A multi-farm assessment of Greek black pig genetic diversity using microsatellite molecular markers

Michailidou, Sofia; Kalivas, Apostolos; Ganopoulos, Ioannis; Stea, Eleni A.; Michailidis, Georgios; Tsaftaris, Athanasios; Argiriou, Anagnostis

doi:10.4238/2014.april.14.4

Cited by 14 publications

(17 citation statements)

References 22 publications

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“…This paper aimed to explore the population structure and genetic diversity of various PhNP populations in Luzon and Visayas and to identify conservation priorities. Our study showed that the PhNP exhibited high allelic richness and a population structure ( In PhNP, we identified higher allelic diversity and heterozygosity (Table 2) than the values reported in indigenous pigs of Bulgaria, Croatia, and Greece, but lower values than those reported in South Africa and the Iberian pig (Fabuel et al, 2004;Gvozdanović et al, 2019;Ishikawa et al, 2021;Michailidou et al, 2014;Swart et al, 2010). Our results show the importance of PhNP as a repository of alleles, and provide clues about how its fitness has been improved despite production constraints.…”

Section: Discussionsupporting

confidence: 55%

Genetic diversity and population structure analysis of Philippine native pigs highlight five priority populations for conservation

Banayo,

Manese,

Furusho

et al. 2023

Ecology and Evolution

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The Philippine native pig (PhNP) is a unique genetic resource composed of multiple domesticated Sus scrofa lineages and interspecific hybrids. No prior study has determined the population structure and genetic diversity of PhNPs on multiple islands and provinces, which is essential for establishing conservation priorities. In this study, we explore the population structure and genetic diversity of various PhNP populations in Luzon and the Visayas, Philippines, to identify conservation priorities. We analyzed seven PhNP populations (n = 20–27 samples each; Benguet [B], Kalinga [K], Nueva Vizcaya [N], Isabela [I], Quezon [Q], Marinduque [M], and Samar [S]) and four transboundary breeds present in the Philippines (n = 9–11 samples each; Duroc, Large White, Landrace, and Berkshire). The pigs were compared against a panel of 20 microsatellite markers recommended by the ISAG–FAO. We tested for population structure at the island, region, and province levels. Strong genetic differentiation between native and transboundary breeds was confirmed by Bayesian clustering (k = 2) and Nei's DA genetic distance (100% bootstrap support for the PhNP cluster). PhNP exhibited high heterozygosity (Ho: 0.737), a high allele count (Na: 7.771), and a low inbreeding coefficient (Fis: −0.040–0.125). Bayesian clustering supported genetic differentiation at the island (k = 2; North Luzon and South Luzon‐Visayas cluster), region (k = 3), and population (k = 8) levels. The pairwise F'st between PhNP populations ranged from 0.084 (N and I) to 0.397 (Q and K), confirming that some PhNP populations exhibited sufficient genetic distance to be considered separate populations. This study shows that native pigs from B, K, I, Q, M, and S are unique genetic units for conservation. Furthermore, the small effective population sizes of B, I, Q, M, and S (Ne: 3.9, 19.1, 14.2, 44.7, and 22.5, respectively) necessitate immediate conservation actions, such as incentivizing PhNP farming.

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Section: Discussionsupporting

confidence: 55%

Genetic diversity and population structure analysis of Philippine native pigs highlight five priority populations for conservation

Banayo,

Manese,

Furusho

et al. 2023

Ecology and Evolution

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“…The inbreeding coefficient ( F IS ) was negative for all farm populations, with most of the values significant. Negative F IS values have been similarly observed in other semi‐wild swine (native breeds) such as the Greek black pig (Michailidou et al, 2014), Ryukyu pig (Takada et al, 2018), and Nero Siciliano pig (Guastella et al, 2010). The negative values suggest that the EBS farms are undertaking mating with other strains and/or non‐random mating to prevent inbreeding.…”

Section: Discussionmentioning

confidence: 72%

Population genetic structure and diversity of the East Balkan Swine (Sus scrofa) in Bulgaria, revealed by mitochondrial DNA and microsatellite analyses

Ishikawa

Doneva²,

Raichev

et al. 2021

Animal Science Journal

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The East Balkan Swine (EBS) is the only indigenous pig breed in Bulgaria. We analyzed the mitochondrial DNA (mtDNA) control region and 21 microsatellite loci for 198 individuals from 11 farms in Bulgaria. Obtained 11 mtDNA haplotypes including three novel ones were grouped to two major clades, European clade E1 (146/198 individuals, 73.7%) and Asian clade A (52/198, 26.3%). The mixture of the two clades may have resulted from historical crossbreeding between the European and Asian pig breeds. Clade A was frequent in southeastern Bulgaria (Burgas Province), but less frequent or absent in northeastern Bulgaria (Varna and Shumen Provinces). The distribution of Europe‐ and Asia‐specific haplotypes relative to EBS farm locations could be attributed to regional differences of breeding systems (e.g., crossbreeding with imported commercial pigs). A microsatellite analysis showed high heterozygosities for all the EBS farms, and negative inbreeding coefficients presumably due to crossing with commercial pigs or wild boars and/or efforts to reduce inbreeding by farmers. Bayesian clustering analyses showed that all farm populations are genetically well distinguishable from one another. Although diversity has been maintained by the efforts of farmers and a breeding association, the effective population size remains small, and conservation efforts should be continued.

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“…distribution than Lanyu pigs (Chang et al 2009). Henan Western Black pigs had a higher heterozygosity (0.6802) than several breeds including European pigs breeds (0.570) (Zhang and Graham, 2011), the Greek black pigs breeds (0.624) (Michailidou et al 2014), the Criollo pigs breeds (0.622) (Revidatti et al 2014), however, Henan Western Black Pigs were lower than Jeju Black Pig (0.706) (Oh et al 2014). Thus, the Black Pig populations of Henan Western Black Pigs appear to have higher levels of genetic polymorphism than the experiment of Sahoo (2015b).The Shannon index reflects the uniformity of genetic variation.…”

Section: Resultsmentioning

confidence: 93%

Microsatellite DNA Markers and Their Correlation with Body Traits in Landrace, Duroc and Henan Western Black Pigs

Yang

Bian

Pang

et al. 2019

IJAR

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Twelve microsatellite loci were selected from the Food and Agriculture Organization of the United Nations to examine the genetic structure and relationship between microsatellite DNA and body traits including height, back height, body length, chest width, chest depth, head Length, Ear area, and forehead width. Twelve microsatellite loci analyzed were polymorphic in Landrace, Duroc and Henan Western Black Pigs. The total number of alleles found for the twelve microsatellite loci amounted to 150.The average expected heterozygositie ranged from 0.1287 to 0.8301 among twelve loci, and the average polymorphic information content ranged from 0.1168 to 0.7894. The results of cluster analysis showed that the genetic distance between Henan Western Black Pigs and Duroc was least 0.1414. Microsatellite loci of SW72 were significantly associated with back height and chest depth (plessthan0.05), while SO002 were significantly associated with chest depth and head Length (plessthan0.05). Finally, the results showed that Henan Western Black Pigs has a high level of genetic polymorphism and genetic differentiation. Cluster analysis shows that the relationship between Black Pigs and Duroc is closer. These were significantly associated with body traits in five microsatellite loci, including SW72, SO002, SW632, SO090 and SW1828 (plessthan0.05). These results provided scientific reference for the further cultivation and utilization of black pigs.

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A multi-farm assessment of Greek black pig genetic diversity using microsatellite molecular markers

Cited by 14 publications

References 22 publications

Genetic diversity and population structure analysis of Philippine native pigs highlight five priority populations for conservation

Genetic diversity and population structure analysis of Philippine native pigs highlight five priority populations for conservation

Population genetic structure and diversity of the East Balkan Swine (Sus scrofa) in Bulgaria, revealed by mitochondrial DNA and microsatellite analyses

Microsatellite DNA Markers and Their Correlation with Body Traits in Landrace, Duroc and Henan Western Black Pigs

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