Italian beef cattle breeds: a genomic determinism of production traits
Creators: name: Rovelli, Giacomo
Publisher: name: figshare
Year: 2022
Subjects: subject: 70201 Animal Breeding
subject: FOS: Animal and dairy science

description: Climate change has the potential to negatively affect livestock health, with consequences for animal welfare, greenhouse gas emissions, productivity, human health, and livelihoods. In the first paper presented in this Ph.D. thesis, phenotypic plasticity is defined as the ability of a genotype to produce different phenotypes, depending on environmental conditions, biotic or abiotic. It is a factor that influences and modifies the genes of animals and plants, adapting them to climate change. Among the climatic variables, it is known that heat stress is the most damaging factor for the economy of the agro-zootechnic industry. There is a large number of candidate genes associated with the adaptation of ruminants, monogastrics, and poultry to heat stress. For example, the genes that code for leptin (LEP), for thyroid hormone (THR) and insulin (IGF) receptors, and for growth factors (TCF), are associated with heat stress in physiological pathways of domestic animals such as dairy cows, beef cattle, buffaloes, poultry, pigs, and horses. In this review, we wanted to highlight genes and traits associated with the thermotolerance of the domestic animals in order to support production and cope with climate change. The selection and experimental evolution approaches have shown that plasticity is a trait that can evolve under direct selection and has a response related to some specific traits. Therefore, new zootechnical strategies should be defined immediately in order to select and raise livestock capable of adapting to current climate change conditions. In the other four papers presented in this doctoral thesis, the main objective was to apply different genetic and genomic techniques on data obtained from the performance test of young bulls of the Marchigiana, Chianina, Romagnola, Maremmana, and Podolica breeds at the genetic selection center of ANABIC (National Association of Italian Beef Cattle Breeders). The second and third papers aim to determine genetic variability, population differentiation by heterozygosity and inbreeding, using genotypes at SNP loci. The initial dataset contained data from 3,581 young bulls (Chianina, N = 909; Marchigiana, N = 879; Maremmana, N = 334; Podolica, N = 555; Romagnola, N = 904), obtained in performance tests from 1985 to 2019. All animals were genotyped with the GeneSeek GGP-LDv4 33k SNP chip containing 30,111 SNPs. After the quality control of the genotype, carried out for each breed, the heterozygosity was calculated using the PLINK v1.9 software, and the FIS index using the “hierstat” package of the R 4.0.1 software. Genetic analysis showed low values of heterozygosity in specialized meat breeds (Marchigiana, Chianina, and Romagnola) compared to rustic breeds (Maremmana, and Podolica). The evolution of inbreeding, over the course of thirty years of selection, was instead estimated through Fhat2 and Fped coefficients. The mean results obtained were very low, on average between years and breeds, with values between 0.121-0.072 and 0.000-0.068 respectively. The annual rates of inbreeding increase were also very low (Fhat2 0.01-0.02%; Fped 0.003-0.004%). The use of a large number of sires combined with the selection strategies implemented by ANABIC to minimize inbreeding could explain these low results. Furthermore, despite the fact that heterozygosity and inbreeding have remained fairly stable over the last two decades, we have found a sustained decrease in the effective population number (Ne) in the five breeds under analysis. Such results must be interpreted with caution, due to the inherent difficulty in estimating Ne from SNP data reliably. As known, beef cattle, globally, have a high economic impact, being the third most important livestock species after poultry and pigs. Italy has a long history in the production of local beef cattle breeds such as Marchigiana, Chianina, Romagnola, Maremmana, and Podolica, which produce high quality meat. Over the years, traits such as meat production, earliness, growth capacity and muscle development have been improved through modern breeding practices, but the genetic determinism of these traits, unlike dairy breeds, is mainly unknown. In the fourth paper of this Ph.D. thesis, the genomic architecture of the growth traits in the five breeds described above was studied. Population studies (PCA and ADMIXTURE) have shown that the rustic Maremmana and Podolica breeds are closely related, while the specialized Marchigiana, Chianina, and Romagnola breeds are more differentiated from each other. A genome-wide association study (GWAS) was also performed for muscle growth and development traits (daily weight gain before and during the performance test, weight at the entrance to the genetic center and at one year of life, and muscularity), which showed a region (4-8 Mbp) on chromosome (BTA) 2 that contains the myostatin gene (MSTN) and shows significant associations at genomic level with muscularity in Marchigiana breed. At chromosomal level, a higher number of SNP markers showed significant associations with the traits under study in Marchigiana (41 significant SNPs), Chianina (19 significant SNPs), Romagnola (15 significant SNPs), Maremmana (12 significant SNPs), and Podolica (12 significant SNPs). Positional concordance of significant SNPs between the breeds was found to be rather low, however, more significantly associated SNPs were found between the two rustic breeds than the other breeds. In general, the determinism of growth and muscle development characteristics showed a remarkable level of genetic heterogeneity among the five Italian breeds considered. In general, in farms and especially in cattle, male fertility is extremely important at a clinical level for the diagnosis of reproductive problems, and at company management level in order to ensure optimal fertility rates for the breeder for efficient reproduction. Male fertility traits usually have low heritability due to the strong impact of non-additive and environmental factors in their genetic determinism. The goal of the fifth paper presented in this Ph.D. thesis was to identify genetic markers and genes associated with eight fertility traits (scrotal circumference, right testicle length and diameter, sperm volume and concentration, percentage of abnormal spermatozoa, and total and progressive sperm motility) recorded in 2,692 young bulls belonging to the three main Italian beef cattle breeds, namely Chianina (N = 909), Marchigiana (N = 879) and Romagnola (N = 904). Genome-wide association studies, performed with the GEMMA software, revealed significant SNPs in all the breeds under analysis. At chromosomal level, a total of 73, 76, and 80 SNPs were identified considering all the phenotypic characters analyzed for Marchigiana, Chianina, and Romagnola respectively. The metabolic and ontological study of the genes located near the significant markers have highlighted the existence of some candidate genes involved in reproduction (SGMS2, FABP5, ZFPM2, MOS, PLK1, HELLS, TRPV4, DYNLL1, and INSL3). Furthermore, in Marchigiana breed we carried out an association study between the polymorphism of the myostatin gene (which in this breed can be mutated) and the fertility traits. Testicular morphometries showed lower values in heterozygous and homozygous mutated animals, while for sperm quality traits the values were higher in heterozygous animals. A possible interpretation of these results would be that heterozygous bulls have a higher fertility than subjects with normal genotype. In conclusion, the determinism of these traits showed a remarkable level of genetic heterogeneity among the three Italian breeds considered.