Proportion Of Breeders Research Articles

SNP panels for the estimation of dairy breed proportion and parentage assignment in African crossbred dairy cattle

BackgroundUnderstanding the relationship between genetic admixture and phenotypic performance is crucial for the optimization of crossbreeding programs. The use of small sets of informative ancestry markers can be a cost-effective option for the estimation of breed composition and for parentage assignment in situations where pedigree recording is difficult. The objectives of this study were to develop small single nucleotide polymorphism (SNP) panels that can accurately estimate the total dairy proportion and assign parentage in both West and East African crossbred dairy cows.MethodsMedium- and high-density SNP genotype data (Illumina BovineSNP50 and BovineHD Beadchip) for 4231 animals sampled from African crossbreds, African Bos taurus, European Bos taurus, Bos indicus, and African indigenous populations were used. For estimating breed composition, the absolute differences in allele frequency were calculated between pure ancestral breeds to identify SNPs with the highest discriminating power, and different combinations of SNPs weighted by ancestral origin were tested against estimates based on all available SNPs. For parentage assignment, informative SNPs were selected based on the highest minor allele frequency (MAF) in African crossbred populations assuming two Scenarios: (1) parents were selected among all the animals with known genotypes, and (2) parents were selected only among the animals known to be a parent of at least one progeny.ResultsFor the medium-density genotype data, SNPs selected for the largest differences in allele frequency between West African indigenous and European Bos taurus breeds performed best for most African crossbred populations and achieved a prediction accuracy (r2) for breed composition of 0.926 to 0.961 with 200 SNPs. For the high-density dataset, a panel with 70% of the SNPs selected on their largest difference in allele frequency between African and European Bos taurus performed best or very near best across all crossbred populations with r2 ranging from 0.978 to 0.984 with 200 SNPs. In all African crossbred populations, unambiguous parentage assignment was possible with ≥ 300 SNPs for the majority of the panels for Scenario 1 and ≥ 200 SNPs for Scenario 2.ConclusionsThe identified low-cost SNP assays could overcome incomplete or inaccurate pedigree records in African smallholder systems and allow effective breeding decisions to produce progeny of desired breed composition.

Genetic Diversity and the Impact of the Breed Proportions of US Brown Swiss in German Brown Cattle.

Simple SummaryThe main aim of modern breeding programs in dairy cows is to improve productivity, functional and health traits. The use of only a few top sires leads to more efficient milk production, but also it could lead to a decline in the gene pool, smaller effective population size and an increase of inbreeding. Deleterious effects of inbreeding in dairy cattle may reduce the benefits of the genetic gains. Due to this fact, it is important to monitor the genetic diversity in dairy cattle breeds. In this study, pedigree data were used to show the losses of genetic variability and its association with the heavy use of imported US Brown Swiss bulls and semen in the German Brown population. Strategies to decrease rate of inbreeding through sires with less relationships to the most important ancestors should be considered in future breeding strategies.Increase of inbreeding and loss of genetic diversity have large impact on farm animal genetic resources. Therefore, the aims of the present study were to analyse measures of genetic diversity as well as recent and ancestral inbreeding using pedigree data of the German Brown population, and to identify causes for loss of genetic diversity. The reference population included 922,333 German Brown animals born from 1990 to 2014. Pedigree depth and completeness reached an average number of complete equivalent generations of 6.24. Estimated effective population size for the German Brown reference population was about 112 with a declining trend from 141 to 95 for the birth years. Individual inbreeding coefficients increased from 0.013 to 0.036. Effective number of founders, ancestors and founder genomes of 63.6, 36.23 and 20.34 indicated unequal contributions to the reference population. Thirteen ancestors explained 50% of the genetic diversity. Higher breed proportions of US Brown Swiss were associated with higher levels of individual inbreeding. Ancestral inbreeding coefficients, which are indicative for exposure of ancestors to identical-by-descent alleles, increased with birth years but recent individual inbreeding was higher than ancestral inbreeding. Given the increase of inbreeding and decline of effective population size, measures to decrease rate of inbreeding and increase effective population size through employment of a larger number of sires are advisable.

Short communication: Heterosis and breed effects for milk production and udder health traits in crosses between Danish Holstein, Danish Red, and Danish Jersey

During the last decade, the use of systematic crossbreeding in dairy cattle herds has increased in several countries of the world. The aim of this study was to estimate the effect of breed proportion and heterosis on milk production traits and udder health traits in dairy cattle. The study was based on records on milk yield (MY), protein yield (PY), fat yield (FY), somatic cell score (SCS), and mastitis (MAST) from 73,695 first-lactation dairy cows in 130 Danish herds applying systematic crossbreeding programs. Around 45% of the cows were crosses between Danish Holstein (DH), Danish Red (DR), or Danish Jersey (DJ), and the remaining were purebred DH, DR, or DJ. The statistical model included the fixed effects of herd-year, calving month, and calving age and an effect representing the lactation status of the cow. In addition, the model included a regression on calving interval from first to second lactation, a regression on the proportion of DH, DR, and DJ genes, and a regression on the degree of heterozygosity between DH and DR, DH and DJ, and DR and DJ. Random effects were the genetic effect of the cow and a residual. The effect of breed proportions was estimated relatively to DH. For MY, a pure DR yielded 461 kg milk less than DH, whereas a pure DJ yielded 2,259 kg milk less than a pure DH. Compared with DH, PY was 41.7 kg less for DJ, whereas PY for DR was 4.0 kg less than for DH. For FY, a DR yielded 10.6 kg less than DH, whereas there was no significant effect of breed proportion between DJ and DH. A DR cow had lower SCS (0.13) than DH, whereas DJ had higher SCS (0.14) than DH. There was no significant effect of breed proportion on MAST between the 3 breeds. Heterosis was significant in all combinations of breeds for MY, FY, and PY. Heterosis for crosses between DH and DR was 257 kg (3.2%), 11.9 kg (3.2%), and 8.9 kg (3.2%) for MY, PY, and FY, respectively. Corresponding figures for crosses between DH and DJ were 314 kg (4.4%), 14.3 kg (4.4%), and 10.4 kg (4.0%), whereas heterosis between DR and DJ was 462 kg (6.7%), 19.6 kg (6.7%), and 13.9 kg (5.4%) for MY, PY, and FY, respectively. Heterosis was only significant for SCS in the crosses between DH and DR. Heterosis effects for MAST were nonsignificant for all the crosses. The results obtained in this study demonstrate that in first lactation cows, there is a positive effect of heterosis on milk production traits, but limited effect on udder health traits.

Animal-level factors associated with the achievement of desirable specifications in Irish beef carcasses graded using the EUROP classification system.

Beef carcasses in Europe are classified on measures of carcass weight, conformation, and fat cover. These measurements provide the basis for payment to producers, with financial penalties for carcasses that do not conform to desirable characteristics. The objective of the present study was to identify animal-level factors associated with the achievement of a desirable carcass weight, conformation score, fat score, and age at harvest, as stipulated by Irish beef processors in accordance with the EUROP carcass classification system. The stipulated specifications were a EUROP conformation score ≥O=, a carcass weight between 270 and 380 kg, a EUROP fat score between 2+ and 4=, and an age at harvest ≤ 30 mo. In the present study, 59% of cattle failed to achieve at least one of these desired specifications. The logit of the probability of achieving the desired specifications was estimated using multivariable logistic regression and carcass data from 4,717,989 cattle finished and harvested in Ireland between the years 2003 and 2017. In comparison to beef-origin carcasses and after accounting for breed differences, the likelihood of dairy-origin carcasses achieving the desired age, conformation, fat, and weight specifications was 0.97, 0.88, 1.14, and 1.05, respectively. In comparison to heifer carcasses, the odds ratio (OR) of bull and steer carcasses simultaneously achieving all of the desired specifications (i.e. the overall specification) was 0.35 and 0.95, respectively. Additionally, after accounting for breed differences, heifers from the dairy herd were half as likely as heifers from the beef herd to achieve the overall specification, whereas the odds of dairy-origin bulls (OR = 3.46) and steers (OR = 2.41) achieving the overall specification was greater than that of their respective beef-origin counterparts. Finally, cattle with a greater breed proportion of Angus were most likely to achieve the overall specification. Results from the present study could provide a deeper understanding as to why animals fail to achieve desirable carcass specifications and could be implemented into the management decisions made on farm to ensure that the supply of beef carcasses that achieve the desired metrics is maximized.

Evaluation of fishing industry clusterization in the russian far east within the context of integration with Asian-Pacific markets

The study’s aim is to assess the potential and processes of formation of sectoral clusters in the Far Eastern regions fishing industry. The paper suggests the strategy for forming the fishing industry clusters in the Russian Far East, analyzes trends, taking place in the fishing industry, from the perspective of its clusterization, interprets locatization and density ratios of capture fisheries and fish-farming businesses in the Far Eastern territories. The research first describes methods used to evaluate localization and geographical density of fishing-industry companies in the Far Eastern regions, and offers methodological recommendations for investigating fishing industry clusters. The second stage outlines trends of the industry such as increasing harvest level, changing proportion of capture fisheries and fish breeding, growing export, emerging exporting clusters, forming fishing industry associations. The third stage analyzes density ratios and specialization of fishing and fish-farming businesses by regions, compares the calculated ratios’ values to other Russian regions’ ones. On the basis of integral ratio we estimate the potential for clusterization of the fishing industry in Russian regions as well as on the territories of the Far Eastern Federal District. The research comes to conclusion that a set of state support measures and effective investment projects, concerned with the fishing industry cluster, can produce an additional synergetic effect for the whole gross regional product.

Population structure and breed composition prediction in a multi-breed sheep population using genome-wide single nucleotide polymorphism genotypes

Knowledge of population structure and breed composition of a population can be advantageous for a number of reasons; these include designing optimal (cross)breeding strategies in order to maximise non-additive genetic effects, maintaining flockbook integrity by authenticating animals being registered and as a quality control measure in the genotyping process. The objectives of the present study were to 1) describe the population structure of 24 sheep breeds, 2) quantify the breed composition of both flockbook-recorded and crossbred animals using single nucleotide polymorphism BLUP (SNP-BLUP), and 3) quantify the accuracy of breed composition prediction from low-density genotype panels containing between 2000 and 6000 SNPs. In total, 9334 autosomal SNPs on 11 144 flockbook-recorded animals and 1172 crossbred animals were used. The population structure of all breeds was characterised by principal component analysis (PCA) as well as the pairwise breed fixation index (Fst). The total number of animals, all of which were purebred, included in the calibration population for SNP-BLUP was 2579 with the number of animals per breed ranging from 9 to 500. The remaining 9559 flockbook-recorded animals, composite breeds and crossbred animals represented the test population; three breeds were excluded from breed composition prediction. The breed composition predicted using SNP-BLUP with 9334 SNPs was considered the gold standard prediction. The pairwise breed Fst ranged from 0.040 (between the Irish Blackface and Scottish Blackface) to 0.282 (between the Border Leicester and Suffolk). Principal component analysis revealed that the Suffolk from Ireland and the Suffolk from New Zealand formed distinct, non-overlapping clusters. In contrast, the Texel from Ireland and that from New Zealand formed integrated, overlapping clusters. Composite animals such as the Belclare clustered close to its founder breeds (i.e., Finn, Galway, Lleyn and Texel). When all 9334 SNPs were used to predict breed composition, an animal that had a majority breed proportion predicted to be ≥0.90 was defined as purebred for the present study. As the panel density decreased, the predicted breed proportion threshold, used to identify animals as purebred, also decreased (≥0.85 with 6000 SNPs to ≥0.60 with 2000 SNPs). In all, results from the study suggest that breed composition for purebred and crossbred animals can be determined with SNP-BLUP using ≥5000 SNPs.

Cryoconservation of Animal Genetic Resources in Europe and Two African Countries: A Gap Analysis

Cryoconservation is one of the main strategies to conserve farm animal genetic resources, providing opportunities for genetic improvement and adaptation to changes in production environments and consumer demands. In this study, we combine livestock breed-related data from the Domesticated Animal Diversity Information System (DAD-IS) and information provided by gene banks from 15 European and 2 non-European countries on material stored for livestock breeds to analyze the gaps in cryomaterial collections according to species, countries and various breed categories. Out of the 2949 breeds registered in DAD-IS for these countries, 15.9% have been reported to have material stored in gene banks, but only 4.3% have material sufficient to allow breed reconstitution. The proportion of breeds with stored cryomaterial was greater than 20% for ruminants and pigs, between 10% and 20% for equids, and below 10% for rabbit and avian species. According to the results of two logistic regressions, countries show significant differences in the proportion of populations collected for cryostorage, while breeds not-at-risk are more likely to have cryomaterial preserved than are other breeds. Also, a relatively larger proportion of transboundary breeds have cryomaterial in gene banks than do local breeds, likely due in part to the fact that multiple countries have the opportunity to collect this material. These results highlight the need for increased efforts in material collection for at-risk local breeds and regional coordination on cryoconservation of material from transboundary breeds.

PHENOTYPE FEATURES APPEARANCE OF DAIRY PRODUCTIVITY OF DIFFERENT UKRAINIAN DAIRY BLACK-AND-WHITE BREED COWS GENOTYPES

The main task of breeding in dairy cattle breeding is to raise dairy productivity of cows. Improvement of productive qualities of domestic dairy cattle with the use of Holstein breeders of high breeding value led to serious disadvantages, including impairment of animal health, reproductive capacity and quality of milk. Therefore, the purpose of our research was to examine the milk productivity of cows of different genotypes of the Ukrainian Black-and-White dairy breed and ascertain the relationship between quantitative and qualitative indicators of milk.
 Research conducted at agricultural limited liability company "Lishche" Lutsk district of Volyn region on cows of different genotypes of the Ukrainian Black-and-White dairy breed. 5 groups of animals were formed: I − cows with a proportion of Holstein breed 75% or less, II − with a share Holstein heredity 75.1–81.25%, III − Holstein heredity share 81.26–87.50%, ІV − with a share of the heredity of the Holstein 87.51–93.75% and V − with a share of the heredity of the Holstein more than 93.75%. Evaluation of milk productivity was carried out by milk yield, fat content in milk and the amount of milk fat for the first, second, third and highest lactations according to the data of zootechnical accounting.
 It was found that the largest number of animals under control (33.7%) was with the relative share of Holstein heredity of 81.26–87.50%, and the lowest (9.3%) was with relative share of the Holstein breed's heredity more than 93.75%. Analysis of the level of milk yield of cows of different genotypes showed that the increase of Holstein heredity increases milk yields, however, significantly reduces the fat content of milk. If the animals have a share of Holstein heredity up to 75% the milk yields was 5154, and the amount of milk fat − 199.7 kg, and cows with hereditary of 75.10–81.25% showed figures increased by 16.4 and 15.5%, with Holstein heredity 81.26–87.50% by 23.3 and 20.8%, Holstein heredity 87.51–93.75% for 26.1 and 23.2% and with Holstein heredity more than 93.75% for 34.8 and 31.4%, and fat content in milk, on the contrary, decreased, depending on the genotype of animals, by 1.6–2.3%. In all in the above cases, these changes were highly significant (P < 0.001).
 The effectiveness of breeding on increasing the milk productivity of cows depends on the efficiency of selection and selection of animals, taking into account the phenotypic and genetic correlation between economically useful features. It was found that the studied cows of all genotypes had highest highly reliable (P < 0.001) positive values of correlation coefficients between milk yield and milk fat (Table 2). These features are the most predicted because strong relationship between them (r = 0.912–0.987). There was also observed direct positive ligament (r = 0.039–0.533, P < 0.05–0.001) between fat content in milk and milk fat content, and mostly weak, and only in some cases correlation coefficients had average values. The cows of the studied genotypes had the lowest and for the most part unreliable values of relative variability by the milk yields and fat content milk. The heifers with conditional share of Holstein heredity, more than 75% had negative and weak relationship features, and the older cows were diversified from weak to average values.
 One of the reliable criteria for determining the level of heredity of features is the coefficient of frequency, which indicates their heredity stability in age. Coefficients of age-related frequency of milk yield, fat content of milk and the highest milk fat content of cows with a conditional share of Holstein heredity of up to 75% had indicating a higher degree of heredity of these features compared to high half-bred cows. With the increasing of heredity of the Holstein breed the genotype of controlled animals values were decreasing for the most part. The most significant and reliable (P < 0.001) genotype of animals affected milk yields (13.3–18.1% of the total variability of this feature), less – the fat content of milk (9.3–13.2% (P < 0.001) and the amount of milk fat (6.6–14.1% (P < 0.001), with the highest genotype influence on the studied features indicated in the first lactation.

Data-driven approach to using individual cattle weights to estimate mean adult dairy cattle weight

BackgroundKnowledge of accurate weights of cattle is crucial for effective dosing of individual animals and for reporting antimicrobial usage. For the first time, we provide an evidence-based estimate of the...

Genetic and nongenetic factors associated with the fate of maiden ewe lambs: slaughtered without ever lambing versus retained for breeding.

The decision on which ewe lamb to retain versus which to sell is likely to vary by producer based on personal preference. What is not known, however, is if any commonality exists among producers in the characteristics of ewe lambs that influence their eventual fate. The objective of the present study was to determine what genetic and nongenetic factors associate with the fate of maiden ewe lambs. The fate of each ewe lamb born in the present study was defined as either subsequently: 1) having lambed in the flock, or 2) was slaughtered without any recorded lambing event. A total of 9,705 ewe lamb records from 41 crossbred flocks were used. The logit of the odds of the ewe lamb being retained for lambing was modeled using logistic regression. Variance components were then estimated for the binary trait representing the fate of the ewe lamb using animal linear and threshold mixed models. The genetic correlations between fate of the ewe lamb and preweaning, weaning, or postweaning liveweight were also estimated. From the edited data set, 45% of ewe lambs born entered the mature flock as ewes. Ewe lambs reared as singles, with greater levels of heterosis but lower levels of recombination loss, born to dams that lambed for the first time as hoggets, with greater breed proportion of the Belclare, Suffolk, Texel, and Llyen breeds were more likely (P < 0.001) to eventually lamb in the flock than be slaughtered without ever lambing. Irrespective of the age of the animal when weighed, heavier ewe lambs were more likely to eventually lamb (P < 0.001). The genetic SD and direct heritability of fate of the ewe lamb estimated in the univariate linear model was 26.58 percentage units and 0.31 (SE = 0.03), respectively; the heritability was 0.30 when estimated using the threshold model. The corresponding direct heritability of fate of the ewe lamb estimated in the bivariate analyses with liveweight ranged from 0.29 (SE = 0.03; preweaning weight) to 0.35 (SE = 0.04; postweaning weight). The genetic correlations estimated between fate of the ewe lamb and the liveweight traits were weak to moderate but strengthened as the age of the ewe lamb at weighing increased. Results from this study provide an understanding of the factors producers consider when selecting females for retention versus slaughter which may form useful parameters in the development of a decision support tool to identify suitable ewe lambs for retention.

Genome-wide scan for runs of homozygosity in the composite Montana Tropical® beef cattle.

The aim of this study was to assess the distribution of runs of homozygosity (ROH) and autozygosity islands in the composite Montana Tropical® beef cattle to explore hotspot regions which could better characterize the different biological types within the composite breed. Montana animals (n=1,436) were genotyped with the GGP-LD BeadChip (~30,000 markers). ROH was identified in every individual using the plink v1.90 software. Medium and long ROH prevailed in the genome, which accounted for approximately 74% of all ROH detected. On an average, 2.0% of the genome was within ROH, agreeing with the pedigree-based inbreeding coefficient. The Montana cattle with a higher proportion of productive breed types showed the highest number of autozygosity islands (n=17), followed by those with a higher proportion of breeds adapted to tropical environments (n=15). Enriched terms (p<.05) associated with the immune and inflammatory response, homeostasis, reproduction, mineral absorption, and lipid metabolism were described within the autozygosity islands. In this regard, over-represented GO terms and KEGG pathways described in this population may play a key role in providing information to explore the genetic and biological mechanisms together with the genomic regions underlying each biological type that favoured their optimal performance ability in tropical and subtropical regions.

Demography of a high‐density tiger population and its implications for tiger recovery

Abstract Prioritizing conservation of source populations within landscapes is proposed as a strategy for recovering tigers globally. We studied population dynamics of tigers in Corbett National Park (CNP) in Indian Terai, which harbours the largest and highest density tiger population in any protected area of the world. Through population viability models, we demonstrate the importance of CNP in tiger recovery within western Terai. We camera trapped 521 km2 of CNP using open population capture–mark–recapture framework between 2010 and 2015 to estimate annual abundance, spatially explicit density, survival, recruitment, temporary movements, sex ratio and proportion of females breeding. We model metapopulation persistence with and without Corbett as a source within western Terai landscape at different levels of poaching and habitat connectivity. In 6 years, we recorded 6,202 photo‐captures of 307 individual tigers. Annual tiger abundance and density were stable at 120 (SE 19) and 14 (SE 3) per 100 km2 respectively. Detection probability of tigers was 0.18 (SE 0.03) and detection‐corrected male:female sex ratio was female biased (0.80 SE 0.13). Apparent annual survival probability was 0.79 (SE 0.05) for females and 0.60 (SE 0.04) for males. Survival of tigers in CNP (0.68 SE 0.12) was lower than that reported for other populations. CNP tigers showed high reproduction with 54.8 (SE 5.1)% females breeding and with addition of 35 (SE 8)% as new recruits to the population each year. Small tiger populations in western Terai with moderate poaching could only persist through dispersal from CNP. Synthesis and applications. Corbett tiger population was characterized by a stable high density, high reproductive rate and low survival, resulting in high turnover rates (32%–48%) between successive years. Such source populations could sustain low‐level poaching and with habitat connectivity, recover tiger populations across the landscape. This study establishes potential thresholds that can likely be achieved by tiger populations under optimal natural conditions and highlights the importance of prioritizing conservation of source populations within tiger landscapes. This information can be used to plan and implement realistic tiger recovery programmes globally.

Breeding systematization of indigenous breed Medjimurje horse

Medjimurje horse is critically endangered breed (Ne = 14.17) and is one of three Croatian indigenous horse breeds. The aim of this research is to systematize the Medjimurje horse breeding, defining stallion and mare lines, and analyzing the prevalence of other breeds in Medjimurje breeding horses. The result of systematization is defining 7 stallion lines and 37 mare lines which are the basis for breeding in the future. By analyzing the pedigree, we established higher rate of other breeds in Medjimurje breeding horses, and the fact that the breeding hasn’t been done pure blooded, which is necessary given that it is the indigenous breed since the year 1999, after founding the breeds registry. A large proportion of other horse breeds in the Medjimurje horse registry leads to the conclusion that it is not an indigenous horse breed, but the type of cold-blooded horse, so the status of current population "authenticity" is doubtful.

The milk production and survival of spring-calving carryover cows in New Zealand

ABSTRACT The objective of this study was to compare breed proportions, genetic merit, milk production and survival of carryover and non-carryover dairy cows in New Zealand. Calving interval was used as a tool to identify cows that had an extended non-lactating period and then returned to a milking herd. A greater proportion of Holstein-Friesian was observed in the breed composition of the carryover cows. Estimated breeding values (EBVs) for milk traits were greater, but the EBVs for fertility were lower for carryover cows, than those for non-carryover cows. Carryover cow genetic merit values were greater than those for non-carryover cows in the year prior to their carryover period. Carryover cow milk production was significantly greater than that of non-carryover cows. The average survival days and probability of survival for second-lactation carryover cows was lower than that for first-lactation and lactation-matched non-carryover cows. These results are important for culling decisions made by pastoral dairy farmers.

Use of hidden Markov capture-recapture models to estimate abundance in the presence of uncertainty: Application to the estimation of prevalence of hybrids in animal populations.

Estimating the relative abundance (prevalence) of different population segments is a key step in addressing fundamental research questions in ecology, evolution, and conservation. The raw percentage of individuals in the sample (naive prevalence) is generally used for this purpose, but it is likely to be subject to two main sources of bias. First, the detectability of individuals is ignored; second, classification errors may occur due to some inherent limits of the diagnostic methods. We developed a hidden Markov (also known as multievent) capture–recapture model to estimate prevalence in free‐ranging populations accounting for imperfect detectability and uncertainty in individual's classification. We carried out a simulation study to compare naive and model‐based estimates of prevalence and assess the performance of our model under different sampling scenarios. We then illustrate our method with a real‐world case study of estimating the prevalence of wolf (Canis lupus) and dog (Canis lupus familiaris) hybrids in a wolf population in northern Italy. We showed that the prevalence of hybrids could be estimated while accounting for both detectability and classification uncertainty. Model‐based prevalence consistently had better performance than naive prevalence in the presence of differential detectability and assignment probability and was unbiased for sampling scenarios with high detectability. We also showed that ignoring detectability and uncertainty in the wolf case study would lead to underestimating the prevalence of hybrids. Our results underline the importance of a model‐based approach to obtain unbiased estimates of prevalence of different population segments. Our model can be adapted to any taxa, and it can be used to estimate absolute abundance and prevalence in a variety of cases involving imperfect detection and uncertainty in classification of individuals (e.g., sex ratio, proportion of breeders, and prevalence of infected individuals).

Finding best exotic breed proportion in crossbred lactating sheep kept under farmers’ conditions in Ethiopia determined by use of nested Legendre polynomials with limited data

ABSTRACTThe present study was conducted to estimate milk production performance and fit lactation curves for groups of ewes of Local and of Awassi crosses, with a variable blood level, reared under farmer’s environment. The Weigh-Suckle-Weigh method plus hand milking was used to estimate milk yield for ewes. A total of 466 observations from 115 ewes were used. Estimated least-squares adjusted means for the milk production over 120 days were 0.56 kg day−1 (Local), 0.67 (<30% Awassi), 0.86 (30–50% Awassi), and 0.96 (>50% Awassi). Groups with 30–50% Awassi and >50% Awassi ewes produced significantly (p < 0.05) more milk than Local ewes. Significant differences were observed between <30% Awassi and >50% Awassi crossbred groups. The best crosses (>50% Awassi) produced over 70% more milk than the local ewes which demonstrates the potential that exists in increasing milk production through the initiated crossbreeding programme with sheep in Ethiopia.

Population Structure and Genomic Breed Composition in an Angus-Brahman Crossbred Cattle Population.

Crossbreeding is a common strategy used in tropical and subtropical regions to enhance beef production, and having accurate knowledge of breed composition is essential for the success of a crossbreeding program. Although pedigree records have been traditionally used to obtain the breed composition of crossbred cattle, the accuracy of pedigree-based breed composition can be reduced by inaccurate and/or incomplete records and Mendelian sampling. Breed composition estimation from genomic data has multiple advantages including higher accuracy without being affected by missing, incomplete, or inaccurate records and the ability to be used as independent authentication of breed in breed-labeled beef products. The present study was conducted with 676 Angus–Brahman crossbred cattle with genotype and pedigree information to evaluate the feasibility and accuracy of using genomic data to determine breed composition. We used genomic data in parametric and non-parametric methods to detect population structure due to differences in breed composition while accounting for the confounding effect of close familial relationships. By applying principal component analysis (PCA) and the maximum likelihood method of ADMIXTURE to genomic data, it was possible to successfully characterize population structure resulting from heterogeneous breed ancestry, while accounting for close familial relationships. PCA results offered additional insight into the different hierarchies of genetic variation structuring. The first principal component was strongly correlated with Angus–Brahman proportions, and the second represented variation within animals that have a relatively more extended Brangus lineage—indicating the presence of a distinct pattern of genetic variation in these cattle. Although there was strong agreement between breed proportions estimated from pedigree and genetic information, there were significant discrepancies between these two methods for certain animals. This was most likely due to inaccuracies in the pedigree-based estimation of breed composition, which supported the case for using genomic information to complement and/or replace pedigree information when estimating breed composition. Comparison with a supervised analysis where purebreds are used as the training set suggest that accurate predictions can be achieved even in the absence of purebred population information.

A comparison of 4 predictive models of calving assistance and difficulty in dairy heifers and cows

The aim of this study was to build and compare predictive models of calving difficulty in dairy heifers and cows for the purpose of decision support and simulation modeling. Models to predict 3 levels of calving difficulty (unassisted, slight assistance, and considerable or veterinary assistance) were created using 4 machine learning techniques: multinomial regression, decision trees, random forests, and neural networks. The data used were sourced from 2,076 calving records in 10 Irish dairy herds. In total, 19.9 and 5.9% of calving events required slight assistance and considerable or veterinary assistance, respectively. Variables related to parity, genetics, BCS, breed, previous calving, and reproductive events and the calf were included in the analysis. Based on a stepwise regression modeling process, the variables included in the models were the dam's direct and maternal calving difficulty predicted transmitting abilities (PTA), BCS at calving, parity; calving assistance or difficulty at the previous calving; proportion of Holstein breed; sire breed; sire direct calving difficulty PTA; twinning; and 2-way interactions between calving BCS and previous calving difficulty and the direct calving difficulty PTA of dam and sire. The models were built using bootstrapping procedures on 70% of the data set. The held-back 30% of the data was used to evaluate the predictive performance of the models in terms of discrimination and calibration. The decision tree and random forest models omitted the effect of twinning and included only subsets of sire breeds. Only multinomial regression and neural networks explicitly included the modeled interactions. Calving BCS, calving difficulty PTA, and previous calving assistance ranked as highly important variables for all 4 models. The area under the receiver operating characteristic curve (ranging from 0.64 to 0.79) indicates that all of the models had good overall discriminatory power. The neural network and multinomial regression models performed best, correctly classifying 75% of calving cases and showing superior calibration, with an average error in predicted probability of 3.7 and 4.5%, respectively. The neural network and multinomial regression models developed are both suitable for use in decision-support and simulation modeling.

Genetic tests for estimating dairy breed proportion and parentage assignment in East African crossbred cattle

BackgroundSmallholder dairy farming in much of the developing world is based on the use of crossbred cows that combine local adaptation traits of indigenous breeds with high milk yield potential of exotic dairy breeds. Pedigree recording is rare in such systems which means that it is impossible to make informed breeding decisions. High-density single nucleotide polymorphism (SNP) assays allow accurate estimation of breed composition and parentage assignment but are too expensive for routine application. Our aim was to determine the level of accuracy achieved with low-density SNP assays.MethodsWe constructed subsets of 100 to 1500 SNPs from the 735k-SNP Illumina panel by selecting: (a) on high minor allele frequencies (MAF) in a crossbred population; (b) on large differences in allele frequency between ancestral breeds; (c) at random; or (d) with a differential evolution algorithm. These panels were tested on a dataset of 1933 crossbred dairy cattle from Kenya/Uganda and on crossbred populations from Ethiopia (N = 545) and Tanzania (N = 462). Dairy breed proportions were estimated by using the ADMIXTURE program, a regression approach, and SNP-best linear unbiased prediction, and tested against estimates obtained by ADMIXTURE based on the 735k-SNP panel. Performance for parentage assignment was based on opposing homozygotes which were used to calculate the separation value (sv) between true and false assignments.ResultsPanels of SNPs based on the largest differences in allele frequency between European dairy breeds and a combined Nelore/N’Dama population gave the best predictions of dairy breed proportion (r2 = 0.962 to 0.994 for 100 to 1500 SNPs) with an average absolute bias of 0.026. Panels of SNPs based on the highest MAF in the crossbred population (Kenya/Uganda) gave the most accurate parentage assignments (sv = −1 to 15 for 100 to 1500 SNPs).ConclusionsDue to the different required properties of SNPs, panels that did well for breed composition did poorly for parentage assignment and vice versa. A combined panel of 400 SNPs was not able to assign parentages correctly, thus we recommend the use of 200 SNPs either for breed proportion prediction or parentage assignment, independently.

At-sea distribution and habitat use in king penguins at sub-Antarctic Marion Island.

King penguins make up the bulk of avian biomass on a number of sub‐Antarctic islands where they have a large functional effect on terrestrial and marine ecosystems. The same applies at Marion Island where a substantial proportion of the world population breeds. In spite of their obvious ecological importance, the at‐sea distribution and behavior of this population has until recently remained entirely unknown. In addressing this information deficiency, we deployed satellite‐linked tracking instruments on 15 adult king penguins over 2 years, April 2008 and 2013, to study their post‐guard foraging distribution and habitat preferences. Uniquely among adult king penguins, individuals by and large headed out against the prevailing Antarctic Circumpolar Current, foraging to the west and southwest of the island. On average, individuals ventured a maximum distance of 1,600 km from the colony, with three individuals foraging close to, or beyond, 3,500 km west of the colony. Birds were mostly foraging south of the Antarctic Polar Front and north of the southern boundary of the Antarctic Circumpolar Current. Habitat preferences were assessed using boosted regression tree models which indicated sea surface temperate, depth, and chorophyll a concentration to be the most important predictors of habitat selection. Interestingly, king penguins rapidly transited the eddy‐rich area to the west of Marion Island, associated with the Southwest Indian Ocean Ridge, which has been shown to be important for foraging in other marine top predators. In accordance with this, the king penguins generally avoided areas with high eddy kinetic energy. The results from this first study into the behavioral ecology and at‐sea distribution of king penguins at Marion Island contribute to our broader understanding of this species.