Estimation of pedigree errors in the UK dairy population using microsatellite markers and the impact on selection

How pedigree errors affect genetic evaluations and validation statistics

Pedigrees used in genetic evaluations contain errors. Because of such errors, assumptions regarding the relatedness among individuals in genetic evaluation models are wrong. Consequences of that have been investigated in earlier studies focusing on models that did not account for genomic information yet. The objective of this work was to investigate the effects of pedigree errors on the results from genetic evaluations using the single-step model, and the effect of such effects on results from validation studies with forward prediction. We used a real pedigree (n = 361,980) and real genotypes (n = 25,950) of Fleckvieh cattle, sampled in a way to provide a good consistency between pedigree and genomic relationships. Given the real pedigree and genotypes, true breeding values (TBV) were simulated to have a covariance structure equal to the matrix H assumed in a single-step model. Based on TBV, phenotypes were simulated with a heritability of 0.25. Genetic evaluations were conducted with a conventional animal model (i.e., without genomic information) and a single-step animal model under scenarios using either the correct pedigree or a pedigree containing 5%, 10%, or 20% of wrong records. Wrong records were simulated by randomly assigning wrong sires to nongenotyped females. The increasing rates of pedigree errors led to decreasing correlations between TBV and EBV and lower standard deviations of predictions. Less variation was observed because pedigree errors operate actually as a random exchange of daughters among bulls, making them look more similar to each other than they actually are. This occurs of course only when animals have progeny. Therefore, this decreased variation was more pronounced for progeny tested bulls than for young selection candidates. In a forward prediction validation scenario, the stronger decrease in variation when animals get progeny caused an apparent inflation of early predictions. This phenomenon may contribute to the usually observed problem of inflation of early predictions observed in validation studies.

Pedigree diversity and implications for genetic selection of Katahdin sheep

The Katahdin hair breed gained popularity in the United States as low input and prolific, with a propensity to exhibit parasite resistance. With the introduction of genomically enhanced estimated breeding values (GEBV) to the Katahdin genetic evaluation, defining the diversity present in the breed is pertinent. Utilizing pedigree records (n = 92,030) from 1984 to 2019 from the National Sheep Improvement Program, our objectives were to (i) estimate the completeness and quality of the pedigree, (ii) calculate diversity statistics for the whole pedigree and relevant reference subpopulations and (iii) assess the impact of current diversity on genomic selection. Reference 1 was Katahdins born from 2017 to 2019 (n = 23,494), while reference 2 was a subset with at least three generations of Katahdin ancestry (n = 9327). The completeness of the whole pedigree, and the pedigrees of reference 1 and reference 2, were above 50% through the fourth, fifth and seventh generation of ancestors, respectively. Effective population size (Ne) averaged 111 animals with a range from 42.2 to 451.0. The average generation interval was 2.9 years for the whole pedigree and reference 1, and 2.8 years for reference 2. The mean individual inbreeding and average relatedness coefficients were 1.62% and 0.91%, 1.74% and 0.90% and 2.94% and 1.46% for the whole pedigree, reference 1, and reference 2, respectively. There were over 300 effective founders in the whole pedigree and reference 1, with 169 in reference 2. Effective number of ancestors were over 150 for the whole pedigree and reference 1, while there were 67 for reference 2. Prediction accuracies increased as the reference population grew from 1k to 7.5k and plateaued at 15k animals. Given the large number of founders and ancestors contributing to the base genetic variation in the breed, the Ne is sufficient to maintain diversity while achieving progress with selection. Stable low rates of inbreeding and relatedness suggest that incorporating genetic conservation in breeding decisions is currently not of high priority. Current Ne suggests that with limited genotyping, high levels of accuracy for genomic prediction can be achieved. However, intense selection on GEBV may cause loss of genetic diversity long term.

Animal board invited review: Practical applications of genomic information in livestock

Access to high-dimensional genomic information in many livestock species is accelerating. This has been greatly aided not only by continual reductions in genotyping costs but also an expansion in the services available that leverage genomic information to create a greater return-on-investment. Genomic information on individual animals has many uses including (1) parentage verification and discovery, (2) traceability, (3) karyotyping, (4) sex determination, (5) reporting and monitoring of mutations conferring major effects or congenital defects, (6) better estimating inbreeding of individuals and coancestry among individuals, (7) mating advice, (8) determining breed composition, (9) enabling precision management, and (10) genomic evaluations; genomic evaluations exploit genome-wide genotype information to improve the accuracy of predicting an animal's (and by extension its progeny's) genetic merit. Genomic data also provide a huge resource for research, albeit the outcome from this research, if successful, should eventually be realised through one of the ten applications already mentioned. The process for generating a genotype all the way from sample procurement to identifying erroneous genotypes is described, as are the steps that should be considered when developing a bespoke genotyping panel for practical application.

Analysis of the Genetic Diversity and Family Structure of the Licha Black Pig Population on Jiaodong Peninsula, Shandong Province, China

Simple Summary

This study investigated the current conservation status, including the genetic diversity, the family structure, and inbreeding, of the Licha black pig population on Jiaodong Peninsula (Shandong Province, China). The results provide insights into the management and conservation of a local pig breed. Breeders are encouraged to utilize genomic data to improve mating schemes based on the family information obtained in this study, such as keeping an equivalent number of boars and sows in each family and selecting individuals with a kinship coefficient of less than 0.1 for mating.

Abstract

The Licha black pig, a popular indigenous Chinese pig breed, is known for its multi-vertebral trait and higher lean meat rate. Understanding the current conservation status, family structure, and degree of inbreeding of the Licha black pig population will be useful to maintain a sufficient level of genetic diversity in these animal resources. In the present study, the genetic diversity, population structure, and inbreeding coefficient of this conserved population were analyzed using SNP genotyping data from 209 Licha black pigs. Based on the genomic information, this population was divided into eight different families with boars. The effective population size (N_e), polymorphic marker ratio (P_N), expected heterozygosity (H_e), and observed heterozygosity (H_o) of this population were 8.7, 0.827, 0.3576, and 0.3512, respectively. In addition, a total of 5976 runs of homozygosity (ROHs) were identified, and most of the ROHs (54.9%) were greater than 5 Mb. The genomic inbreeding coefficient of each individual was estimated based on ROHs (F_ROH) with an average inbreeding coefficient of 0.11 for the population. Five statistics (N_e, P_N, H_o, H_e, and F_ROH) showed a decrease in the level of genetic diversity and a high degree of inbreeding in this population. Thus, special preservation programs need to be implemented in the future, such as introducing new individuals or improving the mating plan. Altogether, our study provides the first genomic overview of the genetic diversity and population structure of Licha black pigs, which will be useful for the management and long-term preservation of this breed.

Discovery of hidden pedigree errors combining genomic information with the genomic relationship matrix in Texel sheep

Genomic variants such as Single Nucleotide Polymorphisms and animal pedigree are now used widely in routine genetic evaluations of livestock in many countries. The use of genomic information not only can be used to enhance the accuracy of prediction but also to verify pedigrees for animals that are extensively managed using natural mating and enabling multiple-sire mating groups to be used. By so doing, the rate of genetic gain is enhanced, and any bias associated with incorrect pedigrees is removed. This study used a set of 8 764 sheep genotypes to verify the pedigree based on both the conventional opposing homozygote method as well as a novel method when combined with the inclusion of the genomic relationship matrix (GRM). The genomic relationship coefficients between verified pairs of animals showed on average a relationship of 0.50 with parent, 0.25 with grandparent, 0.13 with great grandparent, 0.50 with full-sibling and 0.27 with half-sibling. Minimum obtained values from these verified pairs were then used as thresholds to determine the pedigree for unverified pairs of animals, to detect potential errors in the pedigree. Using a case study from a population partially genotyped UK sheep, the results from this study illustrate a powerful way to resolve parentage inconsistencies, when combining the conventional 'opposing homozygote' method using genomic information together with GRM for pedigree checking. In this way, previously undetected pedigree errors can be resolved.

Comparative analysis of inbreeding parameters and runs of homozygosity islands in 2 Italian autochthonous cattle breeds mainly raised in the Parmigiano-Reggiano cheese production region

Reggiana and Modenese are autochthonous cattle breeds, reared in the North of Italy, that can be mainly distinguished for their standard coat color (Reggiana is red, whereas Modenese is white with some pale gray shades). Almost all milk produced by these breeds is transformed into 2 mono-breed branded Parmigiano-Reggiano cheeses, from which farmers receive the economic incomes needed for the sustainable conservation of these animal genetic resources. After the setting up of their herd books in 1960s, these breeds experienced a strong reduction in the population size that was subsequently reverted starting in the 1990s (Reggiana) or more recently (Modenese) reaching at present a total of about 2,800 and 500 registered cows, respectively. Due to the small population size of these breeds, inbreeding is a very important cause of concern for their conservation programs. Inbreeding is traditionally estimated using pedigree data, which are summarized in an inbreeding coefficient calculated at the individual level (F_PED). However, incompleteness of pedigree information and registration errors can affect the effectiveness of conservation strategies. High-throughput SNP genotyping platforms allow investigation of inbreeding using genome information that can overcome the limits of pedigree data. Several approaches have been proposed to estimate genomic inbreeding, with the use of runs of homozygosity (ROH) considered to be the more appropriate. In this study, several pedigree and genomic inbreeding parameters, calculated using the whole herd book populations or considering genotyping information (GeneSeek GGP Bovine 150K) from 1,684 Reggiana cattle and 323 Modenese cattle, were compared. Average inbreeding values per year were used to calculate effective population size. Reggiana breed had generally lower genomic inbreeding values than Modenese breed. The low correlation between pedigree-based and genomic-based parameters (ranging from 0.187 to 0.195 and 0.319 to 0.323 in the Reggiana and Modenese breeds, respectively) reflected the common problems of local populations in which pedigree records are not complete. The high proportion of short ROH over the total number of ROH indicates no major recent inbreeding events in both breeds. ROH islands spread over the genome of the 2 breeds (15 in Reggiana and 14 in Modenese) identified several signatures of selection. Some of these included genes affecting milk production traits, stature, body conformation traits (with a main ROH island in both breeds on BTA6 containing the ABCG2, NCAPG, and LCORL genes) and coat color (on BTA13 in Modenese containing the ASIP gene). In conclusion, this work provides an extensive comparative analysis of pedigree and genomic inbreeding parameters and relevant genomic information that will be useful in the conservation strategies of these 2 iconic local cattle breeds.

Performance of using opposing homozygotes for paternity testing in Japanese Black cattle

Genome-wide single nucleotide polymorphism (SNP) markers in Japanese Black cattle enable genomic prediction and verifying parent-offspring relationships. We assessed the performance of opposing homozygotes (OH) for paternity testing in Japanese Black cattle, using SNP genotype information of 50 sires and 3,420 fattened animals, 1,945 of which were fathered by the 50 genotyped sires. The number of OH was counted for each sire-progeny pair in 28,764 SNPs with minor allele frequencies of ≥0.05 in this population. Across all pairs of animals, the number of OH tended to increase as the pedigree-based coefficient of relationship decreased. With a threshold of 288 (1% of SNPs) for paternity testing, most sire-progeny pairs were detected as true relationships. The frequency of Mendelian inconsistencies was 2.4%, reflecting the high accuracy of pedigree information in Japanese Black cattle population. The results indicate the utility of OH for paternity testing in Japanese Black cattle.

Unintended consequences of selection for increased production on the health and welfare of livestock

Modern farming technologies, including quantitative selection and breeding methods in farm animal species, resulted in increased production and efficiency. Selection for increased output in both intensive and extensive production systems has trade-offs and negative outcomes, often more pronounced in intensive systems. Animal welfare and health are often adversely affected and this influences sustainable production. The relative importance of animal welfare differs among developed and developing countries due to the level of economic development, food security and education, as well as religious and cultural practices which presents challenges for sound scientific research. Due to breeding goals in the past set on growth performance, traits such as fertility, welfare and health have been neglected. Fertility is the single most important trait in all livestock species. Reduced fertility and lameness, claw health and mastitis results in unnecessary culling and reduced longevity. Selection pressure for growth accompanied with inbreeding has resulted in a number of genetic defects in beef, sheep and pigs. This review demonstrated the importance of inclusion of animal welfare concepts into breeding objectives and selection strategies. Accurate phenotyping of welfare traits is a limiting factor in the implementation of mitigating strategies, which include diagnostic testing, control of inbreeding and genomic selection.

Selection and implementation of single nucleotide polymorphism markers for parentage analysis in crossbred cattle population

Crossbreeding is an essential way of improving herd performance. However, frequent parentage record errors appear, which results in the lower accuracy of genetic parameter estimation and genetic evaluation. This study aims to build a single nucleotide polymorphism (SNP) panel with sufficient power for parentage testing in the crossbred population of Simmental and Holstein cattle. The direct sequencing technique in PCR products of pooling DNA along with matrix-assisted laser desorption/ionization time-of-flight MS method for genotyping the individuals was applied. A panel comprising 50 highly informative SNPs for parentage analysis was developed in the crossbred population. The average minor allele frequency for SNPs was 0.43, and the cumulative probability of exclusion for single-parent and both-parent inference met 0.99797 and 0.999999, respectively. The maker-set for parentage verification was then used in a group of 81 trios with aid of the likelihood-based parentage-assignment program of Cervus software. Reconfirmation with on-farm records showed that this 50-SNP system could provide sufficient and reliable information for parentage testing with the parental errors for mother-offspring and sire-offspring being 8.6 and 18.5%, respectively. In conclusion, a set of low-cost and efficient SNPs for the paternity testing in the Simmental and Holstein crossbred population are provided.

Evaluation of the International Society for Animal Genetics bovine single nucleotide polymorphism parentage panel in South African Bonsmara and Drakensberger cattle

A panel of 200 single nucleotide polymorphisms (SNPs) have been recommended by the International Society for Animal Genetics (ISAG) for use in parentage verification of cattle. While the SNPs included on the ISAG panel are segregating in European Bos taurus and Bos indicus breeds, their applicability in South African (SA) Sanga cattle has never been evaluated. This study, therefore, assessed the usefulness of the ISAG panel in SA Bonsmara (BON) and Drakensberger (DRB) cattle. Genotypes of 185 ISAG SNPs from 64 BON and 97 DRB sire-offspring pairs were available, all of which were validated with 119,375 SNPs. Of the 185 ISAG SNPs, 14 and 18 in the BON and DRB, respectively (9 in common to both breeds), were either monomorphic, exhibited at least one discordance between validated sire-offspring pairs, or had poor call rate or clustering issue. The mean minor allele frequency of the 185 ISAG SNPs was 0.331 in the BON and 0.359 in the DRB. The combined probability of parentage exclusion (P_E) was the same (99.46%) for both breeds, while the probability of identity varied from 1.61 × 10^-48 (BON) to 1.11 × 10^-54 (DRB). Fifteen (23.4%) and 32 (33%) of the already validated sire-offspring pairs for the BON and DRB, respectively, were determined by the ISAG panel to be false-negatives based on a threshold of having at least two discordant SNPs. In comparison to sire discovery using the 119,375 SNPs, sire discovery using only the ISAG panel identified correctly 44 (out of 64 identified using the 119,375 SNPs) unique sire-offspring BON pairs and 62 (out of 97 identified using the 119,375 SNPs) unique sire-offspring DRB when all sires were masked. Five BON and three DRB offspring had > 1 sire nominated. This study demonstrated that the use of the ISAG panel may result in incorrect exclusions and multiple candidate sires for a given animal. Selection of more informative SNPs is, therefore, necessary in the pursuit of a low-cost and effective SNP panel for indigenous cattle breeds in SA.

Coat Color Roan Shows Association with KIT Variants and No Evidence of Lethality in Icelandic Horses

Roan (Rn) horses show a typical seasonal change of color. Their body is covered with colored and white hair. We performed a descriptive statistical analysis of breeding records of Icelandic horses to challenge the hypothesis of roan being lethal in utero under homozygous condition. The roan to non-roan ratio of foals from roan × roan matings revealed homozygous roan Icelandic horses to be viable. Even though roan is known to be inherited in a dominant mode and epistatic to other coat colors, the causative mutation is still unknown. Nevertheless, an association between roan phenotype and the KIT gene was shown for different horse breeds. In the present study, we identified KIT variants by Sanger sequencing, and show that KIT is also associated with roan in the Icelandic horse breed.

Single nucleotide polymorphism-based analysis of the genetic structure of Liangshan pig population

Objective

To conserve and utilize the genetic resources of a traditional Chinese indigenous pig breed, Liangshan pig, we assessed the genetic diversity, genetic structure, and genetic distance in this study.

Methods

We used 50K single nucleotide polymorphism (SNP) chip for SNP detection of 139 individuals in the Liangshan Pig Conservation Farm.

Results

The genetically closed conserved population consisted of five overlapping generations, and the total effective content of the population (Ne) was 15. The whole population was divided into five boar families and one non-boar family. Among them, the effective size of each generation subpopulation continuously decreased. However, the proportion of polymorphic markers (P_N) first decreased and then increased. The average genetic distance of these 139 Liangshan pigs was 0.2823±0.0259, and the average genetic distance of the 14 boars was 0.2723±0.0384. Thus, it can be deduced that the genetic distance changed from generation to generation. In the conserved population, 983 runs of homozygosity (ROH) were detected, and the majority of ROH (80%) were within 100 Mb. The inbreeding coefficient calculated based on ROH showed an average value of 0.026 for the whole population. In addition, the inbreeding coefficient of each generation subpopulation initially increased and then decreased. In the pedigree of the whole conserved population, the error rate of paternal information was more than 11.35% while the maternal information was more than 2.13%.

Conclusion

This molecular study of the population genetic structure of Liangshan pig showed loss of genetic diversity during the closed cross-generation reproduction process. It is necessary to improve the mating plan or introduce new outside blood to ensure long-term preservation of Liangshan pig.

On-farm net benefit of genotyping candidate female replacement cattle and sheep

The net benefit from investing in any technology is a function of the cost of implementation and the expected return in revenue. The objective of the present study was to quantify, using deterministic equations, the net monetary benefit from investing in genotyping of commercial females. Three case studies were presented reflecting dairy cows, beef cows and ewes based on Irish population parameters; sensitivity analyses were also performed. Parameters considered in the sensitivity analyses included the accuracy of genomic evaluations, replacement rate, proportion of female selection candidates retained as replacements, the cost of genotyping, the sire parentage error rate and the age of the female when it first gave birth. Results were presented as an annualised monetary net benefit over the lifetime of an individual, after discounting for the timing of expressions. In the base scenarios, the net benefit was greatest for dairy, followed by beef and then sheep. The net benefit improved as the reliability of the genomic evaluations improved and, in fact, a negative net benefit of genotyping was less frequent when the reliability of the genomic evaluations was high. The impact of a 10% point increase in genomic reliability was, however, greatest in sheep, followed by beef and then dairy. The net benefit of genotyping female selection candidates reduced as replacement rate increased. As genotyping costs increased, the net benefit reduced irrespective of the percentage of selection candidates kept, the replacement rate or even the population considered. Nonetheless, the association between the genotyping cost and the net benefit of genotyping differed by the percentage of selection candidates kept. Across all replacement rates evaluated, retaining 25% of the selection candidates resulted in the greatest net benefit when genotyping cost was low but the lowest net benefit when genotyping cost was high. Genotyping breakeven cost was non-linearly associated with the percentage of selection candidates retained, reaching a maximum when 50% of selection candidates were retained, irrespective of replacement rate, genomic reliability or the population. The genotyping breakeven cost was also non-linearly associated with replacement rate. The approaches outlined within provide the back-end framework for a decision support tool to quantify the net benefit of genotyping, once parameterised by the relevant population metrics.

Genomic selection for non-key traits in radiata pine when the documented pedigree is corrected using DNA marker information

Background

Non-key traits (NKTs) in radiata pine (Pinus radiata D. Don) refer to traits other than growth, wood density and stiffness, but still of interest to breeders. Branch-cluster frequency, stem straightness, external resin bleeding and internal checking are examples of such traits and are targeted for improvement in radiata pine research programmes. Genomic selection can be conducted before the performance of selection candidates is available so that generation intervals can be reduced. Radiata pine is a species with a long generation interval, which if reduced could significantly increase genetic gain per unit of time. The aim of this study was to evaluate the accuracy and predictive ability of genomic selection and its efficiency over traditional forward selection in radiata pine for the following NKTs: branch-cluster frequency, stem straightness, internal checking, and external resin bleeding.

Results

Nine hundred and eighty-eight individuals were genotyped using exome capture genotyping by sequencing (GBS) and 67,168 single nucleotide polymorphisms (SNPs) used to develop genomic estimated breeding values (GEBVs) with genomic best linear unbiased prediction (GBLUP). The documented pedigree was corrected using a subset of 704 SNPs. The percentage of trio parentage confirmed was about 49% and about 50% of parents were re-assigned. The accuracy of GEBVs was 0.55–0.75 when using the documented pedigree and 0.61–0.80 when using the SNP-corrected pedigree. A higher percentage of additive genetic variance was explained and a higher predictive ability was observed when using the SNP-corrected pedigree than using the documented pedigree. With the documented pedigree, genomic selection was similar to traditional forward selection when assuming a generation interval of 17 years, but worse than traditional forward selection when assuming a generation interval of 14 years. After the pedigree was corrected, genomic selection led to 37–115% and 13–77% additional genetic gain over traditional forward selection when generation intervals of 17 years and 14 years were assumed, respectively.

Conclusion

It was concluded that genomic selection with a pedigree corrected by SNP information was an efficient way of improving non-key traits in radiata pine breeding.

Genomic selection for non-key traits in radiata pine when the documented pedigree is corrected using DNA marker information

BACKGROUND

Non-key traits (NKTs) in radiata pine (Pinus radiata D. Don) refer to traits other than growth, wood density and stiffness, but still of interest to breeders. Branch-cluster frequency, stem straightness, external resin bleeding and internal checking are examples of such traits and are targeted for improvement in radiata pine research programmes. Genomic selection can be conducted before the performance of selection candidates is available so that generation intervals can be reduced. Radiata pine is a species with a long generation interval, which if reduced could significantly increase genetic gain per unit of time. The aim of this study was to evaluate the accuracy and predictive ability of genomic selection and its efficiency over traditional forward selection in radiata pine for the following NKTs: branch-cluster frequency, stem straightness, internal checking, and external resin bleeding.

RESULTS

Nine hundred and eighty-eight individuals were genotyped using exome capture genotyping by sequencing (GBS) and 67,168 single nucleotide polymorphisms (SNPs) used to develop genomic estimated breeding values (GEBVs) with genomic best linear unbiased prediction (GBLUP). The documented pedigree was corrected using a subset of 704 SNPs. The percentage of trio parentage confirmed was about 49% and about 50% of parents were re-assigned. The accuracy of GEBVs was 0.55-0.75 when using the documented pedigree and 0.61-0.80 when using the SNP-corrected pedigree. A higher percentage of additive genetic variance was explained and a higher predictive ability was observed when using the SNP-corrected pedigree than using the documented pedigree. With the documented pedigree, genomic selection was similar to traditional forward selection when assuming a generation interval of 17 years, but worse than traditional forward selection when assuming a generation interval of 14 years. After the pedigree was corrected, genomic selection led to 37-115% and 13-77% additional genetic gain over traditional forward selection when generation intervals of 17 years and 14 years were assumed, respectively.

CONCLUSION

It was concluded that genomic selection with a pedigree corrected by SNP information was an efficient way of improving non-key traits in radiata pine breeding.

Single Nucleotide Polymorphisms (SNPs) Reveal Sibship Among Founders of a Bangladeshi Rohu (Labeo rohita) Breeding Population

Rohu (Labeo rohita) is a significant freshwater aquaculture species with approximately 1.8 Mt produced annually. Fin clips obtained from the founders of a newly established Bangladesh-based breeding population (∼140 fish from each of the Halda, Jamuna, and Padma rivers) were used to identify 9157 SNPs and 14 411 silicoDArT markers using the Diversity Arrays Technology (DArT) genotyping-by-sequencing platform known as DArTseq. After quality control, 1985 SNPs were retained and used to examine population structure within and among river systems. Examination of genomic relationships revealed evidence of full- and half-sibling relationships among founders. Accordingly, sibship and dummy parents were assigned within each river population using a maximum likelihood approach with COLONY software. Founders that had no dummy parents in common were then identified for population genetic analyses. Only 40 unique dummy parents and 17 founders with no common dummy parents were identified from the Halda river, compared with 206 (96) from the Jamuna and 184 (83) from the Padma. Overall pairwise FST estimates among rivers were low (<0.005) and the optimum number of clusters using unsupervised K-means clustering was one, indicating little genetic divergence among the river populations in our SNPs. These results suggest that observed sibship among founders should be accounted for in future pedigree-based analyses and it cannot be assumed that fertilized spawn collections are representative samples of river populations.

Inbreeding depression in line 1 Hereford cattle population using pedigree and genomic information

This study aimed at assessing inbreeding and its effect on growth and fertility traits using the longtime closed line 1 Hereford cattle population. Inbreeding was estimated based on pedigree (FPED) and genomic information. For the latter, three estimates were derived based on the diagonal elements of the genomic relationship matrix using estimated (FGRM) or fixed (FGRM0.5) minor allele frequencies or runs of homozygosity (ROH) (FROH). A pedigree containing 10,186 animals was used to calculate FPED. Genomic inbreeding was evaluated using 785 animals genotyped for 30,810 SNP. Traits analyzed were birth weight (BWT), weaning weight (WWT), yearling weight (YWT), ADG, and age at first calving (AFC). The number of ROH per animal ranged between 6 and 119 segments with an average of 83. The shortest and longest segments were 1.36 and 64.86 Mb long, respectively, reflecting both ancient and recent inbreeding occurring in the last 30 to 40 generations. The average inbreeding was 29.2%, 16.1%, 30.2%, and 22.9% for FPED, FGRM, FGRM0.5, and FROH, respectively. FROH provided the highest correlations with FPED (r = 0.66). Across paternal half-sib families, with minimal variation in FPED, there were substantial variations in their genomic inbreeding. Inbreeding depression analyses showed that a 1% increase in an animal's FPED resulted in a decrease of 1.20 kg, 2.03 kg, and 0.004 kg/d in WWT, YWT, and ADG, respectively. Maternal inbreeding showed significantly negative effects on progeny growth performance. AFC increased by 1.4 and 0.8 d for each 1% increase in FPED of the cow and her dam, respectively. Using genomic inbreeding, similar impact on growth traits was observed although the magnitude of the effect varied between methods. Across all genomic measures, WWT, YWT, and ADG decreased by 0.21 to 0.53 kg, 0.46 to 1.13 kg, and 0.002 to 0.006 kg/d for each 1% increase in genomic inbreeding, respectively. Four chromosomes (9, 12, 17, and 27) were identified to have a significant association between their homozygosity (FROH-CHR) and growth traits. Variability in genomic inbreeding could be useful when deciding between full and half-sib selection candidates. Despite the high level of inbreeding in this study, its negative impact on growth performance was not as severe as expected, which may be attributed to the purging of the deleterious alleles due to natural or artificial selection over time.

Forensic use of the genomic relationship matrix to validate and discover livestock pedigrees

Correct pedigree is essential to produce accurate genetic evaluations of livestock populations. Pedigree validation has traditionally been undertaken using microsatellites and more recently, based on checks on opposing homozygotes using single nucleotide polymorphisms (SNPs). In this study, the genomic relationship matrix was examined to see whether it was a useful tool to forensically validate pedigree and discover unknown pedigree. Using 5,993 genotyped Limousin animals which were imputed to a core set of 38,907 SNPs, the genomic relationships between animals were assessed to validate the reported pedigree. Using already pedigree-verified animals, the genomic relationships between animals of different relationships were shown to be on average 0.58, 0.59, 0.32, 0.32, 0.19, and 0.14 between animals and their parents, full siblings, half siblings, grandparents, great grandparents, and great great grandparents, respectively. Threshold values were defined based on the minimum genomic relationship reported between already pedigree-verified animals; 0.46, 0.41, 0.17, 0.17, 0.07, and 0.05, respectively for animals and their parents, full siblings, half siblings, grandparents, great grandparents, and great great grandparents. Using the wider population and the above genomic relationship threshold values, potential pedigree conflicts were identified within each relationship type. Pedigree error rates of between 0.9% (animal and great great grandparent) and 4.0% (full siblings) were identified. A forensic genomic pedigree validation and discovery system was developed to enable pedigree to be verified for individual genotyped animals. This system verifies not just the parents, but also a wide number of other genotyped relatives and can therefore identify more potential errors in the pedigree than current conventional methods. A novel aspect to this algorithm is that it can also be used to discover closely related animals on the basis of their genomic relationships although they are not recorded as such in the pedigree. This functionality enables missing pedigree information to be discovered and corrected in the pedigree of livestock populations. The methods in this paper demonstrate that the genomic relationship matrix can be a useful tool in the validation and discovery of pedigree in livestock populations. However, the method does rely on being able to define threshold values appropriate to the specific livestock population, which will require sufficient number of animals to be genotyped and pedigree validated before it can be used.

Pedigree verification and parentage assignment using genomic information in the Mexican Holstein population

Genealogical information is an essential tool for carrying out any genetic improvement program. The objective of this study was to determine the accuracy of pedigree information in the Mexican registered Holstein population using genomic data available in Mexico and for the US Holstein population. The study included 7,508 animals (158 sires and 7,350 cows) that were born from 2002 through 2014, registered with Holstein de México, and genotyped with single nucleotide polymorphism arrays of different densities. Parentage could not be validated for 17% of sires of cows and 12% of sires of bulls. Most (79%) of the dams of cows and the dams of bulls had no genotype available and could not be validated. A parentage test was possible for only 6,104 sires of cows, 139 sires of bulls, 1,519 dams of cows, and 33 dams of bulls. Of the animals with a parentage test, parent assignment was confirmed for 89% of sires of cows, 92% of dams of cows, 95% of sires of bulls, and 97% of dams of bulls. Parent discovery was possible for some animals without confirmed parents: 17% for sires of cows, 2.5% for dams of cows, 43% for sires of bulls, and 0% for dams of bulls. Of the 7,795 progeny tests, 777 had parent conflicts, which is an error rate of 9.97% for parental recording in the population, a rate that is similar to those recently reported for other populations. True parents for some progeny conflicts (15%) were discovered for the Mexican population, and the remaining parents were assigned as unknown. Expected effects of misidentification on rate of genetic gain could be decreased by half if genealogical errors were decreased to 5%. This study indicates that genotyping and genealogy recovery may help in increasing rates of genetic improvement in the Mexican registered Holstein population.

Genetic Improvement in South African Livestock: Can Genomics Bridge the Gap Between the Developed and Developing Sectors?

South Africa (SA) holds a unique position on the African continent with a rich diversity in terms of available livestock resources, vegetation, climatic regions and cultures. The livestock sector has been characterized by a dual system of a highly developed commercial sector using modern technology vs. a developing sector including emerging and smallholder farmers. Emerging farmers typically aim to join the commercial sector, but lag behind with regard to the use of modern genetic technologies, while smallholder farmers use traditional practices aimed at subsistence. Several factors influence potential application of genomics by the livestock industries, which include available research funding, socio-economic constraints and extension services. State funded Beef and Dairy genomic programs have been established with the aim of building reference populations for genomic selection with most of the potential beneficiaries in the well-developed commercial sector. The structure of the beef, dairy and small stock industries is fragmented and the outcomes of selection strategies are not perceived as an advantage by the processing industry or the consumer. The indigenous and local composites represent approximately 40% of the total beef and sheep populations and present valuable genetic resources. Genomic research has mostly provided insight on genetic biodiversity of these resources, with limited attention to novel phenotypes associated with adaptation or disease tolerance. Genetic improvement of livestock through genomic technology needs to address the role of adapted breeds in challenging environments, increasing reproductive and growth efficiency. National animal recording schemes contributed significantly to progress in the developed sector with regard to genetic evaluations and estimated breeding values (EBV) as a selection tool over the past three decades. The challenge remains on moving the focus to novel traits for increasing efficiency and addressing welfare and environmental issues. Genetic research programs are required that will be directed to bridge the gap between the elite breeders and the developing livestock sector. The aim of this review was to provide a perspective on the dichotomy in the South African livestock sector arguing that a realistic approach to the use of genomics in beef, dairy and small stock is required to ensure sustainable long term genetic progress.

Selection and effectiveness of informative SNPs for paternity in Chinese Simmental cattle based on a high-density SNP array

Incorrect paternity assignment in cattle can significantly influence the accuracy of genetic evaluation. Recent advances in high-throughput technology have facilitated the identification of single nucleotide polymorphism (SNP) markers and their applications for filiation and individual identification. We genotyped 1074 bulls from a reference population of Chinese Simmental cattle for genomic selection using a BovineSNP770K BeadChip. Among them, a total of 136 bulls were randomly selected to design a suitable low-density SNP panel for paternity testing in Simmental cattle. Our results showed that 50 SNPs were determined to be the most informative markers in parental testing, with an accuracy of 99.89% for CPE (cumulative probability of exclusion) in the unknown female parent case. The 50 highly informative SNP markers were distributed across 25 chromosomes, and the mean intermarker distance per chromosome was 26.72 Mb. The average minor allele frequency (MAF), expected heterozygosity (HE), and polymorphic information content (PIC) values were 0.3748, 0.4998, and 0.4818, respectively. Finally, the 50 identified SNPs were used to estimate paternity for the remaining 938 of 1074 bulls from 23 farms. Our results revealed that 76.75% of the 938 bulls were assigned parentage to the pedigree sires with 95% confidence, and the rate of pedigree record mistakes ranged from 9.52%-39.29% in different herds. Our study is the first attempt to provide valuable insights into the extraction of informative markers through the application of high-density SNP chips for paternity testing in Chinese Simmental cattle.

The cost-benefit of genomic testing of heifers and using sexed semen in pasture-based dairy herds

Recent improvements in dairy cow fertility and female reproductive technologies offer an opportunity to apply greater selection pressure to females. This means there may be greater incentive to obtain genomic breeding values for females. We modeled the impact of changes to key parameters on the net benefit from genomic testing of heifer calves with and without usage of sexed semen. This paper builds on earlier cost-benefit studies but uses parameters relevant to pasture-based systems. A deterministic model was used to evaluate the effect on net benefit due to changes in (1) reproduction rate, (2) genomic test costs, (3) availability of parent-derived breeding values (EBV_PA), and (4) replacement rate. When the use of sexed semen was included, we also considered (1) the proportion of heifers and cows mated to sexed semen, (2) decreases in conception rate in inseminations with sexed semen, and (3) the marginal return for surplus heifers. Scenarios with lower replacement rates and no availability of EBV_PA had the largest net benefits. Under current Australian parameters, the net benefit of genomic testing realized over the lifetime of genotyped heifers is expected to range from A$204 to A$1,124 per 100 cows for a herd with median reproductive performance. The cost of a genomic test, a perceived barrier to many farmers, had only a small effect on net benefit. Genomic testing alone was always more profitable than using sexed semen and genomic testing together if the only benefit considered was increased genetic gain in heifer replacements. When other benefits (i.e., the higher sale price of a surplus heifer compared with a male calf) were considered, there were combinations of parameters where net benefit from using sexed semen and genomic testing was higher than the equivalent scenario with genomic testing only. Using sexed semen alongside genomic testing is most likely to be profitable when (1) used in heifers, (2) the marginal return for selling surplus heifers (sale price minus rearing costs) is greater than A$400, and (3) conception rates of no more than 10 percentage points lower than those achieved using conventional semen can be realized. Net benefit was highly dependent on the marginal return. Demonstrating that the initial investment in genomic testing can be recouped within the lifetime of the heifers tested may assist in the development of extension messages to explain the value of genomic testing females at the herd level.

Mutation responsible for congenital photosensitivity and hyperbilirubinemia in Southdown sheep

OBJECTIVE To identify the genetic cause for congenital photosensitivity and hyperbilirubinemia (CPH) in Southdown sheep. ANIMALS 73 Southdown sheep from a CPH research flock and 48 sheep of various breeds from commercial flocks without CPH. PROCEDURES Whole-genome sequencing was performed for a phenotypically normal Southdown sheep heterozygous for CPH. Heterozygous variants within Slco1b3 coding exons were identified, and exons that contained candidate mutations were amplified by PCR assay methods for Sanger sequencing. Blood samples from the other 72 Southdown sheep of the CPH research flock were used to determine plasma direct and indirect bilirubin concentrations. Southdown sheep with a plasma total bilirubin concentration < 0.3 mg/dL were classified as controls, and those with a total bilirubin concentration ≥ 0.3 mg/dL and signs of photosensitivity were classified as mutants. Sanger sequencing was used to determine the Slco1b3 genotype for all sheep. Genotypes were compared between mutants and controls of the CPH research flock and among all sheep. Protein homology was measured across 8 species to detect evolutionary conservation of Slco1b. RESULTS A nonsynonymous mutation at ovine Chr3:193,691,195, which generated a glycine-to-arginine amino acid change within the predicted Slco1b3 protein, was significantly associated with hyperbilirubinemia and predicted to be deleterious. That amino acid was conserved across 7 other mammalian species. CONCLUSIONS AND CLINICAL RELEVANCE Results suggested a nonsynonymous mutation in Slco1b3 causes CPH in Southdown sheep. This disease appears to be similar to Rotor syndrome in humans. Sheep with CPH might be useful animals for Rotor syndrome research.

SNP Data Quality Control in a National Beef and Dairy Cattle System and Highly Accurate SNP Based Parentage Verification and Identification

A major use of genetic data is parentage verification and identification as inaccurate pedigrees negatively affect genetic gain. Since 2012 the international standard for single nucleotide polymorphism (SNP) verification in Bos taurus cattle has been the ISAG SNP panels. While these ISAG panels provide an increased level of parentage accuracy over microsatellite markers (MS), they can validate the wrong parent at ≤1% misconcordance rate levels, indicating that more SNP are needed if a more accurate pedigree is required. With rapidly increasing numbers of cattle being genotyped in Ireland that represent 61 B. taurus breeds from a wide range of farm types: beef/dairy, AI/pedigree/commercial, purebred/crossbred, and large to small herd size the Irish Cattle Breeding Federation (ICBF) analyzed different SNP densities to determine that at a minimum ≥500 SNP are needed to consistently predict only one set of parents at a ≤1% misconcordance rate. For parentage validation and prediction ICBF uses 800 SNP (ICBF800) selected based on SNP clustering quality, ISAG200 inclusion, call rate (CR), and minor allele frequency (MAF) in the Irish cattle population. Large datasets require sample and SNP quality control (QC). Most publications only deal with SNP QC via CR, MAF, parent-progeny conflicts, and Hardy-Weinberg deviation, but not sample QC. We report here parentage, SNP QC, and a genomic sample QC pipelines to deal with the unique challenges of >1 million genotypes from a national herd such as SNP genotype errors from mis-tagging of animals, lab errors, farm errors, and multiple other issues that can arise. We divide the pipeline into two parts: a Genotype QC and an Animal QC pipeline. The Genotype QC identifies samples with low call rate, missing or mixed genotype classes (no BB genotype or ABTG alleles present), and low genotype frequencies. The Animal QC handles situations where the genotype might not belong to the listed individual by identifying: >1 non-matching genotypes per animal, SNP duplicates, sex and breed prediction mismatches, parentage and progeny validation results, and other situations. The Animal QC pipeline make use of ICBF800 SNP set where appropriate to identify errors in a computationally efficient yet still highly accurate method.

Justification for setting the individual animal genotype call rate threshold at eighty-five percent

Data quality of SNP arrays impacts the accuracy and precision of downstream data analyses. One such quality control measure often imposed is a threshold on individual animal call rate. Different call rate thresholds have been applied across studies; little is known, however, about the impact of these thresholds on the quality of the genotype data. The objective of the present study was to investigate the effect of different call rate thresholds on the integrity of the genotypes but also to quantify the contribution of different factors to the variability in animal call rate. Data included 142,342 samples genotyped on a custom Illumina genotype panel from 141,591 dairy and beef cattle; the number of Illumina SNP on the panel was 14,371. The mean animal call rate across all samples was 99.09%; 487 animals had both a low call rate (<99%) and a subsequent high call rate (≥99%) after resampling and regenotyping. Several factors were associated ( < 0.001) with individual call rate including animal sex, the sampling herd, the date of genotyping, the genotyping plate, and the plate well. The genotype and allele concordance between the genotypes of the 487 low- and high-call rate individuals improved at a diminishing rate as mean animal call rate increased. Mean genotype and allele concordance rates of 0.987 and 0.997, respectively, existed when animal call rate was between 85 and 90%, increasing to 0.998 and 0.999, respectively, when animal call rate was between 95 and <99%. The mean within-animal allele concordance rate of rare variants (i.e., minor allele frequency < 0.05) between low and high genotype call rate animals increased when animal call rate improved; an allele concordance rate of 1.00 was achieved when animal call rate was between 85 and <99%. The accuracy of imputation of the nonobserved genotypes in the low-call rate animals improved as animal call rate increased; the mean genotype concordance rate of the imputed nonobserved SNP was 0.41 when animal call rate was <40% but increased to 0.95 when animal call rate was between 95 and <99%. Parentage validation, determined by the count of opposing homozygotes in a parent-progeny pair, was unreliable when animal call rate was <85%. Therefore, to ensure the provision of high-quality genotypes while also considering the cost and inconvenience of resampling and regenotyping, we suggest a minimum animal call rate threshold of 85%.

Genetic Parameters and the Impact of Off-Types for Theobroma cacao L. in a Breeding Program in Brazil

Breeding programs of cacao (Theobroma cacao L.) trees share the many challenges of breeding long-living perennial crops, and genetic progress is further constrained by both the limited understanding of the inheritance of complex traits and the prevalence of technical issues, such as mislabeled individuals (off-types). To better understand the genetic architecture of cacao, in this study, 13 years of phenotypic data collected from four progeny trials in Bahia, Brazil were analyzed jointly in a multisite analysis. Three separate analyses (multisite, single site with and without off-types) were performed to estimate genetic parameters from statistical models fitted on nine important agronomic traits (yield, seed index, pod index, % healthy pods, % pods infected with witches broom, % of pods other loss, vegetative brooms, diameter, and tree height). Genetic parameters were estimated along with variance components and heritabilities from the multisite analysis, and a trial was fingerprinted with low-density SNP markers to determine the impact of off-types on estimations. Heritabilities ranged from 0.37 to 0.64 for yield and its components and from 0.03 to 0.16 for disease resistance traits. A weighted index was used to make selections for clonal evaluation, and breeding values estimated for the parental selection and estimation of genetic gain. The impact of off-types to breeding progress in cacao was assessed for the first time. Even when present at <5% of the total population, off-types altered selections by 48%, and impacted heritability estimations for all nine of the traits analyzed, including a 41% difference in estimated heritability for yield. These results show that in a mixed model analysis, even a low level of pedigree error can significantly alter estimations of genetic parameters and selections in a breeding program.

Milk Production and Fertility in Cattle

Evolutionary biology provides reasons for why the intensive selection for milk production reduces reproductive success rates. There is considerable exploitable genetic variation in reproductive performance in both dairy and beef cattle, and examination of national genetic trends demonstrates that genetic gain for both reproductive performance and milk production is possible in a well-structured breeding program. Reproductive failure is often postulated to be a consequence of the greater negative energy balance associated with the genetic selection for increased milk production. However, experimental results indicate that the majority of the decline in reproductive performance cannot be attributed to early lactation energy balance, per se; reproductive success will, therefore, not be greatly improved by nutritional interventions aimed at reducing the extent of negative energy balance. Modeling can aid in better pinpointing the key physiological components governing reproductive success and, also, the impact of individual improvements on overall fertility, helping to prioritize variables for inclusion in breeding programs.

Factors associated with the differential in actual gestational age and gestational age predicted from transrectal ultrasonography in pregnant dairy cows

The objective of the study was to determine (1) how gestational age predicted using transrectal ultrasonography related to actual gestational age derived as the number of days from the most recent artificial insemination date, (2) what factors, if any, were associated with the differential between the two measures, and (3) the association between this differential in gestational age and the likelihood of subsequent pregnancy loss, stillbirth, or calving dystocia. The data set contained 7340 ultrasound records from 6805 Holstein Friesian dairy cows in 175 herds. Ultrasonography assessment underestimated gestational age relative to days since last service by 0.51 days (standard error [SE]: 0.040), although the differential was less during embryonic development phase (i.e., ≤42 days of gestation; mean overestimation of 0.31 days) versus fetal development phase (i.e., >42 days of gestation; mean underestimation of 0.81 days). Predicted calving date calculated from ultrasonography was 1.41 days (SE: 0.040) later than the actual subsequent calving date and was, on average, 0.52 days later than predicted calving date, assuming a gestation length of 282 days. Parity of the dam (P < 0.05), stage of pregnancy (P < 0.001), and sex of the calf born (P < 0.001) were all associated with the differential in gestational age based on ultrasonography versus days since last service. No obvious trend among parities was evident in the difference between the methods in predicting gestational age. Ultrasonography underestimated gestational age by 0.83 (SE: 0.15) days in parity 5+ cows and underestimated gestational age by 0.41 (SE: 0.14) days in the first-parity cows. Relative to gestational age predicted from the most recent service, ultrasonography underestimated gestational age by 0.75 (SE: 0.13) days for heifer fetuses and underestimated gestational age by 0.36 (SE: 0.13) days for bull fetuses. The heritability of the differential in gestational age between the methods of prediction was low 0.05 (SE: 0.022), corroborating heritability estimates for most cow reproductive traits. Overestimation of gestational age using ultrasonography was associated with an increased likelihood of pregnancy loss (P < 0.001). Gender of calf born (P < 0.001), sire breed of calf (P < 0.001), and parity (P < 0.001) were all associated with gestation length. Gestation length was 1.27 days longer (SE: 0.01) for bull calves compared to heifer calves. Calves from beef sires had a longer gestation length than calves from dairy sires, and older parity cows had a longer gestation length than younger cows. The results highlight factors associated with differences in gestational age obtained from ultrasonography and insemination data and illustrate the value of ultrasonography for the prediction of calving date and pregnancy loss.

The contribution of migrant breeds to the genetic gain of beef traits of German Vorderwald and Hinterwald cattle

During the past decades, migrant contributions have accumulated in many local breeds. Cross-breeding was carried out to mitigate the risk of inbreeding depression and to improve the performance of local breeds. However, breeding activities for local breeds were not as intensive and target oriented as for popular high-yielding breeds. Therefore, even if performance improved, the gap between the performance of local and popular breeds increased for many traits. Furthermore, the genetic originality of local breeds declined due to the increasing contributions of migrant breeds. This study examined the importance of migrant breed influences for the realization of breeding progress of beef traits of German Vorderwald and Hinterwald cattle. The results show that there is a high amount of migrant contributions and their effects on performance are substantial for most traits. The effect of the French cattle breed Montbéliard (p-value 0.014) on daily gain of Vorderwald bulls at test station was positive. The effects of Vorderwald ancestors (p-value for daily gain 0.007 and p-value for net gain 0.004) were positive for both traits under consideration in the population of Hinterwald cattle. Additionally, the effect of remaining breeds (p-value 0.030) on net gain of Hinterwald cattle in the field was also positive. The estimated effect of Fleckvieh ancestors on net gain of Hinterwald cattle was even larger but not significant. Breeding values adjusted for the effects of the migrant breeds showed little genetic trend.

A high throughput single nucleotide polymorphism multiplex assay for parentage assignment in New Zealand sheep

Accurate pedigree information is critical to animal breeding systems to ensure the highest rate of genetic gain and management of inbreeding. The abundance of available genomic data, together with development of high throughput genotyping platforms, means that single nucleotide polymorphisms (SNPs) are now the DNA marker of choice for genomic selection studies. Furthermore the superior qualities of SNPs compared to microsatellite markers allows for standardization between laboratories; a property that is crucial for developing an international set of markers for traceability studies. The objective of this study was to develop a high throughput SNP assay for use in the New Zealand sheep industry that gives accurate pedigree assignment and will allow a reduction in breeder input over lambing. This required two phases of development- firstly, a method of extracting quality DNA from ear-punch tissue performed in a high throughput cost efficient manner and secondly a SNP assay that has the ability to assign paternity to progeny resulting from mob mating. A likelihood based approach to infer paternity was used where sires with the highest LOD score (log of the ratio of the likelihood given parentage to likelihood given non-parentage) are assigned. An 84 “parentage SNP panel” was developed that assigned, on average, 99% of progeny to a sire in a problem where there were 3,000 progeny from 120 mob mated sires that included numerous half sib sires. In only 6% of those cases was there another sire with at least a 0.02 probability of paternity. Furthermore dam information (either recorded, or by genotyping possible dams) was absent, highlighting the SNP test’s suitability for paternity testing. Utilization of this parentage SNP assay will allow implementation of progeny testing into large commercial farms where the improved accuracy of sire assignment and genetic evaluations will increase genetic gain in the sheep industry.

Validation of a microsatellite panel for parentage testing of locally adapted and commercial goats in Brazil

Brazilian goats are generally kept in small herds and extensive rearing systems, mainly in the northeastern region of the country. Despite production improvement in recent years, the lack of pedigree control has affected genetic progress. This study aimed to validate a panel of 16 microsatellites for parentage testing in locally adapted and commercial goats breeds raised in Brazil, as well as to compare its efficiency with the panel recommended by the Brazilian Ministry of Agriculture, Livestock and Supplies (MAPA) in 2004. The number of alleles and expected heterozygosity (He) per marker ranged from four to 18, and from 0.051 to 0.831, respectively. Using all markers, 100% of parentage cases of the validation dataset were resolved with a strict confidence level of 95%. The 16 microsatellites panel showed adequate exclusion power (99.99%) and identity accuracy (99.99%). Suggestions for improvement of the marker panel endorsed by MAPA are provided.

A nonsense mutation in TMEM95 encoding a nondescript transmembrane protein causes idiopathic male subfertility in cattle

Genetic variants underlying reduced male reproductive performance have been identified in humans and model organisms, most of them compromising semen quality. Occasionally, male fertility is severely compromised although semen analysis remains without any apparent pathological findings (i.e., idiopathic subfertility). Artificial insemination (AI) in most cattle populations requires close examination of all ejaculates before insemination. Although anomalous ejaculates are rejected, insemination success varies considerably among AI bulls. In an attempt to identify genetic causes of such variation, we undertook a genome-wide association study (GWAS). Imputed genotypes of 652,856 SNPs were available for 7962 AI bulls of the Fleckvieh (FV) population. Male reproductive ability (MRA) was assessed based on 15.3 million artificial inseminations. The GWAS uncovered a strong association signal on bovine chromosome 19 (P = 4.08×10⁻⁵⁹). Subsequent autozygosity mapping revealed a common 1386 kb segment of extended homozygosity in 40 bulls with exceptionally poor reproductive performance. Only 1.7% of 35,671 inseminations with semen samples of those bulls were successful. None of the bulls with normal reproductive performance was homozygous, indicating recessive inheritance. Exploiting whole-genome re-sequencing data of 43 animals revealed a candidate causal nonsense mutation (rs378652941, c.483C>A, p.Cys161X) in the transmembrane protein 95 encoding gene TMEM95 which was subsequently validated in 1990 AI bulls. Immunohistochemical investigations evidenced that TMEM95 is located at the surface of spermatozoa of fertile animals whereas it is absent in spermatozoa of subfertile animals. These findings imply that integrity of TMEM95 is required for an undisturbed fertilisation. Our results demonstrate that deficiency of TMEM95 severely compromises male reproductive performance in cattle and reveal for the first time a phenotypic effect associated with genomic variation in TMEM95.

Impaired male fertility is a prevalent condition in many species and is often explained by aberrant semen quality. In some cases, male fertility is severely compromised although semen quality is without any apparent pathological findings (i.e., idiopathic male subfertility). The genetic mechanisms underlying idiopathic male subfertility often remain unexplained. In the present paper, we report a recessively inherited variant of idiopathic male subfertility in a cattle population. We use 650,000 genome-wide SNP markers genotyped in >7900 artificial insemination bulls to pinpoint the underlying genomic region. We take advantage of whole-genome re-sequencing data of 43 animals to identify a causal loss-of-function mutation in TMEM95 encoding a nondescript transmembrane protein. We demonstrate that transmembrane protein 95 is located at the plasma membrane of spermatozoa of fertile animals whereas it is absent in spermatozoa of subfertile animals. Our results indicate that integrity of transmembrane protein 95 is required for an undisturbed fertilisation. This is the first report to reveal a phenotypic effect associated with genomic variation in TMEM95 in any organism.

Pedigree error due to extra-pair reproduction substantially biases estimates of inbreeding depression

Understanding the evolutionary dynamics of inbreeding and inbreeding depression requires unbiased estimation of inbreeding depression across diverse mating systems. However, studies estimating inbreeding depression often measure inbreeding with error, for example, based on pedigree data derived from observed parental behavior that ignore paternity error stemming from multiple mating. Such paternity error causes error in estimated coefficients of inbreeding (f) and reproductive success and could bias estimates of inbreeding depression. We used complete "apparent" pedigree data compiled from observed parental behavior and analogous "actual" pedigree data comprising genetic parentage to quantify effects of paternity error stemming from extra-pair reproduction on estimates of f, reproductive success, and inbreeding depression in free-living song sparrows (Melospiza melodia). Paternity error caused widespread error in estimates of f and male reproductive success, causing inbreeding depression in male and female annual and lifetime reproductive success and juvenile male survival to be substantially underestimated. Conversely, inbreeding depression in adult male survival tended to be overestimated when paternity error was ignored. Pedigree error stemming from extra-pair reproduction therefore caused substantial and divergent bias in estimates of inbreeding depression that could bias tests of evolutionary theories regarding inbreeding and inbreeding depression and their links to variation in mating system.

Confirmation and discovery of maternal grandsires and great-grandsires in dairy cattle

Selection, mating, and improvement of dairy animals have required accurate pedigrees. Genomic tools allow paternal ancestors to be easily confirmed or discovered because most sires are genotyped for many markers, but maternal ancestors are more difficult to discover because most female ancestors are not genotyped. Three methods to discover maternal grandsires (MGS) were developed and compared. Conflicts were counted one single nucleotide polymorphism (SNP) at a time between genotypes of the animal and potential MGS (duo method) or also using the sire's genotype (trio method). Alternatively, haplotypes of a potential MGS were matched to the animal's maternal haplotype, obtained by using linkage across loci (HAP method). The duo and trio methods can be performed as soon as a genotype is received because no imputation is required. The HAP method improved accuracy because genotypes with 2,683 (3 K) SNP were imputed to the 45,187 (50K) SNP used for genomic evaluation. The HAP method was tested using modified pedigrees with 5% of true MGS replaced by a random genotyped bull from the same birth year and 5% of MGS set to missing for 4,134 Holsteins, 552 Jerseys, and 142 Brown Swiss that had confirmed, genotyped sires. Those same animals were used to test the duo and trio methods, except that some animals had multiple genotypes and imputed dams were excluded. Accuracy measured how often the correct MGS was selected from among 12,152 genotyped Holstein, 2,265 Jersey, and 1,605 Brown Swiss potential MGS. Accuracies were 61, 60, and 65%, respectively, with the duo method; 95, 91, and 94% with the trio method; and 97, 95, and 97% with the HAP method. Accuracy of the duo method was poor (only 52% for animals genotyped with 3 K and 65% with 50K) because additional information from the paternal genotype is not used. Accuracy of the trio method was 97% with 50K but only 78% with 3K because the missing SNP were not imputed. Accuracy of the HAP method was 94% with 3 K genotypes, 98% with 50K, and 92% with nongenotyped, imputed dams. When the HAP method was extended to great-grandsires, the accuracy of maternal great-grandsire discovery was 92% for 652 Holsteins, 95% for 33 Jerseys, and 85% for 20 Brown Swiss. Accuracy was even higher using simulated genotypes. Because most dairy bulls over several generations have been genotyped, percentages of haplotypes shared with candidate males can accurately confirm, correct, or discover the sires, MGS, and even more distant ancestors of most animals.

Short communication: evaluation of bovine milk residues from routine milk testing programs as DNA source for genotyping

Genome-wide association studies and genomic evaluation using a dense set of genetic markers both require a large number of genotyped individuals. Collection of the respective samples contributes substantially to the cost of the approach. In dairy cattle research, the use of residues from routine milk recording would be a cost-saving alternative to obtain samples for an appropriate number of individuals with specific phenotypes in a very short time. To assess the suitability of milk recording residues, we concurrently investigated milk residues obtained after standardized milk recording procedures and blood samples from 115 cows originating from 3 farms with different milking systems by genotyping 15 microsatellite markers. We found that 4% of the milk samples were possibly assigned to the wrong animal (i.e., conflicts) and that at least 27% of the milk residues were contaminated, as indicated by an extra allele not present in the blood sample. These additional alleles primarily originated from a sample with a higher somatic cell score that went through the milk sample analyzer in the milk laboratory before the target sample. Furthermore, additional allele carryover was observed across more than one sample, when the difference in somatic cell count between samples exceeded 100,000 cells/mL. Finally, in several samples, the extra allele could not be traced back to previous samples passing through the milk sample analyzer. One source of those contaminations might be sample collection on-farm due to milk traces from the previously milked cow in the hose. No correlation was found between the farm management and conflicts or contaminations. We conclude that residues from routine milk recording are not suitable for genomic evaluation or genome-wide association studies because of the high prevalence of contamination generated at several steps during the collection and processing of milk residual samples.