Animal Genotype Research Articles

Imputation of non-genotyped sheep from the genotypes of their mates and resulting progeny

Accurate genomic analyses are predicated on access to a large quantity of accurately genotyped and phenotyped animals. Because the cost of genotyping is often less than the cost of phenotyping, interest is increasing in generating genotypes for phenotyped animals. In some instances this may imply the requirement to genotype older animals with greater phenotypic information content. Biological material for these older informative animals may, however, no longer exist. The objective of the present study was to quantify the ability to impute 11 129 single nucleotide polymorphism (SNP) genotypes of non-genotyped animals (in this instance sires) from the genotypes of their progeny with or without including the genotypes of the progenys’ dams (i.e. mates of the sire to be imputed). The impact on the accuracy of genotype imputation by including more progeny (and their dams’) genotypes in the imputation reference population was also quantified. When genotypes of the dams were not available, genotypes of 41 sires with at least 15 genotyped progeny were used for the imputation; when genotypes of the dams were available, genotypes of 21 sires with at least 10 genotyped progeny were used for the imputation. Imputation was undertaken exploiting family and population level information. The mean and variability in the proportion of genotypes per individual that could not be imputed reduced as the number of progeny genotypes used per individual increased. Little improvement in the proportion of genotypes that could not be imputed was achieved once genotypes of seven progeny and their dams were used or genotypes of 11 progeny without their respective dam’s genotypes were used. Mean imputation accuracy per individual (depicted by both concordance rates and correlation between true and imputed) increased with increasing progeny group size. Moreover, the range in mean imputation accuracy per individual reduced as more progeny genotypes were used in the imputation. If the genotype of the mate of the sire was also used, high accuracy of imputation (mean genotype concordance rate per individual of 0.988), with little additional benefit thereafter, was achieved with seven genotyped progeny. In the absence of genotypes on the dam, similar imputation accuracy could not be achieved even using genotypes on up to 15 progeny. Results therefore suggest, at least for the SNP density used in the present study, that it is possible to accurately impute the genotypes of a non-genotyped parent from the genotypes of its progeny and there is a benefit of also including the genotype of the sire’s mate (i.e. dam of the progeny).

Livestock Nutrigenomics Applications and Prospects

Livestock performance is thought to be affected by genotype (heritable) and environment (non-heritable). Nutrition is among the greatest environmental determinants. Genes are turned on and off according to metabolic signals that the nucleus receives from internal factors like hormones and external factors like nutrients. Currently, Nutrigenomics which encompasses the three crucial -omics stages (Transcriptomics, Proteomics and Metabolomics), is emerging in the area of livestock to develop feeds that can be matched to genotypes of animals for a better production, productivity and health. It deciphers how food ingredients and nutrition affect gene expression, metabolic pathways and diet-related disease development. Hence, Nutrigenomics makes clear that how gene interacts with nutrients and how DNA and genetic code affect the needs for certain nutrients and quantities which suggests the possibility to change the way we feed and manage livestock and poultry. The tools of molecular genetics are expected to have much more impact in the future. The interaction between diets and genes could be evaluated through DNA microarray techniques and quantitative real-time polymerase chain reaction (PCR). These profiling techniques are reported to allow examination of nutrient effects that was not possible in the past. Nutrigenomics is feasible to apply in livestock production but can only provide part of the solution in response to non genetic factors involved in livestock health and production. In this paper, the Principles, current status of its application in different areas, challenges and opportunities of livestock Nutrigenomics with emphasis to developing countries like Ethiopia has been thoroughly reviewed.

GDF9 gene polymorphism and its association with litter size in two Russian sheep breeds

The purpose of this work was to study the GDF9 gene polymorphism in two sheep breeds raised in Russia and to identify its association with litter size. A variety of allelic variants of the GDF9 gene (GDF9/G1 and GDF9/G4 sites) in Salsk and Volgograd sheep breeds was studied. Mutations of the GDF9 gene that lead to improvement of reproductive traits in these sheep breeds were revealed. The obtained results of the alleles and genotypes frequencies for the GDF9 gene showed a low level of polymorphism at G1 and G4 sites. The studied populations were found to have high frequencies of G allele and GG genotype at G1 site and of A allele and AA genotype at G4 site of the GDF9 gene. Herewith all the individuals heterozygous at G1 site were also heterozygous at G4 site. Homozygous AA (G1) and GG (G4) genotypes in the study population were not observed. In the Salsk sheep population the individuals with AG genotype at G1 site had the highest fertility. A similar pattern was observed at G4 site. The litter size of Salsk sheep with GG genotype (G1) was 1.13. Among the Volgograd sheep, the individuals with AG genotype were also characterized by the highest fertility; the litter size of the individuals with the GG genotype (G1) was 1.22. A similar pattern was observed at G4 site. The litter size of animals with AG genotype was 1.88 and the AA genotype − 1.22. Thus, the positive and significant relation between the heterozygous AG/GDF9 genotype and litter size of animals has been established.

Multi-year evaluation of stocking rate and animal genotype on milk production per hectare within intensive pasture-based production systems

The objective of this experiment was to evaluate the effect of stocking rate (SR) and animal genotype (BR) on milk production, body weight (BW), and body condition score (BCS) within intensive pasture-based systems. A total of 533 lactation records, from 246 elite genetic merit dairy cows were available for analysis; 68 Holstein-Friesian (HF) and 71 Jersey × Holstein-Friesian (JxHF) crossbred cows in each of 4 consecutive years (2013-2016, inclusive). Cows from each BR were randomly allocated to 1 of 3 whole-farm comparative SR treatments, low (LSR; 1,200 kg of BW/ha), medium (MSR; 1,400 kg of BW/ha), and high (HSR; 1,600 kg of BW/ha), and remained in the same SR treatments for the duration of the experiment. The effects of SR, BR, and their interaction on milk production/cow and per hectare, BW, BCS, and grazing characteristics were analyzed. Total pasture utilization per hectare consumed in the form of grazed pasture increased linearly as SR increased: least in LSR (10,237 kg of dry matter/ha), intermediate in MSR (11,016 kg of dry matter/ha), and greatest in HSR (11,809 kg of dry matter/ha). Milk and milk solids (MS) yield per hectare was greatest for HSR (15,942 and 1,354 kg, respectively), intermediate for MSR (14,191 and 1,220 kg, respectively), and least for LSR (13,186 and 1,139 kg, respectively) with similar trends evident for fat, protein, and lactose yield/ha. At higher SR (MSR and HSR), MS yield per kg of BW per ha was reduced (0.85 and 0.82 kg of MS/kg of BW, respectively) compared with LSR (0.93 kg of MS/kg of BW/ha). Holstein-Friesian cows achieved fewer grazing days per hectare (-37 d), and produced more milk (+561 kg/ha) but less fat plus protein (-57 kg/ha) compared with JxHF cows; the JxHF cows were lighter. At similar BW per hectare, JxHF cows produced more fat plus protein/ha during the grazing season at low (1,164 vs. 1,113 kg), medium (1,254 vs. 1,185 kg), and high (1,327 vs. 1,380 kg) SR. In addition, JxHF cows produced more fat plus protein per kg of BW/ha (0.90 kg) compared with HF cows (0.84 kg). The results highlight the superior productive efficiency of high genetic potential crossbred dairy cows within intensive pasture-based production systems.

CONNECTION g.307 G > A SNP POLYMORPHISM OF THE ALPHA-FUKOZYLTRASFERAZA 1 GENE WITH ECONOMIC-USEFUL TRAITS IN THE LARGE WHITE PIG BREED

One of the top priorities at the present stage of development of pig breeding remains the development of a set of measures aimed at increasing the resistance animals to various diseases, especially – to colibacteriosis .One of the recent and effective approaches to prevent colibacillosis is using markers of selection; it involves pig genotyping by genome locuses. Chosen locuses are associated with animal sensitivity to the disease and selection of the results of genotyping of animals with increased resistance. Due to researches, one of such locuses is alpha-fukozyltrasferаza 1 gene (FUT1). Gene FUT1 is located in chromosome 6. As a result of its sequencing in the swine breeds of Large White and Swedish Landrace, single-nucleotide polymorphism (g.307 G > A SNP) has been detected. AA genotype determines the resistance of animals to colibacteriosis, while AG and GG genotypes are susceptible to this disease. According to the results of previous studies, the positive effect of allele A was determined not only on the resistance of pigs to colibacteriosis, but also on indicators of fattening and meat productivity and on reproductive performance. In Ukraine, the studies of polymorphism FUT1 g.307 G > A SNP were held fragmentedly and only on certain populations of Ukrainian Meat and Large White breed but without establishing its association with the indicators of productivity of pigs. The aim of our work was to study the genetic structure of Ukrainian Large White breeds, type 1 and the establishment of association. g. 307 G > A SNP FUT1 gene with pigs indicators of productivity. For research the 96 samples of hair were used. DNA isolation from samples with biomaterial were carried out using ion exchange resin Chelex-100. Genotyping was performed by PCR-RFLP by method of Jorgensen et al. (2006). Using DNA analysis of this breeds locus FUT1 was determined by genetic structure. Allele frequency of allele G (0,573) and allele A (0,427) was established The distribution of genotype frequencies was not statistically significantly different from the theoretically expected, calculated by the Hardy-Weinberg criterion. Thus, according to the locus of FUT1 g.307 G > A, the breeds investigated are in a state close to the genetic equilibrium. The negative value of the fixation index by the locus FUT1 g.307 G > A indicates an excess of heterozygotes in the population, and hence the lack of targeted selection for this marker. The valuation was performed by calculating the PIC (polymorphic information content) – information content of polymorphism marker. In the analyzed pig herd for this marker, the PIC has an average value (0,367), which indicates the high level of polymorphism of the given locus and is favorable for the possibility of conducting a search for links between individual genotypes and indicators of productivity. To establish the association g.307 G > A SNP FUT1 gene with indicators of animal productivity, a one-way analysis of variance of the experimental data was used. Based on the results of a one-way analysis of variance, a significant effect of the genotypes of the FUT1gene (g.1849 G > C) on the indicator of the average daily weight gain (р ≤ 0,001), the thickness of the bacon at the level of the VI-VII vertebrae (p ≤ 0.01), reaching live weight of 100 kg (р ≤ 0,001) and breeding index of fattening qualities (р ≤ 0,01) was found. The parameter of the influence of the genetic factor on the test feature was 28,54%, 10,4%, 33,4% and 8,8% respectively. According to the investigated indicators of productivity, animals with genotype AA, which determines resistance to colibacteriosis, dominated the animals with genotypes GG and AG. Based on the results of our research and pre-published data, the multiple effect of the g.307 G > A SNP FUT1 gene is observed, which is associated with the indicators of productivity, which again confirms the polygenicity of the quantitative trait loci of farm animals. Taking into account a high level of polymorphism of the investigated gene and reliable associations of genotypes with indicators of productivity found, it can be recommended to carry out breeding of pigs using genetic information of the g.307 G > A SNP gene FUT1.

EVALUATION OF DAIRY PRODUCTIVITY AND REPRODUCTIVE ABILITY OF UKRAINIAN BLACK-AND-WITE AND RED-AND-WITE MILK COWS DEPENDING ON THE SELECTIONAL DIRECTION OF HOLSTEIN BREED

Formation of high-yielding herds is a rather long breeding process (at least 10–12 years), during which animals of the 3rd–4th generation appear. During this period, it is necessary to preserve a certain scientifically justified direction of selection to perform the tasks, the embodiment of which in life is possible only in the presence of a long-term plan of breeding work. Selection of cows for milk productivity primarily depends on the degree of influence on this feature of the main genetic and environmental factors, taking into account that you can significantly improve the desired attributes.
 The purpose of our research was to assess productive and reproductive animal characteristics of Ukrainian red- and black-and-white dairy breeds, search of the most effective breeding methods for improving the reproductive function of cows and heifers.
 Indicators of economically useful signs of the animals under investigation are calculated according to the data of the primary zootechnical account according to the generally accepted methods of biometric analysis. In the course of the work the genealogical, population, genetic and mathematical methods of studying patterns of inheritance, variability, repeatability, estimation of the genotype of animals and other classical methods of research were used.
 According to the results of our research, it is evident that the best milk production is characterized by the animals obtained by using the Holstein breed of North American breeds. A well-defined difference of 234 kg is observed in the cows of the Ukrainian black-and-white milk breed, and in the red- and-white peers there is an insignificant difference between the groups. That indicates that the high-level animals of the Holstein breed do not fully realize their genetic potential by productivity. It should be noted that the bloodiness of the North American selection of Holstein breeds in the genotypes of both breeds, in contrast to the diet, had a negative effect on the protein content of milk (milk protein content decreased by 0.5–0.9%
 In comparison with the animals of the desirable type of daughter from the European bulls of the Holstein breed in the group of Ukrainian black- and red- and-white dairy breeds were significantly superior to or were at the level of the animals of the desired type for fatty milk and milk protein content, unlike the daughters from the bulls of the North American breeding direction.
 Animals derived from the bulls of the North American breeding Holstein breed had the longest service period 166.1 days, which is 36.4 days more than that of the animals of the same breed, but from the bulls of European breeding Holstein breed (P > 0,05). It was also characterized by a longer give birth period, which amounted to 445.4 days, prevailing at the same time of first-born cows with European genetics of Holstein breed for 36 days (P > 0,05).
 According to the indicator of reproductive ability of animals of Ukrainian black-and-white milk breeds holsteinized by the European type of breeding Holstein breed have a better result of 0.89 in contrast to the peers holsteinized by the North American type of selection 0,86 (P > 0,05). In the comparative analysis of the correlation of reproductive ability of cows with different genotypic groups of both breeds, the cows with the European type of selection of the Holstein breed are preferable to the parameters of the animals of the desired type.
 Conclusions. According to the results of the evaluation of milk productivity, the preference is given to the animals obtained from the bulls of the Holstein breed of North American breeding by quantitative indices but this genetics negatively affected the protein content of milk. Compared to the animals of the desired type, – then both breeding directions are considerably inferior to the parameters of the animals of the desired type, but on qualitative indicators of milk productivity the cows from the bulls of European breeding Holstein breed prevail and their peers with the North American selection of Holstein breed and animals of the desired type.
 According to the performance of the reproductive ability of the daughter of the North American bulls Holstein breed had the longest service- and between the give birth period, and shorter dry period. According to the indicator of reproductive ability, dominated cows by the European type of breeding Holstein breed.

FEATURES OF THE PROPAGATION OF GENE BoLA-DRB3 ALLELES IN GRAY CATTLE BREEDS

FEATURES OF THE PROPAGATION OF GENE BoLA-DRB3 ALLELES IN GRAY CATTLE BREEDS

Meta-analysis of sequence-based association studies across three cattle breeds reveals 25 QTL for fat and protein percentages in milk at nucleotide resolution

BackgroundGenotyping and whole-genome sequencing data have been generated for hundreds of thousands of cattle. International consortia used these data to compile imputation reference panels that facilitate the imputation of sequence variant genotypes for animals that have been genotyped using dense microarrays. Association studies with imputed sequence variant genotypes allow for the characterization of quantitative trait loci (QTL) at nucleotide resolution particularly when individuals from several breeds are included in the mapping populations.ResultsWe imputed genotypes for 28 million sequence variants in 17,229 cattle of the Braunvieh, Fleckvieh and Holstein breeds in order to compile large mapping populations that provide high power to identify QTL for milk production traits. Association tests between imputed sequence variant genotypes and fat and protein percentages in milk uncovered between six and thirteen QTL (P < 1e-8) per breed. Eight of the detected QTL were significant in more than one breed. We combined the results across breeds using meta-analysis and identified a total of 25 QTL including six that were not significant in the within-breed association studies. Two missense mutations in the ABCG2 (p.Y581S, rs43702337, P = 4.3e-34) and GHR (p.F279Y, rs385640152, P = 1.6e-74) genes were the top variants at QTL on chromosomes 6 and 20. Another known causal missense mutation in the DGAT1 gene (p.A232K, rs109326954, P = 8.4e-1436) was the second top variant at a QTL on chromosome 14 but its allelic substitution effects were inconsistent across breeds. It turned out that the conflicting allelic substitution effects resulted from flaws in the imputed genotypes due to the use of a multi-breed reference population for genotype imputation.ConclusionsMany QTL for milk production traits segregate across breeds and across-breed meta-analysis has greater power to detect such QTL than within-breed association testing. Association testing between imputed sequence variant genotypes and phenotypes of interest facilitates identifying causal mutations provided the accuracy of imputation is high. However, true causal mutations may remain undetected when the imputed sequence variant genotypes contain flaws. It is highly recommended to validate the effect of known causal variants in order to assess the ability to detect true causal mutations in association studies with imputed sequence variants.

Технологічна оцінка якості м’яса залежно від фізіологічного стану

Впродовж багатьох років в Україні надається велика увага збільшенню виробництва яловичини та покращення її якості завдяки розвитку спеціалізованого м’ясного скотарства. М’ясна продуктивність великої рогатої худоби формується під впливом широкого комплексу морфологічних, біологічних, фізіологічних особливостей, які залежать від породи, генотипу тварин, умов середовища, типу вищої нервової діяльності, повноцінності раціону та оцінюється за такими показниками як: витрати корму на одиницю приросту; маса тіла, абсолютний та відносний прирости; забійний вихід; якість м’яса. Тому дослідження біохімічних процесів у бугайців на відгодівлі поліської м’ясної породи залежно від типів вищої нервової діяльності та вплив згодовування кормової добавки «Мікроліповіт» на основні показники метаболізму та м’ясну продуктивність є надзвичайно важливими. Після припинення життя тварин склад і властивості тканин, насамперед м’язової, істотно змінюються. Внаслідок припинення надходження кисню і призупинення процесів синтезу дезорганізовується обмін речовин і енергії у тканинах. Специфічні автолітичні перетворення протікають у м’язовій тканині відповідно до особливостей метаболізму, концентрації та локалізації ферментів. У основі автолітичних перетворень м’яса лежать зміни вуглеводної системи, системи ресинтезу АТФ і стану міофібрилярних білків, що входять до системи скорочення. Зміни м’яса, зумовлені автолітичними процесами, трапляються у технології м’яса за найрізноманітніших способів його оброблення, під час охолодження та зберігання охолодженого м’яса, заморожування і холодильного зберігання, розморожування, засолювання подрібнення. Характер і глибина автолітичних змін м’яса впливають на його якість і харчову цінність.&#x0D; Аналіз якості харчових продуктів, виявлення потенційних ризиків, пов’язаних з їх забрудненням та псуванням, мають базуватися на науковій основі і нових методах дослідження. Тому, на даний час вивчення питання використання м’яса з ознаками PSE і DFDу технології емульгованих ковбасних виробів залишається актуальним. (PSE – pale, soft, exudative – бліде, м’яке, водянисте; DFD – dark, firm, dry – темне, тверде, сухе, DCB – dark cutting beef – темна на розрізі є актуальним. Проведення оцінки якості яловичини NOR, PSE і DFD є необхідним при виробництві якісних м’ясних продуктів та їх безпеки для здоров’я людей.&#x0D;

Distinct seasonal migration patterns of Japanese native and non-native genotypes of common carp estimated by environmental DNA.

Understanding behavioral differences between intraspecific genotypes of aquatic animals is challenging because we cannot directly observe the animals underwater or visually distinguish morphologically similar counterparts. Here, we tested a new monitoring tool that uses environmental DNA (eDNA), an assemblage of DNA in environmental water, to specifically detect Japanese native and introduced non‐native genotypes of common carp (Cyprinus carpio) in Lake Biwa, Japan, and estimated differences between the two genotypes in the use of inland habitats. We monitored the ratios of native and non‐native single nucleotide polymorphism alleles of a mitochondrial locus of common carp in a lagoon connected to Lake Biwa for 3 years using eDNA. We observed seasonal dynamics in the allele frequency showing that the native genotype frequency peaked every spring, suggesting that native individuals migrated to the lagoon for spawning and then returned to the main lake, whereas non‐native individuals tended to stay in the lagoon. The estimated migration patterns corresponded with the estimates of a previous study, which were based on commercial fish catch data. Our findings suggest that eDNA‐based monitoring can be useful tool for addressing intraspecific behavioral differences underwater.

Effect of stocking rate and animal genotype on dry matter intake, milk production, body weight, and body condition score in spring-calving, grass-fed dairy cows.

The objective of the experiment was to quantify the effect of stocking rate (SR) and animal genotype on milk production, dry matter intake (DMI), energy balance, and production efficiency across 2 consecutive grazing seasons (2014 and 2015). A total of 753 records from 177 dairy cows were available for analysis: 68 Holstein-Friesian and 71 Jersey × Holstein-Friesian (JxHF) cows each year of the experiment under a pasture-based seasonal production system. Animals within each breed group were randomly allocated to 1 of 3 whole-farm SR treatments defined in terms of body weight per hectare (kg of body weight/ha): low (1,200 kg of body weight/ha), medium (1,400 kg of body weight/ha), and high (1,600 kg of body weight/ha), and animals remained in the same SR treatments for the duration of the experiment. Individual animal DMI was estimated 3 times per year at grass using the n-alkane technique: March (spring), June (summer), and September (autumn), corresponding to 45, 111, and 209 d in milk, respectively. The effects of SR, animal genotype, season, and their interactions were analyzed using mixed models. Milk production, body weight, and production efficiency per cow decreased significantly as SR increased due to reduced herbage availability per cow and increased grazing severity. As a percentage of body weight, JxHF cows had higher feed conversion efficiency, higher DMI and milk solids (i.e., kg of fat + kg of protein) production, and also required less energy intake to produce 1 kg of milk solids. The increased production efficiency of JxHF cows at a similar body weight per hectare in the current analysis suggests that factors other than individual cow body weight contribute to the improved efficiency within intensive grazing systems. The results highlight the superior productive efficiency of high genetic potential crossbred dairy cows within intensive pasture-based milk production systems at higher SR where feed availability is restricted.

Invited review: Measurable biomarkers linked to meat quality from different pig production systems

Abstract. Biological processes underlie all livestock traits, including post-mortem meat quality traits. Biomarkers are molecular components of the biological processes showing differential expression associated with the phenotype of the trait. The phenotypes of the meat quality traits are determined by the animal's genotype interacting with the environment affecting the expression of the genome. The omics technologies enable measuring the expression of the genome at all levels: transcriptome, proteome, and metabolome. Associations between the phenotype of the traits and expressions measured with the omics techniques are a first step in developing biomarkers. Biomarkers enable the monitoring, diagnosis, and prediction of changes in meat quality related to external (environmental, e.g. feed and animal management conditions) stimuli and interactions with the genotype. In this paper we review the development of biomarkers for meat quality of pigs in diverse pig breeds, environments, and pork production chains.

Short communication: The role of genotypes from animals without phenotypes in single-step genomic evaluations

In a 2-step genomic system, genotypes of animals without phenotypes do not influence genomic prediction of other animals, but that might not be the case in single-step systems. We investigated the effects of including genotypes from culled bulls on the reliability of genomic predictions from single-step evaluations. Four scenarios with a constant amount of phenotypic information and increasing numbers of genotypes from culled bulls were simulated and compared with respect to prediction reliability. With increasing numbers of genotyped culled bulls, there was a corresponding increase in prediction reliability. For instance, in our simulation scenario the reliability for selection candidates was twice as large when all culled bulls from the last 4 generations were included in the analysis. Single-step evaluations imply the imputation of all nongenotyped animals in the pedigree. We showed that this imputation was increasingly more accurate as increasingly more genotypic information from the culled bulls was taken into account. This resulted in higher prediction reliabilities. The extent of the benefit from including genotypes from culled bulls might be more relevant for small populations with low levels of reliabilities.

Genetic diversity and antibiotic susceptibility of Staphylococcus aureus isolates from wild boars.

We here report the occurrence of S. aureus in wild boars and characterize isolates genotypically and phenotypically in order to get knowledge about the occurrence of clonal lineages and genotypes in free-living wild animals. Forty-one S. aureus isolates obtained from 111 wild boars hunted in Lower Saxony, Germany, were investigated and compared to human and livestock isolates. The S. aureus belonged to multilocus sequence types ST1, ST7, ST30, ST133, ST425, ST804, ST890 and to the new ST3237, ST3238, ST3255 and ST3369. The livestock associated CC398-MRSA lineage, however, was not found. In addition to well-known spa types, the new types t14999, t15000, t15001 and t15002 were detected. Macrorestriction analysis revealed a variety of different SmaI fragment patterns. Most isolates were susceptible to all antimicrobials tested, including methicillin, and resistance was detected only to ampicillin, penicillin and erythromycin. PCR analysis confirmed the presence of staphylococcal enterotoxin genes (seh) in all t127-ST1 isolates. A high degree of genetic diversity was detected with many spa types and clonal lineages previously reported in humans and livestock animals.

Signal function drives phenotypic and genetic diversity: the effects of signalling individual identity, quality or behavioural strategy.

Animal coloration is influenced by selection pressures associated with communication. During communication, signallers display traits that inform receivers and modify receiver behaviour in ways that benefit signallers. Here, we discuss how selection on signallers to convey different kinds of information influences animal phenotypes and genotypes. Specifically, we address the phenotypic and genetic consequences of communicating three different kinds of information: individual identity, behavioural strategy and quality. Previous work has shown signals that convey different kinds of information differ in terms of the (i) type of selection acting on signallers (e.g. directional, stabilizing, or negative frequency dependent), and (ii) developmental basis of signals (i.e. heritability, genetic architecture). These differences result in signals that convey different information having consistently different phenotypic properties, including the amount, modality and continuity of intraspecific variation. Understanding how communication influences animal phenotypes may allow researchers to quickly identify putative functions of colour variation prior to experimentation. Signals that convey different information will also have divergent evolutionary consequences. For example, signalling individual identity can increase genetic diversity, signalling quality may decrease diversity, and signalling strategy can constrain adaptation and contribute to speciation. Considering recent advances in genomic resources, our framework highlights new opportunities to resolve the evolutionary consequences of selection on communication across diverse taxa and signal types.This article is part of the themed issue 'Animal coloration: production, perception, function and application'.

Selection of core animals in the Algorithm for Proven and Young using a simulation model

The Algorithm for Proven and Young (APY) enables the implementation of single-step genomic BLUP (ssGBLUP) in large, genotyped populations by separating genotyped animals into core and non-core subsets and creating a computationally efficient inverse for the genomic relationship matrix (G). As APY became the choice for large-scale genomic evaluations in BLUP-based methods, a common question is how to choose the animals in the core subset. We compared several core definitions to answer this question. Simulations comprised a moderately heritable trait for 95,010 animals and 50,000 genotypes for animals across five generations. Genotypes consisted of 25,500 SNP distributed across 15 chromosomes. Genotyping errors and missing pedigree were also mimicked. Core animals were defined based on individual generations, equal representation across generations, and at random. For a sufficiently large core size, core definitions had the same accuracies and biases, even if the core animals had imperfect genotypes. When genotyped animals had unknown parents, accuracy and bias were significantly better (p≤.05) for random and across generation core definitions.

BANK OF ANIMAL GENETIC RESOURCES OF INSTITUTE OF ANIMALS BREEDING AND GENETICS ND. A. M.V.ZUBETS OF NAAS SYSTEM OF ANIMAL BIODIVERSITY CONSERVATION OF UKRAINE

BANK OF ANIMAL GENETIC RESOURCES OF INSTITUTE OF ANIMALS BREEDING AND GENETICS ND. A. M.V.ZUBETS OF NAAS SYSTEM OF ANIMAL BIODIVERSITY CONSERVATION OF UKRAINE

EFFICIENCY OF SELECTION BY EXTERIOR TYPE IN THE BREEDING HERDS DAIRY BREEDS

The need to study constitutional-exterior features of dairy cattle is due, of course, established in many studies to their positive connectivity with performance and lasting economic use. The vast majority of scientists-breeders thinks, that breeding cattle by technological features should determine the basic direction of work in farming on the threshold of XXI century. Based from the above, the aim of the research was to evaluate the productive and technological features cattle of dairy breeds combined with linear estimation from the body type. The study focused on linear estimation of cattle dairy breeds by the type of body structure and study their impact on economically useful traits – don’t have any doubts.The study was conducted in pedigree cattle breeding farms of Holstein, Ukrainian black- and red-white dairy breeds in stock of 1300 cows. Linear evaluation of cows by external type carried from the method of Hmelnychyi L.M. developed by employees of Institute to breeding and animal genetics. Comparative evaluation of animals for productive characteristics held within the breeding herds and genealogical groups. In the course of the work done was applied genealogical, population, genetics and mathematical methods Study of frequency heritability, variability, estimation of genotype of animals and other classical research methods. A statistical analysis result of research was conducted on algorithms N.A. Plohinskyi.Cows first calves Ukrainian red- and black-white dairy breeds are characterized by the following measurements articles: the height at the withers and sacrum 132.7&amp;132,2 and 141,1 &amp; 140,8 cm, with well-developed breasts in depth (72.0 and 71.5 cm), width (44.6 and 43.1 cm) and girth (189.9 and 187.9 cm), with extensive backwards in tubers of Ilium (51.3 and 50.9 cm) and in buttocks (34.6 and 35.2 cm). Spit length of rump was 52.5 and 51.8 cm, and body length - 162.4 and 161.2 cm. First-born Holstein breed exceeded peers Ukrainian dairy breeds by the withers height on (1.4 and 1.9 cm) and a sacrum (1.2 and 1.5 cm), by breast depth 1.1 and 1.6 cm, but they are inferior on the basis of the width of the breast, especially in comparison with cattle Ukrainian red-white milk breed (1.8 cm). Holstein animals differed broader backwards in tubers of Ilium (0.3 and 0.7 cm), in the hipbone (0.3 and 0.4 cm) and in buttocks (by 2.0 and 1.1 cm), and longer by 1.2 and 2.4 cm trunk, by chest girth of 2.4 and 4.4 cm.Large coefficients of variation measurements describing the distance from the bottom of the udder to hock (Cv = 33,2 - 42,3%), between the front (Cv = 24,2 - 28,1%), back (Cv = 33,3 - 53,9%) and side teat (Cv = 19,1 - 27,0%) indicate the level of not consolidation studied animal herds on these characteristics. Comparative characteristics of the firstborn cow’s udder Ukrainian red- and black-white dairy breeds shows, that animal’s udder great and makes for girth - 132.4 and 135.3 cm, length - 38.7 and 40.0 cm and width - 29.9 and 32.3 cm with advantage of reliable peers Ukrainian black-white dairy cattle for the circumference of 2.9 cm (TD = 2.41), length - 1.3 cm (td = 1,74) and width - 2.4 cm (td = 4,56). Most of the morphological features of the udder is in the positive connection with the largest yield per lactation. These include the circumference (r = 0,430 and 0.335) length (r = 0,376 and 0.353), width (r = 0,347 and 0.232) and depth of the front quarters (r = 0,160 and 0.166).The estimated population of the first-calves is characterized by rather high rates, then ranging within 1.85 - 1.90 kg / min. exceeding the maximum target standards for Ukrainian dairy breeds 0.05 - 0.10 kg / min. During the breeding to improve dairy breeds is important to know and take into account the relationship between the magnitude and intensity of milking yield. When examined the effect of daily yield on the intensity of milk found, that the highest daily yield, the more intense cow milk off. This high correlation coefficients (r = 0,438 - 0,511) in large samples with high reliability (td = 6.11 – 7.87). Share heredity influence the total variability measurements articles of udder varies widely. Most udder traits are positive in relation to the size of yield and total yield of milk fat. A high level of heritability coefficients udder morphological characteristics sufficient for efficient breeding of dairy cattle and there was a positive correlation between the main floors of the udder and the largest yield provide breeding aimed at improvement.

Helitrons and Retrotransposons Are Co-localized in Bos taurus Genomes.

Background: DNA transposons helitrons are mobile genetic elements responsible for major movements of the genetic material within and across different genomes. This ability makes helitrons suitable candidate elements for the development of new approaches of multilocus genotyping of live-stock animals, along with the well-known microsatellite loci.Objective: We aimed to estimate the informativeness of helitron and microsatellite markers in assessing the consolidation and the “gene pool” standards of two commercial dairy cattle breeds (Ayrshire breed and holsteinized Black-and-White cattle) and one local breed of Kalmyk cattle, and to reveal any inter-breed difference in the organization of genomic regions flanked by helitrons in the studied cattle breeds.Method: We used the combination of two highly-polymorphic genomic elements – helitrons and trinu-cleotide microsatellites (AGC)6G and (GAG)6C, respectively – for genome scanning of the sampled groups of cattle. Also, we pyrosequenced the genomic regions flanked by the inverted repeats of 3'-end of Heligloria family of helitron fragments.Results: Generally, the both combinations of markers generated polymorphic spectra, based on which certain interbreed differentiation could be observed. The analysis of the identified interspersed repeats suggests that in factory and local cattle the genomic regions flanked by helitron fragments are shaped differently and contain different superfamilies of transposable elements, especially retrotransposons.Conclusion: Despite the well-known fact of retrotransposon-dependent microsatellite expansion, our data suggest that, in the cattle genome, the DNA transposons and microsatellites can also be found in close neighbourhood, and that helitrons and retrotransposons may form domains of increased variability – targets for factors of artificial selection.

Progesterone receptor (PRG) gene polymorphism and association with litter size in the california rabbit breed

Modern approaches to genetic improvement of species based on genotype-depth evaluation of farm animals and genetic diversity of populations using marker technology. Determination of genotype of animals was carried out using PCR-RFLP. A 558-bp sequence of the rabbit progesterone receptor promoter region (PGR) gene was obtained for 60 animals of the California breed from High Litter Size (HLS) and Low Litter Size (LLS) groups. Found that in individuals with multiple groups rabbit dominated by individuals with heterozygous genotype (0.700), while in animals with low levels litter size – individuals with genotype AA. In addition, the rabbit and the second group were characterized by very high actual heterozygosity (Ho = 0,700), which significantly exceeds the expected heterozygosity (No = 0.455). Among the animals that had low bahatoplidnosti differences between actual and expected assessments heterozygosity less significant (0.400 and 0.320, respectively). Thus, in both groups, there is an excess of heterozygosity, accompanied by negative assessments fixation index. PCR-RFLP for PGR gene (using the Eco31I restriction endonuclease) revealed two genotypes of AA and GA, and the genotype AA yielding a single 558 bp band, and the heterozygote genotype GA yielding all the three bands of 558, 416 and 142 bp. The 2464G &gt; A SNP for PGR gene was not fixed in the HLS and LLS groups, the allele G frequency being 0.350 in the HLS and 0.200 in the LLS group. Whatever belong to a group marked predominance on the number of rabbits for a rabbit genotype GA on individuals who had genotype AA. More significant, the difference was for the rabbit of the I-th group (9.1 and 7.0 rabbits, respectively). The difference in litter size between the AA and GA genotypes was found for rabbits from as the HLS, as LLS group.