Genome-wide association study of footrot in Texel sheep

Background

This is the first study based on a genome-wide association approach that investigates the links between ovine footrot scores and molecular polymorphisms in Texel sheep using the ovine 50 K SNP array (42 883 SNPs (single nucleotide polymorphisms) after quality control). Our aim was to identify molecular predictors of footrot resistance.

Methods

This study used data from animals selected from a footrot-phenotyped Texel sheep population of 2229 sheep with an average of 1.60 scoring records per animal. From these, a subset of 336 animals with extreme trait values for footrot was selected for genotyping based on their phenotypic records. De-regressed estimated breeding values (EBV) for footrot were used as pseudo-phenotypes in the genome-wide association analysis.

Results

Seven SNPs were significant on a chromosome-wise level but the association analysis did not reveal any genome-wise significant SNPs associated with footrot. Based on the current state of knowledge of the ovine genome, it is difficult to clearly link the function of the genes that contain these significant SNPs with a potential role in resistance/susceptibility to footrot. Linkage disequilibrium (LD) was analysed as one of the factors that influence the power of detecting QTL (quantitative trait loci). A mean LD of 0.20 (r² at a distance of 50 kb between two SNPs) in the population analysed was estimated. LD declined from 0.15 to 0.07 and to 0.04 at distances between two SNPs of 100, 1000 and 2000 kb, respectively.

Conclusions

Based on a relatively small number of genotyped animals, this study is a first step to search for genomic regions that are involved in resistance to footrot using the ovine 50 K SNP array. Seven SNPs were found to be significant on a chromosome-wise level. No major genome-wise significant QTL were identified.     

Genetic analyses of live weight and carcass composition traits in purebred Texel,Suffolk and Charollais lambs

Lamb live weight is one of the key drivers of profitability on sheep farms. Previous studies in Ireland have estimated genetic parameters for live weight and carcass composition traits using a multi-breed population rather than on an individual breed basis. The objective of the present study was to undertake genetic analyses of three lamb live weight and two carcass composition traits pertaining to purebred Texel, Suffolk and Charollais lambs born in the Republic of Ireland between 2010 and 2017, inclusive. Traits (with lamb age range in parenthesis) considered in the analyses were: pre-weaning weight (20 to 65 days), weaning weight (66 to 120 days), post-weaning weight (121 to 180 days), muscle depth (121 to 180 days) and fat depth (121 to 180 days). After data edits, 137 402 records from 50 372 lambs across 416 flocks were analysed. Variance components were derived using animal linear mixed models separately for each breed. Fixed effects included for all traits were contemporary group, age at first lambing of the dam, parity of the dam, a gender by age of the lamb interaction and a birth type by rearing type of the lamb interaction. Random effects investigated in the pre-weaning and weaning weight analyses included animal direct additive genetic, dam maternal genetic, litter common environment, dam permanent environment and residual variances. The model of analysis for post-weaning, muscle and fat depth included an animal direct additive genetic and litter common environment effect only. Significant direct additive genetic variation existed in all cases. Direct heritability for pre-weaning weight ranged from 0.14 to 0.30 across the three breeds. Weaning weight had a direct heritability ranging from 0.17 to 0.27 and post-weaning weight had a direct heritability ranging from 0.15 to 0.27. Muscle and fat depth heritability estimates ranged from 0.21 to 0.31 and 0.15 to 0.20, respectively. Positive direct correlations were evident for all traits. Results revealed ample genetic variation among animals for the studied traits and significant differences between breeds to suggest that genetic evaluations could be conducted on a per-breed basis.     

Auction price of Texel, Suffolk and German white-headed mutton rams: A genetic-statistical study

In this study, the impact of various traits and effects on auction price of Texel, Suffolk and German white-headed mutton rams was determined. Furthermore, (co)variance components between auction price and performance traits recorded at licensing were estimated. Data from 1988 to 2007 were extracted from the recording database of the Sheep Breeding Organisation in Schleswig-Holstein, Germany. Auction prices of 1133 Texel, 373 Suffolk and 341 German white-headed mutton rams from the year 2003 to 2007 were analysed. General Linear Models and Multiple Regression Analysis were used to identify the impact of traits and effects on the auction price. Estimation of (co)variance components was carried out using multivariate animal model. From the traits recorded at licensing, live weight, followed by type traits of conformation and muscle mass, had the highest impact on the auction price. Also the effects of breed, PrP (Prion Protein) genotype, and owner of the ram influenced the auction price of rams significantly. A moderate genetic contribution of auction price, with favourable genetic correlations to all collected performance traits (average daily gain from birth until licensing, muscle depth, fat depth, conformation, muscle mass and wool quality), was estimated. Genetic correlations were 0.42, 0.34, 0.17, 0.49, 0.39 and 0.23, respectively. The results showed a high influence of live weight of animal on auction price of the rams contrary to very low influence of carcass quality traits measured with ultrasound technology.     

Deleterious mutations are characterized by higher genomic heterozygosity than other genic variants in plant genomes

Deleterious mutations can reduce the fitness of crop varieties, which limits the plant breeding efficacy. While crop deleterious mutations have been extensively examined, most studies focused on one specific crop with different analyzing methods, which hinders unveiling shared genomic characteristics of deleterious mutations across diverse crops. Here we used standardized approaches to characterize the deleterious mutations in genomes of domesticated inbreeding (i.e., rice, soybean, and tomato) and clonally propagated crops (i.e., grape and pineapple). We found that deleterious mutations are commonly targeted by purifying selection, and are over-presented in a nearly fixed derived allele frequency in the course of plant domestication. Further, a generally negative correlation between genetic load and the artificial selection strength is observed. Importantly, we consistently uncovered the higher derived genomic heterozygosity for deleterious mutations compared to other genic variants. This study broadens our understanding of the evolution of deleterious mutations in plant genomes.     

澳大利亚萨福克羊及无角陶塞特羊对新疆的生态适应性及杂交后代利用研究

测定分析了新疆地区引入澳大利亚萨福克羊及无角陶塞特羊的体温、脉搏、呼吸频率、血清T₃、T₄含量、繁殖率、总适应能力及杂一代公羔的育肥屠宰性能.结果表明,萨福克羊及无角陶塞特羊繁殖率及体重接近或超过原产地澳大利亚的生产水平.萨福克羊总适应能力为98.80%,无角陶赛特羊为98.74%.杂一代公羔日增重、饲料转化率、净肉重较哈萨克羊高,而尾脂重低于哈萨克羊.     

澳大利亚萨福克羊及无角陶塞特羊对新疆的生态适应性及杂交后代利用研究

测量分析了新疆地区引入澳大利亚萨福克羊及无角陶塞特羊的体温、脉搏、呼吸频率、血清T3、T4含量、繁殖率、总适应能力及杂一代公羔的育肥屠宰性能,结果表明,萨福克羊及无角陶塞特羊繁殖率及体重接近或超过原产地澳大利亚的生产水平,萨福克羊总适应能力为98.80%,无角陶塞特羊为98.74%,杂一代公羔日增重、饲料转化率、净肉重较哈萨克羊高,而尾脂重低于哈萨克羊。     

A new transferrin allele in sheep

An electrophoretic variant of sheep transferrin, TfL, has been described. Transferrin L has been shown to be controlled by a single codominant allele, TfL, at the Tf locus. Transferrin L is electrophoretically distinguishable from the very similar transferrin TfKCzech. The value of gradient polyacrylamide gel electrophoresis for transferrin phenotyping in sheep is discussed.     

A new transferrin allele in sheep

Summary. An electrophoretic variant of sheep transferrin, TfL, has been described. Transferrin L has been shown to be controlled by a single codominant allele, TfL, at the Tf locus. Transferrin L is electrophoretically distinguishable from the very similar transferrin TfKCzech. The value of gradient polyacrylamide gel electrophoresis for transferrin phenotyping in sheep is discussed.     

Extensive genomic conservation of cattle microsatellite heterozygosity in sheep

We report the evaluation of 1036 bovine microsatellite primer pairs for their suitability as linkage markers in sheep. Approximately 58% (605/1036) of bovine primer pairs amplified a locus in sheep. Sixty-seven per cent (409/605) of amplified loci were detected as polymorphic. Marker heterozygosity, allele number and range of allele sizes were significantly lower in sheep than cattle sampled in this study. However, median fragment size was similar. These data suggest that high-resolution comparative linkage maps between closely related species can be constructed relatively efficiently.     

The distribution of transferrin and hemoglobin types in families of Suffolk and Targhee sheep1

Transferrin and hemoglobin types were determined for 2133 sheep (Suffolks, Targhees, and Suffolk × Targhee crossbreds) and gene frequencies were calculated. Analysis of ratios of hemoglobin types revealed a significant excess of lambs of hemoglobin B/B type in some matings. For transferrins, there was a deficiency of homozygotes for Tf^B in offspring of matings of Tf^B heterozygotes inter se.     

Loss of heterozygosity in tumor cells requires re-evaluation: the data are biased by the size-dependent differential sensitivity of allele detection

Normal tissue contamination of tumors may eclipse the detection of loss of heterozygosity (LOH) by microsatellite analysis and may also hamper isolation of tumor suppressor genes. To test the potential impact of this problem, we prepared artificial mixtures of mouse-human microcell hybrid lines that carried different alleles of the same chromosome 3 marker. After performing an allele titration assay, we found a consistent difference between the LOH of a high molecular weight (H) allele and the LOH of a low molecular weight (L) allele of the same CA repeat marker. It follows that normal tissue admixtures will be less of a problem when LOH affects a H allele than with a L allele. Random screening of 100 papers published between 1994 and 1999 revealed that the loss of a L allele was recorded at about half the frequency (52%) of loss of a H allele. To avoid this bias, we have developed rules for the evaluation of LOH data. We suggest that the loss of a L allele should be given more weight than the loss of a H allele in LOH studies using microsatellite markers.     

In a shake of a lamb's tail: using genomics to unravel a cause of chondrodysplasia in Texel sheep

Chondrodysplasia in Texel sheep is a recessively inherited disorder characterized by dwarfism and angular deformities of the forelimbs. A genome-wide association study using the Illumina OvineSNP50 BeadChip on 15 sheep diagnosed as affected and eight carriers descended from three affected rams was conducted to uncover the genetic cause. A homozygous region of 25 consecutive single nucleotide polymorphism (SNP) loci was identified in all affected sheep, covering a region of 1 Mbp on ovine chromosome 4. Seven positional candidate genes - including the solute carrier family 13 (sodium/sulphate symporters), member 1 (SLC13A1) - were identified and used to search for new SNPs for fine mapping of the causal locus. The SLC13A1 gene, encoding a sodium/sulphate transporter, was the primary candidate gene attributable to similar phenotypes observed in the Slc13a1 knockout mouse model. We discovered a 1-bp deletion of T (g.25513delT) at the 107 bp position of exon 3 in the SLC13A1 gene. Genotyping by direct sequencing and restriction fragment length polymorphism analysis for this mutation showed that all 15 affected sheep were g.25513delT/g.25513delT; the eight carriers were g.25513delT/T and 54 normal controls were T/T. The mutation g.25513delT shifts the open reading frame of SLC13A1 to introduce a stop codon and truncate C-terminal amino acids. It was concluded that the g.25513delT mutation in the SLC13A1 gene was responsible for the chondrodysplasia seen in these Texel sheep. This knowledge can be used to identify carriers with the defective g.[25513delT] allele to avoid at-risk matings to improve animal welfare and decrease economic losses.     

Growth,carcass and cooked meat characteristics of lambs sired by Dorset rams heterozygous for the Callipyge gene and Suffolk and Texel rams

Dorset (D) rams heterozygous for the Callipyge gene were single—sire mated to non-carrier ewes to produce Callipyge heterozygous (CLPG, n = 49) and normal (D, n = 33) lambs. Suffolk (S) and Texel (T) rams were mated to similar ewes to produce non-carrier crossbred S (n = 55) and T (n = 52) lambs. Lambs were finished on a high-energy diet to a target live weight of 57 kg. Pre-slaughter weight was recorded for each lamb prior to its transfer and slaughter through a commercial facility. Hot carcass weight and kidney and pelvic fat (KPF) were recorded at slaughter. Chilled carcasses were measured then fabricated into trimmed retail cuts by plant personnel. Each cut was weighed, and two loin chops were collected from each carcass for later cooking. CLPG lambs had the highest dressing % (53.6 versus 49.8–50.6; P < 0.05). At the same cold carcass weight, CLPG lambs had larger longissimus muscle areas (19.5 cm² versus 14.0–15.2 cm² for the rest; P < 0.05), less KPF (0.9 kg versus 1.04–1.13 kg; P < 0.05), less carcass fat (P < 0.05 for all measures), shorter carcasses (60.7 cm versus 61.8–64.7 cm; P < 0.05), and heavier trimmed sirloins, legs, and shoulders than any other group (a11 P < 0.05). They were similar to S lambs in receiving the lowest mean USDA yield grade. CLPG carcasses had the highest proportion of carcass weight represented by trimmed cuts (70% versus 65.7–67.8% for the rest; P < 0.05), the highest proportion of trimmed cuts (62.2% versus 59.7–60.6% for the rest; P < 0.05) represented by the most valuable cuts (leg + loin + rack + sirloin), and the highest composite carcass value ($135.8 versus $125–129 for the rest; P < 0.05). CLPG lambs also produced loin chops with the highest mean Warner–Bratzler shear values (5.4 kg versus 2.8–2.9 kg for the rest; P < 0.05) and the highest % cooking loss (31% versus 29–29.6% for the rest; P < 0.05).