The value of cows in reference populations for genomic selection of new functional traits

Today, almost all reference populations consist of progeny tested bulls. However, older progeny tested bulls do not have reliable estimated breeding values (EBV) for new traits. Thus, to be able to select for these new traits, it is necessary to build a reference population. We used a deterministic prediction model to test the hypothesis that the value of cows in reference populations depends on the availability of phenotypic records. To test the hypothesis, we investigated different strategies of building a reference population for a new functional trait over a 10-year period. The trait was either recorded on a large scale (30 000 cows per year) or on a small scale (2000 cows per year). For large-scale recording, we compared four scenarios where the reference population consisted of 30 sires; 30 sires and 170 test bulls; 30 sires and 2000 cows; or 30 sires, 2000 cows and 170 test bulls in the first year with measurements of the new functional trait. In addition to varying the make-up of the reference population, we also varied the heritability of the trait (h2 = 0.05 v. 0.15). The results showed that a reference population of test bulls, cows and sires results in the highest accuracy of the direct genomic values (DGV) for a new functional trait, regardless of its heritability. For small-scale recording, we compared two scenarios where the reference population consisted of the 2000 cows with phenotypic records or the 30 sires of these cows in the first year with measurements of the new functional trait. The results showed that a reference population of cows results in the highest accuracy of the DGV whether the heritability is 0.05 or 0.15, because variation is lost when phenotypic data on cows are summarized in EBV of their sires. The main conclusions from this study are: (i) the fewer phenotypic records, the larger effect of including cows in the reference population; (ii) for small-scale recording, the accuracy of the DGV will continue to increase for several years, whereas the increases in the accuracy of the DGV quickly decrease with large-scale recording; (iii) it is possible to achieve accuracies of the DGV that enable selection for new functional traits recorded on a large scale within 3 years from commencement of recording; and (iv) a higher heritability benefits a reference population of cows more than a reference population of bulls.     

Genetic diversity among Canadienne, Brown Swiss, Holstein, and Jersey cattle of Canada based on 15 bovine microsatellite markers.

The genetic diversity among Canadienne, Brown Swiss, Holstein, and Jersey cattle was estimated from relationships determined by genotyping 20 distantly related animals in each breed for 15 microsatellites located on separate chromosomes. The Canadienne, Holstein, and Jersey cattle had an average of six alleles per loci compared with five alleles for Brown Swiss. Furthermore, a number of potentially breed-specific alleles were identified. The allele size variance among breeds was similar, but varied considerably among loci. All of the loci studied were equally heterozygous, as were Brown Swiss, Canadienne, and Holstein cattle (0.68-0.69) whereas Jersey cattle showed lower heterozygosity (0.59). The within-breed estimates of genetic distance were greater than zero and significant. The genetic distance between Canadienne and Holstein (0.156), Brown Swiss (0.243), and Jersey (0.235) was negligible, suggesting close relationship. Concurrently, Brown Swiss and Holstein (0.211) cattle also demonstrated close relationship. In contrast, the Jersey breed was genetically distant from the Brown Swiss and Holstein cattle (0.427 and 0.320, respectively). The characterization of Canadienne cattle, as part of the genetic resource conservation effort currently underway in Canada, underscores the difficulty in scientifically establishing unique breeds. Therefore, the need to consider all relevant morphological characteristics and production performance in combination with available cultural, historical, pedigree, and molecular information becomes relevant when identifying breeds for conservation.     

Genome‐wide variability and selection signatures in Italian island cattle breeds

In the present study, a sample of 88 animals belonging to four local (Modicana, Sarda, Sardo‐Bruna and Sardo‐Modicana) and one cosmopolitan (Italian Brown Swiss) cattle breeds were genotyped with a medium density SNP beadchip and compared to investigate their genetic diversity and the existence of selection signatures. A total of 43 012 SNPs distributed across all 29 autosomal chromosomes were retained after data quality control. Basic population statistics, Wright fixation index and runs of homozygosity (ROH) analyses confirmed that the Italian Brown Swiss genome was shaped mainly by selection, as underlined by the low values of heterozygosity and minor allele frequency. As expected, local cattle exhibited a large within‐breed genetic heterogeneity. The F_ST comparison revealing the largest number of significant SNPs was Sardo‐Bruna vs. Sardo‐Modicana, whereas the smallest was observed for Italian Brown Swiss vs. Sardo‐Modicana. Modicana exhibited the largest number of detected ROHs, whereas the smallest was observed for Sardo‐Modicana. Signatures of selection were detected in genomic regions that harbor genes involved in milk production traits for Italian Brown Swiss and fitness traits for local breeds. According to the results of multi‐dimensional scaling and the admixture analysis the Sardo‐Bruna is more similar to the Sarda than to the Italian Brown Swiss breed. Moreover, the Sardo‐Modicana is genetically closer to the Modicana than to the Sarda breed. Results of the present work confirm the usefulness of single nucleotide polymorphisms in deciphering the genetic architecture of livestock breeds.     

Genetic distances within and across cattle breeds as indicated by biallelic AFLP markers

We tested the use of biallelic Amplified fragment length polymorphism (AFLP) polymorphisms for the estimation of relative genetic distances of cattle individuals within or across breeds. An allele permutation procedure was developed to estimate the stochastic variation of the genetic distance that is inherent to a given dataset. In a panel of 47 Holstein-Friesian cattle analysed with 248 polymorphic markers, the average genetic distance of bulls selected for breeding was slightly lower than the distance of the cows. The observed standard deviation (SD) of the distance indicated genetic subdivision, which for the bulls was explained by variation in the additive relationship derived from herdbook data. Animals from three different breeds, the highly selected Holstein-Friesian, the Italian Brown and the historic Maremmana, were compared on the basis of 106 polymorphic markers. No breed-specific fragments were observed. The mean pair-wise genetic distance within breeds was 85% of the value across breeds, but principal coordinates analysis clustered the animals according to their breed of origin. Calculation of distances between the breeds indicated a relatively divergent position of the Maremmana, relative to the two other breeds. However, biallelic markers indicate that the process of breed formation had only a limited effect on the diversity at marker loci.     

Breed of cow and herd productivity affect milk nutrient recovery in curd,and cheese yield,efficiency and daily production

Little is known about cheese-making efficiency at the individual cow level, so our objective was to study the effects of herd productivity, individual herd within productivity class and breed of cow within herd by producing, then analyzing, 508 model cheeses from the milk of 508 cows of six different breeds reared in 41 multi-breed herds classified into two productivity classes (high v. low). For each cow we obtained six milk composition traits; four milk nutrient (fat, protein, solids and energy) recovery traits (REC) in curd; three actual % cheese yield traits (%CY); two theoretical %CYs (fresh cheese and cheese solids) calculated from milk composition; two overall cheese-making efficiencies (% ratio of actual to theoretical %CYs); daily milk yield (dMY); and three actual daily cheese yield traits (dCY). The aforementioned phenotypes were analyzed using a mixed model which included the fixed effects of herd productivity, parity, days in milk (DIM) and breed; the random effects were the water bath, vat, herd and residual. Cows reared in high-productivity herds yielded more milk with higher nutrient contents and more cheese per day, had greater theoretical %CY, and lower cheese-making efficiency than low-productivity herds, but there were no differences between them in terms of REC traits. Individual herd within productivity class was an intermediate source of total variation in REC, %CY and efficiency traits (10.0% to 17.2%), and a major source of variation in milk yield and dCY traits (43.1% to 46.3%). Parity of cows was an important source of variation for productivity traits, whereas DIM affected almost all traits. Breed within herd greatly affected all traits. Holsteins produced more milk, but Brown Swiss cows produced milk with higher actual and theoretical %CYs and cheese-making efficiency, so that the two large-framed breeds had the same dCY. Compared with the two large-framed breeds, the small Jersey cows produced much less milk, but with greater actual and theoretical %CYs, similar efficiencies and a slightly lower dCY. Compared with the average of the specialized dairy breeds, the three dual-purpose breeds (Simmental and the local Rendena and Alpine Grey) had, on average, similar dMY, lower actual and theoretical %CY, similar fat and protein REC, and slightly greater cheese-making efficiency.     

Strategies for imputation to whole genome sequence using a single or multi-breed reference population in cattle

Background

The advent of low cost next generation sequencing has made it possible to sequence a large number of dairy and beef bulls which can be used as a reference for imputation of whole genome sequence data. The aim of this study was to investigate the accuracy and speed of imputation from a high density SNP marker panel to whole genome sequence level. Data contained 132 Holstein, 42 Jersey, 52 Nordic Red and 16 Brown Swiss bulls with whole genome sequence data; 16 Holstein, 27 Jersey and 29 Nordic Reds had previously been typed with the bovine high density SNP panel and were used for validation. We investigated the effect of enlarging the reference population by combining data across breeds on the accuracy of imputation, and the accuracy and speed of both IMPUTE2 and BEAGLE using either genotype probability reference data or pre-phased reference data. All analyses were done on Bovine autosome 29 using 387,436 bi-allelic variants and 13,612 SNP markers from the bovine HD panel.

Results

A combined breed reference population led to higher imputation accuracies than did a single breed reference. The highest accuracy of imputation for all three test breeds was achieved when using BEAGLE with un-phased reference data (mean genotype correlations of 0.90, 0.89 and 0.87 for Holstein, Jersey and Nordic Red respectively) but IMPUTE2 with un-phased reference data gave similar accuracies for Holsteins and Nordic Red. Pre-phasing the reference data only lead to a minor decrease in the imputation accuracy, but gave a large improvement in computation time. Pre-phasing with BEAGLE was substantially faster than pre-phasing with SHAPEIT2 (2.5 hours vs. 52 hours for 242 individuals), and imputation with pre-phased data was faster in IMPUTE2 than in BEAGLE (5 minutes vs. 50 minutes per individual).

Conclusion

Combining reference populations across breeds is a good option to increase the size of the reference data and in turn the accuracy of imputation when only few animals are available. Pre-phasing the reference data only slightly decreases the accuracy but gives substantial improvements in speed. Using BEAGLE for pre-phasing and IMPUTE2 for imputation is a fast and accurate strategy.     

Breeding soundness and libido examination of Belgian Blue and Holstein Friesian artificial insemination bulls in Belgium and The Netherlands

Data on breeding soundness and libido evaluations in Belgian Blue (BB) bulls are scarce. The present study compared results of breeding soundness and libido evaluations of young BB bulls to young Holstein Friesian (HF) bulls prior to acceptance into an AI program. Breed differences for breeding soundness exist between BB and HF bulls, as 93.7% of the young BB bulls failed the breeding soundness examination (BSE) compared to 59.3% of the HF bulls (P=0.0005). Within the BB breed, differences were present between bulls of different ages, and bull selection for better fertility with increasing age apparently influenced the results. The number of reasons for which bulls failed the test differed between the age groups in the BB breed, whereas a tendency for more failure reasons in the BB breed was noticed in the breed comparison. The most important reasons for failure were sperm morphology and scrotal circumference (SC), but far more BB bulls failed for these traits compared to the HF breed (82.8% versus 56.0% and 43.8% versus 17.6% in the BB and the HF breed for sperm morphology (P=0.0005) and SC (P<0.0001), respectively). The high proportion of BB bulls with a substandard SC and poor sperm morphology might suggest an increased prevalence of testicular hypoplasia or degeneration within this breed. Concerning libido, the reaction time did not differ either between breeds or between age groups within the BB breed, whereas mounting enthusiasm, although not different between the two breeds, did decline with increasing age, probably due to the greater mating experience of the older bulls. All in all, libido did not seem to be different between the breeds.     

Morphometrics within dog breeds are highly reproducible and dispute Rensch’s rule

Using 27 body measurements, we have identified 13 breed-defining metrics for 109 of 159 domestic dog breeds, most of which are recognized by the American Kennel Club (AKC). The data set included 1,155 dogs at least 1 year old (average 5.4 years), and for 53 breed populations, complete measurement data were collected from at least three males and three females. We demonstrate, first, that AKC breed standards are rigorously adhered to for most domestic breeds with little variation observed within breeds. Second, Rensch’s rule, which describes a scaling among taxa such that sexual dimorphism is greater among larger species if males are the larger sex, with less pronounced differences in male versus female body size in smaller species, is not maintained in domestic dog breeds because the proportional size difference between males and females of small and large breeds is essentially the same. Finally, principal components (PCs) analysis describes both the overall body size (PC1) and the shape (length versus width) of the skeleton (PC2). That the integrity of the data set is sufficiently rich to discern PCs has strong implications for mapping studies, suggesting that individual measurements may not be needed for genetic studies of morphologic traits, particularly in the case of breed-defining traits that are typically under strong selection. Rather, phenotypes derived from data sets such as these, collected at a fraction of the effort and cost, may be used to direct whole-genome association studies aimed at understanding the genetic basis of fixed morphologic phenotypes defining distinct dog breeds.

     

Morphometrics within dog breeds are highly reproducible and dispute Rensch’s rule

Using 27 body measurements, we have identified 13 breed-defining metrics for 109 of 159 domestic dog breeds, most of which are recognized by the American Kennel Club (AKC). The data set included 1,155 dogs at least 1 year old (average 5.4 years), and for 53 breed populations, complete measurement data were collected from at least three males and three females. We demonstrate, first, that AKC breed standards are rigorously adhered to for most domestic breeds with little variation observed within breeds. Second, Rensch’s rule, which describes a scaling among taxa such that sexual dimorphism is greater among larger species if males are the larger sex, with less pronounced differences in male versus female body size in smaller species, is not maintained in domestic dog breeds because the proportional size difference between males and females of small and large breeds is essentially the same. Finally, principal components (PCs) analysis describes both the overall body size (PC1) and the shape (length versus width) of the skeleton (PC2). That the integrity of the data set is sufficiently rich to discern PCs has strong implications for mapping studies, suggesting that individual measurements may not be needed for genetic studies of morphologic traits, particularly in the case of breed-defining traits that are typically under strong selection. Rather, phenotypes derived from data sets such as these, collected at a fraction of the effort and cost, may be used to direct whole-genome association studies aimed at understanding the genetic basis of fixed morphologic phenotypes defining distinct dog breeds.     

A whole genome scan for differences in recombination rates among three Bos taurus breeds

Twenty paternal half-sib families of a granddaughter design were genotyped for 265 genetic markers, most of them microsatellites. These were 16 Holstein families, 3 Simmental families, and 1 Brown Swiss family. The number of sires per breed was 872, 170, and 32, respectively. Two-point recombination rates were estimated both jointly for all breeds and each single breed separately. Of 1168 marker intervals, 865 provided estimates for at least two breeds. Differences between breeds were tested by likelihood ratio tests. Four marker intervals, representing three genomic regions on BTA19, BTA24, and BTA27, show a significant impact of the breed at a false discovery rate of 0.23 and indicate a genetic component of observed heterogeneity of recombination. The variability of recombination rates between cattle breeds might not be a common feature of the whole genome, but rather might be restricted to certain chromosomal segments. Thus, attention should be paid to heterogeneities when pooling data of such regions from different breeds. Received: 14 March 2001 / Accepted: 8 May 2001     

Use of linked loci as individuals or haplotypes for marker-assisted breed assignment

The objective of this study was to use simulation to evaluate the benefits of considering haplotypes of loci when linked single nucleotide polymorphisms are used for breed assignment. Three breeds of 10 000 females each were simulated under eight scenarios that differed according to the number of generations separating the breeds, size of breed founder populations and recombination rate between linked loci. Molecular genotypes consisted of 20 groups of three linked loci each. Breed assignment was performed in the final generation and was based on the frequency method. Haplotypes were reconstructed using the expectation–maximization algorithm. Accuracy of breed assignment was based on the frequency of correct breed assignment. Assignment accuracy increased as more genotypes (loci or haplotypes) were considered and more animals were used to estimate genotypic frequencies within breed. For most scenarios, use of haplotypes yielded equal or greater accuracies than when loci were considered independent. The advantage of haplotypes tended to increase as linkage disequilibrium between adjacent loci increased. The greatest advantage for using haplotypes was observed when recombination rate was low (0.001), breeds were separated by few generations (100), and a relatively large number of founder animals (110) was used to form new breeds. In this situation, 90% accuracy of breed assignment was achieved using nine to 14 haplotypes (i.e. 27–42 loci) depending on breed, vs. 39–57 individual loci.     

Breed differences in the distribution of BoLA-A locus antigens in American cattle

A total of 627 cattle representing seven breeds from south central Nebraska, USA were tested for 37 BoLA antigens which behave as products of 37 distinct alleles of the class I BoLA-A locus. Four antigens were absent from all breeds tested. The other antigens showed marked and statistically significant differences in breed distribution. There was no evidence for blank (null) alleles. The number of alleles in each breed ranged from 10 to 20. The Hereford and Simmental populations tested were less polymorphic than the Angus, Brown Swiss, Charolais, Gelbvieh and Limousin populations.     

Associations of scrotal circumference with semen traits in young beef bulls

Associations of percent live sperm, sperm number, sperm concentration, sperm motility, and potential breeding efficiency score with scrotal circumference were studied using data from the records of 465 Polled Hereford and 264 Simmental bulls. Data were subdivided by breed and within breed into three groups according to scrotal circumference (SC) size. Group I bulls had SC measurements <32 cm. Group II included bulls with SC measurements between 32 cm and the mean measurement of the breed (i.e., 35 cm for Polled Hereford and 38 cm for Simmentals). Group III was comprised of bulls with SC values above their respective breed averages. Age and body weight differences were also evaluated in the three groups. Average age differences among bulls in the three groups differed by not more than nine days in the two breeds. Average body weight differences among the three groups were statistically significant (P<0.05) with the maximum difference between any two groups within breed being 80 pounds. Average differences in percent live sperm and sperm number were greater (P<0.05) in Groups II and III than in Group I. For sperm concentration ratings, sperm motility ratings and potential breeding efficiency score, and for both breeds, Group I had a significantly lower (P<0.05) number of bulls classified satisfactory and a significantly greater (P<0.05) number of bulls classified unsatisfactory than did groups II and III.     

A Function Accounting for Training Set Size and Marker Density to Model the Average Accuracy of Genomic Prediction

Prediction of genomic breeding values is of major practical relevance in dairy cattle breeding. Deterministic equations have been suggested to predict the accuracy of genomic breeding values in a given design which are based on training set size, reliability of phenotypes, and the number of independent chromosome segments (). The aim of our study was to find a general deterministic equation for the average accuracy of genomic breeding values that also accounts for marker density and can be fitted empirically. Two data sets of 5′698 Holstein Friesian bulls genotyped with 50 K SNPs and 1′332 Brown Swiss bulls genotyped with 50 K SNPs and imputed to ∼600 K SNPs were available. Different k-fold (k = 2–10, 15, 20) cross-validation scenarios (50 replicates, random assignment) were performed using a genomic BLUP approach. A maximum likelihood approach was used to estimate the parameters of different prediction equations. The highest likelihood was obtained when using a modified form of the deterministic equation of Daetwyler et al. (2010), augmented by a weighting factor (w) based on the assumption that the maximum achievable accuracy is . The proportion of genetic variance captured by the complete SNP sets () was 0.76 to 0.82 for Holstein Friesian and 0.72 to 0.75 for Brown Swiss. When modifying the number of SNPs, w was found to be proportional to the log of the marker density up to a limit which is population and trait specific and was found to be reached with ∼20′000 SNPs in the Brown Swiss population studied.     

Heritability estimates and adjustment factors for the effects of bull age and age of dam on yearling testicular size in breeds of bulls

Scrotal circumference, testicular length and body weight were measured in 3,090 yearling bulls of 12 breed groups finishing growth performance tests during a 5 yr period. Breeds were Limousin, Hereford, Charolais, Angus, Red Poll, Simmental, Pinzgauer, Brown Swiss, Gelbvieh and three crossbred breed groups. All bulls were born during a 60-d calving season starting in late March of each year and were subjected to similar management and environmental influences during the study. The bulls were the progeny of 307 sires averaging approximately 26 sires per breed group and 10 sons per sire. Breed group, sire within breed group, year and age-of-dam effects were important (P<0.01) for all testicular traits at both a constant age (354 d) and constant body weight (418 kg). Paternal half-sib estimates of heritability were 0.41 +/- 0.06 for ageconstant scrotal circumference, 0.34 +/- 0.06 for testicular length and 0.37 +/- 0.06 for calculated paired testicular volume, respectively. Age-constant genetic correlations between yearling body weight and testicular traits were small, indicating that testicular growth and body growth rates are largely independent, regardless of breed. Testicular size of bulls from 2-yr-old dams was smaller than that of bulls from older dams. Most of these age-of-dam effects on testicular size were removed when testicular size was adjusted for the effects of body weight, suggesting that age-of-dam effects on testicular size are primarily the result of age-of-dam effects on body weight. Age adjustment factors for yearling scrotal circumference did not differ (P>0.20) among breed groups and averaged 0.032 cm per day of age. Adjustment factors for age of dam were +1.3, +0.8, +0.4, and +0.0 cm for sons of 2-, 3-, 4- and 5-yr-old dams, respectively.     

Effects of suckling frequency and breed on productive performance,follicular dynamics and postpartum interval in beef cows

One experiment was conducted to determine the influence of suckling frequency (restricted suckling (RS) versus ad libitum suckling (AS)) and breed (Brown Swiss versus Pirenaica) on productive performance, follicular dynamics and postpartum cyclicity resumption in beef cows. Twenty-four spring-calving cows (12 Brown Swiss and 12 Pirenaica) were used. After calving cows were assigned, within breed, to the two suckling frequencies (RS versus AS). During the postpartum period, cows were fed 100% of the daily energy estimated requirements. The study was conducted from calving to either day 90 postpartum or to detection of the second ovulation whenever it came later. The pattern of follicular development was monitored daily by transrectal ultrasonography, and blood samples were collected three times a week to analyse progesterone concentrations by RIA. Body condition score at calving was 2.5 (from 1 to 5). Productive parameters were not significantly affected by suckling frequency. Pirenaica cows gained more weight (P<0.001), while Brown Swiss cows had higher milk yield (P<0.001) and thus their calves grew faster (P<0.05). In the present moderate conditions of nutrition, either suckling frequency or breed did not affect follicular dynamics (on average there were 6.5 follicles in emergence, growth rate of dominant follicle (DF) was 1.3mm per day and maximum diameter of dominant follicle was 13.9mm). There were gradual increases in maximum diameter and growth rate of dominant follicle related to the proximity of the ovulatory waves, and they were defined by third order polynomial equations. Postpartum anoestrous interval (PPI) was markedly affected by the interaction between suckling frequency and breed (P<0.001): ad libitum suckling prolonged significantly the interval from calving to first ovulation in Brown Swiss cows (31.8 day versus 82.7 day, in RS and AS groups, respectively, P<0.05), but not in Pirenaica cows (43.5 day versus 32.6 day, in RS and AS groups, respectively, not statistically significant). It is concluded that in moderate pre- and postpartum nutritional conditions Brown Swiss cows were more susceptible to the suppressor effect of ad libitum suckling on postpartum anoestrous interval than Pirenaica cows, although this breed difference did not seem to be mediated by differences in energy balance or in ovarian follicular dynamics.     

Genetic structure of seven European cattle breeds assessed using 20 microsatellite markers

Genotype data from 20 microsatellites typed in 253 animals is used here to assess the genetic structure of seven European pedigree cattle breeds. Estimation of genetic subdivision using classical drift-based measures shows that the average proportion of genetic variation among breeds varies between 10 and 11% of the total, depending on the estimator used. We demonstrate that a simple allele-sharing genetic distance parameter can be used to construct a dendrogram of relationships among animals. This phylogenetic tree displays a remarkable degree of breed clustering and reflects an extensive underlying kinship structure, particularly for the Swiss Simmental breed and four breeds originating from the British Isles. Condensation of allele frequencies and individual genotypic compositions using principal component analysis is also used to investigate genetic structure among breeds and individual animals. In addition, the underlying genetic demarcation of European cattle breeds is emphasized in simulations of breed assignment using allele frequency distributions from samples of microsatellite loci. Correct breed designation can be inferred with accuracies approaching 100% using data from a panel of 10 microsatellite loci.     

Effect of the collection method on semen characteristics of Zebu and European type cattle in the tropics

The effect of the collection method on the characteristics of fresh semen and the recovery of spermatozoa after thawing was studied in 30 Zebu bulls (Bos indicus ) and in 30 Brown Swiss (Bos taurus ) bulls. Semen was collected by using an artificial vagina and by electroejaculation; the ejaculates were individually evaluated. Semen was diluted for freezing in skimmed milk and stored in 0.5-ml French straws, at a concentration of 30 x 10(6) spermatozoa. Data were evaluated by analysis of variance using a factorial model which included collection method, breed effect, and interaction between method and breed, with each bull as a block. Higher volume and pH of the semen was obtained following electroejaculation. Conversely, higher concentration prior to freezing and better progressive motility after thawing was observed in semen collected with an artificial vagina. No differences in motility were obtained in fresh semen between methods. Better post-thaw recovery occurred when the semen was collected by an artificial vagina, independently of the breed type.     

Genome‐wide linkage disequilibrium and past effective population size in three Korean cattle breeds

The routine collection and use of genomic data are useful for effectively managing breeding programs for endangered populations. Linkage disequilibrium (LD) using high‐density DNA markers has been widely used to determine population structures and predict the genomic regions that are associated with economic traits in beef cattle. The extent of LD also provides information about historical events, including past effective population size (N_e), and it allows inferences on the genetic diversity of breeds. The objective of this study was to estimate the LD and N_e in three Korean cattle breeds that are genetically similar but have different coat colors (Brown, Brindle and Jeju Black Hanwoo). Brindle and Jeju Black are endangered breeds with small populations, whereas Brown Hanwoo is the main breeding population in Korea. DNA samples from these cattle breeds were genotyped using the Illumina BovineSNP50 Bead Chip. We examined 13 cattle breeds, including European taurines, African taurines and indicines, and hybrids to compare their LD values. Brown Hanwoo consistently had the lowest mean LD compared to Jeju Black, Brindle and the other 13 cattle breeds (0.13, 0.19, 0.21 and 0.15–0.22 respectively). The high LD values of Brindle and Jeju Black contributed to small N_e values (53 and 60 respectively), which were distinct from that of Brown Hanwoo (531) for 11 generations ago. The differences in LD and N_e for each breed reflect the breeding strategy applied. The N_e for these endangered cattle breeds remain low; thus, effort is needed to bring them back to a sustainable tract.