The demographic history and adaptation of Canarian goat breeds to environmental conditions through the use of genome-wide SNP data.

BACKGROUND: The presence of goats in the Canary Islands dates back to the late 1st millennium BC, which coincides with the colonization by the Amazigh settlers. However, the exact geographic origin of Canarian goats is uncertain since the Amazigh peoples were distributed over a wide spatial range. Nowadays, three Canarian breeds (Palmera, Majorera and Tinerfeña) are officially recognized, along with two distinct South and North Tinerfeña ecotypes, with the South Tinerfeña and Majorera goats thriving in arid and dry semi-desertic environments and the Palmera and North Tinerfeña goats are adapted to humid and temperate areas that are influenced by trade winds. Genotypes for 224 Canarian goats were generated using the Illumina Goat single nucleotide polymorphism (SNP)50 BeadChip. By merging these data with the genotypes from 1007 individuals of African and Southern European ancestry, our aim was to ascertain the geographic origin of the Canarian goats and identify genes associated with adaptation to diverse environmental conditions. RESULTS: The diversity indices of the Canarian breeds align with most of those of the analyzed local breeds from Africa and Europe, except for the Palmera goats that showed lower levels of genetic variation. The Canarian breeds demonstrate a significant genetic differentiation compared to other populations, which indicates a history of prolonged geographic isolation. Moreover, the phylogenetic reconstruction indicated that the ancestry of the Canarian goats is fundamentally North African rather than West African. The ADMIXTURE and the TreeMix analyses showed no evidence of gene flow between Canarian goats and other continental breeds. The analysis of runs of homozygosity (ROH) identified 13 ROH islands while the window-based FST method detected 25 genomic regions under selection. Major signals of selection were found on Capra hircus (CHI) chromosomes 6, 7, and 10 using various comparisons and methods. CONCLUSIONS: This genome-wide analysis sheds new light on the evolutionary history of the four breeds that inhabit the Canary Islands. Our findings suggest a North African origin of the Canarian goats. In addition, within the genomic regions highlighted by the ROH and FST approaches, several genes related to body size and heat tolerance were identified.

Single and longitudinal genome-wide association studies for dairy traits available in goats with three recorded lactations.

Milk yield and composition phenotypes are systematically recorded across several lactations in goats, but the majority of genome-wide association studies (GWAS) performed so far have rather ignored the longitudinal nature of such data. Here, we have used two different GWAS approaches to analyse data from three lactations recorded in Murciano-Granadina goats. In Analysis 1, independent GWAS have been carried out for each trait and lactation, while a single longitudinal GWAS, jointly considering all data, has been performed in Analysis 2. In both analyses, genome-wide significant QTL for lactose percentage on chromosome 2 (129.77-131.01 Mb) and for milk protein percentage on the chromosome 6 (74.8-94.6 Mb) casein gene cluster region were detected. In Analysis 1, several QTL were not replicated in all three lactations, possibly due to the existence of lactation-specific genetic determinants. In Analysis 2, we identified several genome-wide significant QTL related to milk yield and protein content that were not uncovered in Analysis 1. The increased number of QTL identified in Analysis 2 suggests that the longitudinal GWAS is particularly well suited for the genetic analysis of dairy traits. Moreover, our data confirm that variability within or close to the casein complex is the main genetic determinant of milk protein percentage in Murciano-Granadina goats.

Univariate and multivariate genome-wide association studies for hematological traits in Murciano-Granadina goats.

Hematological traits are important indicators of health status, and they are frequently used as criteria for clinical diagnosis. In humans, the genomic architecture of blood traits has been investigated in depth and thousands of associations with genetic variants have been found. In contrast, the association between marker genotypes and the variation of hematological traits has not been investigated in goats yet. Herewith, we have recorded 12 hematological parameters in 882 Murciano-Granadina goats that were also genotyped with the Goat SNP50 BeadChip (Illumina). Performance of a univariate genome-wide association study (GWAS) made it possible to detect one genomic region on goat chromosome (CHI) 21 (19.2-19.5 Mb) associated, at the genome-wide level of significance, with 4 red blood cell traits. The three markers displaying the highest significances were rs268272996 (CHI21: 19225290 bp), rs268273004 (CHI21: 19565629 bp) and rs268239059 (CHI13: 9615190 bp). Consistently, a multivariate GWAS indicated that the rs268273004 marker on chromosome 21 is associated with seven blood cell traits. Interestingly, this marker maps close to the FA Complementation Group I (FANCI) gene (CHI21: 20021947-20077025 bp), which is functionally related to Fanconi anemia, a syndrome characterized by bone marrow failure, aplastic anemia, and congenital disorders. We have also uncovered additional chromosome-wide significant associations between genetic markers and erythrocyte and leukocyte traits in the univariate GWAS. These findings evidence that the phenotypic variation of hematological traits in goats is regulated, at least to some extent, by polygenic determinants distributed in multiple chromosomes.

A Matrilineal Study on the Origin and Genetic Relations of the Ecuadorian Pillareño Creole Pig Population through D-Loop Mitochondrial DNA Analysis.

Domestic pig breeds reached America on the second Columbus trip; from this date, Iberian pig genetic resources were disseminated throughout the continent, forming diverse creole breeds. These Ecuadorian Creole pigs are important for food production but have been genetically eroded since the introduction of transboundary breeds. In this study, we sought to characterize this erosion more thoroughly through mitochondrial DNA D-Loop analysis of Ecuadorian Pillareño Creole pigs from seven regions of Ecuador. To allow comparison, we also included in our analysis sequences from wild species, commercial lines, and domestic pigs, which were obtained from the NCBI GenBank database. Creole pigs' population showed overall moderate Hd values and low π values, and a negative value of Tajima's D was observed. The greatest differentiation from the Ecuadorian Pillareño Creole pigs was observed between Asian wild and Asian domestic pigs. The haplotype analysis revealed three different phylogenetic clades (A, E I, and E II) and 65 haplotypes. Ecuadorian Creole populations were grouped into nine haplotypes for Clade E I and E II, which have not previously been reported for Creole Pillareño populations. Our analysis indicates that in the establishment of Creole Pillareño pigs, individuals most likely separated from the Asian pig population and appear to be genetically influenced by European and Iberian populations raised in Spain.