Holstein-Friesian cattle are the most important dairy breed worldwide. The main objective was to carry out a detailed pedigree evaluation of the Ecuadorian Holstein-Friesian cattle to investigate the demographic structure, inbreeding evolution, and genetic diversity of the official paternal lineages to determine the potential GD loss after the inclusion of modern Assisted Reproductive Technologies (ARTs). Official pedigree information from 28,893 Holstein-Friesian sires born between 1950 and 2021 and enrolled with the Ecuadorian Holstein-Friesian Association (AHFE, Ecuador) were recorded and evaluated from USA and Canada genetic official databases. After multiple-trait across-country genetic analyses the total population was divided into four subpopulations; i) 1950–1969: natural mating (NM) period; ii) 1970–1989: NM + artificial insemination (AI) period; iii) 1990–2009: AI + embryo transfer (ET) period; and iv) 2010–2021: AI + ET + genomic selection (GS) period. Demographic parameters [number of males, pedigree integrity (PI), and generation interval (GI)] were analysed. PI was analysed using known ancestors up to 4 generations considering the number of complete (GCom), maximum (GMax) and equivalent (GEqu) generations. Moreover, Inbreeding parameters [inbreeding coefficient (F), average relatedness (AR), coancestry (C), effective size (Ne), genetic conservation index (GCI)] and parameters related to the gene origin probability (number of founders (f), effective number of founders (fe), genetic conservation index (GCI), among others] were also analysed, together with the fe/f ratio, fge/fe ratio, genetic contributions, and genetic diversity loss (GD-loss) derived parameters. The results indicated that nearly all imported sires used in Ecuador born in the beginning of 1990s could be traced to just three countries, who together account for > 90% of paternal lineages. This fact indicates that GD has undergone a dramatic decrease during the past 30 years. The PCI for the three last periods were > 55%, and the trend was enhanced in the fourth chronological period till > 92%. The estimated proportion of random genetic drift in GD loss increased over time as well as the Ne that decreased by the time. In conclusion, the occurrence of AI + ET + GS period led to the major GD loss. Therefore, due to the extremely limited number of paternal lineages the strategy for recovering the minimal GD on the current and future Ecuadorian Holstein-Friesian cattle should reduce the inbreeding values by increasing the Ne using alternately the foreign genetic material and the national breeding stock.

The objective was to evaluate the evolution of the population structure, reproductive performance, inbreeding, and genetic diversity in Charolais cattle. Official genealogical information from the Ecuadorian Charolais Association was divided into five populations: (a) historical (total), (b) 2008–2012 (natural mating period), (c) 2013–2017 (natural mating + artificial insemination period), (d) 2018–2022 (artificial insemination + embryo transfer period), and (e) the reference (known sires and dams) from which the population structure was evaluated using pedigree completeness and the generation interval (GI). Meanwhile, for genetic diversity (GD), inbreeding (F), average relatedness (AR), and the effective population size (Ne) were estimated. The gene origin probability (number of founders, effective number of founders/ancestors, and number of founder genomes) explaining genetic variability, reproductive efficiency, the number of offspring per sire and dam, and the average ages of parents at the birth of their offspring were determined. The database was analyzed using the ENDOG, POPREP, and CFC software programs. The results indicate that pedigree completeness and the GI decreased over time among populations, although the first generation showed higher values. The sire gametic pathway was greater in all populations. F increased over time, although not markedly. Although Ne variations were observed, the levels remained above the recommended limit value. The GD loss increased progressively over time although the most recent population was not significantly affected. Finally, the female reproductive efficiency increased over time as well. In conclusion, the Charolais cattle GI should be reduced. After 2012, the use of Assisted Reproductive Technologies and breeding schemes raised the GD loss. Finally, the F increased over time although it could be reduced using foreign genetic resources in the current Ecuadorian Charolais population.

This comprehensive study on the Andalusian Black cattle breed reveals a substantial population decline, with the average herd size decreasing significantly from 305.54 to 88.28 animals per herd. This decline is primarily attributed to agricultural changes and the introduction of foreign meat-focused breeds. The male-to-female ratio shift is noteworthy, with more cows than bulls, impacting selection intensity for both genders. Inbreeding levels, though relatively low historically (5.94%) and currently (7.23%), raise concerns as 37.08% historically and 48.82% currently of the animals exhibit inbreeding. Positive assortative mating is evident, reflected by the increasing non-random mating coefficient (α). Key ancestors play a crucial role in shaping genetic diversity, with one ancestor significantly influencing the current genetic pool and the top 10 ancestors contributing substantially. Breed maintains a conservation index of 2.75, indicating relatively high genetic diversity. Recent conservation efforts have led to an increase in registered animals. The Cañadas Reales, historical transhumance routes, may have contributed to genetic connections among provinces. Challenges include the historical bottleneck, demographic changes, and potential impacts from reproductive practices. The Andalusian Black breed’s conservation necessitates ongoing efforts in genealogical registration, targeted breeding programs, and collaborative initiatives to address the observed demographic shifts and ensure sustainable genetic diversity.

Recently, a growing interest in dairy cattle selection has been triggered due to specific genetic variations of the β-casein (CSN2) gene which was associated to several human disorders. The aim of the present study was to evaluate the A1/A2 β-casein (CSN2) gene-derived allelic and genotypic frequencies in five Ecuadorian dairy cattle breeds to determine the genetic diversity of the A1/A2 β-casein locus. Genomic Deoxyribonucleic Acid (gDNA) was extracted from hair samples collected from different dairy cattle breeds, namely Holstein Friesian (HF), Brown Swiss (BS), Jersey (J), Gyr (G), and crossbreds (CB) raised commonly in seven different regions in order to identify A1 and A2 variants. Genomic determination of the β-casein (CSN2) gene variants was carried out evaluating the Exon 7 region in order to identify and confirm the accuracy of the A1/A2 β-casein (CSN2) gene-derived polymorphisms related to the genotypes and the allelic profiling. A2 allele frequencies were determined as 0.628, 0.643, 0.727, and 0.644 in HF, BS, J, and CB, respectively. In contrast, the lowest A1 allele frequency (0.145) as well as the greatest A2 allele frequency (0.855) was detected in G. No significant differences for allelic frequency were observed among breeds (p > 0.05). Homozygous A1 genotype frequency in HF, BS, J, and CB was 0.140, 0.110, 0.050 and 0.150, respectively. Interestingly, the A1A1 genotype was absent in G (p < 0.05). A1A2 genotypes were 0.290, 0.490, 0.450, 0.290, and 0.420 in HF, BS, J, G, and CB, respectively. Finally, the A2A2 genotype was 0.400, 0.400, 0.500, and 0.460 in HF, BS, J, and CB, respectively. However, the greatest A2A2 genotype frequency was observed in G (0.710). No deviation from the Hardy–Weinberg equilibrium was found in any breed in terms of β-casein gene (p > 0.05). Moreover, the results revealed a geographically related distribution of A1/A2 allele and genotype frequencies of β-casein (CSN2) gene. In terms of genetic diversity a differential distribution of heterozygosity was observed among breeds being average Ho, He, uHe, and F values determined as 0.429, 0.438, 0.439, and 0.022, respectively. In conclusion, the β-casein (CSN2) gene was polymorphic in all the cattle breeds analyzed. The A1/A2 allele and genotype frequencies varied depending on the breed and the geographic region which may be conditioned by the specificities related to different breeding selection programmes. A2 allele and A2A2 genotype frequency were particularly greater in Gyr cattle which have a great potential for A2 milk production without compromising genetic diversity.

Montbeliarde dairy cattle were introduced in Ecuador with the aim of ameliorating the production performance of other cattle breeds. The aim was to analyze the reproductive performance, demographic structure, inbreeding, and genetic diversity of Montbeliarde cattle obtained by absorption crossing. Official pedigree records from the Ecuadorian Montbeliarde Association were used. The total population was divided into seven populations: (i) historical (all individuals), (ii) 1999–2003, (iii) 2004–2008, (iv) 2009–2013, (v) 2014–2018, (vi) 2019–2023 (current), and (vii) reference (individuals with known parents). Demographic structure variables analyzed: pedigree completeness index (PCI), number of equivalents (GEqu), complete (GCom) and maximum (GMax) generations, and generation interval (GI). Inbreeding-derived variables analyzed: inbreeding (F), inbreeding increment (ΔF), average relatedness (AR), co-ancestry (C), non-random mating (α), effective population size (Ne), and genetic conservation index (GCI). Gene origin probability/genetic diversity variables analyzed: number of founders (f), effective number of founders (fe) and ancestors (fa), number of equivalent genomes (fg), fe/fa and fg/fa ratio, and DG losses. The databases were analyzed by ENDOG, POPREP, and CPC software. PCI in the historical population compared to the current population decreased from 72.95 to 65.87% (sire/dam pathway), while the GI decreased from 7.17 to 3.08 years when the historical and current populations were compared. Dam reproductive efficiency increased over time. Moreover, F = ~1%, AR = 2.06%, ΔF = 0.22%, C = 1.03%, α = −0.0077, GCI = 3.12, and Ne = 58 values were obtained. Gene origin probability in the reference population was f = 439, fa = 37, fe = 71.64, fg = 23.43, and fg/fe = 0.33, showing a GD loss due to unequal contribution of founders (0.55%) and bottleneck and genetic drift (4.25%). In conclusion, the Ecuadorian Montbeliarde cattle population displayed a relatively low diversity and high genetic relationship. Inbreeding levels increased while Ne values decreased over time. The introduction of new purebred bloodlines could be important to minimize the inbreeding levels ensuring the long-term conservation of this breed and minimizing GD loss.

El Caballo Peruano de Paso (CPP) es una raza con ambladura de cuatro tiempos originaria de Perú a partir de los caballos que llegaron en la época de la conquista de América. El objetivo del estudio fue conocer el nivel de consanguinidad y el efecto sobre la variabilidad genética en la raza. Se analizaron 8330 animales que incluyó la población de CPP nacidos en Ecuador y su ascendencia peruana (PT) y dos poblaciones de referencia de animales nacidos en Ecuador (PE) y nacidos entre 2008 y 2018 (PR). Las generaciones trazadas promedio fueron de 9.18 ± 3.89 (PT), 11.14 ± 2.23 (PE) y 12.83 ± 1.42 (PR) y la completitud del pedigrí sobre el 90% en la primera, cuarta y quinta generación de PT, PE y PR, respectivamente. Intervalo generacional promedio de 8.72 ± 4.56 (PT), 8.79 ± 4.30 (PE) y 9.20 ± 4.61 (PR). Promedio de consanguinidad individual: 5.97% (PT), 6.83% (PE) y 8.11% (PR) y relación de parentesco: 9.02% (PT), 10.56% (PE) y 11.56% (PR). Incremento individual de consanguinidad por año fue de 0.13% y por generación de 1.13%. El tamaño efectivo de la población fue menor a 50. Las probabilidades de origen de los genes resultaron mayores a uno. Se concluye la ocurrencia de pérdida de variabilidad genética por efecto de cuello de botella y deriva genética.