered to indicate a significant genetic dissociation of the compared groups of animals, up to 0.80 - of the existing genetic differences, with above 0.80 - for the presence of genetic similarities between the compared groups of livestock. The calculations showed that there is a genetic similarity between the cows of the Florian and Fasadnik lines, as well as the Facadnik and Mergel, in the herd of the “Combine” state farm (the index value was 0.89 and 0.91) The differences were established between the animals of the Florian and the Mergel lines (r = 0.76). The high genetic similarity between the lines is due to the use of crosses between them. The homozygosity coefficient in the lines varies from 9 to 22%.

THE VALUATION OF IMMUNOGENETICAL DISTINCTION BETWEEN THE DESCENDANTS OF DIFFERENT BULLS

The article presents the results of detailed genetical valuation between the descendants of different bulls in the period from 2003 till 2013. The aim of this research was to give a detailed genetic evaluation of the descendants of different bulls used in the herd of STE "Maximovca" at the relevant period of time. The object of the study was the heifers of Moldovan type of black-and-white cattle – the descendants of 11 bulls. Blood groups were determined by standard serological tests with the use of 49 monospecific sera from 9 genetic systems. All the attested livestock of breeding young growth of 2003-2013 are authentic, that is proved by the materials of the expertise of the authenticity of origin. According to AEB-locus at the descendants of all the bulls, common from 25 studied antigens were only 6 – B2, G2, O2, Y2, E′2 and Q′. The low frequency of occurrence of antigens P2, Q, T1, K ', J'2, P' is peculiar mainly for all the analysed descendants. The smallest genetic distance is identified between the descendants of bulls Academic 767 and Senior 7415 – 0,1291, and the highest one – between the descendants of bulls Abhazian 835 and Dikii 788 – 0,3095. The descendants of the evaluated bulls form four separate clusters: the first cluster consists of descendants of bulls Senior – Academic, the second cluster – Abiturient – Captain, the third cluster – Abhazian – Kiperush and the fourth cluster – Meteor – Karas. Herewith the linear belonging of bulls in the first three clusters is different and only both bulls of the fourth cluster (Karas, Meteor) refer to bloodline of Vis Back Ideal. The total frequency of occurrence of the basic alleles varied from 0,2250 (the descendants of bull Kiperush 79) to 0,4071 (the descendants of bull Dikii 788). The lowest coefficient of homozygosity turned out to be at the descendants of Abiturient 861 and Svet 732 – 5,7%. The greatest genetical resemblance is revealed between the descendants of bulls Academic 767 and Senior 7415 (r=0,8709). It is observed the tendency of increasing coefficient of homozygosity (descendants, born in 2009-2013) – 18%, that led to the shortening of numbers of effective working alleles from 17,3 (the descendants of bull Abiturient) to 5,4 (descendants of bull Meteor) and to shortening of the indicator of the degree of the possible genetical changeability to 86,4%. Alleles which are inherent to Holstein American, Canadian and European selection – B2O2Y2D 'and B2G2 are identified in the allele pool of the descendants of bulls Dikii, Svet and Senior. Conclusions. The main specific gravity in the structure of the allele pool of blood groups at the descendants of different bulls occupies the alleles, identified in the previous research of the herd of STE "Maximovca". The descendants of 9 bulls are the carriers of 11 alleles of EAB-locus which are characteristic for Red Steppe breed (B1I1, B2O1Y2, G2O1, G2D′, O2B′, G2O1Y2, O1Y2, Y2D′, Y2Y′, P1I′, O2D′). The tendency of the coefficient of homozygosity growth at the descendants, born in 2009-2013 (Ca=18%), led to reduction of the number of effective alleles from 17,3 to 5,4 and decrease of the indicator of the possible genetic variability to 86.4%.