The Effect of Integrating Genomic Information into Genetic Evaluations of Chinese Merino Sheep

Accuracy of Genomic prediction for fleece traits in Inner Mongolia Cashmere goats

The fleece traits are important economic traits of goats. With the reduction of sequencing and genotyping cost and the improvement of related technologies, genomic selection for goats has become possible. The research collect pedigree, phenotype and genotype information of 2299 Inner Mongolia Cashmere goats (IMCGs) individuals. We estimate fixed effects, and compare the estimates of variance components, heritability and genomic predictive ability of fleece traits in IMCGs when using the pedigree based Best Linear Unbiased Prediction (ABLUP), Genomic BLUP (GBLUP) or single-step GBLUP (ssGBLUP). The fleece traits considered are cashmere production (CP), cashmere diameter (CD), cashmere length (CL) and fiber length (FL). It was found that year of production, sex, herd and individual ages had highly significant effects on the four fleece traits (P < 0.01). All of these factors should be considered when the genetic parameters of fleece traits in IMCGs are evaluated. The heritabilities of FL, CL, CP and CD with ABLUP, GBLUP and ssGBLUP methods were 0.26 ~ 0.31, 0.05 ~ 0.08, 0.15 ~ 0.20 and 0.22 ~ 0.28, respectively. Therefore, it can be inferred that the genetic progress of CL is relatively slow. The predictive ability of fleece traits in IMCGs with GBLUP (56.18% to 69.06%) and ssGBLUP methods (66.82% to 73.70%) was significantly higher than that of ABLUP (36.73% to 41.25%). For the ssGBLUP method is significantly (29% ~ 33%) higher than that with ABLUP, and which is slightly (4% ~ 14%) higher than that of GBLUP. The ssGBLUP will be as an superiors method for using genomic selection of fleece traits in Inner Mongolia Cashmere goats.

Improving Breeding Value Reliability with Genomic Data in Breeding Groups of Charolais

The aim of this study was to assess the impact of incorporating genomic data using the single-step genomic best linear unbiased prediction (ssGBLUP) method compared to the best linear unbiased prediction (BLUP) method on the reliability of breeding values for age at first calving, calving interval, and productive longevity at 78 months in Charolais cattle. The study included 48,590 purebred Charolais individuals classified into four subgroups based on genotyping and performance records. The results showed that considering genotypes significantly improved genomic estimated breeding values (GEBV) reliability across all categories except nongenotyped individuals. For young genotyped individuals, the increase in reliability was up to 27% for both sexes. The highest average reliability was achieved for genotyped proven bulls and cows with performance records, and the inclusion of genomic data further improved the reliability by up to 22% and 21% for cows and bulls, respectively. The gain in reliability was observed mainly during the first three calvings, and then the differences decreased. The imported individuals showed lower estimated breeding values (EBV) and GEBV reliabilities than the domestic population, probably due to the weak genetic connection with the domestic population. However, when the progeny of imported heifers were sired by domestic bulls, the reliability increased by up to 24%. For nongenotyped individuals, only a slight increase in reliability was observed; however, the number of genotyped individuals in the population was still relatively small.

A newly identified small tRNA fragment reveals the regulation of different wool types and oxidative stress in lambs

Novel small RNAs derived from tRNAs are continuously identified, however, their biological functions are rarely reported. Here, we accidentally found the reads peak at 32nt during statistical analysis on the miRNA-seq data of lamb skin tissue, and found that it was related to the wool type of lambs. This 32nt peak was composed of small tRNA fragments. The main component sequence of this peak was a novel small tRNA derived from Glycyl tRNA (tRNAGly), the expression level of tRNAGly-derived tRNA fragments (tRFGly) was 5.77 folds higher in the coarse wool lambs than that in the fine wool lambs. However, in contrast, the expression of tRNAGly in the skin of fine wool lambs is 6.28 folds more than that in coarse wool lambs. tRNAGly promoted the synthesis of high glycine protein including KAP6 in fine wool lamb skin. These proteins were reported as the major genes for fine curly wool. Integrative analysis of target gene prediction, proteomics and metabolomics results revealed that tRFGly reduced the level of reactive oxygen species (ROS) in the skin of coarse wool lambs by targeted inhibition of the Metabolic signal and the corresponding Glutathione metabolic pathway, on the contrary, the level of oxidative stress in the skin of fine wool lambs was significantly higher. This study revealed for the first time the relationship between tRNAGly and its derived tRFGly and animal traits. tRFGly has the function of targeting and regulating protein synthesis. At the same time, tRFGly can reduce the expression of its resource complete tRNA, thereby reducing its ability to transport specific amino acid and affecting the expression of corresponding proteins.

Integration of non-additive genome-wide association study with a multi-tissue transcriptome analysis of growth and carcass traits in Duroc pigs

Growth and carcass traits are of economic importance in the pig production, which affect pork quality and profitability of finishing pig production. This study used whole-genome and transcriptome sequencing technologies to identify potential candidate genes affecting growth and carcass traits in Duroc pigs. The medium (50-60 k) single nucleotide polymorphism (SNP) arrays of 4 154 Duroc pigs from three populations were imputed to whole-genome sequence data, yielding 10 463 227 markers on 18 autosomes. The dominance heritabilities estimated for growth and carcass traits ranged from 0.000 ± 0.041 to 0.161 ± 0.054. Using non-additive genome-wide association study (GWAS), we identified 80 dominance quantitative trait loci for growth and carcass traits at genome-wide significance (false discovery rate < 5%), 15 of which were also detected in our additive GWAS. After fine mapping, 31 candidate genes for dominance GWAS were annotated, and 8 of them were highlighted that have been previously reported to be associated with growth and development (e.g. SNX14, RELN and ENPP2), autosomal recessive diseases (e.g. AMPH, SNX14, RELN and CACNB4) and immune response (e.g. UNC93B1 and PPM1D). By integrating the lead SNPs with RNA-seq data of 34 pig tissues from the Pig Genotype-Tissue Expression project (https://piggtex.farmgtex.org/), we found that the rs691128548, rs333063869, and rs1110730611 have significantly dominant effects for the expression of SNX14, AMPH and UNC93B1 genes in tissues related to growth and development for pig, respectively. Finally, the identified candidate genes were significantly enriched for biological processes involved in the cell and organ development, lipids catabolic process and phosphatidylinositol 3-kinase signalling (P < 0.05). These results provide new molecular markers for meat production and quality selection of pig as well as basis for deciphering the genetic mechanisms of growth and carcass traits.

Estimates of Genomic Heritability and the Marker-Derived Gene for Re(Production) Traits in Xinggao Sheep

Xinggao sheep are a breed of Chinese domestic sheep that are adapted to the extremely cold climatic features of the Hinggan League in China. The economically vital reproductive trait of ewes (litter size, LS) and productive traits of lambs (birth weight, BWT; weaning weight, WWT; and average daily gain, ADG) are expressed in females and later in life after most of the selection decisions have been made. This study estimated the genetic parameters for four traits to explore the genetic mechanisms underlying the variation, and we performed genome-wide association study (GWAS) tests on a small sample size to identify novel marker trait associations (MTAs) associated with prolificacy and growth. We detected two suggestive significant single-nucleotide polymorphisms (SNPs) associated with LS and eight significant SNPs for BWT, WWT, and ADG. These candidate loci and genes also provide valuable information for further fine-mapping of QTLs and improvement of reproductive and productive traits in sheep.

Factor Analysis of Genetic Parameters for Body Conformation Traits in Dual-Purpose Simmental Cattle

Simple Summary

Body conformation traits are closely related to economically important characteristics and should be considered in cattle breeding programs. A variety of body conformation traits recorded by classifiers can complicate the analysis process. Factor analysis can reduce the number of variables by combining two or more variables into a single factor, which has biological significance. The results of this study could be used by breeders to define conformation indexes and implement genetic assessments for conformation traits in dual-purpose breeds.

Abstract

In this study, we estimated the genetic parameters for 6 composite traits and 27 body conformation traits of 1016 dual-purpose Simmental cattle reared in northwestern China from 2010 to 2019 using a linear animal mixed model. To integrate these traits, a variety of methods were used as follows: (1) genetic parameters estimates for composite and individual body conformation traits based on the pedigree relationship matrix (A) and combined genomic-pedigree relationship matrix (H); (2) factor analysis to explore the relationships among body conformation traits; and (3) genetic parameters of factor scores estimated using A and H, and the correlations of EBVs of the factor scores and EBVs of the composite traits. Heritability estimates of the composite traits using A and H were low to medium (0.07–0.47). The 24 common latent factors explained 96.13% of the total variance. Among factors with eigenvalues ≥ 1, F1 was mainly related to body frame, muscularity, and rump; F2 was related to feet and legs; F3, F4, F5, and F6 were related to teat placement, teat size, udder size, and udder conformation; and F7 was related to body frame. Single-trait analysis of factor scores yielded heritability estimates that were low to moderate (0.008–0.43 based on A and 0.04–0.43 based on H). Spearman and Pearson correlations, derived from the best linear unbiased prediction analysis of composite traits and factor scores, showed a similar pattern. Thus, incorporating factor analysis into the morphological evaluation to simplify the assessment of body conformation traits may improve the genetics of dual-purpose Simmental cattle.

Effects of Se-Yeast on Immune and Antioxidant in the Se-Deprived Pishan Red Sheep

The experiments were to study the effects of Se-yeast on immune and antioxidant in Selenium(Se)-deprived Pishan red sheep in Southern Xinjiang, China. The samples of soil, forage, and animal tissues were collected, and used for measuring mineral content, physiological parameter, and biochemical values. These findings showed that the Se contents in affected soil and forage were markedly lower than those from unaffected soil and forage (P < 0.01). Se in affected blood and wool were also extremely lower than those from healthy Pishan red sheep (P < 0.01). The hemoglobin, packed cell volume, platelet count, Glutathione peroxidase, and total antioxidant capacity in the affected Pishan red sheep were markedly lower than those from healthy ones too (P < 0.01). The levels of malondialdehyde, total nitric oxide synthase, and lipid peroxide in Pishan red sheep from affected pastures were extremely higher than those from healthy ones (P < 0.01). The levels of interleukin (IL)-1β, Interleukin-2, tumor necrosis factor-α and interleukin-6 from serum were markedly decreased in affected Pishan red sheep(P < 0.01). The Pishan red sheep in Se-deprived pasture were treated by orally with Se-yeast, the amount of Se in the blood markedly increased in treated animals. Meanwhile, the immune and antioxidant indicator was returned to the healthy values. Consequently, our findings were indicated that Se-deprived forage caused oxidative damage, and a serious threat to the immune function in animals. The Se-yeast is more effective in the Se-deficient Pishan red sheep including blood Se content, immune function and the antioxidant capacity.

Estimation of direct and maternal genetic effects and annotation of potential candidate genes for weight and meat quality traits in a genotyped outdoor dual-purpose cattle breed

With regard to potential applications of genomic selection in small numbered breeds, we evaluated genomic models and focused on potential candidate gene annotations for weight and meat quality traits in the local Rotes Höhenvieh (RHV) breed. Traits included 6,003 birth weights (BWT), 5,719 200 d-weights (200dw), 4,594 365 d-weights (365dw), and 547 records for intramuscular fat content (IMF). A total of 581,304 SNP from 370 genotyped cattle with phenotypic records were included in genomic analyses. Model evaluations focused on single- and multiple-trait models with direct and with direct and maternal genetic effects. Genetic relationship matrices were based on pedigree (A-matrix), SNP markers (G-matrix), or both (H-matrix). Genome-wide association studies (GWASs) were carried out using linear mixed models to identify potential candidate genes for the traits of interest. De-regressed proofs (DRP) for direct and maternal genetic components were used as pseudo-phenotypes in the GWAS. Accuracies of direct breeding values were higher from models based on G or on H compared to A. Highest accuracies (> 0.89) were obtained for IMF with multiple-trait models using the G-matrix. Direct heritabilities with maternal genetic effects ranged from 0.62 to 0.66 for BWT, from 0.45 to 0.55 for 200dW, from 0.40 to 0.44 for 365dW, and from 0.48 to 0.75 for IMF. Maternal heritabilities for BWT, 200dW, and 365dW were in a narrow range from 0.21 to 0.24, 0.24 to 0.27, and 0.21 to 0.25, respectively, and from 0.25 to 0.65 for IMF. Direct genetic correlations among body weight traits were positive and favorable, and very similar from different models but showed a stronger variation with 0.31 (A), −0.13 (G), and 0.45 (H) between BWT and IMF. In gene annotations, we identified 6, 3, 1, and 6 potential candidate genes for direct genetic effect on BWT, 200dW, 365dW, and IMF traits, respectively. Regarding maternal genetic effects, four (SHROOM3, ZNF609, PECAM1, and TEX2) and two (TMEM182 and SEC11A) genes were detected as potential candidate genes for BWT and 365dW, respectively. Potential candidate genes for maternal effect on IMF were GRHL2, FGA, FGB, and CTNNA3. As the most important finding from a practical breeding perspective, a small number of genotyped RHV cattle enabled accurate breeding values for high heritability IMF.

Selective Sweeps Uncovering the Genetic Basis of Horn and Adaptability Traits on Fine-Wool Sheep in China

Long-term natural and artificial selection leads to change in certain regions of the genome, resulting in selection signatures that can reveal genes associated with selected traits, such as horns (i.e., polled/horned), high-quality wool traits, and high-altitude hypoxia adaptability. These are complex traits determined by multiple genes, regulatory pathways, and environmental factors. A list of genes with considerable effects on horn and adaptability traits has not been found, although multiple quantitative trait loci (QTL) have been identified. Selection signatures could be identified using genetic differentiation (F_ST), polymorphism levels θπ, and Tajima’s D. This study aimed to identify selection signatures in fine-wool sheep and to investigate the genes annotated in these regions, as well as the biological pathways involved in horn and adaptability traits. For this purpose, the whole-genome sequence of 120 individuals from four breeds, which come from different elevations and habitats in China, was used to analyze selection signatures for horn and adaptability traits. Annotation of the consensus regions of F_ST and θπ ratios revealed a list of identified genes associated with polled/horned and high-altitude hypoxia adaptability traits, such as RXPF2, EERFC4, MSH6, PP1R12A, THBS1, ATP1B2, RYR2, and PLA2G2E. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified genes related primarily to mismatch repair, metabolism, vascular smooth muscle contraction, and cardiac muscle contraction. This is the first study to demonstrate that selection signatures play an important role in the polled/horned and high-altitude hypoxia adaptability traits of fine-wool sheep breeds that have undergone high-intensity selection and adapted to different ecological environments in China. Changes observed in the genome of fine-wool sheep may have acted on genomic regions that affect performance traits and provide a reference for genome design and breeding.