Investigation of cosmopolitan and local Italian beef cattle breeds uncover common patterns of heterozygosity.

The analysis of livestock heterozygosity is less common compared to the study of homozygous patterns. Heterozygous-Rich Regions (HRRs) may harbor significant loci for functional traits such as immune response, survival rate, and fertility. For this reason, this study was conducted to investigate and characterize the heterozygosity patterns of four beef cattle breeds, which included two cosmopolitan breeds (Limousine and Charolaise) and two local breeds (Sarda and Sardo Bruna). Our analysis identified regions with a high degree of heterozygosity using a consecutive runs approach, the Tajima D test, nucleotide diversity estimation, and Hardy Weinberg equilibrium test. These regions exhibited recurrent heterozygosity peaks and were consistently found on specific chromosomes across all breeds, specifically autosomes 15, 16, 20, and 23. The cosmopolitan and Sardo Bruna breeds also displayed peaks on autosomes 2 and 21, respectively. Thirty-five top runs shared by more than 25% of the populations were identified. These genomic fragments encompassed 18 genes, two of which are directly linked to male fertility, while four are associated with lactation. Two other genes play roles in survival and immune response. Our study also detected a region related to growth and carcass traits in Limousine breed. Our analysis of heterozygosity-rich regions revealed particular segments of the cattle genome linked to various functional traits. It appears that balancing selection is occurring in specific regions within the four examined breeds, and unexpectedly, they are common across cosmopolitan and local breeds. The genes identified hold potential for applications in breeding programs and conservation studies to investigate the phenotypes associated with these heterozygous genotypes. In addition, Tajima D test, Nucleotide diversity, and Hardy Weinberg equilibrium test confirmed the presence of heterozygous fragments found with Heterozygous-Rich Regions analysis.

Identification of candidate genes associated with bacterial and viral infections in wild boars hunted in Tuscany (Italy).

Wild boar (Sus scrofa L.) is one of the large mammals most spread worldwide, highly adaptable, and its population rapidly increased in many areas in Europe, including Italy, where Tuscany is considered particularly suitable for wild boar. Wild boars are potential hosts for different etiological agents, such as Brucella spp., Leptospira spp. and Pseudorabies virus and they can contribute to maintain and/or to disseminate some bacterial or viral pathogens to humans and domestic animals, above all-in free-range farms. In order to identify hypothetical genomic regions associated with these infection diseases, 96 samples of wild boars hunted in Tuscany during the 2018-2019 and 2019-2020 hunting seasons were considered. Diagnosis was achieved by serological tests and 42 Pseudorabies, 31 Leptospira and 15 Brucella positive animals were identified. All animals were genotyped with Geneseek Genomic Profiler Porcine HD (70 k) and a genome-wide scan was then performed. Significant markers were highlighted for Pseudorabies (two SNPs), Brucella (seven SNPs), and Leptospira (four SNPs) and they were located within, or nearby, 29 annotated genes on chromosome 6, 9, 12, 13, 14 and 18. Eight genes are implicated in viral (SEC14L1, JMJD6, SRSF2, TMPRSS2, MX1, MX2) or bacterial (COL8A1, SPIRE1) infections, seven genes (MFSD11, METTL23, CTTNBP2, BACE2, IMPA2, MPPE1 and GNAL) are involved in mental disorders and one gene (MGAT5B) is related to the Golgi complex. Results presented here provide interesting starting points for future research, validation studies and fine mapping of candidate genes involved in bacterial and viral infections in wild boar.

Heritability and genetic correlation of body weight and Kleiber ratio in Limousin and Charolais beef cattle breeds.

Reducing the environmental impact of livestock production is now indispensable and genetic selection can be of great support for this purpose. Measures that can identify high body growth at low maintenance costs in production animals are particularly useful since resources have been increasingly limited. Therefore, the goal of this study was to estimate genetic parameters for BW and Kleiber ratio (KR) in 210-day-old and 365-day-old Charolais and Limousin breeds. A database comprising animals born from 1999 to 2018 was used in a multitrait model applying Bayesian inference. The heritability for BW is high in Charolais (0.39 and 0.42 for BW210 and BW365, respectively) and moderate in Limousin (0.22), indicating possible genetic gains for BW in both breeds. The genetic variability of KR should also allow satisfactory genetic gains. In addition, the genetic correlation between BW and KR ranged from low to moderate. Thus, selection over KR should have no effects on BW, showing that high body growth can be obtained without changes in efficiency.

Genome-wide association study identifies markers associated with carcass and meat quality traits in Italian Large White pigs.

A GWAS was performed using the genotypes obtained by PorcineSNP60 v2 BeadChip and 11 phenotypic traits (carcass lean meat percentage; backfat thickness; Longissimus thoracis muscle thickness; lightness; backfat thickness measured with caliper at the midline; meat pH measured at about 1 h post mortem and 24 h post mortem; CIE L*, a* and b* color parameters; and water-holding capacity). Three markers were associated with three of the phenotypic traits considered: M1GA0009592 (SSC7) with backfat thickness and lean meat content, DIAS0002910 (SSC6) and ALGA0109856 (SSC6) with water-holding capacity. The marker M1GA0009592, associated with backfat thickness, lies in a QTL region near the gene JARID2, which is a transcription factor also involved in the regulation of adipose-derived stem cell pluripotency. The results seem to indicate a possible role of these genomic regions in the regulation of pig carcass fatness (i.e. backfat at last rib) and water-holding capacity.