Genomics of Dwarfism in Italian Local Chicken Breeds

Overview

Journal Genes (Basel)

Publisher MDPI

Date 2023 Mar 29

PMID 36980905

Authors

Francesco Perini

Filippo Cendron

Zhou Wu

Natalia Sevane

Zhiqiang Li

Chunhua Huang

Jacqueline Smith

Emiliano Lasagna

Martino Cassandro

Mauro Penasa

Affiliations

Soon will be listed here.

Abstract

The identification of the dwarf phenotype in chicken is based on body weight, height, and shank length, leaving the differentiation between dwarf and small breeds ambiguous. The aims of the present study were to characterize the sequence variations associated with the dwarf phenotype in three Italian chicken breeds and to investigate the genes associated with their phenotype. Five hundred and forty-one chickens from 23 local breeds (from 20 to 24 animals per breed) were sampled. All animals were genotyped with the 600 K chicken SNP array. Three breeds were described as "dwarf", namely, Mericanel della Brianza (MERI), Mugellese (MUG), and Pepoi (PPP). We compared MERI, MUG, and PPP with the four heaviest breeds in the dataset by performing genome-wide association studies. Results showed significant SNPs associated with dwarfism in the MERI and MUG breeds, which shared a candidate genomic region on chromosome 1. Due to this similarity, MERI and MUG were analyzed together as a meta-population, observing significant SNPs in the and genes, which were previously reported as being responsible for dwarfism in different species. In conclusion, MERI and MUG breeds seem to share a genetic basis of dwarfism, which differentiates them from the small PPP breed.

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References

Carneiro M, Hu D, Archer J, Feng C, Afonso S, Chen C . Dwarfism and Altered Craniofacial Development in Rabbits Is Caused by a 12.1 kb Deletion at the HMGA2 Locus. Genetics. 2016; 205(2):955-965. PMC: 5289862. DOI: 10.1534/genetics.116.196667. View

Popow J, Alleaume A, Curk T, Schwarzl T, Sauer S, Hentze M . FASTKD2 is an RNA-binding protein required for mitochondrial RNA processing and translation. RNA. 2015; 21(11):1873-84. PMC: 4604428. DOI: 10.1261/rna.052365.115. View

Tews D, Fromme T, Keuper M, Hofmann S, Debatin K, Klingenspor M . Teneurin-2 (TENM2) deficiency induces UCP1 expression in differentiating human fat cells. Mol Cell Endocrinol. 2017; 443:106-113. DOI: 10.1016/j.mce.2017.01.015. View

Cho S, Manjula P, Kim M, Cho E, Lee D, Lee S . Comparison of Selection Signatures between Korean Native and Commercial Chickens Using 600K SNP Array Data. Genes (Basel). 2021; 12(6). PMC: 8230197. DOI: 10.3390/genes12060824. View

Li Y, Bian M, Zhou Z, Wu X, Ge X, Xiao T . Circular RNA SIPA1L1 regulates osteoblastic differentiation of stem cells from apical papilla via miR-204-5p/ALPL pathway. Stem Cell Res Ther. 2020; 11(1):461. PMC: 7607702. DOI: 10.1186/s13287-020-01970-7. View

Lambert M, Spinazzola J, Widrick J, Pakula A, Conner J, Chin J . PDE10A Inhibition Reduces the Manifestation of Pathology in DMD Zebrafish and Represses the Genetic Modifier PITPNA. Mol Ther. 2020; 29(3):1086-1101. PMC: 7934586. DOI: 10.1016/j.ymthe.2020.11.021. View

Mannelli F, Franzoni A, Galigani I, Nistri V, Daghio M, Scicutella F . Characterization of morphological, reproductive, and productive performances of Mugellese breed: an update of knowledge. Poult Sci. 2022; 102(1):102259. PMC: 9679384. DOI: 10.1016/j.psj.2022.102259. View

Alyaqoub F, Pyatt R, Bailes A, Brock A, Deeg C, McKinney A . 12q14 microdeletion associated with HMGA2 gene disruption and growth restriction. Am J Med Genet A. 2012; 158A(11):2925-30. DOI: 10.1002/ajmg.a.35610. View

Wang L, Frey M, Kohli R . The Role of FGF19 and MALRD1 in Enterohepatic Bile Acid Signaling. Front Endocrinol (Lausanne). 2022; 12:799648. PMC: 8804323. DOI: 10.3389/fendo.2021.799648. View

10.

Cendron F, Perini F, Mastrangelo S, Tolone M, Criscione A, Bordonaro S . Genome-Wide SNP Analysis Reveals the Population Structure and the Conservation Status of 23 Italian Chicken Breeds. Animals (Basel). 2020; 10(8). PMC: 7460279. DOI: 10.3390/ani10081441. View

11.

Stuck M, Conley S, Naash M . Retinal Degeneration Slow (RDS) Glycosylation Plays a Role in Cone Function and in the Regulation of RDS·ROM-1 Protein Complex Formation. J Biol Chem. 2015; 290(46):27901-13. PMC: 4646032. DOI: 10.1074/jbc.M115.683698. View

12.

COLE R . An autosomal dwarfism in the domestic fowl. Poult Sci. 2000; 79(11):1507-16. DOI: 10.1093/ps/79.11.1507. View

13.

Addis L, Ahn J, Dobson R, Dixit A, Ogilvie C, Pinto D . Microdeletions of ELP4 Are Associated with Language Impairment, Autism Spectrum Disorder, and Mental Retardation. Hum Mutat. 2015; 36(9):842-50. DOI: 10.1002/humu.22816. View

14.

Kranis A, Gheyas A, Boschiero C, Turner F, Yu L, Smith S . Development of a high density 600K SNP genotyping array for chicken. BMC Genomics. 2013; 14:59. PMC: 3598943. DOI: 10.1186/1471-2164-14-59. View

15.

Ahlers-Dannen K, Yang J, Spicer M, Maity B, Stewart A, Koland J . Protein Profiling of RGS6, a Pleiotropic Gene Implicated in Numerous Neuropsychiatric Disorders, Reveals Multi-Isoformic Expression and a Novel Brain-Specific Isoform. eNeuro. 2021; 9(1). PMC: 8805202. DOI: 10.1523/ENEURO.0379-21.2021. View

16.

Colli L, Jessop L, Myers T, Camp S, Machiela M, Choi J . Altered regulation of DPF3, a member of the SWI/SNF complexes, underlies the 14q24 renal cancer susceptibility locus. Am J Hum Genet. 2021; 108(9):1590-1610. PMC: 8456159. DOI: 10.1016/j.ajhg.2021.07.009. View

17.

Saric A, Freeman S, Williamson C, Jarnik M, Guardia C, Fernandopulle M . SNX19 restricts endolysosome motility through contacts with the endoplasmic reticulum. Nat Commun. 2021; 12(1):4552. PMC: 8316374. DOI: 10.1038/s41467-021-24709-1. View

18.

Lange M, Kaynak B, Forster U, Tonjes M, Fischer J, Grimm C . Regulation of muscle development by DPF3, a novel histone acetylation and methylation reader of the BAF chromatin remodeling complex. Genes Dev. 2008; 22(17):2370-84. PMC: 2532927. DOI: 10.1101/gad.471408. View

19.

Kundu A, Nam H, Shelar S, Chandrashekar D, Brinkley G, Karki S . PRDM16 suppresses HIF-targeted gene expression in kidney cancer. J Exp Med. 2020; 217(6). PMC: 7971134. DOI: 10.1084/jem.20191005. View

20.

Li Z, Gilbert J, Zhang Y, Zhang M, Qiu Q, Ramanujan K . An HMGA2-IGF2BP2 axis regulates myoblast proliferation and myogenesis. Dev Cell. 2012; 23(6):1176-88. PMC: 3645921. DOI: 10.1016/j.devcel.2012.10.019. View