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Vasu M, Ahlawat S, Chhabra P, Sharma U, Arora R, Sharma R, Mir MA, Singh MK. Genetic insights into fiber quality, coat color and adaptation in Changthangi and Muzzafarnagri sheep: A comparative skin transcriptome analysis. Gene 2024; 891:147826. [PMID: 37748630 DOI: 10.1016/j.gene.2023.147826] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/15/2023] [Accepted: 09/22/2023] [Indexed: 09/27/2023]
Abstract
Changthangi sheep, which inhabit the high-altitude regions of Ladakh, are known for their fine fiber production and are characterized by grey skin and either black or white coats. In contrast, Muzzafarnagri sheep from the plains of Uttar Pradesh produce coarse wool and have white skin and coats. We conducted comparative global gene expression profiling on four biological replicates of skin from each breed. Notably, our analysis identified 149 up-regulated genes and 2,139 down-regulated genes in Changthangi sheep compared to Muzzafarnagri sheep, with a p-adjusted value (padj) of ≤0.05 and a Log2 fold change of ≥1.5. Gene Ontology analysis of the up-regulated genes revealed an enrichment of terms related to melanin biosynthesis and developmental pigmentation. Additionally, enriched KEGG pathways included tyrosine metabolism and metabolic pathways. Among the melanogenesis-related genes that exhibited higher expression in Changthangi sheep were TYR, TYRP1, DCT, SLC45A2, PMEL, MLANA, and OCA2. These findings confirm melanin's role in both the animals' black coat color and UV protection at high-altitude. Furthermore, we observed more pronounced expression of genes related to fiber quality, namely KRTAP6, KRTAP7, KRTAP13, and KRTAP2, in the fine wool-producing sheep from Ladakh. The results of the RNA sequencing were validated using real-time PCR on 10 genes governing fiber quality and coat color, with ACTB and PPIB serving as reference genes. In conclusion, our comparative skin transcriptome analysis of Changthangi and Muzzafarnagri sheep sheds light on the genetic differences associated with distinct phenotypic traits and environmental adaptability, offering valuable insights into the underlying mechanisms.
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Affiliation(s)
- Mahanthi Vasu
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India; ICAR-National Dairy Research Institute, Karnal, India
| | - Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India.
| | - Pooja Chhabra
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Upasna Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - M A Mir
- Mountain Research Centre for Sheep and Goat, Shuhama (Aulestang), SKUAST-Kashmir, India
| | - Manoj Kumar Singh
- ICAR-Central Institute for Research on Goats, Makhdoom, Mathura, India
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Zhang CL, Zhang J, Tuersuntuoheti M, Zhou W, Han Z, Li X, Yang R, Zhang L, Zheng L, Liu S. Landscape genomics reveals adaptive divergence of indigenous sheep in different ecological environments of Xinjiang, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166698. [PMID: 37683864 DOI: 10.1016/j.scitotenv.2023.166698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 08/22/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023]
Abstract
Sheep are important livestock animals that have evolved under various ecological pressures. Xinjiang is a region with diverse and harsh environments that have shaped many local sheep breeds with unique characteristics and environmental adaptability. However, these breeds are losing ecological flexibility due to the promotion of intensive farming practices. Here we sequenced 14 local sheep breeds from Xinjiang and analyzed their genetic structure and gene flow with other sheep breeds from neighboring regions. The Tibetan Plateau was the geographic origin of Xinjiang native sheep evolution. We performed genome-environment association analysis and identified Bio9: Mean Temperature of Driest Quarter and Bio15: Precipitation Seasonality as the key environmental factors affecting Xinjiang local sheep and the key genes involved in their survival and adaptation. We classified Xinjiang native sheep breeds into six groups based on their differential genes by pairwise selective sweep analysis and Community Network Analysis. We analyzed transcriptome expression data of 832 sheep tissues and detected tissue-specific enrichment of six group-specific genes in different biological systems. Our results revealed the genetic basis of year-round estrus, drought tolerance, hypoxia resistance, and cold tolerance traits of Xinjiang sheep breeds. Moreover, we proposed conservation strategies for Xinjiang local sheep breeds and provided theoretical guidance for breeding new sheep breeds under global extreme environments.
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Affiliation(s)
- Cheng-Long Zhang
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Jihu Zhang
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Mirenisa Tuersuntuoheti
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Wen Zhou
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Zhipeng Han
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Xiaopeng Li
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Ruizhi Yang
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Lulu Zhang
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Langman Zheng
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Shudong Liu
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China.
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Chen Z, Cao J, Zhao F, He Z, Sun H, Wang J, Liu X, Li S. Identification of the Keratin-Associated Protein 22-2 Gene in the Capra hircus and Association of Its Variation with Cashmere Traits. Animals (Basel) 2023; 13:2806. [PMID: 37685070 PMCID: PMC10487131 DOI: 10.3390/ani13172806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/20/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
The Cashmere goat is an excellent local goat breed in Gansu Province of China, and it is expected to improve cashmere production and cashmere quality through selection and breeding to enhance its commercial value. Keratin-associated proteins (KAPs) play an important role in maintaining wool structure. The gene encoding the keratin-associated protein 22-2 (KAP22-2) gene has been identified in selected species other than goats, such as humans, mice, and sheep. In this study, the sequence of the sheep KAP22-2 gene (KRTAP22-2) was aligned into the goat genome, and the sequence with the highest homology was assumed to be the goat KRTAP22-2 sequence and used to design primers to amplify the goat gene sequence. A total of 356 Longdong Cashmere goats (Gansu Province, China) were used for screening of genetic variants. Four specific bands were detected by polymerase chain reaction-single-stranded conformational polymorphism (PCR-SSCP) analysis, and they formed a total of six band types individually or in combination. Four alleles were identified by DNA sequencing of PCR amplification products. A total of four single nucleotide polymorphic sites (SNPs) were detected in the four sequenced KRTAP22-2 alleles. Two of them are in the 5'UTR region and the other two are in the coding region, and the variants in the coding region are all non-synonymous mutations. In addition, there was a 6 bp length variation in allele C. The gene was expressed in the cortical layer of primary and secondary hair follicles, the inner root sheath, as well as hair papillae and hair maternal cells in goats. The results of the correlation analysis between genotypes and cashmere traits showed that after excluding genotypes with a gene frequency of less than 5%, the mean fiber diameter (MFD) of cashmere was significantly higher in the AB genotype than in the AA and AC genotypes. That is, the KRTAP22-2 gene variants are associated with mean fiber diameter in cashmere. The above results suggest that the goat KRTAP22-2 variant can be utilized as a molecular marker candidate gene for cashmere traits.
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Affiliation(s)
- Zhanzhao Chen
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Z.C.); (F.Z.); (Z.H.); (H.S.); (J.W.); (X.L.)
| | - Jian Cao
- Faculty of Bioengineering, Jiuquan Vocational Technical College, Jiuquan 735000, China;
| | - Fangfang Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Z.C.); (F.Z.); (Z.H.); (H.S.); (J.W.); (X.L.)
| | - Zhaohua He
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Z.C.); (F.Z.); (Z.H.); (H.S.); (J.W.); (X.L.)
| | - Hongxian Sun
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Z.C.); (F.Z.); (Z.H.); (H.S.); (J.W.); (X.L.)
| | - Jiqing Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Z.C.); (F.Z.); (Z.H.); (H.S.); (J.W.); (X.L.)
| | - Xiu Liu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Z.C.); (F.Z.); (Z.H.); (H.S.); (J.W.); (X.L.)
| | - Shaobin Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Z.C.); (F.Z.); (Z.H.); (H.S.); (J.W.); (X.L.)
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Sallam AM, Gad-Allah AA, Albetar EM. Genetic variation in the ovine KAP22-1 gene and its effect on wool traits in Egyptian sheep. Arch Anim Breed 2022; 65:293-300. [PMID: 36035880 PMCID: PMC9399921 DOI: 10.5194/aab-65-293-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 07/19/2022] [Indexed: 11/11/2022] Open
Abstract
The objective of this study was to investigate the genetic polymorphisms in
the keratin-associated protein (KAP22-1) gene in Barki (n=206), Rahmani (n=28)
and Ossimi (n=28) as the three major sheep breeds in Egypt. Subsequently,
the detected variants were correlated with important wool traits. The traits
included greasy fleece weight (GFW, g), staple length (SL, cm), prickle
factor (PF, %), medullated fiber (MF, %), fiber diameter (FD, µm), crimp percentage (CR, %) and the standard deviation of FD
(SDfd, µm), as well as the subjectively assessed traits of
kemp score (KS), handle grade (HG), greasy color grade (GCG), bulk grade
(BG), luster grade (LG) and staple structure (SST). Animals were
genotyped by polymerase chain reaction (PCR) – single strand conformation
polymorphism (SSCP). Five SSCP banding patterns representing three different
nucleotide variants (A, B and C) were detected. DNA sequencing confirmed
three single nucleotide polymorphisms (SNPs). Animal age significantly
affected GFW (P=0.007), SDfd (P=0.006), SL (P=0.002), CR
(P=0.006), KS (P=0.001), LG (P=0.006) and SST (P=0.013). Likewise, the
breed had a significant effect on all studied traits except HG and BG, which
was not significant. Results showed significant associations between the
KAP22-1 variants and CR (P=0.01), SL (P=0.012), KS (P<0.001) and GCG
(P=0.01). Interestingly, animals with BB genotypes tended to produce more
wool yield (1163.63±65.91 g) with high SL (8.38±0.20 cm), CR
(8.38±0.21 %) and KS (1.98±1.88). Results of this study
strongly recommend the KAP22-1 gene as a candidate gene for wool production traits
in Egyptian sheep, with new useful insights into the visually assessed wool
traits. The identified genetic markers may be incorporated into breeding
strategies and genetic improvement programs of wool traits in Egyptian
sheep.
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Affiliation(s)
- Ahmed M. Sallam
- Animal and Poultry Division, Desert Research Center, 1st
Mathaf El-Mataryia, 11735, Cairo, Egypt
| | - Aymen A. Gad-Allah
- Department of Wool Technology and Production, Desert
Research Center, 1st Mathaf El-Mataryia, 11735, Cairo, Egypt
| | - Essam M. Albetar
- Department of Wool Technology and Production, Desert
Research Center, 1st Mathaf El-Mataryia, 11735, Cairo, Egypt
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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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