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Ji G, Zhang M, Tu Y, Liu Y, Shan Y, Ju X, Zou J, Shu J, Sheng Z, Li H. Molecular Regulatory Mechanisms in Chicken Feather Follicle Morphogenesis. Genes (Basel) 2023; 14:1646. [PMID: 37628697 PMCID: PMC10454116 DOI: 10.3390/genes14081646] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/10/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
In China, the sale of freshly slaughtered chickens is becoming increasingly popular in comparison with that of live chickens, and due to this emerging trend, the skin and feather follicle traits of yellow-feathered broilers have attracted a great deal of research attention. The feather follicle originates from the interaction between the epidermis and dermis in the early embryonic stage. Feather follicle morphogenesis is regulated by the Wnt, ectodysplasin (Eda), epidermal growth factor (EGF), fibroblast growth factor (FGF), bone morphogenetic protein (BMP), sonic hedgehog (Shh), Notch, and other signaling pathways that exist in epithelial and mesenchymal cells. The Wnt pathway is essential for feather follicle and feather morphogenesis. Eda interacts with Wnt to induce FGF expression, which attracts mesenchymal cell movement and aggregates to form feather follicle primordia. BMP acts as an inhibitor of the above signaling pathways to limit the size of the feather tract and distance between neighboring feather primordia in a dose-dependent manner. The Notch/Delta pathway can interact with the FGF pathway to promote feather bud formation. While not a part of the early morphogenesis of feather follicles, Shh and BMP signaling are involved in late feather branching. This review summarizes the roles of miRNAs/lncRNA in the regulation of feather follicle and feather growth and development and suggests topics that need to be solved in a future study. This review focuses on the regulatory mechanisms involved in feather follicle morphogenesis and analyzes the impact of SNP sites on feather follicle traits in poultry. This work may help us to understand the molecular regulatory networks influencing feather follicle growth and provide basic data for poultry carcass quality.
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Affiliation(s)
- Gaige Ji
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Chinese Academy of Agricultural Science, Institute of Poultry Science, Yangzhou 225125, China
| | - Ming Zhang
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Chinese Academy of Agricultural Science, Institute of Poultry Science, Yangzhou 225125, China
| | - Yunjie Tu
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Chinese Academy of Agricultural Science, Institute of Poultry Science, Yangzhou 225125, China
| | - Yifan Liu
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Chinese Academy of Agricultural Science, Institute of Poultry Science, Yangzhou 225125, China
| | - Yanju Shan
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Chinese Academy of Agricultural Science, Institute of Poultry Science, Yangzhou 225125, China
| | - Xiaojun Ju
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Chinese Academy of Agricultural Science, Institute of Poultry Science, Yangzhou 225125, China
| | - Jianmin Zou
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Chinese Academy of Agricultural Science, Institute of Poultry Science, Yangzhou 225125, China
| | - Jingting Shu
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Chinese Academy of Agricultural Science, Institute of Poultry Science, Yangzhou 225125, China
| | - Zhongwei Sheng
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Chinese Academy of Agricultural Science, Institute of Poultry Science, Yangzhou 225125, China
| | - Hua Li
- School of Life Science and Engineering, Foshan University, Foshan 528231, China
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Becker GM, Woods JL, Schauer CS, Stewart WC, Murdoch BM. Genetic association of wool quality characteristics in United States Rambouillet sheep. Front Genet 2023; 13:1081175. [PMID: 36755873 PMCID: PMC9901206 DOI: 10.3389/fgene.2022.1081175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/20/2022] [Indexed: 01/24/2023] Open
Abstract
Introduction: Fine wool production is an important source of revenue, accounting for up to 13% of total revenue in extensively managed wool sheep production systems of the United States. The Rambouillet are a predominant breed that excels in wool quality characteristics. Understanding the genetic basis of wool quality characteristics would aid in the development of genomic breeding strategies to facilitate genetic improvement. Methods: Wool characteristics and DNA were collected for rams enrolled in the North Dakota State University and University of Wyoming annual central performance ram tests over a three-year period (2019-2021, N = 313). The relationships of wool quality characteristics including grease fleece weight adjusted 365 days (wt. 365 adj.), clean fleece wt. 365 adj., staple length 365 adj., average fiber diameter, face wool cover, amount of skin wrinkles and belly wool were evaluated through genome-wide association studies (GWAS), Pearson correlation and ANOVA. Results: The GWAS identified four genome-wide significant genetic markers (p-value <1.19e-06) and five chromosome-wide significant markers (p-value <1.13e-05) on chromosomes 1, 2, 4, 15, and 19. Significant markers were associated with genes notable for relevant wool biological functions, including the gene ABCC8 which codes for SUR1, an ATP-sensitive potassium channel known to affect hair growth and 60S ribosomal protein L17-like, previously found to be expressed during follicle formation. The strongest Pearson correlation coefficients were identified between clean fleece wt. 365 adj. and grease fleece wt. 365 adj. (r = 0.83) and between clean fleece wt. 365 adj. and staple length 365 adj. (r = 0.53). Additionally, clean fleece wt. 365 adj. was correlated with final body weight (r = 0.35) and scrotal circumference (r = 0.16). Staple length 365 adj. (p-value = 5e-04), average fiber diameter (p-value = .0053) and clean fleece wt. 365 adj. (p-value = .014) were significantly associated with belly wool score. Discussion: The results of this study provide important insight into the relationships between wool quality characteristics and report specific markers that Rambouillet sheep producers may use to help inform selection and breeding decisions for improved wool quality.
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Affiliation(s)
- Gabrielle M. Becker
- Department of Animal, Veterinary and Food Science, University of Idaho, Moscow, ID, United States
| | - Julia L. Woods
- Department of Animal, Veterinary and Food Science, University of Idaho, Moscow, ID, United States
| | - Christopher S. Schauer
- Hettinger Research Extension Center, North Dakota State University, Hettinger, ND, United States
| | - Whit C. Stewart
- Department of Animal Science, University of Wyoming, Laramie, WY, United States
| | - Brenda M. Murdoch
- Department of Animal, Veterinary and Food Science, University of Idaho, Moscow, ID, United States,*Correspondence: Brenda M. Murdoch,
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m6A Methylation Analysis Reveals Networks and Key Genes Underlying the Coarse and Fine Wool Traits in a Full-sib Merino Family. BIOLOGY 2022; 11:biology11111637. [PMID: 36358338 PMCID: PMC9687456 DOI: 10.3390/biology11111637] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 10/28/2022] [Accepted: 11/05/2022] [Indexed: 11/11/2022]
Abstract
Simple Summary Artificial breeding makes traits move forward in one direction and reach the extreme, such as ultra-fine wool covering the whole body of fine wool sheep. Nevertheless, many other domestic sheep remain the coarse wool type, and some mendelian genome loci have been identified as having major genes for these traits; however, the epigenetic regulation is still unclear. Abstract In our study, a set of lambs with coarse wool type all over their bodies were discovered within a full-sib family during an embryo transfer experiment of merino fine wool sheep. The difference between coarse and fine wool traits were studied from the perspective of RNA modification-N6-methyladenosine. A total of 31,153 peaks were collected, including 15,968 peaks in coarse skin samples and 15,185 peaks in fine skin samples. In addition, 7208 genes were differentially m6A methylated, including 4167 upregulated and 3041 downregulated in coarse skin samples. Four key genes (EDAR, FGF5, TCHH, KRT2) were obtained by comprehensive analysis of the MeRIP-seq and RNA sequence, which are closely related to primary wool follicle morphogenesis and development. The PI3K/AKT pathway was enriched through different m6A-related genes. These results provided new insights to understand the role of epigenetics in wool sheep domestication and breeding.
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miR-143 Targeting CUX1 to Regulate Proliferation of Dermal Papilla Cells in Hu Sheep. Genes (Basel) 2021; 12:genes12122017. [PMID: 34946965 PMCID: PMC8700861 DOI: 10.3390/genes12122017] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/13/2021] [Accepted: 12/16/2021] [Indexed: 01/19/2023] Open
Abstract
Wool curvature is the determining factor for lambskin quality of Hu lambs. However, the molecular mechanism of wool curvature formation is not yet known. miRNA has been proved to play an important role in hair follicle development, and we have discovered a differentially expressed miRNA, miR-143, in hair follicles of different curl levels. In this study, we first examined the effects of miR-143 on the proliferation and cell cycle of dermal papilla cells using CCK8, EdU and flow cytometry and showed that miR-143 inhibited the proliferation of dermal papilla cells and slowed down the cell cycle. Bioinformatics analysis was performed to predict the target genes KRT71 and CUX1 of miR-143, and both two genes were expressed at significantly higher levels in small waves than in straight lambskin wool (p < 0.05) as detected by qPCR and Western blot (WB). Then, the target relationships between miR-143 and KRT71 and CUX1 were verified through the dual-luciferase assay in 293T cells. Finally, after overexpression and suppression of miR-143 in dermal papilla cells, the expression trend of CUX1 was contrary to that of miR-143. Meanwhile, KRT71 was not detected because KRT71 was not expressed in dermal papilla cells. Therefore, we speculated that miR-143 can target CUX1 to inhibit the proliferation of dermal papilla cells, while miR-143 can target KRT71 to regulate the growth and development of hair follicles, so as to affect the development of hair follicles and ultimately affect the formation of wool curvature.
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Bi Y, Luo B, Zhang S, Li J, Yang Y, Lan X, Pan C. Investigation of Genetic Effects of Nucleotide Variants Within the Goat PRNT Gene on Growth Performance. Anim Biotechnol 2021; 34:321-326. [PMID: 34424814 DOI: 10.1080/10495398.2021.1964514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Our previous study has firstly pointed that three nucleotide variants (g.-11C > T, g.117A > G, and g.149C > T) of the goat PRNT gene can significantly influence litter size. Given litter size is positively correlated with growth performance, we consider whether the PRNT gene also acts on the growth performance in goats. In this work, a correlation analysis among different litter size types and growth traits of Shaanbei white cashmere (SBWC) goats was performed, and results showed that a positive correlation did exist in our detected population (P < 0.01). Then, the association among different genotypes of three variations and goat growth performance was measured. Our results pointed to g.117A > G being significantly associated with the cannon circumference (P = 4.60E-05) while no significant effect was found between another two SNPs and growth traits after the Bonferroni's correction (P*n < 0.05). Together, this is the first report about the influence of the PRNT gene on the growth of goat and g.117A > G can be regarded as a possible DNA marker applying for MAS breeding.
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Affiliation(s)
- Yi Bi
- College of Animal Science and Technology, Northwest A&F University, Yanggling, China
| | - Bihao Luo
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Shaoli Zhang
- College of Animal Science and Technology, Northwest A&F University, Yanggling, China
| | - Jie Li
- College of Animal Science and Technology, Northwest A&F University, Yanggling, China
| | - Yuta Yang
- College of Animal Science and Technology, Northwest A&F University, Yanggling, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yanggling, China
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Yanggling, China
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Ding Y, Xue X, Liu Z, Ye Y, Xiao P, Pu Y, Guan W, Mwacharo JM, Ma Y, Zhao Q. Expression Profiling and Functional Characterization of miR-26a and miR-130a in Regulating Zhongwei Goat Hair Development via the TGF-β/SMAD Pathway. Int J Mol Sci 2020; 21:ijms21145076. [PMID: 32708395 PMCID: PMC7404276 DOI: 10.3390/ijms21145076] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/09/2020] [Accepted: 07/14/2020] [Indexed: 12/26/2022] Open
Abstract
The Zhongwei goat is an important and unique goat breed indigenous to China. It has a natural hair curling phenotype at birth, but the degree of curling gradually decreases with growth. The molecular mechanism underlying the dynamic changes in the wool curvature in Zhongwei goats is poorly understood. MicroRNAs (miRNAs) play important roles in many biological processes, including hair growth and development. In this study, we selected skins from Zhongwei goats at different ages (45 and 108 days) that exhibited different levels of hair curvature and performed miRNA sequencing to explore the molecular mechanism of hair bending. In total, 28 significantly differentially expressed miRNAs (DE miRNAs) were identified in the three groups of samples between the two developmental stages. An analysis of the target genes of the above-mentioned DE miRNAs by the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses indicated that the DE miRNAs were involved in signal pathways which were previously associated with hair bending and hair follicle development, such as the TGF-β/SMAD, PI3K-Akt, JAK-STAT, and MAPK pathways. A comprehensive analysis of the correlations between the miRNA-seq results and issued transcriptional findings indicated that SMAD1 was a target gene of miR-26a and SMAD5 was a target gene of miR-130a. Furthermore, goat dermal papilla cells were successfully isolated and purified to determine the role of miRNAs in follicle development in vitro. The study results demonstrated that miR-130a and miR-26a had significant effects on the proliferation of dermal papilla cells. In addition, the detection results of mRNA and protein levels indicate that the overexpression of miR-26a can promote the expression of related genes in the TGF-β/SMAD pathway, while miR-130a has the opposite substitution effect. The dual luciferase report test showed that miR-26a targeted the SMAD1 gene and reduced the expression of the SMAD1 protein in hair papillary cells. Our results identified DE microRNAs which perhaps change at the time of hair straightening in Zhongwei goats and explore the role of miR-26a and miR-130a in dermal papilla cells proliferation. The present study provided a theoretical basis to explore the mechanisms underlying the Zhongwei hair growth and curly phenotype.
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Affiliation(s)
- Yangyang Ding
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Y.D.); (X.X.); (Y.P.); (W.G.)
| | - Xianglan Xue
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Y.D.); (X.X.); (Y.P.); (W.G.)
| | - Zhanfa Liu
- The Ningxia Hui Autonomous Region Breeding Ground of Zhongwei Goat, Zhongwei 755000, China; (Z.L.); (Y.Y.)
| | - Yong Ye
- The Ningxia Hui Autonomous Region Breeding Ground of Zhongwei Goat, Zhongwei 755000, China; (Z.L.); (Y.Y.)
| | - Ping Xiao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 625014, China;
| | - Yabin Pu
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Y.D.); (X.X.); (Y.P.); (W.G.)
| | - Weijun Guan
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Y.D.); (X.X.); (Y.P.); (W.G.)
| | | | - Yuehui Ma
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Y.D.); (X.X.); (Y.P.); (W.G.)
- Correspondence: (Y.M.); (Q.Z.)
| | - Qianjun Zhao
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
- Correspondence: (Y.M.); (Q.Z.)
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Wei C, Luo H, Zhao B, Tian K, Huang X, Wang Y, Fu X, Tian Y, Di J, Xu X, Wu W, Tulafu H, Yasen M, Zhang Y, Zhao W. The Effect of Integrating Genomic Information into Genetic Evaluations of Chinese Merino Sheep. Animals (Basel) 2020; 10:ani10040569. [PMID: 32231053 PMCID: PMC7222387 DOI: 10.3390/ani10040569] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 03/24/2020] [Accepted: 03/24/2020] [Indexed: 01/06/2023] Open
Abstract
Simple Summary Genetic improvement of wool production and quality traits in fine-wool sheep is an appealing option for enhancing the market value of wool products. We estimated genetic parameters and the accuracies of estimated breeding values for various wool production and quality traits in fine-wool sheep using pedigree-based best linear unbiased prediction (PBLUP) and single-step genomic best linear unbiased prediction (ssGBLUP) strategies. ssGBLUP performed slightly better than PBLUP for the studied traits. Therefore, the single-step genetic evaluation method could be successfully implemented in genomic evaluations of fine-wool sheep and the prediction of future breeding values in young Merino sheep as part of an early preselection strategy in the near future. Abstract Genomic evaluations are a method for improving the accuracy of breeding value estimation. This study aimed to compare estimates of genetic parameters and the accuracy of breeding values for wool traits in Merino sheep between pedigree-based best linear unbiased prediction (PBLUP) and single-step genomic best linear unbiased prediction (ssGBLUP) using Bayesian inference. Data were collected from 28,391 yearlings of Chinese Merino sheep (classified in 1992–2018) at the Xinjiang Gonaisi Fine Wool Sheep-Breeding Farm, China. Subjectively-assessed wool traits, namely, spinning count (SC), crimp definition (CRIM), oil (OIL), and body size (BS), and objectively-measured traits, namely, fleece length (FL), greasy fleece weight (GFW), mean fiber diameter (MFD), crimp number (CN), and body weight pre-shearing (BWPS), were analyzed. The estimates of heritability for wool traits were low to moderate. The largest h2 values were observed for FL (0.277) and MFD (0.290) with ssGBLUP. The heritabilities estimated for wool traits with ssGBLUP were slightly higher than those obtained with PBLUP. The accuracies of breeding values were low to moderate, ranging from 0.362 to 0.573 for the whole population and from 0.318 to 0.676 for the genotyped subpopulation. The correlation between the estimated breeding values (EBVs) and genomic EBVs (GEBVs) ranged from 0.717 to 0.862 for the whole population, and the relative increase in accuracy when comparing EBVs with GEBVs ranged from 0.372% to 7.486% for these traits. However, in the genotyped population, the rank correlation between the estimates obtained with PBLUP and ssGBLUP was reduced to 0.525 to 0.769, with increases in average accuracy of 3.016% to 11.736% for the GEBVs in relation to the EBVs. Thus, genomic information could allow us to more accurately estimate the relationships between animals and improve estimates of heritability and the accuracy of breeding values by ssGBLUP.
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Affiliation(s)
- Chen Wei
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China;
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830011, China (J.D.)
| | - Hanpeng Luo
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Bingru Zhao
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Kechuan Tian
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830011, China (J.D.)
- Correspondence: (K.T.); (X.H.); (Y.W.); Tel.: +86-1590-900-1963 (K.T.); +86-1399-999-6861 (X.H.); +86-1580-159-5851 (Y.W.)
| | - Xixia Huang
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China;
- Correspondence: (K.T.); (X.H.); (Y.W.); Tel.: +86-1590-900-1963 (K.T.); +86-1399-999-6861 (X.H.); +86-1580-159-5851 (Y.W.)
| | - Yachun Wang
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- Correspondence: (K.T.); (X.H.); (Y.W.); Tel.: +86-1590-900-1963 (K.T.); +86-1399-999-6861 (X.H.); +86-1580-159-5851 (Y.W.)
| | - Xuefeng Fu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830011, China (J.D.)
| | - Yuezhen Tian
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830011, China (J.D.)
| | - Jiang Di
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830011, China (J.D.)
| | - Xinming Xu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830011, China (J.D.)
| | - Weiwei Wu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830011, China (J.D.)
| | - Hanikezi Tulafu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830011, China (J.D.)
| | - Maerziya Yasen
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830011, China (J.D.)
| | - Yajun Zhang
- Xinjiang Gonaisi Fine Wool Sheep-Breeding Farm, Ili Kazak Autonomous Prefecture 835800, China
| | - Wensheng Zhao
- Xinjiang Gonaisi Fine Wool Sheep-Breeding Farm, Ili Kazak Autonomous Prefecture 835800, China
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Megdiche S, Mastrangelo S, Ben Hamouda M, Lenstra JA, Ciani E. A Combined Multi-Cohort Approach Reveals Novel and Known Genome-Wide Selection Signatures for Wool Traits in Merino and Merino-Derived Sheep Breeds. Front Genet 2019; 10:1025. [PMID: 31708969 PMCID: PMC6824410 DOI: 10.3389/fgene.2019.01025] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 09/24/2019] [Indexed: 12/24/2022] Open
Abstract
Merino sheep represents a valuable genetic resource worldwide. In this study, we investigated selection signatures in Merino (and Merino-derived) sheep breeds using genome-wide SNP data and two different approaches: a classical FST-outlier method and an approach based on the analysis of local ancestry in admixed populations. In order to capture the most reliable signals, we adopted a combined, multi-cohort approach. In particular, scenarios involving four Merino breeds (Spanish Merino, Australian Merino, Chinese Merino, and Sopravissana) were tested via the local ancestry approach, while nine pair-wise breed comparisons contrasting the above breeds, as well as the Gentile di Puglia breed, with non-Merino breeds from the same geographic area were tested via the FST-outlier method. Signals observed using both methods were compared with genome-wide patterns of distribution of runs of homozygosity (ROH) islands. Novel and known selection signatures were detected. The most reliable signals were observed on OAR 3 (MSRB3 and LEMD3), OAR10 (FRY and RXFP2), OAR 13 (RALY), OAR17 (FAM101A), and OAR18 (NFKBIA, SEC23A, and PAX9). All the above overlapped with known QTLs for wool traits, and evidences from the literature of their involvement in skin/hair/wool biology, as well as gene network analysis, further corroborated these results. The signal on OAR10 also contains well known evidence for association with horn morphology and polledness. More elusive biological evidences of association with the Merino phenotype were observed for a number of other genes, notably LOC101120019 and TMEM132B (OAR17), LOC105609948 (OAR3), LOC101110773 (OAR10), and EIF2S2 (OAR17). Taken together, the above results further contribute to decipher the genetic basis underlying the Merino phenotype.
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Affiliation(s)
- Sami Megdiche
- Départment des Ressources Animales, Agroalimentaire et Développement Rural, Institut Supérieur Agronomique de Chott-Mariem, Université de Sousse, Sousse, Tunisia
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, University of Bari “Aldo Moro,”Bari, Italy
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | | | | | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, University of Bari “Aldo Moro,”Bari, Italy
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Mu F, Rong E, Jing Y, Yang H, Ma G, Yan X, Wang Z, Li Y, Li H, Wang N. Structural Characterization and Association of Ovine Dickkopf-1 Gene with Wool Production and Quality Traits in Chinese Merino. Genes (Basel) 2017; 8:E400. [PMID: 29261127 PMCID: PMC5748718 DOI: 10.3390/genes8120400] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 12/06/2017] [Accepted: 12/15/2017] [Indexed: 12/20/2022] Open
Abstract
Dickkopf-1 (DKK1) is an inhibitor of canonical Wnt signaling pathway and regulates hair follicle morphogenesis and cycling. To investigate the potential involvement of DKK1 in wool production and quality traits, we characterized the genomic structure of ovine DKK1, performed polymorphism detection and association analysis of ovine DKK1 with wool production and quality traits in Chinese Merino. Our results showed that ovine DKK1 consists of four exons and three introns, which encodes a protein of 262 amino acids. The coding sequence of ovine DKK1 and its deduced amino acid sequence were highly conserved in mammals. Eleven single nucleotide polymorphisms (SNPs) were identified within the ovine DKK1 genomic region. Gene-wide association analysis showed that SNP5 was significantly associated with mean fiber diameter (MFD) in the B (selected for long wool fiber and high-quality wool), PW (selected for high reproductive capacity, high clean wool yield and high-quality wool) and U (selected for long wool fiber with good uniformity, high wool yield and lower fiber diameter) strains (p < 4.55 × 10-3 = 0.05/11). Single Nucleotide Polymorphisms wide association analysis showed that SNP8 was significantly associated with MFD in A strain and fleece weight in A (selected for large body size), PM (selected for large body size, high reproductive capacity and high meat yield) and SF (selected for mean fiber diameter less than 18 μm and wool fiber length between 5 and 9 cm) strains (p < 0.05), SNP9 was significantly associated with curvature in B and U strains (p < 0.05) and SNP10 was significantly associated with coefficient of variation of fiber diameter in A, PW and PM strains and standard deviation of fiber diameter in A and PM strains (p < 0.05). The haplotypes derived from these 11 identified SNPs were significantly associated with MFD (p < 0.05). In conclusion, our results suggest that DKK1 may be a major gene controlling wool production and quality traits, also the identified SNPs (SNPs5, 8, 9 and 10) might be used as potential molecular markers for improving sheep wool production and quality in sheep breeding.
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Affiliation(s)
- Fang Mu
- Key Laboratory of Chicken Genetics and Breeding at Ministry of Agriculture, Key Laboratory of Animal Genetics, Breeding and Reproduction at Education Department of Heilongjiang Province, Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Harbin 150030, China.
| | - Enguang Rong
- Key Laboratory of Chicken Genetics and Breeding at Ministry of Agriculture, Key Laboratory of Animal Genetics, Breeding and Reproduction at Education Department of Heilongjiang Province, Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Harbin 150030, China.
| | - Yang Jing
- Key Laboratory of Chicken Genetics and Breeding at Ministry of Agriculture, Key Laboratory of Animal Genetics, Breeding and Reproduction at Education Department of Heilongjiang Province, Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Harbin 150030, China.
| | - Hua Yang
- Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agriculture and Reclamation Science, Shihezi 832000, China.
| | - Guangwei Ma
- Key Laboratory of Chicken Genetics and Breeding at Ministry of Agriculture, Key Laboratory of Animal Genetics, Breeding and Reproduction at Education Department of Heilongjiang Province, Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Harbin 150030, China.
| | - Xiaohong Yan
- Key Laboratory of Chicken Genetics and Breeding at Ministry of Agriculture, Key Laboratory of Animal Genetics, Breeding and Reproduction at Education Department of Heilongjiang Province, Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Harbin 150030, China.
| | - Zhipeng Wang
- Key Laboratory of Chicken Genetics and Breeding at Ministry of Agriculture, Key Laboratory of Animal Genetics, Breeding and Reproduction at Education Department of Heilongjiang Province, Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Harbin 150030, China.
| | - Yumao Li
- Key Laboratory of Chicken Genetics and Breeding at Ministry of Agriculture, Key Laboratory of Animal Genetics, Breeding and Reproduction at Education Department of Heilongjiang Province, Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Harbin 150030, China.
| | - Hui Li
- Key Laboratory of Chicken Genetics and Breeding at Ministry of Agriculture, Key Laboratory of Animal Genetics, Breeding and Reproduction at Education Department of Heilongjiang Province, Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Harbin 150030, China.
| | - Ning Wang
- Key Laboratory of Chicken Genetics and Breeding at Ministry of Agriculture, Key Laboratory of Animal Genetics, Breeding and Reproduction at Education Department of Heilongjiang Province, Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Harbin 150030, China.
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10
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A comparison of transcriptomic patterns measured in the skin of Chinese fine and coarse wool sheep breeds. Sci Rep 2017; 7:14301. [PMID: 29085060 PMCID: PMC5662721 DOI: 10.1038/s41598-017-14772-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 10/12/2017] [Indexed: 12/17/2022] Open
Abstract
We characterised wool traits, and skin gene expression profiles of fine wool Super Merino (SM) and coarse wool Small Tail Han (STH) sheep. SM sheep had a significantly higher total density of wool follicles, heavier fleeces, finer fibre diameter, and increased crimp frequency, staple length and wool grease (lanolin) production. We found 435 genes were expressed at significantly different levels in the skin of the two breeds (127 genes more highly in SM and 308 genes more highly in STH sheep). Classification of the genes more highly expressed in SM sheep revealed numerous lipid metabolic genes as well as genes encoding keratins, keratin-associated proteins, and wool follicle stem cell markers. In contrast, mammalian epidermal development complex genes and other genes associated with skin cornification and muscle function were more highly expressed in STH sheep. Genes identified in this study may be further evaluated for inclusion in breeding programs, or as targets for therapeutic or genetic interventions, aimed at altering wool quality or yield. Expression of the lipid metabolic genes in the skin of sheep may be used as a novel trait with the potential to alter the content or properties of lanolin or the fleece.
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11
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Ebrahimi F, Gholizadeh M, Rahimi-Mianji G, Farhadi A. Detection of QTL for greasy fleece weight in sheep using a 50 K single nucleotide polymorphism chip. Trop Anim Health Prod 2017; 49:1657-1662. [PMID: 28801813 DOI: 10.1007/s11250-017-1373-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 08/02/2017] [Indexed: 12/27/2022]
Abstract
Genome-wide association studies (GWAS) have introduced an influential tool in the search for quantitative trait loci (QTL) influencing economically important traits in sheep. To identify QTL associated with greasy fleece weight, a GWAS with 50 K single nucleotide polymorphisms (SNPs) was performed in a Baluchi sheep population. Association with greasy fleece weights was tested using the software Plink. The results of our GWAS provided three novel SNP markers and candidate genes associated with greasy fleece weight. A total of three chromosome-wide significant associations were detected for SNP on chromosomes 17 and 20 affecting greasy fleece weight across the four shearing. One of the significant SNP markers was located within ovine known genes namely FAM101A. Further investigation of these identified regions in validation studies will facilitate the identification of strong candidate genes for wool production in sheep.
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Affiliation(s)
- Fatemeh Ebrahimi
- Department of Animal Science, Faculty of Animal and Aquatic Science, Sari Agricultural Sciences and Natural Resources University, P.O. Box -578, Sari, Iran
| | - Mohsen Gholizadeh
- Department of Animal Science, Faculty of Animal and Aquatic Science, Sari Agricultural Sciences and Natural Resources University, P.O. Box -578, Sari, Iran.
| | - Ghodrat Rahimi-Mianji
- Department of Animal Science, Faculty of Animal and Aquatic Science, Sari Agricultural Sciences and Natural Resources University, P.O. Box -578, Sari, Iran
| | - Ayoub Farhadi
- Department of Animal Science, Faculty of Animal and Aquatic Science, Sari Agricultural Sciences and Natural Resources University, P.O. Box -578, Sari, Iran
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12
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Darwish H, El-Shorbagy H, Abou-Eisha A, El-Din A, Farag I. New polymorphism in the 5' flanking region of IGF-1 gene and its association with wool traits in Egyptian Barki sheep. J Genet Eng Biotechnol 2017; 15:437-441. [PMID: 30647684 PMCID: PMC6296639 DOI: 10.1016/j.jgeb.2017.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 05/06/2017] [Accepted: 08/01/2017] [Indexed: 11/17/2022]
Abstract
Insulin-like growth factor-1 gene (IGF-1) is considered as a major candidate gene for the economic traits of animal production. Polymorphism of 5′ flanking region of IGF-1 gene in Barki sheep (n = 91) and its association with wool traits were studied using the polymerase chain reaction coupled with single-strand conformation polymorphism technique (PCR-SSCP), PCR-restriction fragment length polymorphism (PCR-RFLP), sequence analysis and different measurements of wool traits (clean fleece weight and fiber diameter). PCR-SSCP analysis revealed three different banding patterns corresponding with three genotypes frequencies GG (0.25), GA (0.58), AA (0.17). PCR-RFLP and corresponding sequence analysis revealed nucleotide transversion from Guanine (G) to Cytosine (C) at nucleotide position 85 and transition from (G) to Adenine (A) at position 87. This is the first study that recorded two SNPs within the 5′ flanking region of IGF-1 gene in Egyptian Barki sheep, which were submitted to DNA Data Bank OF Japan (DDBJ) with Accession No. LC151463.1. The genotype GG showed positive significant association (P < 0.001) with clean fleece weight (CFW) trait (Odd Ratio = 2.83). By contrast, genotype AA had negative significant association (P < 0.05) with such trait (Odd Ratio = 0.15). On the other hand, fiber diameter (FD) measurements showed no significant association (P > 0.05) with different IGF-1 genotypes. This study adds evidence of the association between IGF-1 gene polymorphism and CFW of wool in Egyptian Barki sheep. Therefore; it is important to consider IGF-1 gene as a candidate gene marker for wool weight traits and it should be identified before using successful breeding program.
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Affiliation(s)
- H.R. Darwish
- Cell Biology Department, National Research Centre, Dokki, Giza, P.O. Box 12622, Egypt
| | - H.M. El-Shorbagy
- Zoology Department, Faculty of Science, Cairo University, Giza, P.O. Box 12613, Egypt
- Corresponding author.
| | - A.M. Abou-Eisha
- Cell Biology Department, National Research Centre, Dokki, Giza, P.O. Box 12622, Egypt
| | - A.E. El-Din
- Cell Biology Department, National Research Centre, Dokki, Giza, P.O. Box 12622, Egypt
| | - I.M. Farag
- Cell Biology Department, National Research Centre, Dokki, Giza, P.O. Box 12622, Egypt
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13
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Ma GW, Chu YK, Zhang WJ, Qin FY, Xu SS, Yang H, Rong EG, Du ZQ, Wang SZ, Li H, Wang N. Polymorphisms of FST gene and their association with wool quality traits in Chinese Merino sheep. PLoS One 2017; 12:e0174868. [PMID: 28384189 PMCID: PMC5383234 DOI: 10.1371/journal.pone.0174868] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 03/16/2017] [Indexed: 11/19/2022] Open
Abstract
Follistatin (FST) is involved in hair follicle morphogenesis. However, its effects on hair traits are not clear. This study was designed to investigate the effects of FST gene single nucleotide polymorphisms (SNP) on wool quality traits in Chinese Merino sheep (Junken Type). We performed gene expression analysis, SNP detection, and association analysis of FST gene with sheep wool quality traits. The real-time RT-PCR analysis showed that FST gene was differentially expressed in adult skin between Chinese Merino sheep (Junken Type) and Suffolk sheep. Immunostaining showed that FST was localized in inner root sheath (IRS) and matrix of hair follicle (HF) in both SF and Suffolk sheep. Sequencing analysis identified a total of seven SNPs (termed SNPs 1-7) in the FST gene in Chinese Merino sheep (Junken Type). Association analysis showed that SNP2 (Chr 16. 25,633,662 G>A) was significantly associated with average wool fiber diameter, wool fineness SD, and wool crimp (P < 0.05). SNP4 (Chr 16. 25,633,569 C>T) was significantly associated with wool fineness SD and CV of fiber diameter (P < 0.05). Similarly, the haplotypes derived from these seven identified SNPs were also significantly associated with average wool fiber diameter, wool fineness SD, CV of fiber diameter, and wool crimp (P < 0.05). Our results suggest that FST influences wool quality traits and its SNPs 2 and 4 might be useful markers for marker-assisted selection and sheep breeding.
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Affiliation(s)
- Guang-Wei Ma
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, P. R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, P. R. China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P. R. China
| | - Yan-Kai Chu
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, P. R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, P. R. China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P. R. China
| | - Wen-Jian Zhang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, P. R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, P. R. China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P. R. China
| | - Fei-Yue Qin
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, P. R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, P. R. China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P. R. China
| | - Song-Song Xu
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, P. R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, P. R. China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P. R. China
| | - Hua Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, P. R. China
| | - En-Guang Rong
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, P. R. China
| | - Zhi-Qiang Du
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, P. R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, P. R. China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P. R. China
| | - Shou-Zhi Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, P. R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, P. R. China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P. R. China
| | - Hui Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, P. R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, P. R. China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P. R. China
| | - Ning Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, P. R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, P. R. China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P. R. China
- * E-mail:
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