Nuevas metodologías genéticas para la evaluación del nivel de endogamia y su repercusión sobre caracteres de interés económico en la población equina "Pura Raza Española"

Résumé

The Pura Raza Española (PRE) horse is a native Spanish equine breed and the most important in terms of its census, with 275,018 active individuals. Its current Breeding Program, which includes the Improvement Program, was approved in 2020 and aims to improve morphology, conformation, and functionality while minimizing the level of inbreeding and ensuring the conservation of the breed. Over the past four generations (40 years approximately), paternity controls have been systematically carried out using different molecular tools such as blood groups, biochemical polymorphisms, and microsatellite markers. This makes the population of PRE horses ideal for determining the evaluation of different methodologies for estimating inbreeding and studying different models that estimate deviations in the gene transmission ratio from parents to offspring in economically important traits within this breed. The present Thesis is structured into three chapters. Chapter I: "Genetic Structure of the Pure Spanish Horse Population and Evaluation of Inbreeding." Since 1912, with the creation of the first Stud Book for PRE horses, it was established as a closed population, where only animals from registered parents in the Genealogical Book can be registered as breeding animals. From that moment, mating between related animals became inevitable, and inbreeding, related to the increase in homozygosity in the genome, progressively increased. Nowadays, estimating inbreeding, which is omnipresent and unavoidable in purebred production systems, is the main objective in livestock management, especially for breeders interested in mitigating its negative consequences. The first objective of this chapter was to analyze, based on genealogical information, the classical coefficient of inbreeding (F), the coefficient of relationship (AR), and the partial coefficient of inbreeding (Fij) in the total PRE population, and determine the ancestors that contribute to 50% of the total genetic variability of the current population. This study has allowed us to verify that the average F of the entire population (328,706 horses) has decreased by almost 1% in the last 20 years. Additionally, it was determined that a total of 10,244 common ancestors (those generating consanguinity) contributed partial inbreeding to an average of 5,370 descendants, where each descendant has an average of 170 common ancestors in their pedigree. It was also determined that over generations, the number of common ancestors has increased, while the proportion of Fij transmitted by each of them has decreased. In the second part of this chapter, different methodologies were used to estimate inbreeding, evaluating their respective advantages and disadvantages. From the total PRE population (344,718 horses), coefficients of classical inbreeding (F), Ballou's ancestral, Kalinowski's ancestral, new Kalinowski's, and historical ancestral were estimated. Additionally, genotypic data from a selected population of 805 PRE individuals were used to determine individual coefficients of inbreeding through SNP-by-SNP techniques (moment-based methods -FHOM-, diagonal elements of the genome -FG-, and hybrid matrices -FH-) and measures of ROH (FRZ). The average values of the pedigree-based coefficients of inbreeding ranged from 0.01 (F for the last 3 generations -F3-) to 0.44 (historical ancestral coefficient), and the average values of the genome-based coefficients of inbreeding ranged from 0.05 (FRZ for 3 generations, FH, and FHOM) to 0.11 (FRZ for 9 generations). Significant correlations were also found between pedigree and genomic inbreeding values, ranging from 0.58 (F3 with FHOM) to 0.79 (F with FRZ). Chapter II: "Analysis of Alterations to Mendelian Inheritance and Their Impact on Economically Important Traits in the PRE Horse. Mendel's Law of Segregation states that each offspring receives, with equal probability, one allele from each character from each of its parents. However, in practice, this does not always occur, and distortions in the transmission ratio (TRD) occur, resulting in certain genotypes being overrepresented or underrepresented in the offspring of a specific mating. TRD can be due to mechanisms that affect germ cells (such as meiotic drive, germ line selection, gametic competition, embryonic lethality, or postnatal survival) or mechanisms that affect the proportion of expected genotypic frequencies in the population (such as inbreeding depression, imprinting, or dominance, among others). In the first part of this chapter, genetic parameters for 9 reproductive traits in PRE mares were estimated, the proportion of each trait affected by increased inbreeding (inbreeding depression), and, for the first time in an equine breed, the inbreeding depression load (PDC) associated with common ancestors of the breed. The idea behind the design of these models is based on the notion that inbreeding depression does not always have a negative impact on inbred individuals, but rather inbreeding has heterogeneous effects in the population and sometimes results in neutral or even positive effects. To achieve this, phenotypic data from a total of 22,799 mares were analyzed, and models were developed that included the PDC generated by the individual's ancestor as a random genetic effect to explain their phenotype. Heritability estimates ranged from 0.05 (interval between the first and second foaling) to 0.16 (age at first foaling), while PDC ratios ranged from 0.06 (reproductive efficiency at the sixth foaling) to 0.17 (age at first foaling), for a partial coefficient of inbreeding of 10%. In the second part of this chapter, models were developed for the first time in a horse breed to quantify the "parent of origin" effect, also known as imprinting, on reproductive and morphological traits in the current population of PRE horses. The parent of origin effect occurs when the expression of a gene in offspring can vary depending on the parent of that gene or due to preferential management associated with the genetic merit of one of the parents. The first consequence of this, from a genetic point of view, is that the average phenotypes of reciprocal heterozygotes may no longer be equal, as would be expected based on Mendelian inheritance. Between 44,030 and 144,191 PRE horses were analyzed for a total of 3 reproductive traits and 3 morphological traits. Subsequently, four genetic models were designed and compared, with and without the parent of origin effect. It was determined that both maternal and paternal gametic effects influence all analyzed traits. The maternal gametic effect had a greater influence on most traits, accounting for 3% to 11% of the total phenotypic variance, while the paternal gametic effect accounted for a higher proportion of variance in age at first foaling (4%). As expected, the Pearson correlations between the additive genetic values of the models that consider the parent of origin effect and those that do not were very high. However, the percentage of coincident animals decreases when comparing animals with the highest estimated genetic values. In the third part of this chapter, the mechanisms affecting TRD due to germline cell influences were further explored, specifically focusing on factors occurring during the reproductive process and early neonatal development. Genomic information from 126,394 trios composed of the stallion, mare, and offspring was used for this study, utilizing a panel of 17 microsatellite markers. The number of available alleles for each marker ranged from 13 to 18, with a total of 268 alleles analyzed. After completing the analysis using TRDscan v.2.0, a total of 12 alleles (from 11 microsatellites) with decisive evidence of genotypic TRD were identified, with 3 showing additive patterns and 9 showing heterosis patterns. Additionally, 19 alleles (from 10 microsatellites) with allelic TRD patterns were identified. Among them, 14 exhibited non-specific TRD for the stallion, and 5 for the mare. From the TRD regions, 24 genes were identified and annotated, predominantly associated with cholesterol metabolism and homeostasis but primarily linked to fertility problems, growth delay, and general health deterioration. Chapter III. "Early Selection Index for Reproductive Parameters in Purebred Spanish Horse Mares Using Morphological Traits". In this chapter, a series of indices were developed for the preselection and early selection of reproductive efficiency and fertility parameters in PRE mares, based on morphological variables. A partial least squares analysis was conducted to determine the morphological variables that have the greatest impact on reproductive efficiency parameters. These variables included height at withers, lateral hock angle, dorsal-sternal diameter, perimeter of anterior cannon bone, angle of shoulder, thoracic perimeter, hip-stifle distance, and croup angle. Subsequently, morphological and fertility records from 16,620 to 19,758 mares, depending on the analyzed variable, were used to estimate genetic parameters using a multivariate animal model. The model included age, geographic region, coat color, and average stud size at the mare's first foaling decade as fixed effects. Heritabilities ranged from 0.1 (interval between first and second foaling) to 0.9 (height at withers), and genetic correlations between morphological and reproductive variables ranged from -0.47 (hip-stifle distance with age at last foaling) to 0.16 (angle of shoulder with interval between first and second foaling). It was determined that, for all studied fertility variables, the response to selection increased when comparing indices that included morphological information to those that did not. The fertility variable that showed the highest response was the interval between first and second foaling, with a response increase of 46%, followed by age at last foaling with a 28% increase.