Genomic Tools for the Characterization of Local Animal Genetic Resources: Application in Mascaruna Goat

Tolone, Marco; Sardina, Maria Teresa; Senczuk, Gabriele; Chessari, Giorgio; Criscione, Andrea; Moscarelli, Angelo; Riggio, Silvia; Rizzuto, Ilaria; Gerlando, Rosalia Di; Portolano, Baldassare; Mastrangelo, Salvatore

doi:10.3390/ani12202840

Cited by 7 publications

(7 citation statements)

References 53 publications

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“…In this context, it is well-known that body size is strongly related to warm climate responses and might impose severe constraints on adaptive variation [ 52 , 53 ]. Moreover, this genomic region also overlapped with previously reported ROH islands in southern Italian goats [ 18 , 54 , 55 ] and in Merino and Merino-derived sheep breeds reared in different climatic zones [ 56 ]. One last genomic region shared between the two approaches was detected on CHI6 (16.4–18.2 Mb) in both the PAL-TIS window-based F ST comparisons and in the Palmera ROH islands.…”

Section: Discussionsupporting

confidence: 76%

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

Senczuk,

Macrì,

Di Civita

et al. 2024

Genet Sel Evol

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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.

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Section: Discussionsupporting

confidence: 76%

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

Senczuk,

Macrì,

Di Civita

et al. 2024

Genet Sel Evol

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“…A population’s genetic structure is determined by the interaction of processes such as gene flow, mutation, selection, and mating strategy ( Muriira et al, 2018 ). The population structure of Uganda’s indigenous goats has, for the first time, been analyzed based on whole genome SNP genotyping with the Goat_IGGC_65K_v2 SNP chip ( Tolone et al, 2022 ). The genetic population structure was assessed through PCA, admixture analysis, and discriminant analysis of principal components (DAPC).…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity, population structure and kinship relationships highlight the environmental influence on Uganda’s indigenous goat populations

Nantongo,

Birungi,

Opiyo

et al. 2024

Front. Genet.

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Knowledge about genetic diversity and population structure among goat populations is essential for understanding environmental adaptation and fostering efficient utilization, development, and conservation of goat breeds. Uganda’s indigenous goats exist in three phenotypic groups: Mubende, Kigezi, and Small East African. However, a limited understanding of their genetic attributes and population structure hinders the development and sustainable utilization of the goats. Using the Goat Illumina 60k chip International Goat Genome Consortium V2, the whole-genome data for 1,021 indigenous goats sourced from 10 agroecological zones in Uganda were analyzed for genetic diversity and population structure. A total of 49,337 (82.6%) single-nucleotide polymorphism markers were aligned to the ARS-1 goat genome and used to assess the genetic diversity, population structure, and kinship relationships of Uganda’s indigenous goats. Moderate genetic diversity was observed. The observed and expected heterozygosities were 0.378 and 0.383, the average genetic distance was 0.390, and the average minor allele frequency was 0.30. The average inbreeding coefficient (Fis) was 0.014, and the average fixation index (Fst) was 0.016. Principal component analysis, admixture analysis, and discriminant analysis of principal components grouped the 1,021 goat genotypes into three genetically distinct populations that did not conform to the known phenotypic populations but varied across environmental conditions. Population 1, comprising Mubende (90%) and Kigezi (8.1%) goats, is located in southwest and central Uganda, a warm and humid environment. Population 2, which is 59% Mubende and 49% Small East African goats, is located along the Nile Delta in northwestern Uganda and around the Albertine region, a hot and humid savannah grassland. Population 3, comprising 78.4% Small East African and 21.1% Mubende goats, is found in northeastern to eastern Uganda, a hot and dry Commiphora woodlands. Genetic diversity and population structure information from this study will be a basis for future development, conservation, and sustainable utilization of Uganda’s goat genetic resources.

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“…These 2 subpopulations behave differently; in fact the individuals here sampled exhibited an admixed patterns, whereas those from Cendron et al (2020) clustered homogeneously. The low levels of admixture in the first subgroup indicated the few remaining genomic components of any other ancestral populations that may have interacted with them, as well as a potential typical signal of inbreeding ( Tolone et al, 2022 ). Therefore, the genetic structure detected for Val Platani could be due to the introgression of genes from other populations (VPL) and/or to geographical isolation for a long time with genetic drift (VLP).…”

Section: Discussionmentioning

confidence: 99%

High-density single nucleotide polymorphism markers reveal the population structure of 2 local chicken genetic resources

Tolone¹,

Sardina²,

Criscione³

et al. 2023

Poultry Science

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Genomic Tools for the Characterization of Local Animal Genetic Resources: Application in Mascaruna Goat

Cited by 7 publications

References 53 publications

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

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

Genetic diversity, population structure and kinship relationships highlight the environmental influence on Uganda’s indigenous goat populations

High-density single nucleotide polymorphism markers reveal the population structure of 2 local chicken genetic resources

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