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

Abstract

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.

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

“…We also identified candidate genes related to adaptation to hot temperatures in chicken species, such as FGF14 ( Coble et al, 2014 ) and NALCN ( Gu et al, 2020 ). The genes within the ROH island on GGA03 ( CLIC5, ENPP4, RCAN2, TDRD6, PLA2G7 IMP3, ANKRD66 MEP1A, ADGRF5 ) overlapped with an island reported in Italian turkey ( Bernini et al, 2021 ). Among these, we identified genes involved in immune responses, such as PLA2G7 ( Abasht et al, 2019 ) or reported as differentially expressed in dwarf and normal chickens ( ENPP4 ) ( Ye et al, 2014 ).…”

“…We identified genes associated with adaptation and survival in hot conditions, such as TRMT1L ( Walugembe et al, 2019 ), TBC1D5 ( Fleming et al, 2017 ), and PTGS2 ( Zhao et al, 2022 ), as well as genes associated with immune ( KCNH8 ) ( He et al, 2015 ) and inflammatory response ( SATB1 ) ( Zhang et al, 2016 ). It is also interesting to note within the ROH island on GGA08 mapped candidate genes related to reproductive physiology in avian species ( PTGS2 and PLA2G4 ) ( Bernini et al, 2021 ), or associated with the regulation of growth and body size ( COL11A1 ) ( Wang et al, 2017 ) and feed intake efficiency ( AMY1A ) ( Zhang et al, 2021 ).…”

Genome-wide mapping of signatures of selection using a high-density array identified candidate genes for growth traits and local adaptation in chickens

“…In chicken, several studies have reported that ROH regions can harbour candidate genes associated with production traits, immune response, and environmental adaptation [ 41 , 46 , 69 , 70 ]. For the group of heavy chickens, several genes in three regions of GGA3 have been reported as candidates related to muscle growth and overlap with ROH islands detected in Italian autochthonous turkey breeds [ 71 ]: BEND6 , which was identified as a candidate gene for intramuscular fat content in chicken [ 72 ]; COL21A1 , which is regulated by growth factors and is involved in muscle growth [ 73 ]; and BMP5 , which is a strong candidate gene for body size in livestock [ 74 ]. In the group of light chickens, we identified the AFF1 gene within a ROH island on GGA4, which is known to have a lower expression level in mallards (wild ancestors with a low weight) than in Pekin ducks (large body size), and thus is related with body weight [ 75 ].…”

Unraveling signatures of chicken genetic diversity and divergent selection in breed-specific patterns of early myogenesis, nitric oxide metabolism and post-hatch growth

“… Larkina et al (2021) proposed a phenotypic clustering model, supplementing the evolutionary model with two more breed types, i.e., dual purpose and fancy breeds (see breed examples in Table 1 ; Supplementary Material S2 ). Assessment of genetic diversity in various breeds is an important element in developing new strategies and applications for poultry breeding and production, as well as germplasm preservation ( Romanov and Weigend, 1999 ; 2001 ; Huang et al, 2016 ; Romanov et al, 2017 ; Romanov et al, 2021 ; Bernini et al, 2021 ; Dementieva et al, 2021 ).…”