A meta-analysis of genetic and phenotypic diversity of European local pig breeds reveals genomic regions associated with breed differentiation for production traits

BACKGROUND

Intense selection of modern pig breeds has resulted in genetic improvement of production traits while the performance of local pig breeds has remained lower. As local pig breeds have been bred in extensive systems, they have adapted to specific environmental conditions, resulting in a rich genotypic and phenotypic diversity. This study is based on European local pig breeds that have been genetically characterized using DNA-pool sequencing data and phenotypically characterized using breed level phenotypes related to stature, fatness, growth, and reproductive performance traits. These data were analyzed using a dedicated approach to detect signatures of selection linked to phenotypic traits in order to uncover potential candidate genes that may underlie adaptation to specific environments.

RESULTS

Analysis of the genetic data of European pig breeds revealed four main axes of genetic variation represented by the Iberian and three modern breeds (i.e. Large White, Landrace, and Duroc). In addition, breeds clustered according to their geographical origin, for example French Gascon and Basque breeds, Italian Apulo Calabrese and Casertana breeds, Spanish Iberian, and Portuguese Alentejano breeds. Principal component analysis of the phenotypic data distinguished the larger and leaner breeds with better growth potential and reproductive performance from the smaller and fatter breeds with low growth and reproductive efficiency. Linking the signatures of selection with phenotype identified 16 significant genomic regions associated with stature, 24 with fatness, 2 with growth, and 192 with reproduction. Among them, several regions contained candidate genes with possible biological effects on stature, fatness, growth, and reproductive performance traits. For example, strong associations were found for stature in two regions containing, respectively, the ANXA4 and ANTXR1 genes, for fatness in a region containing the DNMT3A and POMC genes and for reproductive performance in a region containing the HSD17B7 gene.

CONCLUSIONS

In this study on European local pig breeds, we used a dedicated approach for detecting signatures of selection that were supported by phenotypic data at the breed level to identify potential candidate genes that may have adapted to different living environments and production systems.

A missense SNP in the proopiomelanocortin (POMC) gene is associated with growth traits in Awassi and Karakul sheep

This study was conducted to assess the association between proopiomelanocortin (POMC) gene and growth traits in Awassi and Karakul sheep. PCR-single strand conformation polymorphism (SSCP) method was utilized to assess the polymorphism of POMC PCR amplicons with body weight and length, wither and rump height, chest and abdominal circumference measured at birth, 3, 6, 9, and 12 months intervals. Only one missense SNP (rs424417456:C > A) was detected in exon-2, in which glycine was converted to cysteine in the 65th position in POMC (p.65Gly > Cys). rs424417456 SNP showed significant associations with all growth traits in the third, sixth, ninth, and twelfth months. At the age of 3 months onward, lambs with CC genotype showed higher body weight, body length, wither and rump heights, and chest and abdominal circumferences than lambs with CA and AA genotypes, respectively. Prediction analyses indicated a deleterious effect of p.65Gly > Cys on POMC structure, function, and stability. Owing to the strong correlation between rs424417456:CC and better growth characteristics, this genotype is proposed as a promising marker to enhance growth traits in Awassi and Karakul sheep. The predicted damaging effects caused by rs424417456:CA and rs424417456:AA genotypes may entail a putative mechanism through which lambs with these genotypes exhibit lower growth traits.

Favoring Expression of Yak Alleles in Interspecies F1 Hybrids of Cattle and Yak Under High-Altitude Environments

Both cis- and trans-regulation could cause differential expression between the parental alleles in diploid species that might have broad biological implications. Due to the relatively distant genetic divergence between cattle and yak, as well as their differential adaptation to high-altitude environments, we investigated genome-wide allelic differential expression (ADE) in their F1 hybrids using Nanopore long-read RNA-seq technology. From adult F1 hybrids raised in high-altitude, ten lung and liver tissues were individually sequenced for producing 31.6 M full-length transcript sequences. Mapping against autosomal homologous regions between cattle and yak, we detected 17,744 and 14,542 protein-encoding genes expressed in lung and liver tissues, respectively. According to the parental assignments of transcript sequences, a total of 3,381 genes were detected to show ADE in at least one sample. There were 186 genes showing ubiquitous ADE in all the studied animals, and among them 135 and 37 genes had consistent higher expression of yak and cattle alleles, respectively. Functional analyses revealed that the genes with favoring expression of yak alleles have been involved in the biological progresses related with hypoxia adaptation and immune response. In contrast, the genes with favoring expression of cattle alleles have been enriched into different biological progresses, such as secretion of endocrine hormones and lipid metabolism. Our results would support unequal contribution of parental genes to environmental adaptation in the F1 hybrids of cattle and yak.

Genetic and environmental analysis of female calf survival in the Israel Holstein cattle population

The objectives were to estimate the effects of various environmental factors on female calf survival of Israeli Holsteins, to estimate the economic value of calf survival under Israeli conditions, to estimate the genetic and environmental variance components for calf and cow survival using the individual animal model, to perform GWAS analyses of survival to first calving and herd life after first calving, to estimate the genetic and environmental trends for calf survival since 1985, to estimate genetic correlations of calf survival with the traits included in the current Israeli breeding index, and to estimate the consequences of inclusion of calf survival in the national selection index. Mean calf survival rate of Israeli Holsteins from 2001 through 2008 was 0.85, and the mean economic value of survival to first calving was $526. Birth month, gestation length, dystocia, and twin birth significantly affected calf survival rate. Dystocia and twin birth each reduced survival rate by 0.034. Survival rate was highest for calves born in October and lowest for calves born in February. The difference between these months was 3.4%. Maximum survival was at a gestation length of 276 d, the mean gestation length for this population. Survival rate was reduced to 0.76 for calves born after a gestation length of 260 d. The individual animal model was applied for all the genetic analyses. Heritability for calf survival to first calving, as estimated by REML, was 0.009, whereas heritability of herd life from first calving was 0.15. The complete data set for genetic analysis of survival to first calving included 1,235,815 calves born between 1985 and 2017. Annual genetic and phenotypic trends for calf survival were 0.019 and 0.015%, respectively. Correlations of transmitting abilities of 226 sires born since 2010 for calf survival with the traits included in the Israeli breeding index were significant only for the maternal effects of dystocia and stillbirth. The GWAS analysis was based on the transmitting abilities of 1,493 bulls with genotypes and reliabilities >0.5 for calf survival and cow herd life. There were 7 single nucleotide polymorphisms with coefficients of determination >0.03 for calf survival and 12 single nucleotide polymorphisms with coefficients of determination >0.05 for cow survival. There was no overlap between the genome-wide significant markers for the GWAS analyses of calf survival and cow herd life. This corresponds to the conclusion from the REML results and the low correlations between the sire evaluations that the genetic control of the 2 traits are not similar. Inclusion of calf survival in the Israeli breeding would result in a 0.5% increase in calf survival over 10 yr but reduce progress for the other traits by 8%.

Integrating Single-Step GWAS and Bipartite Networks Reconstruction Provides Novel Insights into Yearling Weight and Carcass Traits in Hanwoo Beef Cattle

Simple Summary

Hanwoo is an indigenous cattle breed in Korea and popular for meat production owing to its rapid growth and high-quality meat. Its yearling weight and carcass traits (backfat thickness, carcass weight, eye muscle area, and marbling score) are economically important for the selection of young and proven bulls. In recent decades, the advent of high throughput genotyping technologies has made it possible to perform genome-wide association studies (GWAS) for the detection of genomic regions associated with traits of economic interest in different species. In this study, we conducted a weighted single-step genome-wide association study which combines all genotypes, phenotypes and pedigree data in one step (ssGBLUP). It allows for the use of all SNPs simultaneously along with all phenotypes from genotyped and ungenotyped animals. Our results revealed 33 relevant genomic regions related to the traits of interest. Gene set enrichment analysis indicated that the identified candidate genes were related to biological processes and functional terms that were involved in growth and lipid metabolism. In conclusion, these results suggest that the incorporation of GWAS results and network analysis can help us to better understand the genetic bases underlying growth and carcass traits.

Abstract

In recent years, studies on the biological mechanisms underlying complex traits have been facilitated by innovations in high-throughput genotyping technology. We conducted a weighted single-step genome-wide association study (WssGWAS) to evaluate backfat thickness, carcass weight, eye muscle area, marbling score, and yearling weight in a cohort of 1540 Hanwoo beef cattle using BovineSNP50 BeadChip. The WssGWAS uncovered thirty-three genomic regions that explained more than 1% of the additive genetic variance, mostly located on chromosomes 6 and 14. Among the identified window regions, seven quantitative trait loci (QTL) had pleiotropic effects and twenty-six QTL were trait-specific. Significant pathways implicated in the measured traits through Gene Ontology (GO) term enrichment analysis included the following: lipid biosynthetic process, regulation of lipid metabolic process, transport or localization of lipid, regulation of growth, developmental growth, and multicellular organism growth. Integration of GWAS results of the studied traits with pathway and network analyses facilitated the exploration of the respective candidate genes involved in several biological functions, particularly lipid and growth metabolism. This study provides novel insight into the genetic bases underlying complex traits and could be useful in developing breeding schemes aimed at improving growth and carcass traits in Hanwoo beef cattle.

POMC gene expression, polymorphism, and the association with reproduction traits in chickens

Reproduction trait is one of the most important economic traits in poultry industry. This study was aimed to investigate the mRNA expression levels, single nucleotide polymorphisms (SNP) of POMC gene, and the association with reproduction traits in chickens. Five SNP (g.958 G > A, g.1374 G > C, g.1393 G > A, g.1817 C > T, and g.1918G > A) were detected in introns of POMC gene in 317 Zhenning yellow chickens. Association analysis revealed that g.958 G > A and g.1817 C > T showed significantly associations with fertilization rate, hatching rate of hatching eggs, and hatching rate of fertilized eggs in chickens. Simultaneously, g.1374 G > C and g.1918G > A were both associated with egg weight at 300 D of age (P < 0.05). The SNP of g.958 G > A, g.1393 G > A, and g.1817 C > T were all associated with E2 hormone levels (P < 0.05). The result of mRNA expression levels in different tissues showed that POMC mRNA expression level in the pituitary was higher than those in the other tissues and varied in different genotypes. In conclusion, the results in this study provided new evidences that polymorphisms of the POMC gene have potential effects on reproduction traits in chickens. The 5 SNP detected in this study could be potential markers for improving reproduction traits in chickens.

Relationship between polymorphism in the CRH gene and the traits of body conformation of Salers cows

The study analyzed three SNP polymorphisms located in exon 2 of the corticotropin-coding genes (rs110167397, rs381116984, rs109244394), later referred to as CRH1, CRH2, CRH3, respectively. The research was conducted in a Salers cattle herd. Identification of genotypes of individual animals was carried out using polymerase chain reaction - restriction fragments length polymorphism (PCR-RFLP). The heterozygous genotypes of all analyzed polymorphisms they determined the most extensive body mass of the analyzed animals. Other traits, such as cow size, muscularity, hip height and chest girth, were the most favorable for homozygous GG individuals concerning CRH1 polymorphism. Studying the relationship between CRH2 polymorphism and the animals with the genotype TT was preferred for traits such as muscularity and chest girth. It was shown that the CRH3 polymorphism significantly affected the muscularity and higher values of the zoometric measurement (hip height, chest girth) in the case of cows with the genotype CC. Significant differences were found in the study (p ≤ 0.01; p ≤ 0.05).

Functional Partitioning of Genomic Variance and Genome-Wide Association Study for Carcass Traits in Korean Hanwoo Cattle Using Imputed Sequence Level SNP Data

Quantitative traits are usually controlled by numerous genomic variants with small individual effects, and variances associated with those traits are explained in a continuous manner. However, the relative contributions of genomic regions to observed genetic variations have not been well explored using sequence level single nucleotide polymorphism (SNP) information. Here, imputed sequence level SNP data (11,278,153 SNPs) of 2109 Hanwoo steers (Korean native cattle) were partitioned according to functional annotation, chromosome, and minor allele frequency (MAF). Genomic relationship matrices (GRMs) were constructed for each classified region and fitted in the model both separately and together for carcass weight (CWT), eye muscle area (EMA), backfat thickness (BFT), and marbling score (MS) traits. A genome-wide association study (GWAS) was performed to identify significantly associated variants in genic and exon regions using a linear mixed model, and the genetic contribution of each exonic SNP was determined using a Bayesian mixture model. Considering all SNPs together, the heritability estimates for CWT, EMA, BFT, and MS were 0.57 ± 0.05, 0.46 ± 0.05, 0.45 ± 0.05, and 0.49 ± 0.05, respectively, which reflected substantial genomic contributions. Joint analysis revealed that the variance explained by each chromosome was proportional to its physical length with weak linear relationships for all traits. Moreover, genomic variances explained by functional category and MAF class differed greatly among the traits studied in joint analysis. For example, exon regions had larger contributions for BFT (0.13 ± 0.08) and MS (0.22 ± 0.08), whereas intron and intergenic regions explained most of the total genomic variances for CWT and EMA (0.22 ± 0.09–0.32 ± 0.11). Considering different functional classes of exon regions and the per SNP contribution revealed the largest proportion of genetic variance was attributable to synonymous variants. GWAS detected 206 and 27 SNPs in genic and exon regions, respectively, on BTA4, BTA6, and BTA14 that were significantly associated with CWT and EMA. These SNPs were harbored by 31 candidate genes, among which TOX, FAM184B, PPARGC1A, PRKDC, LCORL, and COL1A2 were noteworthy. BayesR analysis found that most SNPs (>93%) had very small effects and the 4.02–6.92% that had larger effects (10^-4 × σA2, 10^-3 × σA2, and 10^-2 × σA2) explained most of the total genetic variance, confirming polygenic components of the traits studied.

Multiplex Assay for Identifying Animal Species Found in the Tibetan Area Using the Mitochondrial 12S rRNA Gene

Southwestern China has an area with unique natural conditions located in alpine regions at altitudes from 2000 to 5000 m; this area is referred to as the Qinghai-Tibetan plateau (QTP). Unique animals, such as yaks (Bos grunniens), are found extensively on the plateau of Southwestern China due to its unique environment. In recent years, the prevalence of fake meat products such as fake jerky has increased in this area. This research was conducted as an attempt to develop a reliable multiplex polymerase chain reaction (mPCR) detection method for identifying nine animal species found in QTP. We developed the mPCR method using the specific sites found in 12S rRNA region of these nine species, which was effective in discriminating between the nine species and was successful in terms of validated reproducibility, detection limit (<6 pg total DNA), discrimination of mixed samples, and specificity (approximately 99%) using real meat samples. Our results show that the mPCR detection method can overcome the limitations of prior detection methods, such as restriction fragment length polymorphism or high-resolution melting analysis methods.