Genome-wide analysis reveals the patterns of genetic diversity and population structure of 8 Italian local chicken breeds

Cendron, Filippo; Mastrangelo, Salvatore; Tolone, Marco; Perini, Francesco; Lasagna, Emiliano; Cassandro, Martino

doi:10.1016/j.psj.2020.10.023

Cited by 22 publications

(23 citation statements)

References 34 publications

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“…A similar high level of homozygosity has been identified in Italian local chicken breeds [ 30 ], where low values of heterozygosity underline the difficulties of maintaining a fair level of genetic variability in breeds under an in situ conservation plan.…”

Section: Discussionsupporting

confidence: 58%

Genetic Diversity and Identification of Homozygosity-Rich Genomic Regions in Seven Italian Heritage Turkey (Meleagris gallopavo) Breeds

Bernini

Bagnato

Marelli

et al. 2021

Genes

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Italian autochthonous turkey breeds are an important reservoir of genetic biodiversity that should be maintained with an in vivo approach. The aim of this study, part of the TuBAvI national project on biodiversity, was to use run of homozygosity (ROH), together with others statistical approaches (e.g., Wright’s F-statistics, principal component analysis, ADMIXTURE analysis), to investigate the genomic diversity in several heritage turkey breeds. We performed a genome-wide characterization of ROH-rich regions in seven autochthonous turkey breeds, i.e., Brianzolo (Brzl), Bronzato Comune Italiano (BrCI), Bronzato dei Colli Euganei (CoEu), Parma e Piacenza (PrPc), Nero d’Italia (NeIt), Ermellinato di Rovigo (ErRo) and Romagnolo (Roma). ROHs were detected based on a 650K SNP genotyping. ROH_islands were identified as homozygous ROH regions shared by at least 75% of birds (within breed). Annotation of genes was performed with DAVID. The admixture analyses revealed that six breeds are unique populations while the Roma breed consists in an admixture of founder populations. Effective population size estimated on genomic data shows a numeric contraction. ROH_islands harbour genes that may be interesting for target selection in commercial populations also. Among them the PTGS2 and PLA2G4A genes on chr10 were related to reproduction efficiency. This is the first study mapping genetic variation in autochthonous turkey populations. Breeds were genetically different among them, with the Roma breed proving to be a mixture of the other breeds. The ROH_islands identified harboured genes peculiar to the selection that occurred in heritage breeds. Finally, this study releases previously undisclosed information on existing genetic variation in the turkey species.

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Section: Discussionsupporting

confidence: 58%

Genetic Diversity and Identification of Homozygosity-Rich Genomic Regions in Seven Italian Heritage Turkey (Meleagris gallopavo) Breeds

Bernini

Bagnato

Marelli

et al. 2021

Genes

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“…Generally, the within-breed genetic diversity of the studied chicken breeds is low (Ho = 0.44 and K BW = 0.53) similar to the results obtained by Zanetti et al (2011) in a survey carried out on a group of native chicken breed from Veneto region and by Ceccobelli et al (2013) in a study carried out on five native chicken breeds reared in Middle Italy. He and Ho were markedly different among the breeds as reported by Cendron et al (2021), wavering between 0.17 and 0.69 in Bianca di Saluzzo and Livorno Bianca, respectively. The average Ho in some breeds was lower than that reported in previous studies based on microsatellite markers (Zanetti et al, 2010(Zanetti et al, , 2011) and more similar with SNP genetic variability reported by Cendron et al (2020Cendron et al ( , 2021; this Ho deficit could be due to an increase in inbreeding linked to a reduction in the number of individuals within the breed over the years.…”

Section: Potential Shortcomingsmentioning

confidence: 69%

“…He and Ho were markedly different among the breeds as reported by Cendron et al (2021), wavering between 0.17 and 0.69 in Bianca di Saluzzo and Livorno Bianca, respectively. The average Ho in some breeds was lower than that reported in previous studies based on microsatellite markers (Zanetti et al, 2010(Zanetti et al, , 2011) and more similar with SNP genetic variability reported by Cendron et al (2020Cendron et al ( , 2021; this Ho deficit could be due to an increase in inbreeding linked to a reduction in the number of individuals within the breed over the years. This is highlighted by a small number of alleles per locus detected in many breeds (6.71-1.86; mean = 3.62) but also by low heterozygosity estimates (0.69-0.17), and high within-breed inbreeding (0.67-0.31).…”

Section: Potential Shortcomingsmentioning

confidence: 69%

“…Microsatellites are a reliable tool to investigate the genetic variability due to their high polymorphism, the codominant inheritance, and the even distribution throughout the genome ( Cheng et al, 1995 ) and were used in other autochthonous chicken breeds ( De Marchi et al, 2005a , b ; Tadano et al, 2007 ; Zanetti et al, 2010 , 2011 ), although some results were also obtained from the investigation of the mt-DNA polymorphism in some European chicken breeds ( Revay et al, 2010 ; Englund et al, 2014 ). Moreover, in Malomane et al (2019) with the aid of a single-nucleotide polymorphism (SNP) investigation, provided an interesting picture of the genetic variability of 201 chicken breeds spread all over the world and included the Padovana breed; more recent articles ( Cendron et al, 2020 , 2021 ) reported a markedly different level of genomic inbreeding among Italian chicken breeds based on runs of homozygosity (FROH). We investigated the level of genetic diversity, molecular kinship, inbreeding, contribution to overall genetic diversity, and rate of extinction of each breed.…”

Section: Introductionmentioning

confidence: 99%

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Genetic Diversity of 17 Autochthonous Italian Chicken Breeds and Their Extinction Risk Status

et al. 2021

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The preservation of genetic variability of autochthonous poultry breeds is crucial in global biodiversity. A recent report revealed small breed size and potential risk of extinction of all native Italian poultry breeds; therefore, a correct assessment of their genetic diversity is necessary for a suitable management of their preservation. In this work, we provided an overview of the contribution to poultry biodiversity of some Italian autochthonous breeds reared in conservation centers devoted to local biodiversity preservation. The level of genetic diversity, molecular kinship, inbreeding, contribution to overall genetic diversity, and rate of extinction of each breed were analyzed with a set of 14 microsatellite loci in 17 autochthonous chicken breeds. To evaluate genetic variability, total number (Na), and effective number (Ne) of alleles, observed (Ho) and expected (He) heterozygosity, and F (Wright’s inbreeding coefficient) index were surveyed. The contribution of each analyzed breed to genetic diversity of the whole dataset was assessed using MolKin3.0; global genetic diversity and allelic richness contributions were evaluated. All the investigated loci were polymorphic; 209 alleles were identified (94 of which private alleles). The average number of alleles per locus was 3.62, and the effective number of alleles was 2.27. The Ne resulted lower in all breeds due to the presence of low-frequency alleles that can be easily lost by genetic drift, thus reducing the genetic variability of the breeds, and increasing their risk of extinction. The global molecular kinship was 27%, the average breed molecular kinship was 53%, and the mean inbreeding rate 43%, with a self-coancestry of 78%. Wright’s statistical analysis showed a 41% excess of homozygous due to breed genetic differences (34%) and to inbreeding within the breed (9%). Genetic variability analysis showed that 11 breeds were in endangered status. The contribution to Italian poultry genetic diversity, estimated as global genetic diversity, and ranged from 30.2 to 98.5%. In conclusion, the investigated breeds maintain a unique genetic pattern and play an important role in global Italian poultry biodiversity, providing a remarkable contribution to genetic variability.

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“…In chickens, ROH has been applied to assess the genome-wide diversity in local and imported genetic resources, which contributes to maintain an effective program for conservation of endangered populations [10][11][12][13]. The long-term selection molded the presence of ROHs and their associated genomic regions resulting in unique population adaptation to environment-imposed challenges in broilers, suggesting that ROHs are likely the result of selection events and not attributable only to demographic and population history [14].…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Run of Homozygosity Analysis Reveals Candidate Genomic Regions Associated with Environmental Adaptations of Tibetan Native Chickens

Yuan

Sheng

et al. 2021

Preprint

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Background In Tibet, two most important breeds are Tibetan chicken and Lhasa white chicken, and the duo exhibit specific adaptations to high altitude and produce indispensable protein for humans living in the plateau. These breeds were partly included in conservation plans as their biodiversity is important as a genetic resource. However, population genetic analysis of the chickens is rarely investigated. Based on whole-genome sequencing data of 113 chickens from 4 Tibetan chicken population including Shigatse (SH), Nyemo (NM), Dagze (DZ) and Nyingchi (LZ), as well as Lhasa white (LW) chicken population, we performed genetic diversity and differentiation, run of homozygosity (ROH), genomic inbreeding and selection signature analyses. Results Our results showed high genetic diversity across the five chicken populations. The linkage disequilibrium decay was highest in LZ, and moderate level of genetic differentiation was found between LZ and other populations (Fst ranging from 0.05 to 0.10). Furthermore, the highest ROH-based inbreeding estimate (FROH) was 0.11 in LZ, whereas it ranges from 0.04 to 0.06 in the other four chicken populations. In total, 74, 111, 62, 42 and 54 ROHs containing SNPs with concurrency ranked top 1% were identified for SH, NM, DZ, LZ and LW, respectively. BDNF, CCDC34, LGR4, LIN7C, GLS, LOC101747789, MYO1B, STAT1 and STAT4 were shared genes harbored by these ROHs in the five populations, suggesting their important roles in adaptation of the chickens. Combined with selection signature analysis, we also identified a common candidate genomic region harboring AMY2A, NTNG1 and VAV3 genes. These genes have been reported to contribute to digestion, neurite growth and high-altitude adaptation, which could be involved in selection during evolution process. Conclusions High genetic diversity was observed in Tibetan native chickens. Nyingchi population, possessing highest FROH, is genetically distant from other chicken population. Candidate genes in ROH islands could aid the genetic characterization of the five Tibetan native chicken populations. Our findings contribute to the understanding of genetic diversity and offer valuable insights for the genetic mechanism of adaptation, as well as provide veritable tools that can help in the design and implementation of breeding and conservation strategies for Tibetan native chickens.

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Genome-wide analysis reveals the patterns of genetic diversity and population structure of 8 Italian local chicken breeds

Cited by 22 publications

References 34 publications

Genetic Diversity and Identification of Homozygosity-Rich Genomic Regions in Seven Italian Heritage Turkey (Meleagris gallopavo) Breeds

Genetic Diversity and Identification of Homozygosity-Rich Genomic Regions in Seven Italian Heritage Turkey (Meleagris gallopavo) Breeds

Genetic Diversity of 17 Autochthonous Italian Chicken Breeds and Their Extinction Risk Status

Genome-Wide Run of Homozygosity Analysis Reveals Candidate Genomic Regions Associated with Environmental Adaptations of Tibetan Native Chickens

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