Dog–human translational genomics: state of the art and genomic resources

Pallotti, Stefano; Piras, Ignazio S.; Marchegiani, Andrea; Cerquetella, Matteo; Napolioni, Valerio

doi:10.1007/s13353-022-00721-z

Cited by 9 publications

(1 citation statement)

References 87 publications

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“…Indeed, recent efforts were only made to evaluate either the use of Bovine SNP-chip [ 18 ] or to design ad-hoc SNP-chip [ 19 ] for performing genomic studies in alpaca, thus further highlighting the need of genomic studies on SACs. However, the advent of next-generation sequencing led to an enormous amount of genomic data from several species, freely available for evolutionary and zootechnical research [ 20 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide scan for runs of homozygosity in South American Camelids

Pallotti,

Picciolini,

Antonini

et al. 2023

BMC Genomics

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Background Alpaca (Vicugna pacos), llama (Lama glama), vicugna (Vicugna vicugna) and guanaco (Lama guanicoe), are the camelid species distributed over the Andean high-altitude grasslands, the Altiplano, and the Patagonian arid steppes. Despite the wide interest on these animals, most of the loci under selection are still unknown. Using whole-genome sequencing (WGS) data we investigated the occurrence and the distribution of Runs Of Homozygosity (ROHs) across the South American Camelids (SACs) genome to identify the genetic relationship between the four species and the potential signatures of selection. Results A total of 37 WGS samples covering the four species was included in the final analysis. The multi-dimensional scaling approach showed a clear separation between the four species; however, admixture analysis suggested a strong genetic introgression from vicugna and llama to alpaca. Conversely, very low genetic admixture of the guanaco with the other SACs was found. The four species did not show significant differences in the number, length of ROHs (100-500 kb) and genomic inbreeding values. Longer ROHs (> 500 kb) were found almost exclusively in alpaca. Seven overlapping ROHs were shared by alpacas, encompassing nine loci (FGF5, LOC107034918, PRDM8, ANTXR2, LOC102534792, BSN, LOC116284892, DAG1 and RIC8B) while nine overlapping ROHs were found in llama with twenty-five loci annotated (ERC2, FZD9, BAZ1B, BCL7B, LOC116284208, TBL2, MLXIPL, PHF20, TRNAD-AUC, LOC116284365, RBM39, ARFGEF2, DCAF5, EXD2, HSPB11, LRRC42, LDLRAD1, TMEM59, LOC107033213, TCEANC2, LOC102545169, LOC116278408, SMIM15, NDUFAF2 and RCOR1). Four overlapping ROHs, with three annotated loci (DLG1, KAT6B and PDE4D) and three overlapping ROHs, with seven annotated genes (ATP6V1E1, BCL2L13, LOC116276952, BID, KAT6B, LOC116282667 and LOC107034552), were detected for vicugna and guanaco, respectively. Conclusions The signatures of selection revealed genomic areas potentially selected for production traits as well as for natural adaptation to harsh environment. Alpaca and llama hint a selection driven by environment as well as by farming purpose while vicugna and guanaco showed selection signals for adaptation to harsh environment. Interesting, signatures of selection on KAT6B gene were identified for both vicugna and guanaco, suggesting a positive effect on wild populations fitness. Such information may be of interest to further ecological and animal production studies.

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Section: Introductionmentioning

confidence: 99%

Genome-wide scan for runs of homozygosity in South American Camelids

Pallotti,

Picciolini,

Antonini

et al. 2023

BMC Genomics

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Single-cell hemoprotein (heme-SCP) exerts the prebiotic potential to establish a healthy gut microbiota in small pet dogs

Lee

Choi

Park³

et al. 2022

Food Sci Biotechnol

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To investigate the effect of the single-cell hemoprotein (heme-SCP) source on animals, a dog-treat (100 g for each dog) harboring 0.2% heme-SCP was manufactured and fed to seven pet dogs (< 10 kg) in a randomized manner (irrespective of owner’s feeding style, dogs’ health conditions, and staple diets), and the feces before and after the dog-treat diet were analyzed to define the structure of the microbiota. The total bacterial species of the seven dogs showed no difference (564–584), although the bacterial compositions varied significantly. The Firmicutes phylum increased (54.7–73.7%), showing differential species composition before and after heme-SCP intake. Proteobacteria, Bacteroidetes, and Fusobacteria decreased (5.4–3.8%, 32.9–16.8%, and 6.3–3.6%, respectively), which agreed with the previous observation of deliberate feeding. Therefore, it is conceivable that heme-SCP as a prebiotic can shape the gut microbiota regardless of the administration method.

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