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Shi A, Lv J, Ma Q, Liu Z, Ma L, Zhou J, Tao J. Study on the expression patterns of inner root sheath-specific genes in Tan sheep hair follicle during different developmental stages. Gene 2024; 927:148751. [PMID: 38971547 DOI: 10.1016/j.gene.2024.148751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 06/14/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
By analyzing the expression patterns of inner root sheath (IRS) specific genes during different developmental stages of hair follicle (HF) in Tan sheep embryos and at birth, this study aims to reveal the influence of the IRS on crimped wool. Skin tissues from the scapular region of male Tan sheep were collected at 85 days (E85) and 120 days (E120) of fetal development, and at 0 days (D0), 35 days (D35), and 60 days (D60) after birth, with four samples at each stage. Real-time quantitative polymerase chain reaction (RT-qPCR) was employed to determine the relative expression levels of IRS type I keratin genes (KRT25, KRT26, KRT27, KRT28), type II keratin genes (KRT71, KRT72, KRT73, KRT74), and the trichohyalin gene (TCHH) in the skin of Tan sheep at different stages. Results showed that the expression levels of all IRS-specific genes peaked at D0, with the expression of all genes significantly higher than at E85 (P < 0.01), except for KRT73 and TCHH. The expression levels of KRT25, KRT26, and KRT72 were also significantly higher than at E120 (P < 0.01). Furthermore, the expression levels of KRT27, KRT28, KRT71, and KRT74 were significantly higher than both at E120 and D35 (P < 0.01). The expression levels of other genes at different stages showed no significant difference (P > 0.05). Conclusion: The IRS-specific genes exhibit the highest expression levels in Tan sheep at the neonatal stage. The expression levels of KRT71, KRT72, and TCHH, which are consistent with the pattern of wool crimp, may influence the morphology of the IRS and thereby affect the crimp of Tan sheep wool.
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Affiliation(s)
- An Shi
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Jiangjiang Lv
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Qing Ma
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China
| | - Zhanfa Liu
- Ningxia Yanchi Tan Sheep Breeding Center, Yanchi 751506, China
| | - Lina Ma
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China
| | - Junsheng Zhou
- Ningxia Yanchi Tan Sheep Breeding Center, Yanchi 751506, China
| | - Jinzhong Tao
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China.
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Variation in caprine KRTAP1-3 and its association with cashmere fibre diameter. Gene X 2022; 823:146341. [PMID: 35219814 DOI: 10.1016/j.gene.2022.146341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/12/2021] [Accepted: 02/14/2022] [Indexed: 11/24/2022] Open
Abstract
Keratin-associated proteins (KAPs) are components of cashmere fibres. The gene encoding the KAP1-3 protein (KRTAP1-3) has been described in goats, but little is known about sequence variation in this gene and if it affects cashmere fibre traits. In this study, we used a polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) technique to screen for nucleotide sequence variation in caprine KRTAP1-3 in 327 Longdong cashmere goats, then analysed association between the genetic variation that was revealed and some cashmere fibre traits. Six PCR-SSCP patterns representing six different variant sequences of KRTAP1-3 (named A to F) were revealed. Among these variant sequences, seven single nucleotide polymorphisms (SNPs) were detected, with two of them being non-synonymous. Goats with genotype AC had higher mean fibre diameter (MFD) than those with genotype AB (P < 0.001), while goats with genotype AB had higher MFD than those with AA (P < 0.001). The presence of C (P < 0.001) and B (P = 0.006) in a genotype was associated with increased MFD, and together this suggests that variation in caprine KRTAP1-3 affects the key fibre trait of MFD.
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Ovine Toll-like Receptor 9 ( TLR9) Gene Variation and Its Association with Flystrike Susceptibility. Animals (Basel) 2021; 11:ani11123549. [PMID: 34944323 PMCID: PMC8697942 DOI: 10.3390/ani11123549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/09/2021] [Indexed: 11/21/2022] Open
Abstract
Simple Summary Flystrike is a major ectoparasitic disease of sheep and it creates both an economic impact and welfare issue for the sheep industry. Several factors control the responses of sheep to flystrike, and among these, immune response is regarded as an important factor. Toll-like receptors (TLRs) plays a crucial role in the innate immune system by recognizing pathogen-associated molecular patterns derived from various microbes. Of these receptors, TLR9 recognises unmethylated cytosine-phosphate-guanine (CpG) motifs that are known to be prevalent in bacterial genomes and are also reported in Dipteran insects, including Lucilia cuprina, one of the main species associated with flystrike in sheep. In this study, we used a polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) technique to investigate TLR9 variation in sheep with and without flystrike, and found that variation in a gene region containing the coding sequence of the putative CpG-DNA binding domain was associated with the likelihood of flystrike occurrence. This suggests that variation in ovine TLR9 may affect a sheep’s response to flystrike. Abstract Toll-like receptors (TLRs) are a family of proteins that play a role in innate immune responses by recognising pathogen-associated molecular patterns derived from various microbes. Of these receptors, TLR9 recognises bacterial and viral DNA containing unmethylated cytosine-phosphate-guanine (CpG) motifs, and variation in TLR9 has been associated with resistance to various infectious diseases. Flystrike is a problem affecting the sheep industry globally and the immune response of the sheep has been suggested as one factor that influences the response to the disease. In this study, variation in ovine TLR9 from 178 sheep with flystrike and 134 sheep without flystrike was investigated using a polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) approach. These sheep were collected from both commercial and stud farms throughout New Zealand and they were of 13 different breeds, cross-breds and composites. Four alleles of TLR9 were detected, including three previously identified alleles (*01, *02 and *03) and a new allele (*04). In total six single nucleotide polymorphisms (SNPs) were found. Of the three common alleles in the sheep studied, the presence of *03 was found to be associated with a reduced likelihood of flystrike being present (OR = 0.499, p = 0.024). This suggests that variation in ovine TLR9 may affect a sheep’s response to flystrike, and thus the gene may have value as a genetic marker for improving resistance to the disease.
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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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Du X, Zhou H, Liu X, Li Y, Hickford JGH. Sequence Variation in the Bovine Lipin-1 Gene ( LPIN1) and Its Association with Milk Fat and Protein Contents in New Zealand Holstein-Friesian × Jersey (HF × J)-cross Dairy Cows. Animals (Basel) 2021; 11:ani11113223. [PMID: 34827956 PMCID: PMC8614294 DOI: 10.3390/ani11113223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/04/2021] [Accepted: 11/09/2021] [Indexed: 11/16/2022] Open
Abstract
Lipin-1 is known to play a regulatory role in tissues that function in lipid metabolism. In dairy cows, the lipin-1 gene (LPIN1) is highly expressed in the mammary gland, but its function in milk production is less understood. In this study, we used PCR-single strand conformation polymorphism analysis to investigate sequence variation in three regions of bovine LPIN1 in New Zealand Holstein-Friesian × Jersey (HF × J)-cross dairy cows, including part of the 5' non-coding region, the region containing the LPIN1β-spliced exon, and the sixth coding exon that encodes the putative transcriptional activating domain of the protein. No variation was found in the LPIN1β-spliced exon, but two sequence variants containing one single nucleotide polymorphism (SNP) were identified in the 5' non-coding region and four sequence variants containing four non-synonymous SNPs were identified in the sixth coding exon. Among the three common variants of the sixth coding exon, variant C was found to be associated with an increase in milk fat percentage (presence 4.96 ± 0.034% vs. absence 4.81 ± 0.050%; p = 0.006) and milk protein percentage (presence 4.09 ± 0.017% vs. absence 3.99 ± 0.025%; p = 0.001), but no associations (p > 0.01) were detected for milk yield. These results suggest that variation in LPIN1 affect the synthesis of fat and proteins in milk and has potential as a gene-marker to improve milk production traits.
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Affiliation(s)
- Xiaohua Du
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China;
| | - Huitong Zhou
- Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (H.Z.); (Y.L.)
| | - Xia Liu
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- Correspondence: (X.L.); (J.G.H.H.)
| | - Yunhai Li
- Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (H.Z.); (Y.L.)
| | - Jonathan G. H. Hickford
- Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (H.Z.); (Y.L.)
- Correspondence: (X.L.); (J.G.H.H.)
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6
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Zhao M, Zhou H, Luo Y, Wang J, Hu J, Liu X, Li S, Zhang K, Zhen H, Hickford JGH. Variation in a Newly Identified Caprine KRTAP Gene Is Associated with Raw Cashmere Fiber Weight in Longdong Cashmere Goats. Genes (Basel) 2021; 12:genes12050625. [PMID: 33922107 PMCID: PMC8143586 DOI: 10.3390/genes12050625] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 11/30/2022] Open
Abstract
Keratin-associated proteins (KAPs) and keratins determine the physical and chemical properties of cashmere fibers as they are the main components of the fibers. It has been reported that ovine KRTAP1-2 affects clean fleece weight, greasy fleece weight and yield in sheep, but the gene has not been described in goats and its effects on fiber traits are unknown. In this study, we identify the keratin-associated protein 1-2 gene (KRTAP1-2) in the goat genome and describe its effect on cashmere fiber traits in 359 Longdong cashmere goats. Six sequence variants (named CAPHI-KRTAP1-2*A to CAPHI-KRTAP1-2*F) were revealed using polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) analysis. These sequences have the highest homology with ovine KRTAP1-2 sequences. There were a 60-bp deletion, a 15-bp insertion and five single nucleotide polymorphisms (SNPs) including two non-synonymous SNPs in the coding sequence. The caprine KRTAP1-2 gene was expressed in the skin tissue, but a signal was not observed for the kidneys, liver, lungs, spleen, heart and longissimus dorsi muscle. Variation in caprine KRTAP1-2 was found to be associated with raw cashmere fiber weight, but not with fiber diameter and length.
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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.); (H.Z.)
- International Wool Research Institute, Gansu Agricultural University, Lanzhou 730070, China;
| | - Huitong Zhou
- International Wool Research Institute, 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.); (H.Z.)
- International Wool Research Institute, 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.); (H.Z.)
- International Wool Research Institute, 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.); (H.Z.)
- International Wool Research Institute, 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.); (H.Z.)
- International Wool Research Institute, 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.); (H.Z.)
- International Wool Research Institute, Gansu Agricultural University, Lanzhou 730070, China;
| | - Kaiwen Zhang
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, University of Toronto, Toronto, ON M5G 0A4, Canada;
| | - Huimin Zhen
- 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.); (H.Z.)
- 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 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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Gong H, Zhou H, Wang J, Li S, Luo Y, Hickford JGH. Characterisation of an Ovine Keratin Associated Protein (KAP) Gene, Which Would Produce a Protein Rich in Glycine and Tyrosine, but Lacking in Cysteine. Genes (Basel) 2019; 10:genes10110848. [PMID: 31717789 PMCID: PMC6896175 DOI: 10.3390/genes10110848] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/18/2019] [Accepted: 10/23/2019] [Indexed: 01/01/2023] Open
Abstract
The keratin-associated proteins (KAPs) are structural components of hair/wool fibres. All of the KAPs identified to date contain cysteine, which is thought to form disulphide bonds cross-linking the keratin intermediate filaments. Here, we report the identification of a KAP gene in sheep that would produce a protein that contains a high proportion (63.2 mol%) of glycine and tyrosine, but would not contain any cysteine. This suggests that other forms of intra- and inter-strand interaction may occur with this KAP, such as interactions via ring-stacking and hydrogen-bonding. The gene was dissimilar to any previously reported KAP gene, and was therefore assigned to a new family, and named KRTAP36-1. The KRTAP36-1 genome sequence was almost identical to some EST sequences from sheep and goat skin follicles, suggesting that it is present and expressed in sheep and goats. A BLAST search of the human genome assembly sequence did not reveal any human homologue. Three variant sequences (named A to C) of ovine KRTAP36-1 were identified and four single nucleotide polymorphisms (SNPs) were detected. One SNP was located 32 bp upstream of the coding region, and all of the others were in the coding region and were nonsynonymous. After correcting for potential linkage to the proximal KRTAP20-1, variant B of KRTAP36-1 was found to be associated with increased prickle factor (PF) in wool, suggesting that variation in the gene may have the potential to be used as gene marker for breeding sheep with lower PF.
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Affiliation(s)
- Hua Gong
- International Wool Research Institute, Gansu Agricultural University, Lanzhou 730070, China; (H.G.); (H.Z.); (J.W.); (S.L.)
- Gene Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Huitong Zhou
- International Wool Research Institute, Gansu Agricultural University, Lanzhou 730070, China; (H.G.); (H.Z.); (J.W.); (S.L.)
- Gene Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Jiqing Wang
- International Wool Research Institute, Gansu Agricultural University, Lanzhou 730070, China; (H.G.); (H.Z.); (J.W.); (S.L.)
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Shaobin Li
- International Wool Research Institute, Gansu Agricultural University, Lanzhou 730070, China; (H.G.); (H.Z.); (J.W.); (S.L.)
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Yuzhu Luo
- International Wool Research Institute, Gansu Agricultural University, Lanzhou 730070, China; (H.G.); (H.Z.); (J.W.); (S.L.)
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- Correspondence: (Y.L.); (J.G.H.H.)
| | - Jonathan G. H. Hickford
- International Wool Research Institute, Gansu Agricultural University, Lanzhou 730070, China; (H.G.); (H.Z.); (J.W.); (S.L.)
- Gene Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
- Correspondence: (Y.L.); (J.G.H.H.)
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Diversity of Trichocyte Keratins and Keratin Associated Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1054:21-32. [PMID: 29797265 DOI: 10.1007/978-981-10-8195-8_3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
Wool and hair fibres are primarily composed of proteins of which the keratins and keratin associated proteins (KAPs) are the major component. Considerable diversity is known to exist within these two groups of proteins. In the case of the keratins two major families are known, of which there are 11 members in the acidic Type I family and 7 members in the neutral-basic Type II family. The KAPs are even more diverse than the keratins, with 35 families being known to exist when the KAPs found in monotremes, marsupials and other mammalian species are taken into consideration. Human hair and wool are known to have 88 and 73 KAPs respectively, though this number rises for wool when polymorphism within KAP families is included.
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9
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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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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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11
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Li S, Zhou H, Gong H, Zhao F, Hu J, Luo Y, Hickford JGH. Identification of the Ovine Keratin-Associated Protein 26-1 Gene and Its Association with Variation in Wool Traits. Genes (Basel) 2017; 8:E225. [PMID: 28902131 PMCID: PMC5615358 DOI: 10.3390/genes8090225] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/01/2017] [Accepted: 09/06/2017] [Indexed: 01/22/2023] Open
Abstract
Keratin-associated proteins (KAPs) are structural components of wool and hair fibres, and are believed to play a role in defining the physico-mechanical properties of the wool fibre. In this study, the putative ovine homologue of the human KAP26-1 gene (KRTAP26-1) was sequenced and four variants (named A-D) were identified. The sequences shared some identity with each other and with other KRTAPs, but they had the greatest similarity with the human KRTAP26-1 sequence. This suggests they represent different variants of ovine KRTAP26-1. The association of these KRTAP26-1 variants with wool traits was investigated in the 383 Merino-Southdown cross sheep. The presence of B was associated (p < 0.05) with an increase in mean fibre diameter (MFD), mean fibre curvature, and prickle factor (PF). The presence of C was found to be associated (p < 0.05) with an increase in wool yield (Yield) and mean staple length (MSL), and a decrease in MFD, fibre diameter standard deviation (FDSD), and PF. The results suggest that sheep with C have, on average, higher wool quality. These results may be useful in the future development of breeding programs based on decreasing wool MFD and FDSD, or on increasing wool MSL.
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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
- 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.
| | - 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
- 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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Gong H, Zhou H, Forrest RHJ, Li S, Wang J, Dyer JM, Luo Y, Hickford JGH. Wool Keratin-Associated Protein Genes in Sheep-A Review. Genes (Basel) 2016; 7:E24. [PMID: 27240405 PMCID: PMC4929423 DOI: 10.3390/genes7060024] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 05/03/2016] [Accepted: 05/25/2016] [Indexed: 12/18/2022] Open
Abstract
The importance of sheep's wool in making textiles has inspired extensive research into its structure and the underlying genetics since the 1960s. Wool keratin-associated proteins (KAPs) are a key structural component of the wool fibre. The characterisation of the genes encoding these proteins has progressed rapidly with advances in the nucleotide and protein sequencing. This review describes our knowledge of ovine KAPs, their categorisation into families, polymorphism in the proteins and genes, the clustering and chromosomal location of the genes, some characteristics of gene expression and some potential effects of the KAPs on wool traits. The extent and nature of genetic variation in wool KAP genes and its association with fibre characteristics, provides an opportunity for the development of gene-markers for selective breeding of sheep to produce better wool with properties highly matched to specific end-uses.
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Affiliation(s)
- Hua Gong
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
- Gene-marker Laboratory, Faculty of Agricultural and Life 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, Faculty of Agricultural and Life Sciences, Lincoln University, Lincoln 7647, New Zealand.
| | - Rachel H J Forrest
- Faculty of Health and Sport Sciences, Eastern Institute of Technology, Private Bag 1201, Napier 4142, New Zealand.
| | - Shaobin Li
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Jiqing Wang
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Jolon M Dyer
- Food & Bio-Based Products, Lincoln Research Centre, AgResearch Limited, Lincoln 7608, New Zealand.
| | - Yuzhu Luo
- 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, Faculty of Agricultural and Life Sciences, Lincoln University, Lincoln 7647, New Zealand.
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Identification of four new gene members of the KAP6 gene family in sheep. Sci Rep 2016; 6:24074. [PMID: 27045687 PMCID: PMC4820716 DOI: 10.1038/srep24074] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 03/18/2016] [Indexed: 11/23/2022] Open
Abstract
KAP6 is a high glycine-tyrosine keratin-associated protein (HGT-KAP) family. This family is thought to contain multiple genes. In this study, we used a KRTAP6 coding sequence to search the Ovine Genome (v3.1) and identified five homologous regions (R1–R5). All these regions contained an open reading frame, and they were either identical to, or highly similar to, sheep skin Expressed Sequence Tags (ESTs). Phylogenetic analysis revealed that R1–R5 were clustered with KAP6 sequences from different species and formed a group distinct to other HGT-KAPs. R1 was very similar to the characterised KRTAP6-1 sequence, but the remaining genes appeared to be new. PCR primers were designed to amplify and confirm the presence of these new genes. Amplicons were obtained for all of the 96 sheep investigated. Six, five, three and six PCR-SSCP patterns representing six, five, three and six DNA sequences were observed for KRTAP6-2 to KRTAP6-5 respectively. KRTAP6-2 and KRTAP6-4 had five and three SNPs respectively. Three SNPs and a 45-bp insertion/deletion were detected for KRTAP6-3, and five SNPs and an 18-bp insertion/deletion were identified for KRTAP6-5. Allele frequencies for these KAP6 genes differed between Merino and Romney sheep.
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Li S, Zhang Y, Wang J, Yang Y, Miao C, Guo Y, Zhang Z, Cao Q, Shui W. Combining Untargeted and Targeted Proteomic Strategies for Discrimination and Quantification of Cashmere Fibers. PLoS One 2016; 11:e0147044. [PMID: 26789629 PMCID: PMC4720366 DOI: 10.1371/journal.pone.0147044] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 12/28/2015] [Indexed: 01/28/2023] Open
Abstract
Cashmere is regarded as a specialty and luxury fiber due to its scarcity and high economic value. For fiber quality assessment, it is technically very challenging to distinguish and quantify the cashmere fiber from yak or wool fibers because of their highly similar physical appearance and substantial protein sequence homology. To address this issue, we propose a workflow combining untargeted and targeted proteomics strategies for selecting, verifying and quantifying biomarkers for cashmere textile authentication. Untargeted proteomic surveys were first applied to identify 174, 157, and 156 proteins from cashmere, wool and yak fibers, respectively. After marker selection at different levels, peptides turned out to afford much higher selectivity than proteins for fiber species discrimination. Subsequently, parallel reaction monitoring (PRM) methods were developed for ten selected peptide markers. The PRM-based targeted analysis of peptide markers enabled accurate determination of fiber species and cashmere percentages in different fiber mixtures. Furthermore, collective use of these peptide makers allowed us to discriminate and quantify cashmere fibers in commercial finished fabrics that have undergone heavy chemical treatments. Cashmere proportion measurement in fabric samples using our proteomic approach was in good agreement with results from traditional light microscopy, yet our method can be more readily standardized to become an objective and robust assay for assessing authenticity of fibers and textiles. We anticipate that the proteomic strategies presented in our study could be further implicated in discovery of quality trait markers for other products containing highly homologous proteomes.
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Affiliation(s)
- Shanshan Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Yong Zhang
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Jihua Wang
- Tianjin Textile Engineering Research Institute, Tianjin, 300308, China
| | - Yunfei Yang
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Chen Miao
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Yufeng Guo
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Zhidan Zhang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Qichen Cao
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Wenqing Shui
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
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Gong H, Zhou H, Hodge S, Dyer JM, Hickford JG. Association of wool traits with variation in the ovine KAP1-2 gene in Merino cross lambs. Small Rumin Res 2015. [DOI: 10.1016/j.smallrumres.2015.01.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Haplotyping using a combination of polymerase chain reaction–single-strand conformational polymorphism analysis and haplotype-specific PCR amplification. Anal Biochem 2014; 466:59-64. [DOI: 10.1016/j.ab.2014.08.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 08/19/2014] [Accepted: 08/20/2014] [Indexed: 11/19/2022]
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Khan I, Maldonado E, Vasconcelos V, O'Brien SJ, Johnson WE, Antunes A. Mammalian keratin associated proteins (KRTAPs) subgenomes: disentangling hair diversity and adaptation to terrestrial and aquatic environments. BMC Genomics 2014; 15:779. [PMID: 25208914 PMCID: PMC4180150 DOI: 10.1186/1471-2164-15-779] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 07/30/2014] [Indexed: 11/24/2022] Open
Abstract
Background Adaptation of mammals to terrestrial life was facilitated by the unique vertebrate trait of body hair, which occurs in a range of morphological patterns. Keratin associated proteins (KRTAPs), the major structural hair shaft proteins, are largely responsible for hair variation. Results We exhaustively characterized the KRTAP gene family in 22 mammalian genomes, confirming the existence of 30 KRTAP subfamilies evolving at different rates with varying degrees of diversification and homogenization. Within the two major classes of KRTAPs, the high cysteine (HS) subfamily experienced strong concerted evolution, high rates of gene conversion/recombination and high GC content. In contrast, high glycine-tyrosine (HGT) KRTAPs showed evidence of positive selection and low rates of gene conversion/recombination. Species with more hair and of higher complexity tended to have more KRATP genes (gene expansion). The sloth, with long and coarse hair, had the most KRTAP genes (175 with 141 being intact). By contrast, the “hairless” dolphin had 35 KRTAPs and the highest pseudogenization rate (74% relative to the 19% mammalian average). Unique hair-related phenotypes, such as scales (armadillo) and spines (hedgehog), were correlated with changes in KRTAPs. Gene expression variation probably also influences hair diversification patterns, for example human have an identical KRTAP repertoire as apes, but much less hair. Conclusions We hypothesize that differences in KRTAP gene repertoire and gene expression, together with distinct rates of gene conversion/recombination, pseudogenization and positive selection, are likely responsible for micro and macro-phenotypic hair diversification among mammals in response to adaptations to ecological pressures. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-779) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Agostinho Antunes
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas 177, 4050-123 Porto, Portugal.
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Association of microsatellite markers with fiber diameter trait in Peruvian alpacas (Vicugna pacos). Livest Sci 2014. [DOI: 10.1016/j.livsci.2013.12.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Zhou H, Gong H, Yan W, Luo Y, Hickford JGH. Identification and sequence analysis of the keratin-associated protein 24-1 (KAP24-1) gene homologue in sheep. Gene 2012; 511:62-5. [PMID: 22995344 DOI: 10.1016/j.gene.2012.08.049] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 08/13/2012] [Accepted: 08/28/2012] [Indexed: 11/18/2022]
Abstract
Keratin-associated proteins (KAPs) are major structural components of hair and wool fibres, and play a critical role in determining the properties of the fibre. While over 100 KAP genes that have been grouped into 27 KAP families have been identified in mammals, most homologues remain unidentified in sheep. A BLAST search of the Ovine Genome Assembly v2.0 using a human KRTAP24-1 coding sequence (NM_001085455), identified a putative ovine KAP24-1 gene clustered with six other known KAP genes on chromosome 1. The KAP24-1 gene was amplified from the genomic DNA of 260 New Zealand Romney-cross sheep and stem-loop conformational polymorphism (SLCP) analysis of the amplicons revealed four unique banding-patterns, representing four different DNA sequences. These sequences were not closely homologous with any known ovine KRTAP and the highest similarity was with KRTAP24-1 sequences from humans, cattle, dog, pig, Sumatran orangutan and northern white-cheeked gibbon. This suggests that the sequences were allelic variants of ovine KRTAP24-1. Among these four sequences, seven nucleotide substitutions in the coding region were identified and four of the substitutions were non-synonymous. The putative ovine KAP24-1 polypeptide consisted of 252 amino acids. While probably belonging to the high-sulphur KAP group, the polypeptide had a moderate level of cysteine, but a high content of serine and tyrosine. The polypeptide possesses two putative N-glycosylation sites and a number of residues that may be O-glycosylated and/or phosphorylated.
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Affiliation(s)
- Huitong Zhou
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou, Gansu, PR China
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Unravelling the proteome of wool: Towards markers of wool quality traits. J Proteomics 2012; 75:4315-24. [DOI: 10.1016/j.jprot.2012.03.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 03/13/2012] [Accepted: 03/16/2012] [Indexed: 11/21/2022]
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Gong H, Zhou H, Dyer JM, Plowman JE, Hickford JGH. Identification of the keratin-associated protein 13-3 (KAP13-3) gene in sheep. ACTA ACUST UNITED AC 2011. [DOI: 10.4236/ojgen.2011.13011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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