A genome-wide perspective about the diversity and demographic history of seven Spanish goat breeds

Manunza, Arianna; Noce, Antonia; Serradilla, J. M.; Goyache, F.; Martínez, Amparo Martínez; Capote, J.; Delgado, Juan Vicente; Jordana, J.; Muñoz, Eva; Molina, A.; Landi, Vincenzo; Pons, A.; Balteanu, Valentin A.; Traoré, Amadou; Vidilla, M.; Sánchez-Rodríguez, Manuel; Sánchez, Armand; Cardoso, Tainã Figueiredo; Amills, Marcel

doi:10.1186/s12711-016-0229-6

Cited by 71 publications

(75 citation statements)

References 25 publications

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“…; Manunza et al . ). The F ROH and average lengths of the ROHs were higher in the BARI, BTAP, BUGI and KAMO than in the PATE, TAP and WTAP breeds.…”

Section: Discussionmentioning

confidence: 97%

Population structure, genetic diversity and selection signatures within seven indigenous Pakistani goat populations

et al. 2018

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Goat farming in Pakistan depends on indigenous breeds that have adapted to specific agro-ecological conditions. Pakistan has a rich resource of goat breeds, and the genetic diversity of these goat breeds is largely unknown. In this study, genetic diversity and population structure were characterized from seven indigenous goat breeds using the goat 50K SNP chip. The genetic diversity analysis showed that Bugi toori goats have the highest inbreeding level, consistent with the highest linkage disequilibrium, lowest diversity and long run of heterozygosity segments. This indicates that this breed should be prioritized in future conservation activities. The population structure analysis revealed four fairly distinct clusters (including Bugi toori, Bari, Black Tapri and some Kamori) and three other breeds that are seemingly the results of admixture between these or related groups (some Kamori, Pateri, Tapri and White Tapri). The selection signatures were evaluated in each breed. A total of 2508 putative selection signals were reported. The 26 significant windows were identified in more than four breeds, and selection signatures spanned several genes that directly or indirectly influence traits included coat colour variation (KIT), reproduction (BMPR1B, GNRHR, INSL6, JAK2 and EGR4), body size (SOCS2), ear size (MSRB3) and milk composition (ABCG2, SPP1, CSN1S2, CSN2, CSN3 and PROLACTIN).

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“…; Manunza et al . ). The F ROH and average lengths of the ROHs were higher in the BARI, BTAP, BUGI and KAMO than in the PATE, TAP and WTAP breeds.…”

Section: Discussionmentioning

confidence: 97%

Population structure, genetic diversity and selection signatures within seven indigenous Pakistani goat populations

et al. 2018

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“…To date, the global diversity of local goats has been assessed using various molecular tools, and such studies have been conducted in Spain (Ferrando et al., ; Manunza et al., ), Africa (Awotunde et al., ; Kibegwa, Githui, Jung'a, Badamana, & Nyamu, ; Mdladla, Dzomba, Huson, & Muchadeyi, ), the Americas (Carvalho, Paiva, Araújo, Mariante, & Blackburn, ), Europe (Bulut, Kurar, Ozsensoy, Altunok, & Nizamlioglu, ; Windig et al., ), and Asia (Lin et al., ; Nicoloso et al., ; Waki, Sasazaki, Kobayashi, & Mannen, ; Yadav, Gahlot, Gahlot, Asraf, & Yadav, ).…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity of the Chinese goat in the littoral zone of the Yangtze River as assessed by microsatellite and mtDNA

Guang‐Xin

Zhao

Chen

et al. 2018

Ecology and Evolution

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The objective of this study was to assess the genetic diversity and population structure of goats in the Yangtze River region using microsatellite and mtDNA to better understand the current status of those goat genetic diversity and the effects of natural landscape in fashion of domestic animal genetic diversity. The genetic variability of 16 goat populations in the littoral zone of the Yangtze River was estimated using 21 autosomal microsatellites, which revealed high diversity and genetic population clustering with a dispersed geographical distribution. A phylogenetic analysis of the mitochondrial D‐loop region (482 bp) was conducted in 494 goats from the Yangtze River region. In total, 117 SNPs were reconstructed, and 173 haplotypes were identified, 94.5% of which belonged to lineages A and B. Lineages C, D, and G had lower frequencies (5.2%), and lineage F haplotypes were undetected. Several high‐frequency haplotypes were shared by different ecogeographically distributed populations, and the close phylogenetic relationships among certain low‐frequency haplotypes indicated the historical exchange of genetic material among these populations. In particular, the lineage G haplotype suggests that some west Asian goat genetic material may have been transferred to China via Muslim migration.

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“…), Spain (Manunza et al . ) and Italy (Nicoloso et al . ) as well as for commercial goats from Canada and Australia (Brito et al .…”

Section: Discussionmentioning

confidence: 99%

Genome‐wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds

et al. 2018

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SummaryUganda has a large population of goats, predominantly from indigenous breeds reared in diverse production systems, whose existence is threatened by crossbreeding with exotic Boer goats. Knowledge about the genetic characteristics and relationships among these Ugandan goat breeds and the potential admixture with Boer goats is still limited. Using a medium‐density single nucleotide polymorphism (SNP) panel, we assessed the genetic diversity, population structure and admixture in six goat breeds in Uganda: Boer, Karamojong, Kigezi, Mubende, Small East African and Sebei. All the animals had genotypes for about 46 105 SNPs after quality control. We found high proportions of polymorphic SNPs ranging from 0.885 (Kigezi) to 0.928 (Sebei). The overall mean observed (HO) and expected (HE) heterozygosity across breeds was 0.355 ± 0.147 and 0.384 ± 0.143 respectively. Principal components, genetic distances and admixture analyses revealed weak population sub‐structuring among the breeds. Principal components separated Kigezi and weakly Small East African from other indigenous goats. Sebei and Karamojong were tightly entangled together, whereas Mubende occupied a more central position with high admixture from all other local breeds. The Boer breed showed a unique cluster from the Ugandan indigenous goat breeds. The results reflect common ancestry but also some level of geographical differentiation. admixture and f4 statistics revealed gene flow from Boer and varying levels of genetic admixture among the breeds. Generally, moderate to high levels of genetic variability were observed. Our findings provide useful insights into maintaining genetic diversity and designing appropriate breeding programs to exploit within‐breed diversity and heterozygote advantage in crossbreeding schemes.

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A genome-wide perspective about the diversity and demographic history of seven Spanish goat breeds

Cited by 71 publications

References 25 publications

Population structure, genetic diversity and selection signatures within seven indigenous Pakistani goat populations

Population structure, genetic diversity and selection signatures within seven indigenous Pakistani goat populations

Genetic diversity of the Chinese goat in the littoral zone of the Yangtze River as assessed by microsatellite and mtDNA

Genome‐wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds

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