1
|
Dai D, Sari EM, Si J, Ashari H, Dagong MIA, Pauciullo A, Lenstra JA, Han J, Zhang Y. Genomic analysis reveals the association of KIT and MITF variants with the white spotting in swamp buffaloes. BMC Genomics 2024; 25:713. [PMID: 39048931 PMCID: PMC11267946 DOI: 10.1186/s12864-024-10634-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 07/18/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND Swamp-type buffaloes with varying degrees of white spotting are found exclusively in Tana Toraja, South Sulawesi, Indonesia, where spotted buffalo bulls are highly valued in accordance with the Torajan customs. The white spotting depigmentation is caused by the absence of melanocytes. However, the genetic variants that cause this phenotype have not been fully characterized. The objective of this study was to identify the genomic regions and variants responsible for this unique coat-color pattern. RESULTS Genome-wide association study (GWAS) and selection signature analysis identified MITF as a key gene based on the whole-genome sequencing data of 28 solid and 39 spotted buffaloes, while KIT was also found to be involved in the development of this phenotype by a candidate gene approach. Alternative candidate mutations included, in addition to the previously reported nonsense mutation c.649 C > T (p.Arg217*) and splice donor mutation c.1179 + 2T > A in MITF, a nonsense mutation c.2028T > A (p.Tyr676*) in KIT. All these three mutations were located in the genomic regions that were highly conserved exclusively in Indonesian swamp buffaloes and they accounted largely (95%) for the manifestation of white spotting. Last but not the least, ADAMTS20 and TWIST2 may also contribute to the diversification of this coat-color pattern. CONCLUSIONS The alternative mutations identified in this study affect, at least partially and independently, the development of melanocytes. The presence and persistence of such mutations may be explained by significant financial and social value of spotted buffaloes used in historical Rambu Solo ceremony in Tana Toraja, Indonesia. Several de novo spontaneous mutations have therefore been favored by traditional breeding for the spotted buffaloes.
Collapse
Affiliation(s)
- Dongmei Dai
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Eka Meutia Sari
- Department of Animal Science, Agriculture Faculty, Universitas Syiah Kuala (USK), Banda Aceh, 23111, Indonesia.
| | - Jingfang Si
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Hidayat Ashari
- Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Cibinong, 16911, Indonesia
| | - Muhammad Ihsan Andi Dagong
- Animal Production Department, Faculty of Animal Science, Hasanuddin University, Makassar, 90245, Indonesia
| | - Alfredo Pauciullo
- Department of Agricultural, Forest and Food Sciences, University of Turin, Grugliasco (TO), 10095, Italy
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, 3584 CM, Utrecht, The Netherlands
| | - Jianlin Han
- Yazhouwan National Laboratory, Sanya, 572024, China
| | - Yi Zhang
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
2
|
Ward JA, Ng'ang'a SI, Randhawa IAS, McHugo GP, O'Grady JF, Flórez JM, Browne JA, Pérez O’Brien AM, Landaeta-Hernández AJ, Garcia JF, Sonstegard TS, Frantz LAF, Salter-Townshend M, MacHugh DE. Genomic insights into the population history and adaptive traits of Latin American Criollo cattle. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231388. [PMID: 38571912 PMCID: PMC10990470 DOI: 10.1098/rsos.231388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 01/04/2024] [Accepted: 01/31/2024] [Indexed: 04/05/2024]
Abstract
Criollo cattle, the descendants of animals brought by Iberian colonists to the Americas, have been the subject of natural and human-mediated selection in novel tropical agroecological zones for centuries. Consequently, these breeds have evolved distinct characteristics such as resistance to diseases and exceptional heat tolerance. In addition to European taurine (Bos taurus) ancestry, it has been proposed that gene flow from African taurine and Asian indicine (Bos indicus) cattle has shaped the ancestry of Criollo cattle. In this study, we analysed Criollo breeds from Colombia and Venezuela using whole-genome sequencing (WGS) and single-nucleotide polymorphism (SNP) array data to examine population structure and admixture at high resolution. Analysis of genetic structure and ancestry components provided evidence for African taurine and Asian indicine admixture in Criollo cattle. In addition, using WGS data, we detected selection signatures associated with a myriad of adaptive traits, revealing genes linked to thermotolerance, reproduction, fertility, immunity and distinct coat and skin coloration traits. This study underscores the remarkable adaptability of Criollo cattle and highlights the genetic richness and potential of these breeds in the face of climate change, habitat flux and disease challenges. Further research is warranted to leverage these findings for more effective and sustainable cattle breeding programmes.
Collapse
Affiliation(s)
- James A. Ward
- Animal Genomics Laboratory, School of Agriculture and Food Science, University College Dublin, DublinD04 V1W8, Ireland
| | - Said I. Ng'ang'a
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, MunichD-80539, Germany
- School of Biological and Chemical Sciences, Queen Mary University of London, LondonE1 4NS, UK
| | | | - Gillian P. McHugo
- Animal Genomics Laboratory, School of Agriculture and Food Science, University College Dublin, DublinD04 V1W8, Ireland
| | - John F. O'Grady
- Animal Genomics Laboratory, School of Agriculture and Food Science, University College Dublin, DublinD04 V1W8, Ireland
| | - Julio M. Flórez
- Acceligen, Eagan, MN55121, USA
- Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, Brazil
| | - John A. Browne
- Animal Genomics Laboratory, School of Agriculture and Food Science, University College Dublin, DublinD04 V1W8, Ireland
| | | | - Antonio J. Landaeta-Hernández
- Unidad de Investigaciones Zootécnicas, Facultad de Ciencias Veterinarias, Universidad del Zulia, Maracaibo, Venezuela
| | - Jóse F. Garcia
- Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, Brazil
| | | | - Laurent A. F. Frantz
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, MunichD-80539, Germany
- School of Biological and Chemical Sciences, Queen Mary University of London, LondonE1 4NS, UK
| | | | - David E. MacHugh
- Animal Genomics Laboratory, School of Agriculture and Food Science, University College Dublin, DublinD04 V1W8, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, DublinD04 V1W8, Ireland
| |
Collapse
|
3
|
Breed Distribution and Allele Frequencies of Base Coat Color, Dilution, and White Patterning Variants across 28 Horse Breeds. Genes (Basel) 2022; 13:genes13091641. [PMID: 36140807 PMCID: PMC9498372 DOI: 10.3390/genes13091641] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 08/30/2022] [Accepted: 09/05/2022] [Indexed: 11/25/2022] Open
Abstract
Since domestication, horses have been selectively bred for various coat colors and white spotting patterns. To investigate breed distribution, allele frequencies, and potential lethal variants for recommendations on genetic testing, 29 variants within 14 genes were investigated in 11,281 horses from 28 breeds. The recessive chestnut ea allele in melanocortin 1 receptor (MC1R) (p.D84N) was identified in four breeds: Knabstrupper, Paint Horse, Percheron, and Quarter Horse. After filtering for relatedness, ea allele frequency in Knabstruppers was estimated at 0.035, thus illustrating the importance of testing for mate selection for base coat color. The Rocky Mountain Horse breed had the highest allele frequency for two of the dilution variants under investigation (Za.f. = 0.32 and Cha.f. = 0.026); marker-assisted selection in this breed could aid in the production of horses with desirable dilute coats with less severe ocular anomalies caused by the silver (Z) allele. With regard to white patterning, nine horses homozygous for the paired box 3 (PAX3) splashed white 2 (SW2) allele (p.C70Y) and six horses homozygous for the KIT proto-oncogene, receptor tyrosine kinase (KIT) sabino 1 (SB1) allele (ECA3g.79544206A>T) were identified, thus determining they are rare and confirming that homozygosity for SW2 is not embryonic lethal. The KIT dominant white 20 (W20) allele (p.R682H) was identified in all but three breeds: Arabian (n = 151), Icelandic Horse (n = 66), and Norwegian Fjord Horse (n = 90). The role of W20 in pigmentation across breeds is not well understood; given the different selection regimes of the breeds investigated, these data provide justification for further evaluating the functional role of this allele in pigmentation. Here, we present the largest dataset reported for coat color variants in horses to date, and these data highlight the importance of breed-specific studies to inform on the proper use of marker-assisted selection and to develop hypotheses related to pigmentation for further testing in horses.
Collapse
|
4
|
Magdesian KG, Tanaka J, Bellone RR. A De Novo MITF Deletion Explains a Novel Splashed White Phenotype in an American Paint Horse. J Hered 2021; 111:287-293. [PMID: 32242630 PMCID: PMC7238438 DOI: 10.1093/jhered/esaa009] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 04/01/2020] [Indexed: 11/14/2022] Open
Abstract
Splashed white is a coat color pattern in horses characterized by extensive white patterning on the legs, belly, and face often accompanied by blue eyes and deafness. Three mutations in microphthalmia-associated transcription factor (MITF) and two mutations in Paired Box 3 (PAX3) have been identified that explain splashed white patterns (SW1-SW5). An American Paint Horse stallion with a splashed white phenotype and blue eyes, whose parents were not white patterned, was negative for the 5 known splashed white variants and other known white spotting alleles. This novel splashed white phenotype (SW6) was hypothesized to be caused by a de novo mutation in MITF or PAX3. Analysis of whole-genome sequencing using the EquCab3.0 reference genome for comparison identified an 8.7 kb deletion in MITF on ECA16 (NC_009159.3:g.21551060-21559770del). The deletion encompassed part of intron 7 through the 3' UTR of exon 9 of MITF, including the helix-loop-helix DNA-binding domain (ENSECAT00000006375.3). This variant is predicted to truncate protein and impair binding to DNA. Sanger sequencing confirmed the stallion was heterozygous for the MITF deletion. No single nucleotide polymorphisms (SNPs) or structural variants were identified in PAX3 or any of the other candidate genes that were unique to the stallion or predicted to affect protein function. Genotyping five of the stallion's splashed white offspring, including one all white foal, found that they were also heterozygous for the deletion. Given the role of MITF in producing white pattern phenotypes, and the predicted deleterious effect of this mutation, this 8.7 kb deletion is the likely causal variant for SW6.
Collapse
Affiliation(s)
- K Gary Magdesian
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California-Davis, Davis, CA
| | - Jocelyn Tanaka
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA
| | - Rebecca R Bellone
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA
| |
Collapse
|
5
|
Brooks SA, Palermo KM, Kahn A, Hein J. Impact of white‐spotting alleles, including
W20
, on phenotype in the American Paint Horse. Anim Genet 2020; 51:707-715. [DOI: 10.1111/age.12960] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2020] [Indexed: 01/09/2023]
Affiliation(s)
- S. A. Brooks
- Department of Animal Sciences UF Genetics Institute University of Florida Gainesville FL 32611‐0910 USA
| | - K. M. Palermo
- Department of Animal Sciences UF Genetics Institute University of Florida Gainesville FL 32611‐0910 USA
| | - A. Kahn
- Department of Animal Sciences UF Genetics Institute University of Florida Gainesville FL 32611‐0910 USA
| | - J. Hein
- American Paint Horse Association Fort Worth TX 76161‐0023 USA
| |
Collapse
|
6
|
E G, Yang BG, Basang WD, Zhu YB, An TW, Luo XL. Screening for signatures of selection of Tianzhu white yak using genome-wide re-sequencing. Anim Genet 2019; 50:534-538. [PMID: 31246332 DOI: 10.1111/age.12817] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2019] [Indexed: 12/13/2022]
Abstract
The Tianzhu white yak, a domestic yak indigenous to the Qilian Mountains, migrated inland from the Qinghai-Tibet Plateau. Specific ecological and long-term artificial selection influenced the evolution of its pure white coat and physiological characteristics. Therefore, it is not only a natural population that represents a genomic selective region of environmental adaptability but is also an animal model for studying the pigmentation of the yak coat. A total of 24 261 829 variants, including 22 445 252 SNPs, were obtained from 29 yaks by genome-wide re-sequencing. According to the results of a selective sweep analysis of Tianzhu white yak in comparison to Tibetan yaks, nine candidate genes under selection in Tianzhu white yak were identified by combining π, Tajima's D, πA/πB and FST statistics, with threshold standards of 5%. These genes include PDCD1, NUP210, ABCG8, NEU4, LOC102287650, D2HGDH, COL4A1, RTP5 and HDAC11. Five of the nine genes were classified into 12 molecular signaling pathways, and most of these signaling pathways are involved in environmental information processing, organismal systems and metabolism. A majority of these genes has not been implicated in previous studies of yak coat color and high-altitude animals. Our findings are helpful not only for explaining the molecular mechanism of yak coat pigmentation but also for exploring the genetic changes in Tianzhu white yak due to environmental adaptation.
Collapse
Affiliation(s)
- Guangxin E
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, 400715, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - B-G Yang
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, 400715, China
| | - W-D Basang
- Institute of Animal Husbandryand Veterinary Medicine, Tibet Academy of Agriculture and Animal Husandry Science, Lasa, 850009, China
| | - Y-B Zhu
- Institute of Animal Husbandryand Veterinary Medicine, Tibet Academy of Agriculture and Animal Husandry Science, Lasa, 850009, China
| | - T-W An
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, 611731, China
| | - X-L Luo
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, 611731, China
| |
Collapse
|