Searching for homozygous haplotype deficiency in Manech Tête Rousse dairy sheep revealed a nonsense variant in the MMUT gene affecting newborn lamb viability.

BACKGROUND: Recessive deleterious variants are known to segregate in livestock populations, as in humans, and some may be lethal in the homozygous state. RESULTS: We used phased 50 k single nucleotide polymorphism (SNP) genotypes and pedigree data to scan the genome of 6845 Manech Tête Rousse dairy sheep to search for deficiency in homozygous haplotypes (DHH). Five Manech Tête Rousse deficient homozygous haplotypes (MTRDHH1 to 5) were identified, with a homozygous deficiency ranging from 84 to 100%. These haplotypes are located on Ovis aries chromosome (OAR)1 (MTRDHH2 and 3), OAR10 (MTRDHH4), OAR13 (MTRDHH5), and OAR20 (MTRDHH1), and have carrier frequencies ranging from 7.8 to 16.6%. When comparing at-risk matings between DHH carriers to safe matings between non-carriers, two DHH (MTRDHH1 and 2) were linked with decreased insemination success and/or increased stillbirth incidence. We investigated the MTRDHH1 haplotype, which substantially increased stillbirth rate, and identified a single nucleotide variant (SNV) inducing a premature stop codon (p.Gln409*) in the methylmalonyl-CoA mutase (MMUT) gene by using a whole-genome sequencing approach. We generated homozygous lambs for the MMUT mutation by at-risk mating between heterozygous carriers, and most of them died within the first 24 h after birth without any obvious clinical symptoms. Reverse transcriptase-qPCR and western blotting on post-mortem liver and kidney biological samples showed a decreased expression of MMUT mRNA in the liver and absence of a full-length MMUT protein in the mutant homozygous lambs. CONCLUSIONS: We identified five homozygous deficient haplotypes that are likely to harbor five independent deleterious recessive variants in sheep. One of these was detected in the MMUT gene, which is associated with lamb lethality in the homozygous state. A specific management of these haplotypes/variants in the MTR dairy sheep selection program would help enhance the overall fertility and lamb survival.

Unfavorable genetic correlations between fecal egg count and milk production traits in the French blond-faced Manech dairy sheep breed.

BACKGROUND: Genetic selection has proven to be a successful strategy for the sustainable control of gastrointestinal parasitism in sheep. However, little is known on the relationship between resistance to parasites and production traits in dairy breeds. In this study, we estimated the heritabilities and genetic correlations for resistance to parasites and milk production traits in the blond-faced Manech breed. The resistance to parasites of 951 rams from the selection scheme was measured through fecal egg counts (FEC) at 30 days post-infection under experimental conditions. Six milk production traits [milk yield (MY), fat yield (FY), protein yield (PY), fat content (FC), protein content (PC) and somatic cell score (LSCS)], were used in this study and were collected on 140,127 dairy ewes in first lactation, as part of the official milk recording. These ewes were related to the 951 rams (65% of the ewes were daughters of the rams). RESULTS: Fecal egg counts at the end of the first and second infections were moderately heritable (0.19 and 0.37, respectively) and highly correlated (0.93). Heritabilities were moderate for milk yields (ranging from 0.24 to 0.29 for MY, FY and PY) and high for FC (0.35) and PC (0.48). MY was negatively correlated with FC and PC (- 0.39 and - 0.45, respectively). FEC at the end of the second infection were positively correlated with MY, FY and PY (0.28, 0.29 and 0.24, respectively with standard errors of ~ 0.10). These slightly unfavorable correlations indicate that the animals with a high production potential are genetically more susceptible to gastrointestinal parasite infections. A low negative correlation (- 0.17) was also found between FEC after the second infection and LSCS, which suggests that there is a small genetic antagonism between resistance to gastrointestinal parasites and resistance to mastitis, which is another important health trait in dairy sheep. CONCLUSIONS: Our results indicate an unfavorable but low genetic relationship between resistance to gastrointestinal parasites and milk production traits in the blond-faced Manech breed. These results will help the breeders' association make decisions about how to include resistance to parasites in the selection objective.

Identification of homozygous haplotypes carrying putative recessive lethal mutations that compromise fertility traits in French Lacaune dairy sheep.

BACKGROUND: Homozygous recessive deleterious mutations can cause embryo/fetal or neonatal lethality, or genetic defects that affect female fertility and animal welfare. In livestock populations under selection, the frequency of such lethal mutations may increase due to inbreeding, genetic drift, and/or the positive pleiotropic effects of heterozygous carriers on selected traits. RESULTS: By scanning the genome of 19,102 Lacaune sheep using 50 k single nucleotide polymorphism (SNP) phased genotypes and pedigree data, we identified 11 Lacaune deficient homozygous haplotypes (LDHH1 to LDHH11) showing a highly significant deficit of homozygous animals ranging from 79 to 100%. These haplotypes located on chromosomes 3, 4, 13, 17 and 18, spanned regions from 1.2 to 3.0 Mb long with a frequency of heterozygous carriers between 3.7 and 12.1%. When we compared at-risk matings (between carrier rams and daughters of carrier rams) and safe matings, seven of the 11 haplotypes were associated with a significant alteration of two fertility traits, a reduced success of artificial insemination (LDHH1, 2, 8 and 9), and/or an increased stillbirth rate (LDHH3, 6, 8, 9, and 10). The 11 haplotypes were also tested for a putative selective advantage of heterozygous carrier rams based on their daughter yield deviation for six dairy traits (milk, fat and protein yields, fat and protein contents and lactation somatic cell score). LDHH1, 3, 4, 5, 7, 9 and 11 were associated with positive effects on at least one selected dairy trait, in particular milk yield. For each haplotype, the most probable candidate genes were identified based on their roles in lethality of mouse knock-out models and in mammalian genetic disorders. CONCLUSIONS: Based on a reverse genetic strategy, we identified at least 11 haplotypes with homozygous deficiency segregating in French Lacaune dairy sheep. This strategy represents a first tool to limit at-risk matings in the Lacaune dairy selection scheme. We assume that most of the identified LDHH are in strong linkage disequilibrium with a recessive lethal mutation that affects embryonic or juvenile survival in sheep but is yet to be identified.

Bias and accuracy of dairy sheep evaluations using BLUP and SSGBLUP with metafounders and unknown parent groups.

BACKGROUND: Bias has been reported in genetic or genomic evaluations of several species. Common biases are systematic differences between averages of estimated and true breeding values, and their over- or under-dispersion. In addition, comparing accuracies of pedigree versus genomic predictions is a difficult task. This work proposes to analyse biases and accuracies in the genetic evaluation of milk yield in Manech Tête Rousse dairy sheep, over several years, by testing five models and using the estimators of the linear regression method. We tested models with and without genomic information [best linear unbiased prediction (BLUP) and single-step genomic BLUP (SSGBLUP)] and using three strategies to handle missing pedigree [unknown parent groups (UPG), UPG with QP transformation in the [Formula: see text] matrix (EUPG) and metafounders (MF)]. METHODS: We compared estimated breeding values (EBV) of selected rams at birth with the EBV of the same rams obtained each year from the first daughters with phenotypes up to 2017. We compared within and across models. Finally, we compared EBV at birth of the rams with and without genomic information. RESULTS: Within models, bias and over-dispersion were small (bias: 0.20 to 0.40 genetic standard deviations; slope of the dispersion: 0.95 to 0.99) except for model SSGBLUP-EUPG that presented an important over-dispersion (0.87). The estimates of accuracies confirm that the addition of genomic information increases the accuracy of EBV in young rams. The smallest bias was observed with BLUP-MF and SSGBLUP-MF. When we estimated dispersion by comparing a model with no markers to models with markers, SSGBLUP-MF showed a value close to 1, indicating that there was no problem in dispersion, whereas SSGBLUP-EUPG and SSGBLUP-UPG showed a significant under-dispersion. Another important observation was the heterogeneous behaviour of the estimates over time, which suggests that a single check could be insufficient to make a good analysis of genetic/genomic evaluations. CONCLUSIONS: The addition of genomic information increases the accuracy of EBV of young rams in Manech Tête Rousse. In this population that has missing pedigrees, the use of UPG and EUPG in SSGBLUP produced bias, whereas MF yielded unbiased estimates, and we recommend its use. We also recommend assessing biases and accuracies using multiple truncation points, since these statistics are subject to random variation across years.

Alternative methods improve the accuracy of genomic prediction using information from a causal point mutation in a dairy sheep model.

BACKGROUND: Genomic evaluation is usually based on a set of markers assumed to be linked with causal mutations. Selection and precise management of major genes and the remaining polygenic component might be improved by including causal polymorphisms in the evaluation models. In this study, various methods involving a known mutation were used to estimate prediction accuracy. The SOCS2 gene, which influences body growth, milk production and somatic cell scores, a proxy for mastitis, was studied as an example in dairy sheep. METHODS: The data comprised 1,503,148 phenotypes and 9844 54K SNPs genotypes. The SOCS2 SNP was genotyped for 4297 animals and imputed in the above 9844 animals. Breeding values and their accuracies were estimated for each of nine traits by using single-step approaches. Pedigree-based BLUP, single-step genomic BLUP (ssGBLUP) involving the 54K ovine SNPs chip, and four weighted ssGBLUP (WssGBLUP) methods were compared. In WssGBLUP methods, weights are assigned to SNPs depending on their effect on the trait. The ssGBLUP and WssGBLUP methods were again tested after including the SOCS2 causal mutation as a SNP. Finally, the Gene Content approach was tested, which uses a multiple-trait model that considers the SOCS2 genotype as a trait. RESULTS: EBV accuracies were increased by 14.03% between the pedigree-based BLUP and ssGBLUP methods and by 3.99% between ssGBLUP and WssGBLUP. Adding the SOCS2 SNP to ssGBLUP methods led to an average gain of 0.26%. Construction of the kinship matrix and estimation of breeding values was generally improved by placing emphasis on SNPs in regions with a strong effect on traits. In the absence of chip data, the Gene Content method, compared to pedigree-based BLUP, efficiently accounted for partial genotyping information on SOCS2 as accuracy was increased by 6.25%. This method also allowed dissociation of the genetic component due to the major gene from the remaining polygenic component. CONCLUSIONS: Causal mutations with a moderate to strong effect can be captured with conventional SNP chips by applying appropriate genomic evaluation methods. The Gene Content method provides an efficient way to account for causal mutations in populations lacking genome-wide genotyping.

A validation study of loci associated with mastitis resistance in two French dairy sheep breeds.

BACKGROUND: The identification of loci associated with resistance to mastitis or of the causative mutations may be helpful in breeding programs for dairy sheep as it is for cattle worldwide. Seven genomic regions that control milk somatic cell counts, an indirect indicator of udder infection, have already been identified in sheep (Spanish Churra, French Lacaune and Italian Sardinian-Lacaune backcross populations). In this study, we used a 960 custom-designed ovine single nucleotide polymorphism (SNP) chip in Lacaune and Manech Tête Rousse dairy sheep to validate these seven genomic regions associated with mastitis. RESULTS: The most significant SNP (rs868996547) on Ovis aries chromosome (OAR) 3 was a previously described mutation in the suppressor of cytokine signalling 2 (SOCS2) gene. An antagonist effect of this causal candidate between health and growth in Lacaune sheep was confirmed. Effects of the mutation on the infectious status of the udder, i.e. increases in milk somatic cell counts and bacteria shedding, were also identified. This SNP was not present in the data available on Manech Tête Rousse. Three other regions associated with mastitis were also confirmed on OAR16 (Manech Tête Rousse), 19 (Lacaune) and 2 (both breeds). For the OAR2 region, we validated previously detected SNPs in several other breeds (Sarda, Churra, and Chios). For significant SNPs in the four mastitis regions, the effect varied from 0.24 to 0.67 phenotypic standard deviation of the traits. Two of the mastitis quantitative trait loci (QTL) regions (OAR2 and 16) that we validated here were also associated in opposite ways with milk production traits in both populations. CONCLUSIONS: These results indicate, at least in part, a genomic basis for the trade-off between milk production and mastitis resistance. Four of the seven mastitis QTL regions that were previously identified in independent populations, were confirmed in this study, which demonstrates partial sharing of mastitis-related genetic mechanisms between different distant dairy sheep populations.

Variation in Recombination Rate and Its Genetic Determinism in Sheep Populations.

Recombination is a complex biological process that results from a cascade of multiple events during meiosis. Understanding the genetic determinism of recombination can help to understand if and how these events are interacting. To tackle this question, we studied the patterns of recombination in sheep, using multiple approaches and data sets. We constructed male recombination maps in a dairy breed from the south of France (the Lacaune breed) at a fine scale by combining meiotic recombination rates from a large pedigree genotyped with a 50K SNP array and historical recombination rates from a sample of unrelated individuals genotyped with a 600K SNP array. This analysis revealed recombination patterns in sheep similar to other mammals but also genome regions that have likely been affected by directional and diversifying selection. We estimated the average recombination rate of Lacaune sheep at 1.5 cM/Mb, identified ∼50,000 crossover hotspots on the genome, and found a high correlation between historical and meiotic recombination rate estimates. A genome-wide association study revealed two major loci affecting interindividual variation in recombination rate in Lacaune, including the RNF212 and HEI10 genes and possibly two other loci of smaller effects including the KCNJ15 and FSHR genes. The comparison of these new results to those obtained previously in a distantly related population of domestic sheep (the Soay) revealed that Soay and Lacaune males have a very similar distribution of recombination along the genome. The two data sets were thus combined to create more precise male meiotic recombination maps in Sheep. However, despite their similar recombination maps, Soay and Lacaune males were found to exhibit different heritabilities and QTL effects for interindividual variation in genome-wide recombination rates. This highlights the robustness of recombination patterns to underlying variation in their genetic determinism.