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Perini F, Cendron F, Lasagna E, Cassandro M, Penasa M. Genomic insights into shank and eggshell color in Italian local chickens. Poult Sci 2024; 103:103677. [PMID: 38593544 PMCID: PMC11004871 DOI: 10.1016/j.psj.2024.103677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 04/11/2024] Open
Abstract
Eggshell and shank color in poultry is an intriguing topic of research due to the roles in selection, breed recognition, and environmental adaptation. This study delves into the genomics foundations of shank and eggshell pigmentation in Italian local chickens through genome-wide association studies analysis to uncover the mechanisms governing these phenotypes. To this purpose, 483 animals from 20 local breeds (n = 466) and 2 commercial lines (n = 17) were considered and evaluated for shank and eggshell color. All animals were genotyped using the Affymetrix Axiom 600 K Chicken Genotyping Array. As regards shank color, the most interesting locus was detected on chromosome Z, close to the TYRP1 gene, known to play a key role in avian pigmentation. Additionally, several novel loci and genes associated with shank pigmentation, skin pigmentation, UV protection, and melanocyte regulation were identified (e.g., MTAP, CDKN2A, CDKN2B). In eggshell, fewer significant loci were identified, including SLC7A11 and MITF on chromosomes 4 and 12, respectively, associated with melanocyte processes and pigment synthesis. This comprehensive study shed light on the genetic architecture underlying shank and eggshell color in Italian native chicken breeds, contributing to a better understanding of this phenomenon which plays a role in breed identification and conservation, and has ecological and economic implications.
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Affiliation(s)
- Francesco Perini
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Legnaro, Padua 35020, Italy
| | - Filippo Cendron
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Legnaro, Padua 35020, Italy.
| | - Emiliano Lasagna
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia 06121, Italy
| | - Martino Cassandro
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Legnaro, Padua 35020, Italy
| | - Mauro Penasa
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Legnaro, Padua 35020, Italy
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Elblinger E, Bokor J, Bokor Á, Altbäcker V, Nagy J, Szabó J, Sárdi B, Bâlteanu A, Rónai Z, Rózsa L, Rátky J, Anton I, Zsolnai A. Parentage testing and looking for single nucleotide markers associated with antler quality in deer ( Cervus elaphus). Arch Anim Breed 2022; 65:267-274. [PMID: 36035877 PMCID: PMC9399935 DOI: 10.5194/aab-65-267-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 07/12/2022] [Indexed: 11/22/2022] Open
Abstract
To provide a cost-efficient parentage testing kit for red deer (Cervus elaphus), a 63 SNP set has been developed from a high-density Illumina
BovineHD BeadChip containing 777 962 SNPs after filtering of genotypes of 50
stags. The successful genotyping rate was 38.6 % on the chip. The ratio
of polymorphic loci among effectively genotyped loci was 6.5 %. The
selected 63 SNPs have been applied to 960 animals to perform parentage
control. Thirty SNPs out of the 63 had worked on the OpenArray platform. Their
combined value of the probability of identity and exclusion probability was
4.9×10-11 and 0.99803, respectively. A search for loci linked with antler quality was also performed on the
genotypes of the above-mentioned stags. Association studies revealed 14 SNPs
associated with antler quality, where low-quality antlers with short and
thin main beam antlers had values from 1 to 2, while high-quality antlers
with long and strong main beams had values between 4 and 5. The chance for a
stag to be correctly identified as having high-value antlers is expected to
be over 88 %.
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Affiliation(s)
- Edith Elblinger
- Kaposvár
Campus, Hungarian University of Agriculture and Life Sciences, Kaposvár, 7400, Hungary
| | - Julianna Bokor
- Game Management
Landscape Center, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, Bőszénfa, 7475, Hungary
| | - Árpád Bokor
- Kaposvár
Campus, Hungarian University of Agriculture and Life Sciences, Kaposvár, 7400, Hungary
| | - Vilmos Altbäcker
- Kaposvár
Campus, Hungarian University of Agriculture and Life Sciences, Kaposvár, 7400, Hungary
| | - János Nagy
- Game Management
Landscape Center, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, Bőszénfa, 7475, Hungary
| | - József Szabó
- Game Management
Landscape Center, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, Bőszénfa, 7475, Hungary
| | - Bertalan Sárdi
- Game Management
Landscape Center, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, Bőszénfa, 7475, Hungary
| | - Adrian Valentin Bâlteanu
- Institute of Life Sciences, University of Agricultural Sciences and Veterinary Medicine,
Cluj-Napoca, Romania
| | - Zsolt Rónai
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Eötvös Loránd University, Budapest, 1053, Hungary
| | - László Rózsa
- Kaposvár
Campus, Hungarian University of Agriculture and Life Sciences, Herceghalom, 2053, Hungary
| | - József Rátky
- Department of Obstetrics
and Food Animal Medicine Clinic, University of Veterinary Medicine Budapest, Budapest, 1078, Hungary
| | - István Anton
- Kaposvár
Campus, Hungarian University of Agriculture and Life Sciences, Herceghalom, 2053, Hungary
| | - Attila Zsolnai
- Kaposvár
Campus, Hungarian University of Agriculture and Life Sciences, Herceghalom, 2053, Hungary
- Institute for Farm Animal Gene Conservation, National Centre for
Biodiversity and Gene Conservation, Gödöllő, 2100, Hungary
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