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Abstract Background Black bone sheep was first discovered in Yunnan province of China in 1970, with unique black pigmentation on the body and internal organs. Endothelin 3 (EDN3) has been known as a key gene causing hyperpigmentation in black bone chicken, the Silky fowl. Methods In this study, EDN3 was employed as a candidate gene for regulating b...
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Context 1
... PCR products from the liver tissue were 1,235 bp. The products obtained from the RACE experiment were 500 bp and 350 bp for the 5′-and 3′-fragments, respect- ively (Fig. 2). The data obtained by GenScan software showed that the full length of EDN3 mRNA was 1,578 bp in- Fig. ...
Context 2
... file 1: Figure S1. Alignments of EDN3 protein with different species. Figure S2. Prediction secondary structure of EDN3 protein. t, refers to Beta turn; c, to Random coil; h, to Alpha helices; e, to Extended strand. (DOCX 13238 kb) Additional file 2: IgG: Immunoglobulin G; IgM: Immunoglobulin M; Kit 1: Kit ligand 1; Kit: KIT proto-oncogene receptor tyrosine kinase; MALDI-TOF MS: Matrix assisted laser desorption-ionization time-of-flight mass spectrometry; MC1R: Melanocortin 1 receptor; MITF: Microphthalmia-associated transcription factor; NCCs: Neural crest cells; ORF: Open reading frame; qRT- PCR: Quantitative real-time PCR; RACE: Rapid amplification of cDNA ends; RT- PCR: Reverse transcription PCR; SNPs: Single nucleotide polymorphisms; TRP1: Tyrosinase-related protein 1; TRP2: Tyrosinase-related protein 2; TYR: Tyrosinase; UTR: Untranslated region Funding This work was supported by National Nature Science Foundation of China (U1136605), the Innovation Base Cultivation and Development Project- research on Precise genetic modification in sheep (Z171100002217072) and Program for Changjiang Scholar and Innovation Research Team in University (IRT1191). The funders had no role in study design, data collection, analysis, and interpretation, decision to publish, or preparation of the ...
Citations
... In general, black-boned sheep show higher levels of melanin and related pigments in tissues and organs compared to the other examined breeds with white bone color [101]. Another gene, EDN3, known to cause hyperpigmentation in black-boned chickens (the silky fowl), was also analyzed in sheep [102]. However, the results of this study showed non-significant differences in genotype and allele frequencies of the identified SNPs and copy number of EDN3 gene among blackboned and non-black-boned sheep. ...
Background
After domestication, the evolution of phenotypically-varied sheep breeds has generated rich biodiversity. This wide phenotypic variation arises as a result of hidden genomic changes that range from a single nucleotide to several thousands of nucleotides. Thus, it is of interest and significance to reveal and understand the genomic changes underlying the phenotypic variation of sheep breeds in order to drive selection towards economically important traits.
Review
Various traits contribute to the emergence of variation in sheep phenotypic characteristics, including coat color, horns, tail, wool, ears, udder, vertebrae, among others. The genes that determine most of these phenotypic traits have been investigated, which has generated knowledge regarding the genetic determinism of several agriculturally-relevant traits in sheep. In this review, we discuss the genomic knowledge that has emerged in the past few decades regarding the phenotypic traits in sheep, and our ultimate aim is to encourage its practical application in sheep breeding. In addition, in order to expand the current understanding of the sheep genome, we shed light on research gaps that require further investigation.
Conclusions
Although significant research efforts have been conducted in the past few decades, several aspects of the sheep genome remain unexplored. For the full utilization of the current knowledge of the sheep genome, a wide practical application is still required in order to boost sheep productive performance and contribute to the generation of improved sheep breeds. The accumulated knowledge on the sheep genome will help advance and strengthen sheep breeding programs to face future challenges in the sector, such as climate change, global human population growth, and the increasing demand for products of animal origin.
... Dermal hyperpigmentation, also known as fibromelanosis (FM), is a typical skin pigmentation trait in chickens, and FM is linked to higher EDN3 expression (Arora et al., 2011). However, the EDN3 gene may not be a crucial gene for the black phenotype in sheep, which is marked by black pigmentation throughout the body and on internal organs (Darwish et al., 2018). Lentigines and freckles are common skin hyperpigmentations in humans. ...
Hyperpigmentation of the visceral peritoneum (HVP) has been becoming one of the most challenging problems in yellow-feathered chicken production, which seriously affected chicken carcass quality traits. Detecting which genes dominantly impact pigmentation in the peritoneum tissues is of great benefit to the genetic improvement of HVP. To investigate the genetic mechanism of HVP in yellow-feathered broilers, genome-wide association studies (GWASs) were conducted in the F2 generation of a cross broiler population with 395 birds. A total of 115,706 single-nucleotide polymorphisms (SNPs) of 122,415 were retained to identify quantitative trait loci (QTL) associated to HVP in chicken. The GWAS results based on the logistic mixed model (LMM) revealed that a narrow genomic location on chromosomes 1 (49.2–51.3 Mb) was significantly associated (p ≤ 4.32 × 10⁻⁷) with HVP, which contained 23 SNP makers related to 14 functional genes (MFNG, POLDIP3, POLR2F, PICK1, PDXP, SGSM3, RANGAP1, MYH9, RPL3, GALP3, LGALS1, MICALL1, ATF4, and CYP2D6). Four highly associated (p < 10⁻⁵) haplotype blocks of 0.80 kb (two SNPs), 0.06 kb (two SNPs), 0.95 kb (two SNPs), and 0.03 kb (two SNPs) were identified with two, two, four, and four distinct haplotypes, respectively. As a melanoma-associated gene, CYP2D6 were also possibly involved in the development of HVP occurring in chicken with two significant variations (rs314284996 and rs317955795) in the promoter regions. Further tests revealed that the expression of CYP2D6 was obviously higher in the visceral peritoneum tissue of chicken with HVP than that in the normal group (p < 0.05). Our results provide a novel clue to understand the genetic mechanism of HVP generation in chicken, and the mapped QTL or candidate genes might serve for genomic selection to improve carcass quality in the yellow-feathered chicken industry.
... Multiple genes affect skin and shank color. Many genes related to coat and skin color, such as SLC45A2, SLC24A2, SLMO2, ATP5e, CDKN2A, GRAMD3, FGF10, and EDN3, have been found in genomic regions under selective sweep [44][45][46][47][48][49]. ...
Background: Domesticated chickens have a wide variety of phenotypes, in contrast with their wild progenitors. Unlike other chicken breeds, Xichuan black-bone chickens have blue-shelled eggs, and black meat, beaks, skin, bones, and legs. The breeding history and the economically important traits of this breed have not yet been explored at the genomic level. We therefore used whole genome resequencing to analyze the breeding history of the Xichuan black-bone chickens and to identify genes responsible for its unique phenotype.
Results: Principal component and population structure analysis showed that Xichuan black-bone chicken is in a distinct clade apart from eight other breeds. Linkage disequilibrium analysis showed that the selection intensity of Xichuan black-bone chickens is higher than for other chicken breeds. The estimated time of divergence between the Xichuan black-bone chickens and other breeds is 2.89 ka years ago. Fst analysis identified a selective sweep that contains genes related to melanogenesis. This region is probably associated with the black skin of the Xichuan black-bone chickens and may be the product of long-term artificial selection. A combined analysis of genomic and transcriptomic data suggests that the candidate gene related to the black-bone trait, EDN3, might interact with the upstream ncRNA LOC101747896 to generate black skin color during melanogenesis.
Conclusions: These findings help explain the unique genetic and phenotypic characteristics of Xichuan black-bone chickens, and provide basic research data for studying melanin deposition in animals.
Keywords: Xichuan black-bone chicken, Structural variants, Selective sweep, Black skin, Integration of whole genome and transcriptome
... To date, genes related to the mechanism of black pigmentation traits on LPBB have been studied such as TYR (Deng et al., 2008), MC1R (Deng et al., 2009a), TYRP1, TYRP2 (Deng et al., 2009b), and EDN3 (Darwish et al., 2018). However, the genetic background of LPBB has not yet been reported. ...
Lanping black-boned sheep was first discovered in the 1950s in Lanping county of China and characterized by black pigmentation on skin and internal organs. Due to the novel and unique trait, the genetic background of Lanping black-boned sheep is of great interest. Here, we genotyped genome-wide SNPs (single nucleotide polymorphisms) of Lanping black-boned sheep and Lanping normal sheep using Illumina OvineSNP50 BeadChip to investigate the genetic diversity and genetic origin of Lanping black-boned sheep. We also downloaded a subset SNP dataset of two Tibet-lineage sheep breeds and four other sheep breeds from the International Sheep Genomics Consortium (ISGC) as a reference for interpreting. Lanping black-boned sheep had a lower genetic diversity level when compared to seven other sheep breeds. Principal component analysis (PCA) showed that Lanping black-boned sheep and Lanping normal sheep were clustered into the Asian group, but there was no clear separation between the two breeds. Structure analysis demonstrated a high ancestry coefficient in Lanping black-boned sheep and Lanping normal sheep. However, the two populations were separated into two distinct branches in a neighbor-joining (NJ) tree. We further evaluated the genetic divergence using population
F
ST
, which showed that the genetic differentiation that existed between Lanping black-boned sheep and Lanping normal sheep was higher than that between Tibet sheep and Changthangi sheep, which revealed that Lanping black-boned sheep is a different breed from Lanping normal sheep on the genetic level. In addition, structure analysis and NJ tree showed that Lanping black-boned sheep had a relatively close relation with Tibet sheep. The results reported herein are a first step toward understanding the genetic background of Lanping black-boned sheep, and it will provide informative knowledge on the unique genetic resource conservation and mechanism of novel breed formation.
Mastitis is one of the most common diseases of dairy cattle that appreciates the enormous losses of farm worldwide. Current treatment and prevention developed at the moment does not guarantee the reliable protection of animals from the disease, given the polyethological nature of mastitis. An important method of combating this problem may be a selection aimed at improving the immunity of livestock to the inflammation of the breast.The purpose of the article was to search and systematize information on genes associated with the sustainability of dairy cattle towards the development of clinical mastitis and SCS in milk, mainly among the Holstein breed. Also, the publication presents data on the genomic assessment of the bull leader 395, obtained on the basis of St. Petersburg University of Veterinary Medicine, in terms of indicators related to the sustainability of the offspring to the Master.The relationship between the markers of high milk productivity and is low-resistant to the mastel, the protein composition of milk and the frequency of the inflammatory processes of udder. The general mechanisms for the formation of immunity, nonspecific resistance and stability to the mastel are illustrated. A correlation is indicated between allele variants of genes regulating cell cycle or modulating autoimmune processes, and the SCS level in milk. When implementing a genomic estimate of the bull, the leader 395 was identified by its potential as an improved indicators such as SCS, mastotustability, the form of udder, the fatness of milk in daughters.
