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Ghildiyal K, Panigrahi M, Kumar H, Rajawat D, Nayak SS, Lei C, Bhushan B, Dutt T. Selection signatures for fiber production in commercial species: A review. Anim Genet 2023; 54:3-23. [PMID: 36352515 DOI: 10.1111/age.13272] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/11/2022] [Accepted: 10/11/2022] [Indexed: 11/11/2022]
Abstract
Natural fibers derived from diverse animal species have gained increased attention in recent years due to their favorable environmental effects, long-term sustainability benefits, and remarkable physical and mechanical properties that make them valuable raw materials used for textile and non-textile production. Domestication and selective breeding for the economically significant fiber traits play an imperative role in shaping the genomes and, thus, positively impact the overall productivity of the various fiber-producing species. These selection pressures leave unique footprints on the genome due to alteration in the allelic frequencies at specific loci, characterizing selective sweeps. Recent advances in genomics have enabled the discovery of selection signatures across the genome using a variety of methods. The increased demand for 'green products' manufactured from natural fibers necessitates a detailed investigation of the genomes of the various fiber-producing plant and animal species to identify the candidate genes associated with important fiber attributes such as fiber diameter/fineness, color, length, and strength, among others. The objective of this review is to present a comprehensive overview of the concept of selection signature and selective sweeps, discuss the main methods used for its detection, and address the selection signature studies conducted so far in the diverse fiber-producing animal species.
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Affiliation(s)
- Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | | | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Bareilly, India
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Kalds P, Zhou S, Gao Y, Cai B, Huang S, Chen Y, Wang X. Genetics of the phenotypic evolution in sheep: a molecular look at diversity-driving genes. Genet Sel Evol 2022; 54:61. [PMID: 36085023 PMCID: PMC9463822 DOI: 10.1186/s12711-022-00753-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/29/2022] [Indexed: 12/22/2022] Open
Abstract
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.
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Affiliation(s)
- Peter Kalds
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- Department of Animal and Poultry Production, Faculty of Environmental Agricultural Sciences, Arish University, El-Arish, 45511 Egypt
| | - Shiwei Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100 China
| | - Yawei Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Bei Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Shuhong Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Yulin Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs, Yangling, 712100 China
| | - Xiaolong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs, Yangling, 712100 China
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The Complexity of the Ovine and Caprine Keratin-Associated Protein Genes. Int J Mol Sci 2021; 22:ijms222312838. [PMID: 34884644 PMCID: PMC8657448 DOI: 10.3390/ijms222312838] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/25/2021] [Accepted: 11/25/2021] [Indexed: 01/01/2023] Open
Abstract
Sheep (Ovis aries) and goats (Capra hircus) have, for more than a millennia, been a source of fibres for human use, be it for use in clothing and furnishings, for insulation, for decorative and ceremonial purposes, or for combinations thereof. While use of these natural fibres has in some respects been superseded by the use of synthetic and plant-based fibres, increased accounting for the carbon and water footprint of these fibres is creating a re-emergence of interest in fibres derived from sheep and goats. The keratin-associated proteins (KAPs) are structural components of wool and hair fibres, where they form a matrix that cross-links with the keratin intermediate filaments (KIFs), the other main structural component of the fibres. Since the first report of a complete KAP protein sequence in the late 1960s, considerable effort has been made to identify the KAP proteins and their genes in mammals, and to ascertain how these genes and proteins control fibre growth and characteristics. This effort is ongoing, with more and more being understood about the structure and function of the genes. This review consolidates that knowledge and suggests future directions for research to further our understanding.
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Ullah F, Jamal SM, Zhou H, Hickford JGH. Variation in ovine KRTAP8-1 affects mean staple length and opacity of wool fiber. Anim Biotechnol 2021:1-7. [PMID: 34666626 DOI: 10.1080/10495398.2021.1990078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
In this study, keratin-associated proteins gene (KRTAP8-1) from five different sheep breeds and breed-crosses (n = 310) was genotyped using a Polymerase Chain Reaction-Single Strand confirmation Polymorphism (PCR-SSCP). Six unique genotypes were observed: AA, AC, AD, AE, DD and EE, with AA being the most common in the different breeds and crosses. Twelve wool characteristics: yield, mean staple length (MSL), bulk, mean fiber diameter (MFD), fiber diameter standard deviation (FDSD), coefficient of variation of fiber diameter (CVFD), medullation, standard deviation of medullation (MeSD), coefficient of variation of medullation (CVMed), opacity, standard deviation of opacity (OpSD), and coefficient of variation of opacity (CVOp) were measured on wool derived from the sheep. Variation in KRTAP8-1 was found to have strong association with MSL, OpSD and CVOp (p ≤ 0.027). The MSL of sheep of genotype AE was greater (p = 0.027) than for sheep of genotype AA. The OpSD of sheep of genotype AA was less (p = 0.017) than sheep with the AE genotype, and the CVOp of sheep with genotype AA was less (p = 0.018) than sheep with genotype AE. Further studies are required to confirm the role of variation in KRTAP8-1 in improving quality wool production.
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Affiliation(s)
- Farman Ullah
- Department of Biotechnology, University of Malakand, Chakdara, Pakistan
| | - Syed M Jamal
- Department of Biotechnology, University of Malakand, Chakdara, Pakistan
| | - Huitong Zhou
- Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, New Zealand
| | - Jon G H Hickford
- Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, New Zealand
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Ullah F, Jamal SM, Zhou H, Hickford JGH. Variation in the KRTAP6-3 gene and its association with wool characteristics in Pakistani sheep breeds and breed-crosses. Trop Anim Health Prod 2020; 52:3035-3043. [DOI: 10.1007/s11250-020-02322-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 06/09/2020] [Indexed: 10/24/2022]
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Characterization and functional analysis of Krtap11-1 during hair follicle development in Angora rabbits (Oryctolagus cuniculus). Genes Genomics 2020; 42:1281-1290. [PMID: 32955717 DOI: 10.1007/s13258-020-00995-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 09/07/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND Keratin-associated protein (KAP), the structural protein molecule of hair fibers, plays a key role in determining the physical properties of hair. Studies of Krtap11-1 have focused only on its localization. Functional studies of Krtap11-1 in hair follicle development have so far not been reported. OBJECTIVE This study aimed to provide evidence for the role of Krtap11-1 in skin and hair development. METHODS Full-length cloning and analysis of Krtap11-1 were conducted to ascertain its function. Overexpression vectors and interference sequences were constructed and transfected into RAB-9 cells. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to investigate the hair follicle developmental stage of Krtap11-1, the expression of different tissues, and the effects on other hair follicle development-related genes. RESULTS The full length of cloned Krtap11-1 was 947 bp. Krtap11-1 was confirmed to be a hydrophilic protein localized mostly in mitochondria. The greatest mRNA expression was observed in skin. Using a follicle synchronization model, it was found that Krtap11-1 mRNA expression levels first increased then decreased over the passage of time, principally during hair follicle catagen and telogen. Following the overexpression of Krtap11-1, mRNA expression levels of the WNT-2, KRT17, BMP-2, and TGF-β-1 genes increased, and LEF-1 decreased (P < 0.05), the converse after the corresponding use of si-RNA interference. CONCLUSIONS Krtap11-1 exerts a promoting effect. The results provide novel insight into the relationship between hair follicle development and Krtap11-1 gene expression.
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Zhao M, Zhou H, Luo Y, Wang J, Hu J, Liu X, Li S, Hao Z, Jin X, Song Y, Wu X, Hu L, Hickford JGH. Variation in the Caprine Keratin-Associated Protein 27-1 Gene is Associated with Cashmere Fiber Diameter. Genes (Basel) 2020; 11:genes11080934. [PMID: 32823629 PMCID: PMC7463587 DOI: 10.3390/genes11080934] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/04/2020] [Accepted: 08/06/2020] [Indexed: 12/22/2022] Open
Abstract
Variation in some caprine keratin-associated protein (KAP) genes has been associated with cashmere fiber traits, but many KAP genes remain unidentified in goats. In this study, we confirm the identification of a KAP27-1 gene (KRTAP27-1) and describe its effect on cashmere traits in 248 Longdong cashmere goats. A polymerase chain reaction–single strand conformation polymorphism (PCR-SSCP) analysis was used to screen for sequence variation in this gene, and three sequence variants (named A to C) were found. These sequences have the highest similarity (77% identity) to a human KRTAP27-1 sequence, while sharing some homology with a predicted caprine KRTAP27-1 sequence ENSCHIG00000023347 in the goat genome construct (ARS1:CM004562.1) at chromosome 1 position 3,966,193–3,973,677 in the forward strand. There were two single nucleotide polymorphisms (SNPs) detected in the coding sequence, including one nonsynonymous SNP (c.413C/T; p.Ala138Val) and one synonymous SNP (c.495C/T). The C variant differed from A and B at c.413C/T, having cytosine in its nucleotide sequence, while the B variant differed from A and C at c.495C/T, having thymine in its nucleotide sequence. Goats of the genotypes AB and BB produced cashmere fibers of higher mean fiber diameter (MFD) than goats of genotype AA, but no difference in MFD was detected between the AB and BB goats. These results suggest that B is associated with increased MFD. Expression of the caprine KRTAP27-1 sequence was predominantly detected in the skin tissue of goats but not or only weakly detected in other tissues, including longissimus dorsi muscle, heart, kidney, liver, lung and spleen.
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Affiliation(s)
- Mengli Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (M.Z.); (Y.L.); (J.H.); (X.L.); (S.L.); (Z.H.); (X.J.); (Y.S.); (X.W.); (L.H.)
- International Wool Research Institute, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China;
| | - Huitong Zhou
- International Wool Research Institute, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China;
- Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Yuzhu Luo
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (M.Z.); (Y.L.); (J.H.); (X.L.); (S.L.); (Z.H.); (X.J.); (Y.S.); (X.W.); (L.H.)
- International Wool Research Institute, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China;
| | - Jiqing Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (M.Z.); (Y.L.); (J.H.); (X.L.); (S.L.); (Z.H.); (X.J.); (Y.S.); (X.W.); (L.H.)
- International Wool Research Institute, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China;
- Correspondence: (J.W.); (J.G.H.H.); Tel.: +86-931-763-2469 (J.W.); +64-3423-0665 (J.G.H.H.)
| | - Jiang Hu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (M.Z.); (Y.L.); (J.H.); (X.L.); (S.L.); (Z.H.); (X.J.); (Y.S.); (X.W.); (L.H.)
- International Wool Research Institute, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China;
| | - Xiu Liu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (M.Z.); (Y.L.); (J.H.); (X.L.); (S.L.); (Z.H.); (X.J.); (Y.S.); (X.W.); (L.H.)
- International Wool Research Institute, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China;
| | - Shaobin Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (M.Z.); (Y.L.); (J.H.); (X.L.); (S.L.); (Z.H.); (X.J.); (Y.S.); (X.W.); (L.H.)
- International Wool Research Institute, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China;
| | - Zhiyun Hao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (M.Z.); (Y.L.); (J.H.); (X.L.); (S.L.); (Z.H.); (X.J.); (Y.S.); (X.W.); (L.H.)
- International Wool Research Institute, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China;
| | - Xiayang Jin
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (M.Z.); (Y.L.); (J.H.); (X.L.); (S.L.); (Z.H.); (X.J.); (Y.S.); (X.W.); (L.H.)
- International Wool Research Institute, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China;
| | - Yize Song
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (M.Z.); (Y.L.); (J.H.); (X.L.); (S.L.); (Z.H.); (X.J.); (Y.S.); (X.W.); (L.H.)
- International Wool Research Institute, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China;
| | - Xinmiao Wu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (M.Z.); (Y.L.); (J.H.); (X.L.); (S.L.); (Z.H.); (X.J.); (Y.S.); (X.W.); (L.H.)
- International Wool Research Institute, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China;
| | - Liyan Hu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (M.Z.); (Y.L.); (J.H.); (X.L.); (S.L.); (Z.H.); (X.J.); (Y.S.); (X.W.); (L.H.)
- International Wool Research Institute, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China;
| | - Jon G. H. Hickford
- International Wool Research Institute, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China;
- Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
- Correspondence: (J.W.); (J.G.H.H.); Tel.: +86-931-763-2469 (J.W.); +64-3423-0665 (J.G.H.H.)
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Wang J, Zhou H, Hickford JGH, Luo Y, Gong H, Hu J, Liu X, Li S, Song Y, Ke N, Qiao L, Wang J. Identification of the Ovine Keratin-Associated Protein 2-1 Gene and Its Sequence Variation in Four Chinese Sheep Breeds. Genes (Basel) 2020; 11:E604. [PMID: 32485962 PMCID: PMC7349075 DOI: 10.3390/genes11060604] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/21/2020] [Accepted: 05/27/2020] [Indexed: 11/16/2022] Open
Abstract
Keratin-associated proteins are important components of wool fibers. The gene encoding the high-sulfur keratin-associated protein 2-1 has been described in humans, but it has not been described in sheep. A basic local alignment search tool nucleotide search of the Ovine Genome Assembly version 4.0 using a human keratin-associated protein 2-1 gene sequence revealed a 399-base pair open reading frame, which was clustered among nine previously identified keratin-associated protein genes on chromosome 11. Polymerase chain reaction-single strand conformation polymorphism analysis revealed four different banding patterns, with these representing four different sequences (A-D) in Chinese sheep breeds. These sequences had the highest similarity to human keratin-associated protein 2-1 gene, suggesting that they represent variants of ovine keratin-associated protein 2-1 gene. Nine single nucleotide variations were detected in the gene, including one non-synonymous nucleotide substitution. Differences in variant frequencies between fine-wool sheep breeds and coarse-wool sheep breeds were detected. The gene was found to be expressed in various tissues, with the highest expression level in skin, and moderate expression levels in heart and lung tissue. These results reveal that the ovine keratin-associated protein 2-1 gene is variable and suggest the gene might affect variation in mean fiber diameter.
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Affiliation(s)
- Jianqing Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (J.W.); (H.Z.); (J.G.H.H.); (Y.L.); (H.G.); (J.H.); (X.L.); (S.L.); (Y.S.); (N.K.); (L.Q.)
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Huitong Zhou
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (J.W.); (H.Z.); (J.G.H.H.); (Y.L.); (H.G.); (J.H.); (X.L.); (S.L.); (Y.S.); (N.K.); (L.Q.)
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Jon G. H. Hickford
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (J.W.); (H.Z.); (J.G.H.H.); (Y.L.); (H.G.); (J.H.); (X.L.); (S.L.); (Y.S.); (N.K.); (L.Q.)
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Yuzhu Luo
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (J.W.); (H.Z.); (J.G.H.H.); (Y.L.); (H.G.); (J.H.); (X.L.); (S.L.); (Y.S.); (N.K.); (L.Q.)
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Hua Gong
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (J.W.); (H.Z.); (J.G.H.H.); (Y.L.); (H.G.); (J.H.); (X.L.); (S.L.); (Y.S.); (N.K.); (L.Q.)
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Jiang Hu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (J.W.); (H.Z.); (J.G.H.H.); (Y.L.); (H.G.); (J.H.); (X.L.); (S.L.); (Y.S.); (N.K.); (L.Q.)
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiu Liu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (J.W.); (H.Z.); (J.G.H.H.); (Y.L.); (H.G.); (J.H.); (X.L.); (S.L.); (Y.S.); (N.K.); (L.Q.)
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Shaobin Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (J.W.); (H.Z.); (J.G.H.H.); (Y.L.); (H.G.); (J.H.); (X.L.); (S.L.); (Y.S.); (N.K.); (L.Q.)
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Yize Song
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (J.W.); (H.Z.); (J.G.H.H.); (Y.L.); (H.G.); (J.H.); (X.L.); (S.L.); (Y.S.); (N.K.); (L.Q.)
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Na Ke
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (J.W.); (H.Z.); (J.G.H.H.); (Y.L.); (H.G.); (J.H.); (X.L.); (S.L.); (Y.S.); (N.K.); (L.Q.)
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Lirong Qiao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (J.W.); (H.Z.); (J.G.H.H.); (Y.L.); (H.G.); (J.H.); (X.L.); (S.L.); (Y.S.); (N.K.); (L.Q.)
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiqing Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (J.W.); (H.Z.); (J.G.H.H.); (Y.L.); (H.G.); (J.H.); (X.L.); (S.L.); (Y.S.); (N.K.); (L.Q.)
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
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Li S, Zhou H, Gong H, Zhao F, Wang J, Liu X, Hu J, Luo Y, Hickford JG. The Mean Staple Length of Wool Fibre Is Associated with Variation in the Ovine Keratin-Associated Protein 21-2 Gene. Genes (Basel) 2020; 11:E148. [PMID: 32019077 PMCID: PMC7073969 DOI: 10.3390/genes11020148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/20/2020] [Accepted: 01/24/2020] [Indexed: 11/16/2022] Open
Abstract
Wool and hair fibres consist of a variety of proteins, including the keratin-associated proteins (KAPs). In this study, a putative ovine homologue of the human KAP21-2 gene (KRTAP21-2) was identified. It was located on chromosome 1 as a 201-bp open reading frame (ORF) in the ovine genome assembly from a Texel sheep (v.4 NC_019458.2: nt122932727 to 122932927). A polymerase chain reaction- single strand conformation polymorphism (PCR-SSCP) analysis of this ORF, and subsequent DNA sequencing, identified five sequences (named A-E). The putative amino acid sequences that would be produced, shared some identity with each other and with other KAPs, but they were most similar to ovine KAP21-1, and phylogenetically related to human KAP21-2. The location of the ovine KRTAP21-2 sequence was consistent with the location of human KRTAP21-2, and this suggests they represent different variant forms of ovine KRTAP21-2. Variation in this gene was investigated in 389 Merino (sire) × Southdown-cross (ewe) lambs. These were derived from four independent sire-lines. The sequence variation was found to be associated with variation in five wool traits: including mean staple length (MSL), mean fibre diameter (MFD), fibre diameter standard deviation (FDSD), prickle factor (PF), and greasy fleece weight (GFW). The most persistent effect of KRTAP21-2 variation was with variation in MSL; with the MSL of sheep of genotype AC being 12.5% greater than those of genotype CE. A similar effect was observed from individual variant absence/presence models. This suggests that KRTAP21-2 should be further investigated as a possible gene-marker for improving MSL.
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Affiliation(s)
- Shaobin Li
- Faculty of Animal Science and Technology, Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (S.L.); (J.W.); (X.L.); (J.H.)
- International Wool Research Institute, Gansu Agricultural University, Lanzhou 730070, China; (H.Z.); (H.G.)
| | - Huitong Zhou
- International Wool Research Institute, Gansu Agricultural University, Lanzhou 730070, China; (H.Z.); (H.G.)
- Gene-marker Laboratory, Faculty of Agricultural and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Hua Gong
- International Wool Research Institute, Gansu Agricultural University, Lanzhou 730070, China; (H.Z.); (H.G.)
- Gene-marker Laboratory, Faculty of Agricultural and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Fangfang Zhao
- Faculty of Animal Science and Technology, Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (S.L.); (J.W.); (X.L.); (J.H.)
| | - Jiqing Wang
- Faculty of Animal Science and Technology, Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (S.L.); (J.W.); (X.L.); (J.H.)
- International Wool Research Institute, Gansu Agricultural University, Lanzhou 730070, China; (H.Z.); (H.G.)
| | - Xiu Liu
- Faculty of Animal Science and Technology, Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (S.L.); (J.W.); (X.L.); (J.H.)
- International Wool Research Institute, Gansu Agricultural University, Lanzhou 730070, China; (H.Z.); (H.G.)
| | - Jiang Hu
- Faculty of Animal Science and Technology, Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (S.L.); (J.W.); (X.L.); (J.H.)
- International Wool Research Institute, Gansu Agricultural University, Lanzhou 730070, China; (H.Z.); (H.G.)
| | - Yuzhu Luo
- Faculty of Animal Science and Technology, Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (S.L.); (J.W.); (X.L.); (J.H.)
- International Wool Research Institute, Gansu Agricultural University, Lanzhou 730070, China; (H.Z.); (H.G.)
| | - Jon G.H. Hickford
- International Wool Research Institute, Gansu Agricultural University, Lanzhou 730070, China; (H.Z.); (H.G.)
- Gene-marker Laboratory, Faculty of Agricultural and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
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11
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Wang J, Zhou H, Hickford JGH, Zhao M, Gong H, Hao Z, Shen J, Hu J, Liu X, Li S, Luo Y. Identification of Caprine KRTAP28-1 and Its Effect on Cashmere Fiber Diameter. Genes (Basel) 2020; 11:E121. [PMID: 31979055 PMCID: PMC7074440 DOI: 10.3390/genes11020121] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/20/2020] [Accepted: 01/21/2020] [Indexed: 12/31/2022] Open
Abstract
The keratin-associated proteins (KAPs) are constituents of cashmere fibers and variation in many KAP genes (KRTAPs) has been found to be associated with fiber traits. The gene encoding the high-sulphur KAP28-1 has been described in sheep, but it has not been identified in the goat genome. In this study, a 255-bp open reading frame on goat chromosome 1 was identified using a search of similar sequence to ovine KRTAP28-1, and that would if transcribed and translated encode a high sulphur KAP. Based on the analysis of polymerase chain reaction (PCR) amplicons for the goat nucleotide sequences in 385 Longdong cashmere goats in China, five unique banding patterns were detected using single-stranded conformational polymorphism (SSCP). These represented five DNA sequences (named variants A to E) and they had the highest resemblance to KRTAP28-1 sequences from sheep, suggesting A-E are variants of caprine KRTAP28-1. DNA sequencing revealed a 2 or 4-bp deletion and eleven nucleotide sequence differences, including four non-synonymous substitutions. Of the four common variants (A, B, C and D) found in these goats, the presence of variant A was associated with decreased mean fiber diameter and this effect appeared to be additive. These results indicate that caprine KRTAP28-1 variation might have value as a molecular marker for reducing cashmere mean fiber diameter.
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Affiliation(s)
- Jiqing Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (J.W.); (H.Z.); (J.G.H.H.); (M.Z.); (H.G.); (Z.H.); (J.S.); (J.H.); (X.L.); (S.L.)
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Huitong Zhou
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (J.W.); (H.Z.); (J.G.H.H.); (M.Z.); (H.G.); (Z.H.); (J.S.); (J.H.); (X.L.); (S.L.)
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Jon G. H. Hickford
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (J.W.); (H.Z.); (J.G.H.H.); (M.Z.); (H.G.); (Z.H.); (J.S.); (J.H.); (X.L.); (S.L.)
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Mengli Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (J.W.); (H.Z.); (J.G.H.H.); (M.Z.); (H.G.); (Z.H.); (J.S.); (J.H.); (X.L.); (S.L.)
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Hua Gong
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (J.W.); (H.Z.); (J.G.H.H.); (M.Z.); (H.G.); (Z.H.); (J.S.); (J.H.); (X.L.); (S.L.)
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Zhiyun Hao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (J.W.); (H.Z.); (J.G.H.H.); (M.Z.); (H.G.); (Z.H.); (J.S.); (J.H.); (X.L.); (S.L.)
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiyuan Shen
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (J.W.); (H.Z.); (J.G.H.H.); (M.Z.); (H.G.); (Z.H.); (J.S.); (J.H.); (X.L.); (S.L.)
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiang Hu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (J.W.); (H.Z.); (J.G.H.H.); (M.Z.); (H.G.); (Z.H.); (J.S.); (J.H.); (X.L.); (S.L.)
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiu Liu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (J.W.); (H.Z.); (J.G.H.H.); (M.Z.); (H.G.); (Z.H.); (J.S.); (J.H.); (X.L.); (S.L.)
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Shaobin Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (J.W.); (H.Z.); (J.G.H.H.); (M.Z.); (H.G.); (Z.H.); (J.S.); (J.H.); (X.L.); (S.L.)
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Yuzhu Luo
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (J.W.); (H.Z.); (J.G.H.H.); (M.Z.); (H.G.); (Z.H.); (J.S.); (J.H.); (X.L.); (S.L.)
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
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12
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Ullah F, Jamal SM, Ekegbu UJ, Haruna IL, Zhou H, Hickford JGH. Polymorphism in the ovine keratin-associated protein gene KRTAP7-1 and its association with wool characteristics. J Anim Sci 2020; 98:5682607. [PMID: 31863114 DOI: 10.1093/jas/skz381] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 12/17/2019] [Indexed: 01/28/2023] Open
Abstract
The keratin-associated proteins (KAPs) are structural components of wool fibers and variation in the genes encoding the KAPs can affect wool traits. In this study, sequence variation in the ovine KAP7-1 gene (KRTAP7-1) was investigated in 222 sheep across 5 different Pakistani breeds and breed crosses. Two previously identified variants (A and B) of the KRTAP7-1 coding sequence were identified. The frequency of the genotypes AA and AB was 76% and 23%, respectively, and that of BB was 1%. The association of sequence variation with various wool traits and measurements included yield (the proportion of greasy fleece weight that is clean fleece), mean staple length (MSL), wool bulk, mean fiber diameter, fiber diameter SD, the coefficient of variation of fiber diameter, medullation, the SD of medullation, the coefficient of variation of medullation, fiber opacity, the SD of opacity, and the coefficient of variation of opacity. Variation in KRTAP7-1 was found to be associated with yield (P = 0.017). The adjusted mean yield of sheep of genotype AA (n = 169) was 79.9 ± 2.72%, while that of genotype AB (n = 51) was 81.9 ± 3.37%. There was also an association between variation in KRTAP7-1 and MSL (P = 0.024), with sheep of genotype AA (n = 169) having an adjusted mean MSL of 47.3 ± 0.57 mm compared with sheep of genotype AB (n = 51, 50.9 ± 0.65 mm). Yield and MSL are both important wool production traits, hence variation in KRTAP7-1 needs to be further investigated in more sheep of differing breed.
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Affiliation(s)
- Farman Ullah
- Department of Biotechnology, University of Malakand, Chakdara, Pakistan
| | - Syed M Jamal
- Department of Biotechnology, University of Malakand, Chakdara, Pakistan
| | - Ugonna J Ekegbu
- Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, New Zealand
| | - Ishaku L Haruna
- Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, New Zealand
| | - Huitong Zhou
- Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, New Zealand
| | - Jon G H Hickford
- Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, New Zealand
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13
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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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14
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Bai L, Zhou H, Gong H, Tao J, Ma Q, Ding W, Hickford JG. Variation in the ovine KAP8-1 gene affects wool fibre uniformity in Chinese Tan sheep. Small Rumin Res 2019. [DOI: 10.1016/j.smallrumres.2019.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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15
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Li W, Gong H, Zhou H, Wang J, Li S, Liu X, Luo Y, Hickford J. Variation in KRTAP6-1 affects wool fibre diameter in New Zealand Romney ewes. Arch Anim Breed 2019; 62:509-515. [PMID: 31807662 PMCID: PMC6853137 DOI: 10.5194/aab-62-509-2019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 07/09/2019] [Indexed: 01/17/2023] Open
Abstract
Variation in KRTAP6-1 has been reported to affect wool fibre traits in Merino cross-breed sheep and Chinese Tan sheep, but little is known about whether these effects persist in other breeds. In this study, variation in KRTAP6-1 was investigated in 290 New Zealand (NZ) Romney ewes sired by 16 different rams. Polymerase chain reaction single-stranded conformational polymorphism (PCR-SSCP) analysis revealed four variants ( A , B , E and F ) of KRTAP6-1, and nine genotypes (AA, AB, AE, AF, BB, BE, BF, EE and FF) in these ewes. Among the 243 ewes that had genotypes with a frequency of over 5 % (i.e. AA, AB and BB), the presence of A was found to be associated with reduced mean fibre diameter (MFD) and increased coefficient of variation in fibre diameter (CVFD), whereas the presence of B had a trend of association with decreased coarse edge measurement (CEM). A genotype effect was also detected for MFD and CVFD. No associations were detected for fibre diameter standard deviation (FDSD), mean fibre curvature (MFC) and medulation. These results suggest that variation in KRTAP6-1 affects wool fibre diameter in NZ Romney ewes, confirming the finding in Merino cross-breed sheep.
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Affiliation(s)
- Wenhao Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of
Animal Science and Technology, Gansu Agricultural University, Lanzhou
730070, China
- International Wool Research Institute, Gansu Agricultural University,
Lanzhou 730070, China
| | - Hua Gong
- International Wool Research Institute, Gansu Agricultural University,
Lanzhou 730070, China
- Gene-marker Laboratory, Faculty of Agricultural and Life Sciences,
Lincoln University, Lincoln 7647, New Zealand
| | - Huitong Zhou
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of
Animal Science and Technology, Gansu Agricultural University, Lanzhou
730070, China
- International Wool Research Institute, Gansu Agricultural University,
Lanzhou 730070, China
- Gene-marker Laboratory, Faculty of Agricultural and Life Sciences,
Lincoln University, Lincoln 7647, New Zealand
| | - Jiqing Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of
Animal Science and Technology, Gansu Agricultural University, Lanzhou
730070, China
- International Wool Research Institute, Gansu Agricultural University,
Lanzhou 730070, China
| | - Shaobin Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of
Animal Science and Technology, Gansu Agricultural University, Lanzhou
730070, China
- International Wool Research Institute, Gansu Agricultural University,
Lanzhou 730070, China
| | - Xiu Liu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of
Animal Science and Technology, Gansu Agricultural University, Lanzhou
730070, China
- International Wool Research Institute, Gansu Agricultural University,
Lanzhou 730070, China
| | - Yuzhu Luo
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of
Animal Science and Technology, Gansu Agricultural University, Lanzhou
730070, China
- International Wool Research Institute, Gansu Agricultural University,
Lanzhou 730070, China
| | - Jon G. H. Hickford
- International Wool Research Institute, Gansu Agricultural University,
Lanzhou 730070, China
- Gene-marker Laboratory, Faculty of Agricultural and Life Sciences,
Lincoln University, Lincoln 7647, New Zealand
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16
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Li S, Zhou H, Gong H, Zhao F, Wang J, Liu X, Hu J, Luo Y, Hickford JGH. Identification of the Ovine Keratin-Associated Protein 21-1 Gene and Its Association with Variation in Wool Traits. Animals (Basel) 2019; 9:E450. [PMID: 31315271 PMCID: PMC6680380 DOI: 10.3390/ani9070450] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 07/08/2019] [Accepted: 07/12/2019] [Indexed: 12/27/2022] Open
Abstract
Keratin-associated proteins (KAPs) are key constituents of wool and hair fibers. In this study, an ovine KAP gene encoding a HGT-KAP protein was identified. The gene was different from all of the HGT-KAP genes identified in sheep, but was closely related to the human KAP21-1 gene, suggesting that it represented the unidentified ovine KRTAP21-1. Four variants (named A to D) of ovine KRTAP21-1 were found in 360 Merino × Southdown-cross lambs from four sire lines. Three sequence variations were detected among these variants. Two of the sequence variations were located upstream of the coding region and the remaining one was a synonymous variation in the coding sequence. Six genotypes were found in the Merino-cross lambs, with only two of the genotypes (AA and AC) occurring at a frequency of over 5%. Wool from sheep of genotype AA had a higher yield than that from AC sheep (p = 0.014), but tended to have a lower greasy fleece weight (GFW) than that of genotype AC (P = 0.078). This suggests that variation in KRTAP21-1 affects wool yield and the gene may have potential for use as a genetic maker for improving wool yield.
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Affiliation(s)
- Shaobin Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- International Wool Research Institute, Gansu Agricultural University, Lanzhou 730070, China
| | - Huitong Zhou
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- International Wool Research Institute, Gansu Agricultural University, Lanzhou 730070, China
- Gene-Marker Laboratory, Faculty of Agricultural and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Hua Gong
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- International Wool Research Institute, Gansu Agricultural University, Lanzhou 730070, China
- Gene-Marker Laboratory, Faculty of Agricultural and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Fangfang Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiqing Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- International Wool Research Institute, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiu Liu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- International Wool Research Institute, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiang Hu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- International Wool Research Institute, Gansu Agricultural University, Lanzhou 730070, China
| | - Yuzhu Luo
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
- International Wool Research Institute, Gansu Agricultural University, Lanzhou 730070, China.
| | - Jon G H Hickford
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
- International Wool Research Institute, Gansu Agricultural University, Lanzhou 730070, China.
- Gene-Marker Laboratory, Faculty of Agricultural and Life Sciences, Lincoln University, Lincoln 7647, New Zealand.
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17
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Gong H, Zhou H, Bai L, Li W, Li S, Wang J, Luo Y, Hickford JGH. Associations between variation in the ovine high glycine-tyrosine keratin-associated protein gene KRTAP20-1 and wool traits. J Anim Sci 2019; 97:587-595. [PMID: 30535023 DOI: 10.1093/jas/sky465] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/06/2018] [Indexed: 11/12/2022] Open
Abstract
The keratin-associated proteins (KAPs) are important constituents of wool fibers. Of the many mammalian KAP genes (KRTAPs) identified, KRTAP20-1 has been described in humans, but it has not been described in any other species. A search of the sheep genome using the human KRTAP20-1 sequence revealed a homologous open reading frame on chromosome 1, which would encode a high glycine-tyrosine KAP. PCR-single-stranded conformational polymorphism (PCR-SSCP) analysis identified 8 different banding patterns representing 8 unique DNA sequences (named A to H). The sequences had highest similarity to the human KRTAP20-1 sequence, and this suggests that they are variants of ovine KRTAP20-1. Among these variants, a 12-bp insertion/deletion and 6 single nucleotide poly- morphisms (SNPs), including one 5' untranslated region (UTR) SNP, one 3' UTR SNP, and 2 nonsynonymous SNPs, were detected. Variant A was found to be associated with a decrease in mean fiber diameter, fiber diameter standard deviation, and prickle factor, whereas variant C was associated with increased greasy fleece weight and decreased wool yield. These associations persisted after adjusting for the effect of 2 nearby KRTAPs (KRTAP6-3 and KRTAP22-1) that have also been reported to associate with these wool traits. This suggests that variation in KRTAP20-1 affects wool yield and mean fiber diameter-associated traits, and that this effect is unlikely to be the result of the clustering of these KRTAPs on chromosome 1.
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Affiliation(s)
- Hua Gong
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China.,Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, New Zealand
| | - Huitong Zhou
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China.,Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, New Zealand
| | - Lingrong Bai
- Agricultural College, Ningxia University, Yinchuan, China
| | - Wenhao Li
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China.,Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou, China
| | - Shaobin Li
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China.,Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou, China
| | - Jiqing Wang
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China.,Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou, China
| | - Yuzhu Luo
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China.,Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou, China
| | - Jon G H Hickford
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China.,Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, New Zealand
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18
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Bai L, Wang J, Zhou H, Gong H, Tao J, Hickford JGH. Identification of Ovine KRTAP28-1 and Its Association with Wool Fibre Diameter. Animals (Basel) 2019; 9:ani9040142. [PMID: 30987059 PMCID: PMC6523819 DOI: 10.3390/ani9040142] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 03/25/2019] [Accepted: 03/29/2019] [Indexed: 11/18/2022] Open
Abstract
Simple Summary Keratin-associated proteins (KAPs) are fundamental components of wool and hair fibres. They are split into three broad groups: the high sulphur (HS), the ultra-high sulphur (UHS) and the high glycine-tyrosine (HGT) KAPs. KRTAP25-1 encodes a HS-KAP protein and the gene has recently been identified in humans. Here, we report the absence of a KRTAP25-1 in sheep, and we describe a new HS-KRTAP (named KRTAP28-1) in the chromosome region where KRTAP25-1 was expected to be found. Six variants (A−F) of KRTAP28-1 containing eight single nucleotide polymorphisms (SNPs) and a TG dinucleotide repeat polymorphism were detected. One SNP was located upstream of the start codon and all the others were non-synonymous SNPs, including a nonsense SNP. The TG repeat polymorphism would lead to a reading frame shift at the carboxyl-terminal end. The association of KRTAP28-1 with wool traits was investigated with 383 Southdown × Merino-cross lambs from seven sire lines. Of the four genotypes with a frequency over 5%, lambs of genotypes AB and BD produced wool of a smaller mean fibre diameter (MFD) than lambs of genotype BC. This shows that KRTAP28-1 is associated with a key wool trait, and variation in this gene might therefore have value as a marker for improving that trait. Abstract Keratin-associated proteins (KAPs) are a diverse group of proteins and form a matrix that cross-links keratin intermediate filaments in hair and wool fibres. From over 100 KAP genes (KRTAPs) identified in mammalian species, KRTAP25-1 is a high sulphur (HS)-KAP gene, which has recently been described in humans. Here, we report the absence of KRTAP25-1 in sheep, and describe a new HS-KRTAP (named KRTAP28-1) in the chromosome region where KRTAP25-1 was expected to be found. Six variants (A−F) of KRTAP28-1 containing eight single nucleotide polymorphisms (SNPs) and a TG repeat polymorphism were detected. One was positioned 30 bp upstream of the transcription start codon and all the others were non-synonymous SNPs, including a nonsense SNP. The TG repeat polymorphism would lead to a reading frame shift at the carboxyl-terminal end. The effect of KRTAP28-1 on wool traits was investigated with 383 Southdown × Merino-cross lambs from seven sire lines. Of the four genotypes with a frequency of over 5%, lambs of genotypes AB and BD produced wool of a smaller MFD than lambs of genotype BC. This shows that KRTAP28-1 is associated with wool fibre diameter, and that variation in this gene might have potential for use as a gene marker for reducing wool fibre diameter.
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Affiliation(s)
- Lingrong Bai
- Agricultural College, Ningxia University, Yinchuan 750021, China.
| | - Jing Wang
- College of Animal Science and Technology, Hebei North University, Zhangjiakou, Hebei 075131, China.
| | - Huitong Zhou
- Faculty of Agricultural and Life Sciences, Lincoln University, Lincoln 7647, New Zealand.
| | - Hua Gong
- Faculty of Agricultural and Life Sciences, Lincoln University, Lincoln 7647, New Zealand.
| | - Jinzhong Tao
- Agricultural College, Ningxia University, Yinchuan 750021, China.
| | - Jon G H Hickford
- Faculty of Agricultural and Life Sciences, Lincoln University, Lincoln 7647, New Zealand.
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19
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Zhao M, Zhou H, Hickford JGH, Gong H, Wang J, Hu J, Liu X, Li S, Hao Z, Luo Y. Variation in the caprine keratin-associated protein 15-1 (KAP15-1) gene affects cashmere fibre diameter. Arch Anim Breed 2019; 62:125-133. [PMID: 31807622 PMCID: PMC6852866 DOI: 10.5194/aab-62-125-2019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/05/2019] [Indexed: 11/23/2022] Open
Abstract
Keratin-associated proteins (KAPs) are a
structural component of cashmere fibre, and variation in some KAP
genes (KRTAPs) has been associated with a number of caprine fibre
traits. In this study, we report the identification of
KRTAP15-1 in goats. Sequence variation in the gene was
detected using the polymerase chain reaction single-strand conformation
polymorphism (PCR-SSCP) technique in 250 Longdong goats, and six variants
(named A to F) containing eight single nucleotide
polymorphisms (SNPs) were identified. Five of the SNPs were non-synonymous
and would lead to putative amino acid changes. Reverse-transcription
polymerase chain reaction (RT-PCR) analysis revealed that
KRTAP15-1 was expressed in secondary hair follicles but not
in heart tissue, liver tissue, lung tissue, kidney tissue or the longissimus
dorsi muscle. Despite being rich in cysteine, the caprine KAP15-1 protein
possesses a high content of serine and moderate content of glycine and
phenylalanine. Association analyses revealed that KRTAP15-1
variant A was associated with decreased mean fibre diameter (MFD), and this
effect appeared to be dominant; while variant C was found to be associated
with increased MFD, the effect being recessive. The findings suggest that
caprine KRTAP15-1 is highly polymorphic and that variation in this
gene affects cashmere MFD.
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Affiliation(s)
- Mengli Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.,International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Huitong Zhou
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.,International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.,Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Jon G H Hickford
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.,International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.,Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Hua Gong
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.,Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Jiqing Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.,International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiang Hu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.,International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiu Liu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.,International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Shaobin Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.,International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Zhiyun Hao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.,International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Yuzhu Luo
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.,International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
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20
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Wang J, Zhou H, Luo Y, Zhao M, Gong H, Hao Z, Hu J, Hickford JGH. Variation in the Caprine KAP24-1 Gene Affects Cashmere Fibre Diameter. Animals (Basel) 2019; 9:E15. [PMID: 30621287 PMCID: PMC6357099 DOI: 10.3390/ani9010015] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 12/10/2018] [Accepted: 12/29/2018] [Indexed: 01/02/2023] Open
Abstract
The keratin-associated proteins (KAPs) are structural components of cashmere fibres. The gene encoding the high-sulphur (HS)-KAP24-1 (KRTAP24-1) has been identified in humans and sheep, but it has not been described in goats. In this study, we report the identification of caprine KRTAP24-1, describe variation in this gene, and investigate the effect of this variation on cashmere traits. A search for sequences orthologous to the ovine gene in the goat genome revealed a 774 bp open reading frame on chromosome 1, which could encode an HS-KAP. Based on this goat genome sequence and comparison with ovine KRTAP24-1 sequences, polymerase chain reaction (PCR) primers were designed to amplify an 856 bp fragment that would contain the entire coding region of the putative caprine KRTAP24-1. Use of this PCR amplification with subsequent single-strand conformation polymorphism (SSCP) analysis of the amplicons identified four distinct patterns of DNA bands on gel electrophoresis, with these representing four different DNA sequences (A to D), in 340 Longdong cashmere goats reared in China. The variant sequences had the highest similarity to KRTAP24-1 sequences from sheep and humans, suggesting that they are variants of caprine KRTAP24-1. Nine single-nucleotide polymorphisms (SNPs) were detected in the gene, including four non-synonymous SNPs and an SNP in proximity to the ATG start codon. Of the three common genotypes (AA, AB, and BB) found in these Longdong cashmere goats, cashmere fibres from goats of genotype AA had lower mean fibre diameter (MFD) than did those of genotype AB, and cashmere fibres from goats of genotype AB had lower MFD than did those from goats of genotype BB.
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Affiliation(s)
- Jiqing Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Huitong Zhou
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
- Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand.
| | - Yuzhu Luo
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Mengli Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Hua Gong
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
- Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand.
| | - Zhiyun Hao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Jiang Hu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Jon G H Hickford
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
- Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand.
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21
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Contrasting patterns of coding and flanking region evolution in mammalian keratin associated protein-1 genes. Mol Phylogenet Evol 2018; 133:352-361. [PMID: 30599197 DOI: 10.1016/j.ympev.2018.12.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/15/2018] [Accepted: 12/26/2018] [Indexed: 12/17/2022]
Abstract
Mammalian genomes contain a number of duplicated genes, and sequence identity between these duplicates can be maintained by purifying selection. However, between-duplicate recombination can also maintain sequence identity between copies, resulting in a pattern known as concerted evolution where within-genome repeats are more similar to each other than to orthologous repeats in related species. Here we investigated the tandemly-repeated keratin-associated protein 1 (KAP1) gene family, KRTAP1, which encodes proteins that are important components of hair and wool in mammals. Comparison of eutherian mammal KRTAP1 gene repeats within and between species shows a strong pattern of concerted evolution. However, in striking contrast to the coding regions of these genes, we find that the flanking regions have a divergent pattern of evolution. This contrast in evolutionary pattern transitions abruptly near the start and stop codons of the KRTAP1 genes. We reveal that this difference in evolutionary patterns is not explained by conventional purifying selection, nor is it likely a consequence of codon adaptation or reverse transcription of KRTAP1-n mRNA. Instead, the evidence suggests that these contrasting patterns result from short-tract gene conversion events that are biased to the KRTAP1 coding region by selection and/or differential sequence divergence. This work demonstrates the power that gene conversion has to finely shape the evolution of repetitive genes, and provides another distinctive pattern of contrasting evolutionary outcomes that results from gene conversion. A greater emphasis on exploring the evolution of multi-gene eukaryotic families will reveal how common different contrasting evolutionary patterns are in gene duplicates.
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22
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Wang J, Hao Z, Zhou H, Luo Y, Hu J, Liu X, Li S, Hickford JG. A keratin-associated protein (KAP) gene that is associated with variation in cashmere goat fleece weight. Small Rumin Res 2018. [DOI: 10.1016/j.smallrumres.2018.08.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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23
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Bai L, Gong H, Zhou H, Tao J, Hickford JGH. A nucleotide substitution in the ovine KAP20-2 gene leads to a premature stop codon that affects wool fibre curvature. Anim Genet 2018; 49:357-358. [DOI: 10.1111/age.12668] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Lingrong Bai
- Agricultural College; Ningxia University; Yinchuan 750021 China
- International Wool Research Institute; Faculty of Animal Science and Technology; Gansu Agricultural University; Lanzhou 730070 China
| | - Hua Gong
- International Wool Research Institute; Faculty of Animal Science and Technology; Gansu Agricultural University; Lanzhou 730070 China
- Gene-Marker Laboratory; Department of Agricultural Sciences; Lincoln University; Lincoln 7647 New Zealand
| | - Huitong Zhou
- International Wool Research Institute; Faculty of Animal Science and Technology; Gansu Agricultural University; Lanzhou 730070 China
- Gene-Marker Laboratory; Department of Agricultural Sciences; Lincoln University; Lincoln 7647 New Zealand
| | - Jingzhong Tao
- Agricultural College; Ningxia University; Yinchuan 750021 China
- International Wool Research Institute; Faculty of Animal Science and Technology; Gansu Agricultural University; Lanzhou 730070 China
| | - Jon G. H. Hickford
- International Wool Research Institute; Faculty of Animal Science and Technology; Gansu Agricultural University; Lanzhou 730070 China
- Gene-Marker Laboratory; Department of Agricultural Sciences; Lincoln University; Lincoln 7647 New Zealand
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