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Wang X, Wang L, Hong X, Li M, Gu X, Liu M, Li S. Genome-wide re-sequencing reveals regulatory genes and variants involved in the regulation of intermittent fertilization intensity in Wenchang chickens. Anim Genet 2024. [PMID: 39343428 DOI: 10.1111/age.13471] [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: 06/20/2024] [Revised: 06/20/2024] [Accepted: 08/02/2024] [Indexed: 10/01/2024]
Abstract
Intermittent fertilization intensity (IFI) is closely related to higher fertilization in chickens, but the genetic basis of IFI is not clearly understood. Here, we sampled a total of 939 Wenchang chickens with IFI. The IFI traits had negative correlation with the fertilization rate and exhibited huge phenotypic variations among individuals of the same strain. Based on SNPs derived from a subset of 499 whole genome data, a genome-wide association study with mixed linear model and further linkage disequilibrium analysis were performed to test potential associations between IFI traits and genomic variants. We identified 35 SNP variants and a 19.82 kb linkage disequilibrium block on chr8 significantly associated with IFI. This block is in the intron of LOC101750715, which shows significant homology with the human LMO4. Therefore, LOC101750715 and LMO4 may regulate IFI. The oviduct's immune regulation is crucial for fertilization. LMO4, activated by IL-6 and IL-23, promotes inflammation in epithelial cells. Thus, LOC101750715 and LMO4 may affect fertilization by regulating oviductal inflammation, impacting IFI. Our findings will provide targets for molecular-marker selection and genetic manipulation for lines of chickens with lower IFI.
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Affiliation(s)
- Xiuping Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Lei Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Xing Hong
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Mingze Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Xianyuan Gu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Minhui Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - ShiJun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, China
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Fontanesi L. Genetics and genomics of pigmentation variability in pigs: A review. Livest Sci 2022. [DOI: 10.1016/j.livsci.2022.105079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Kawakami T, Jensen MK, Slavney A, Deane PE, Milano A, Raghavan V, Ford B, Chu ET, Sams AJ, Boyko AR. R-locus for roaned coat is associated with a tandem duplication in an intronic region of USH2A in dogs and also contributes to Dalmatian spotting. PLoS One 2021; 16:e0248233. [PMID: 33755696 PMCID: PMC7987146 DOI: 10.1371/journal.pone.0248233] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 02/22/2021] [Indexed: 11/18/2022] Open
Abstract
Structural variations (SVs) represent a large fraction of all genetic diversity, but how this genetic diversity is translated into phenotypic and organismal diversity is unclear. Explosive diversification of dog coat color and patterns after domestication can provide a unique opportunity to explore this question; however, the major obstacle is to efficiently collect a sufficient number of individuals with known phenotypes and genotypes of hundreds of thousands of markers. Using customer-provided information about coat color and patterns of dogs tested on a commercial canine genotyping platform, we identified a genomic region on chromosome 38 that is strongly associated with a mottled coat pattern (roaning) by genome-wide association study. We identified a putative causal variant in this region, an 11-kb tandem duplication (11,131,835–11,143,237) characterized by sequence read coverage and discordant reads of whole-genome sequence data, microarray probe intensity data, and a duplication-specific PCR assay. The tandem duplication is in an intronic region of usherin gene (USH2A), which was perfectly associated with roaning but absent in non-roaned dogs. We detected strong selection signals in this region characterized by reduced nucleotide diversity (π), increased runs of homozygosity, and extended haplotype homozygosity in Wirehaired Pointing Griffons and Australian Cattle Dogs (typically roaned breeds), as well as elevated genetic difference (FST) between Wirehaired Pointing Griffon (roaned) and Labrador Retriever (non-roaned). Surprisingly, all Dalmatians (N = 262) carried the duplication embedded in identical or similar haplotypes with roaned dogs, indicating this region as a shared target of selection during the breed’s formation. We propose that the Dalmatian’s unique spots were a derived coat pattern by establishing a novel epistatic interaction between roaning “R-locus” on chromosome 38 and an uncharacterized modifier locus. These results highlight the utility of consumer-oriented genotype and phenotype data in the discovery of genomic regions contributing to phenotypic diversity in dogs.
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Affiliation(s)
- Takeshi Kawakami
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
- * E-mail: (ARB); (TK)
| | - Meghan K. Jensen
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Andrea Slavney
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Petra E. Deane
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Ausra Milano
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Vandana Raghavan
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Brett Ford
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Erin T. Chu
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Aaron J. Sams
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Adam R. Boyko
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
- * E-mail: (ARB); (TK)
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Talenti A, Bertolini F, Williams J, Moaeen-Ud-Din M, Frattini S, Coizet B, Pagnacco G, Reecy J, Rothschild MF, Crepaldi P. Genomic Analysis Suggests KITLG is Responsible for a Roan Pattern in two Pakistani Goat Breeds. J Hered 2019; 109:315-319. [PMID: 29099936 DOI: 10.1093/jhered/esx093] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 10/25/2017] [Indexed: 11/12/2022] Open
Abstract
The roan coat color pattern is described as the presence of white hairs intermixed with pigmented hairs. This kind of pigmentation pattern has been observed in many domestic species, including the goat. The molecular mechanisms and inheritance that underlie this pattern are known for some species and the KITLG gene has been shown associated with this phenotype. To date, no research effort has been carried out to find the gene(s) that control(s) roan coat color pattern in goats. In the present study, after genotyping with the GoatSNP50 BeadChip, 35 goats that showed a roan pattern and that belonged to two Pakistan breeds (Group A) were analyzed and then compared to 740 goats of 39 Italian and Pakistan goat breeds that did not have the same coat color pattern (Group B). Runs of homozygosity-based and XP-EHH analyses were used to identify unique genomic regions potentially associated with the roan pattern. A total of 3 regions on chromosomes 5, 6, and 12 were considered unique among the group A versus group B comparisons. The A region > 1.7 Mb on chromosome 5 was the most divergent between the two groups. This region contains six genes, including the KITLG gene. Our findings support the hypothesis that the KITLG gene may be associated with the roan phenotype in goats.
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Affiliation(s)
- Andrea Talenti
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | | | - Jamie Williams
- Department of Animal Science, Iowa State University, Ames, Iowa, USA
| | - Muhammad Moaeen-Ud-Din
- Laboratories of Animal Breeding & Genetics, PMAS-Arid Agriculture University, Rawalpindi, Pakistan
| | - Stefano Frattini
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Beatrice Coizet
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Giulio Pagnacco
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - James Reecy
- Department of Animal Science, Iowa State University, Ames, Iowa, USA
| | - Max F Rothschild
- Department of Animal Science, Iowa State University, Ames, Iowa, USA
| | - Paola Crepaldi
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
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Alhaddad H, Alhajeri BH. Cdrom Archive: A Gateway to Study Camel Phenotypes. Front Genet 2019; 10:48. [PMID: 30804986 PMCID: PMC6370635 DOI: 10.3389/fgene.2019.00048] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/21/2019] [Indexed: 11/30/2022] Open
Abstract
Camels are livestock that exhibit unique morphological, biochemical, and behavioral traits, which arose by natural and artificial selection. Investigating the molecular basis of camel traits has been limited by: (1) the absence of a comprehensive record of morphological trait variation (e.g., diseases) and the associated mode of inheritance, (2) the lack of extended pedigrees of specific trait(s), and (3) the long reproductive cycle of the camel, which makes the cost of establishing and maintaining a breeding colony (i.e., monitoring crosses) prohibitively high. Overcoming these challenges requires (1) detailed documentation of phenotypes/genetic diseases and their likely mode of inheritance (and collection of related DNA samples), (2) conducting association studies to identify phenotypes/genetic diseases causing genetic variants (instead of classical linkage analysis, which requires extended pedigrees), and (3) validating likely causative variants by screening a large number of camel samples from different populations. We attempt to address these issues by establishing a systematic way of collecting camel DNA samples, and associated phenotypic information, which we call the "Cdrom Archive." Here, we outline the process of building this archive to introduce it to other camel researchers (as an example). Additionally, we discuss the use of this archive to study the phenotypic traits of Arabian Peninsula camel breeds (the "Mezayen" camels). Using the Cdrom Archive, we report variable phenotypic traits related to the coat (color, length, and texture), ear and tail lengths, along with other morphological measurements.
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Affiliation(s)
- Hasan Alhaddad
- Department of Biological Sciences, Kuwait University, Kuwait City, Kuwait
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Divergent Evolutional Mode and Purifying Selection of the KIT Gene in European and Asian Domestic Pig Breeds. BIOMED RESEARCH INTERNATIONAL 2018; 2018:8932945. [PMID: 30211229 PMCID: PMC6120332 DOI: 10.1155/2018/8932945] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 06/15/2018] [Accepted: 06/20/2018] [Indexed: 11/17/2022]
Abstract
The recent geographic expansion of wild boars and the even more recent development of numerous domestic pigs have spurred exploration on pig domestic origins. The porcine KIT gene has been showed to affect pleiotropic effects, blood parameters, and coat colour phenotypes, especially the white colour phenotype formation in European commercial breeds. Here, we described the use of SNPs to identify different selection patterns on the porcine KIT gene and the phylogenetic relationships of the inferred haplotypes. The phylogenetic tree revealed four clades in European and Asian wild and domestic pigs: two major clades with European and Asian origins and one minor clade with Iberian origins as well as the other minor clade in Asia, consistent with the major introgression of domestic Asian pigs in Europe around 18th -19th century. The domestication history of pigs, which occurred in the domestication centers (Europe and Asia), has also been demonstrated by mtDNA analysis. Furthermore, both Asian and European domestic pigs evolved under purifying selection. This study indicated that domestic pigs in Europe and Asia have different lineage origins but the porcine KIT gene was undergoing a purifying selection during their evolutional histories.
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Edea Z, Dadi H, Dessie T, Kim IH, Kim KS. Association of MITF loci with coat color spotting patterns in Ethiopian cattle. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0493-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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8
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Jackling FC, Johnson WE, Appleton BR. The genetic inheritance of the blue-eyed white phenotype in alpacas (Vicugna pacos). J Hered 2012; 105:847-57. [PMID: 23144493 DOI: 10.1093/jhered/ess093] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
White-spotting patterns in mammals can be caused by mutations in the gene KIT, whose protein is necessary for the normal migration and survival of melanocytes from the neural crest. The alpaca (Vicugna pacos) blue-eyed white (BEW) phenotype is characterized by 2 blue eyes and a solid white coat over the whole body. Breeders hypothesize that the BEW phenotype in alpacas is caused by the combination of the gene causing gray fleece and a white-spotting gene. We performed an association study using KIT flanking and intragenic markers with 40 unrelated alpacas, of which 17 were BEW. Two microsatellite alleles at KIT-related markers were significantly associated (P < 0.0001) with the BEW phenotype (bew1 and bew2). In a larger cohort of 171 related individuals, we identify an abundance of an allele (bew1) in gray animals and the occurrence of bew2 homozygotes that are solid white with pigmented eyes. Association tests accounting for population structure and familial relatedness are consistent with a proposed model where these alleles are in linkage disequilibrium with a mutation or mutations that contribute to the BEW phenotype and to individual differences in fleece color.
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Affiliation(s)
- Felicity C Jackling
- From the Department of Genetics, The University of Melbourne, Melbourne 3010, Australia Laboratory of Genomic Diversity, NCI-Frederick, National Institutes of Health, Frederick, MD 21702
| | - Warren E Johnson
- From the Department of Genetics, The University of Melbourne, Melbourne 3010, Australia Laboratory of Genomic Diversity, NCI-Frederick, National Institutes of Health, Frederick, MD 21702
| | - Belinda R Appleton
- From the Department of Genetics, The University of Melbourne, Melbourne 3010, Australia Laboratory of Genomic Diversity, NCI-Frederick, National Institutes of Health, Frederick, MD 21702
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Lim HT, Zhong T, Cho IC, Seo BY, Kim JH, Lee SS, Ko MS, Park HB, Kim BW, Lee JH, Jeon JT. Novel alternative splicing by exon skipping in KIT associated with whole-body roan in an intercrossed population of Landrace and Korean Native pigs. Anim Genet 2011; 42:451-5. [PMID: 21749430 DOI: 10.1111/j.1365-2052.2011.02225.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The KIT locus has been suggested to be a strong candidate region linked with whole-body roan in the F(2) population produced by intercrosses between Landrace and Korean Native pigs. In this manuscript, we report the finding of a novel alternative splicing event in the porcine KIT gene that results in the skipping of exon 5 in the I(Rn) allele. KIT mRNAs that lack exon 5 were identified in the large intestine and skin, suggesting that the mechanism responsible for the skipping of exon 5 may be tissue specific. A U(26) repeat in intron 5 showed complete linkage (LOD = 11.8) with the roan phenotype and absolute association with the black phenotype of the Korean Native pig (KNP) population samples, inferring that the repeat pattern may alter the complementary base-pairing-mediated looping-out of introns 4 and 5, which may mediate the exon 5-skipping event. Although the sample size in our study was relatively small, we speculate that the R3 allele containing the U(26) repeat is a causative element for the roan phenotype via alternative control of the exon skipping in our roan pedigree.
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Affiliation(s)
- H T Lim
- Division of Applied Life Science, BK21 Program, Graduate School of Gyeongsang National University, Jinju, Korea. s_htim @gnu.ac.kr
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10
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Characterization of an alternative splicing by a NAGNAG splice acceptor site in the porcine KIT gene. Genes Genomics 2011. [DOI: 10.1007/s13258-010-0156-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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