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Mastrangelo S, Ciani E, Sardina MT, Sottile G, Pilla F, Portolano B. Runs of homozygosity reveal genome-wide autozygosity in Italian sheep breeds. Anim Genet 2018; 49:71-81. [PMID: 29333609 DOI: 10.1111/age.12634] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2017] [Indexed: 02/03/2023]
Abstract
The availability of dense single nucleotide polymorphism (SNP) assays allows for the determination of autozygous segments based on runs of consecutive homozygous genotypes (ROH). The aim of the present study was to investigate the occurrence and distribution of ROH in 21 Italian sheep breeds using medium-density SNP genotypes in order to characterize autozygosity and identify genomic regions that frequently appeared in ROH within individuals, namely ROH islands. After filtering, the final number of animals and SNPs retained for analyses were 502 and 46 277 respectively. A total of 12 302 ROH were identified. The mean number of ROH per breed ranged from 10.58 (Comisana) to 44.54 (Valle del Belice). The average length of ROH across breeds was 4.55 Mb and ranged from 3.85 Mb (Biellese) to 5.51 Mb (Leccese). Valle del Belice showed the highest value of inbreeding on the basis of ROH (FROH = 0.099), whereas Comisana showed the lowest (FROH = 0.016), and high standard deviation values revealed high variability in autozygosity levels within each breed. Differences also existed in the length of ROH. Analysis of the distribution of ROH according to their size showed that, for all breeds, the majority of the detected ROH were <10 Mb in length, with a few long ROH >25 Mb. The levels of ROH that we estimated here reflect the inbreeding history of the investigated sheep breeds. These results also highlight that ancient and recent inbreeding have had an impact on the genome of the Italian sheep breeds and suggest that several animals have experienced recent autozygosity events. Comisana and Bergamasca appeared as the less consanguineous breeds, whereas Barbaresca, Leccese and Valle del Belice showed ROH patterns typically produced by recent inbreeding. Moreover, within the genomic regions most commonly associated with ROH, several candidate genes were detected.
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Affiliation(s)
- S Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy
| | - E Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica University of Bari, 70124, Bari, Italy
| | - M T Sardina
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy
| | - G Sottile
- Dipartimento Scienze Economiche, Aziendali e Statistiche, University of Palermo, 90128, Palermo, Italy
| | - F Pilla
- Dipartimento Agricoltura, Ambiente e Alimenti, University of Molise, 86100, Campobasso, Italy
| | - B Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy
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Gutiérrez-Gil B, Esteban-Blanco C, Wiener P, Chitneedi PK, Suarez-Vega A, Arranz JJ. High-resolution analysis of selection sweeps identified between fine-wool Merino and coarse-wool Churra sheep breeds. Genet Sel Evol 2017; 49:81. [PMID: 29115919 PMCID: PMC5674817 DOI: 10.1186/s12711-017-0354-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 10/19/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND With the aim of identifying selection signals in three Merino sheep lines that are highly specialized for fine wool production (Australian Industry Merino, Australian Merino and Australian Poll Merino) and considering that these lines have been subjected to selection not only for wool traits but also for growth and carcass traits and parasite resistance, we contrasted the OvineSNP50 BeadChip (50 K-chip) pooled genotypes of these Merino lines with the genotypes of a coarse-wool breed, phylogenetically related breed, Spanish Churra dairy sheep. Genome re-sequencing datasets of the two breeds were analyzed to further explore the genetic variation of the regions initially identified as putative selection signals. RESULTS Based on the 50 K-chip genotypes, we used the overlapping selection signals (SS) identified by four selection sweep mapping analyses (that detect genetic differentiation, reduced heterozygosity and patterns of haplotype diversity) to define 18 convergence candidate regions (CCR), five associated with positive selection in Australian Merino and the remainder indicating positive selection in Churra. Subsequent analysis of whole-genome sequences from 15 Churra and 13 Merino samples identified 142,400 genetic variants (139,745 bi-allelic SNPs and 2655 indels) within the 18 defined CCR. Annotation of 1291 variants that were significantly associated with breed identity between Churra and Merino samples identified 257 intragenic variants that caused 296 functional annotation variants, 275 of which were located across 31 coding genes. Among these, four synonymous and four missense variants (NPR2_His847Arg, NCAPG_Ser585Phe, LCORL_Asp1214Glu and LCORL_Ile1441Leu) were included. CONCLUSIONS Here, we report the mapping and genetic variation of 18 selection signatures that were identified between Australian Merino and Spanish Churra sheep breeds, which were validated by an additional contrast between Spanish Merino and Churra genotypes. Analysis of whole-genome sequencing datasets allowed us to identify divergent variants that may be viewed as candidates involved in the phenotypic differences for wool, growth and meat production/quality traits between the breeds analyzed. The four missense variants located in the NPR2, NCAPG and LCORL genes may be related to selection sweep regions previously identified and various QTL reported in sheep in relation to growth traits and carcass composition.
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Affiliation(s)
- Beatriz Gutiérrez-Gil
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071 Spain
| | - Cristina Esteban-Blanco
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071 Spain
- Fundación Centro Supercomputación de Castilla y León, Campus de Vegazana, León, 24071 Spain
| | - Pamela Wiener
- Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG UK
| | - Praveen Krishna Chitneedi
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071 Spain
| | - Aroa Suarez-Vega
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071 Spain
| | - Juan-Jose Arranz
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071 Spain
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A comparison of transcriptomic patterns measured in the skin of Chinese fine and coarse wool sheep breeds. Sci Rep 2017; 7:14301. [PMID: 29085060 PMCID: PMC5662721 DOI: 10.1038/s41598-017-14772-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 10/12/2017] [Indexed: 12/17/2022] Open
Abstract
We characterised wool traits, and skin gene expression profiles of fine wool Super Merino (SM) and coarse wool Small Tail Han (STH) sheep. SM sheep had a significantly higher total density of wool follicles, heavier fleeces, finer fibre diameter, and increased crimp frequency, staple length and wool grease (lanolin) production. We found 435 genes were expressed at significantly different levels in the skin of the two breeds (127 genes more highly in SM and 308 genes more highly in STH sheep). Classification of the genes more highly expressed in SM sheep revealed numerous lipid metabolic genes as well as genes encoding keratins, keratin-associated proteins, and wool follicle stem cell markers. In contrast, mammalian epidermal development complex genes and other genes associated with skin cornification and muscle function were more highly expressed in STH sheep. Genes identified in this study may be further evaluated for inclusion in breeding programs, or as targets for therapeutic or genetic interventions, aimed at altering wool quality or yield. Expression of the lipid metabolic genes in the skin of sheep may be used as a novel trait with the potential to alter the content or properties of lanolin or the fleece.
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Bolormaa S, Swan AA, Brown DJ, Hatcher S, Moghaddar N, van der Werf JH, Goddard ME, Daetwyler HD. Multiple-trait QTL mapping and genomic prediction for wool traits in sheep. Genet Sel Evol 2017; 49:62. [PMID: 28810834 PMCID: PMC5558709 DOI: 10.1186/s12711-017-0337-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 07/31/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The application of genomic selection to sheep breeding could lead to substantial increases in profitability of wool production due to the availability of accurate breeding values from single nucleotide polymorphism (SNP) data. Several key traits determine the value of wool and influence a sheep's susceptibility to fleece rot and fly strike. Our aim was to predict genomic estimated breeding values (GEBV) and to compare three methods of combining information across traits to map polymorphisms that affect these traits. METHODS GEBV for 5726 Merino and Merino crossbred sheep were calculated using BayesR and genomic best linear unbiased prediction (GBLUP) with real and imputed 510,174 SNPs for 22 traits (at yearling and adult ages) including wool production and quality, and breech conformation traits that are associated with susceptibility to fly strike. Accuracies of these GEBV were assessed using fivefold cross-validation. We also devised and compared three approximate multi-trait analyses to map pleiotropic quantitative trait loci (QTL): a multi-trait genome-wide association study and two multi-trait methods that use the output from BayesR analyses. One BayesR method used local GEBV for each trait, while the other used the posterior probabilities that a SNP had an effect on each trait. RESULTS BayesR and GBLUP resulted in similar average GEBV accuracies across traits (~0.22). BayesR accuracies were highest for wool yield and fibre diameter (>0.40) and lowest for skin quality and dag score (<0.10). Generally, accuracy was higher for traits with larger reference populations and higher heritability. In total, the three multi-trait analyses identified 206 putative QTL, of which 20 were common to the three analyses. The two BayesR multi-trait approaches mapped QTL in a more defined manner than the multi-trait GWAS. We identified genes with known effects on hair growth (i.e. FGF5, STAT3, KRT86, and ALX4) near SNPs with pleiotropic effects on wool traits. CONCLUSIONS The mean accuracy of genomic prediction across wool traits was around 0.22. The three multi-trait analyses identified 206 putative QTL across the ovine genome. Detailed phenotypic information helped to identify likely candidate genes.
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Affiliation(s)
- Sunduimijid Bolormaa
- Agriculture Victoria Research, AgriBio Centre, Bundoora, VIC, 3083, Australia. .,Cooperative Research Centre for Sheep Industry Innovation, Armidale, NSW, 2351, Australia.
| | - Andrew A Swan
- Animal Genetics and Breeding Unit, University of New England, Armidale, NSW, 2351, Australia.,Cooperative Research Centre for Sheep Industry Innovation, Armidale, NSW, 2351, Australia
| | - Daniel J Brown
- Animal Genetics and Breeding Unit, University of New England, Armidale, NSW, 2351, Australia.,Cooperative Research Centre for Sheep Industry Innovation, Armidale, NSW, 2351, Australia
| | - Sue Hatcher
- NSW Department of Primary Industries, Orange Agricultural Institute, Orange, NSW, 2800, Australia.,Cooperative Research Centre for Sheep Industry Innovation, Armidale, NSW, 2351, Australia
| | - Nasir Moghaddar
- School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia.,Cooperative Research Centre for Sheep Industry Innovation, Armidale, NSW, 2351, Australia
| | - Julius H van der Werf
- School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia.,Cooperative Research Centre for Sheep Industry Innovation, Armidale, NSW, 2351, Australia
| | - Michael E Goddard
- Agriculture Victoria Research, AgriBio Centre, Bundoora, VIC, 3083, Australia.,School of Land and Environment, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Hans D Daetwyler
- Agriculture Victoria Research, AgriBio Centre, Bundoora, VIC, 3083, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3086, Australia.,Cooperative Research Centre for Sheep Industry Innovation, Armidale, NSW, 2351, Australia
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Ebrahimi F, Gholizadeh M, Rahimi-Mianji G, Farhadi A. Detection of QTL for greasy fleece weight in sheep using a 50 K single nucleotide polymorphism chip. Trop Anim Health Prod 2017; 49:1657-1662. [PMID: 28801813 DOI: 10.1007/s11250-017-1373-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 08/02/2017] [Indexed: 12/27/2022]
Abstract
Genome-wide association studies (GWAS) have introduced an influential tool in the search for quantitative trait loci (QTL) influencing economically important traits in sheep. To identify QTL associated with greasy fleece weight, a GWAS with 50 K single nucleotide polymorphisms (SNPs) was performed in a Baluchi sheep population. Association with greasy fleece weights was tested using the software Plink. The results of our GWAS provided three novel SNP markers and candidate genes associated with greasy fleece weight. A total of three chromosome-wide significant associations were detected for SNP on chromosomes 17 and 20 affecting greasy fleece weight across the four shearing. One of the significant SNP markers was located within ovine known genes namely FAM101A. Further investigation of these identified regions in validation studies will facilitate the identification of strong candidate genes for wool production in sheep.
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Affiliation(s)
- Fatemeh Ebrahimi
- Department of Animal Science, Faculty of Animal and Aquatic Science, Sari Agricultural Sciences and Natural Resources University, P.O. Box -578, Sari, Iran
| | - Mohsen Gholizadeh
- Department of Animal Science, Faculty of Animal and Aquatic Science, Sari Agricultural Sciences and Natural Resources University, P.O. Box -578, Sari, Iran.
| | - Ghodrat Rahimi-Mianji
- Department of Animal Science, Faculty of Animal and Aquatic Science, Sari Agricultural Sciences and Natural Resources University, P.O. Box -578, Sari, Iran
| | - Ayoub Farhadi
- Department of Animal Science, Faculty of Animal and Aquatic Science, Sari Agricultural Sciences and Natural Resources University, P.O. Box -578, Sari, Iran
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56
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Genetic Traits of Relevance to Sustainability of Smallholder Sheep Farming Systems in South Africa. SUSTAINABILITY 2017. [DOI: 10.3390/su9081225] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Estimates of linkage disequilibrium and effective population sizes in Chinese Merino (Xinjiang type) sheep by genome-wide SNPs. Genes Genomics 2017; 39:733-745. [PMID: 28706593 PMCID: PMC5486679 DOI: 10.1007/s13258-017-0539-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 03/19/2017] [Indexed: 12/14/2022]
Abstract
Knowledge of linkage disequilibrium (LD) is important for effective genome-wide association studies and accurate genomic prediction. Chinese Merino (Xinjiang type) is well-known fine wool sheep breed. However, the extent of LD across the genome remains unexplored. In this study, we calculated autosomal LD based on genome-wide SNPs of 635 Chinese Merino (Xinjiang type) sheep by Illumina Ovine SNP50 BeadChip. A moderate level of LD (r2 ≥ 0.25) across the whole genome was observed at short distances of 0–10 kb. Further, the ancestral effective population size (Ne) was analyzed by extent of LD and found that Ne increased with the increase of generations and declined rapidly within the most recent 50 generations, which is consistent with the history of Chinese Merino sheep breeding, initiated in 1971. We also noted that even when the effective population size was estimated across different single chromosomes, Ne only ranged from 140.36 to 183.33 at five generations in the past, exhibiting a rapid decrease compared with that at ten generations in the past. These results indicated that the genetic diversity in Chinese Merino sheep recently decreased and proper protective measures should be taken to maintain the diversity. Our datasets provided essential genetic information to track molecular variations which potentially contribute to phenotypic variation in Chinese Merino sheep.
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Ma GW, Chu YK, Zhang WJ, Qin FY, Xu SS, Yang H, Rong EG, Du ZQ, Wang SZ, Li H, Wang N. Polymorphisms of FST gene and their association with wool quality traits in Chinese Merino sheep. PLoS One 2017; 12:e0174868. [PMID: 28384189 PMCID: PMC5383234 DOI: 10.1371/journal.pone.0174868] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 03/16/2017] [Indexed: 11/19/2022] Open
Abstract
Follistatin (FST) is involved in hair follicle morphogenesis. However, its effects on hair traits are not clear. This study was designed to investigate the effects of FST gene single nucleotide polymorphisms (SNP) on wool quality traits in Chinese Merino sheep (Junken Type). We performed gene expression analysis, SNP detection, and association analysis of FST gene with sheep wool quality traits. The real-time RT-PCR analysis showed that FST gene was differentially expressed in adult skin between Chinese Merino sheep (Junken Type) and Suffolk sheep. Immunostaining showed that FST was localized in inner root sheath (IRS) and matrix of hair follicle (HF) in both SF and Suffolk sheep. Sequencing analysis identified a total of seven SNPs (termed SNPs 1-7) in the FST gene in Chinese Merino sheep (Junken Type). Association analysis showed that SNP2 (Chr 16. 25,633,662 G>A) was significantly associated with average wool fiber diameter, wool fineness SD, and wool crimp (P < 0.05). SNP4 (Chr 16. 25,633,569 C>T) was significantly associated with wool fineness SD and CV of fiber diameter (P < 0.05). Similarly, the haplotypes derived from these seven identified SNPs were also significantly associated with average wool fiber diameter, wool fineness SD, CV of fiber diameter, and wool crimp (P < 0.05). Our results suggest that FST influences wool quality traits and its SNPs 2 and 4 might be useful markers for marker-assisted selection and sheep breeding.
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Affiliation(s)
- Guang-Wei Ma
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, P. R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, P. R. China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P. R. China
| | - Yan-Kai Chu
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, P. R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, P. R. China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P. R. China
| | - Wen-Jian Zhang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, P. R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, P. R. China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P. R. China
| | - Fei-Yue Qin
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, P. R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, P. R. China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P. R. China
| | - Song-Song Xu
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, P. R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, P. R. China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P. R. China
| | - Hua Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, P. R. China
| | - En-Guang Rong
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, P. R. China
| | - Zhi-Qiang Du
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, P. R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, P. R. China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P. R. China
| | - Shou-Zhi Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, P. R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, P. R. China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P. R. China
| | - Hui Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, P. R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, P. R. China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P. R. China
| | - Ning Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, P. R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, P. R. China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P. R. China
- * E-mail:
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de Simoni Gouveia JJ, Paiva SR, McManus CM, Caetano AR, Kijas JW, Facó O, Azevedo HC, de Araujo AM, de Souza CJH, Yamagishi MEB, Carneiro PLS, Braga Lôbo RN, de Oliveira SMP, da Silva MVG. Genome-wide search for signatures of selection in three major Brazilian locally adapted sheep breeds. Livest Sci 2017. [DOI: 10.1016/j.livsci.2017.01.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Seroussi E, Rosov A, Shirak A, Lam A, Gootwine E. Unveiling genomic regions that underlie differences between Afec-Assaf sheep and its parental Awassi breed. Genet Sel Evol 2017; 49:19. [PMID: 28187715 PMCID: PMC5301402 DOI: 10.1186/s12711-017-0296-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 02/06/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Sheep production in Israel has improved by crossing the fat-tailed local Awassi breed with the East Friesian and later, with the Booroola Merino breed, which led to the formation of the highly prolific Afec-Assaf strain. This strain differs from its parental Awassi breed in morphological traits such as tail and horn size, coat pigmentation and wool characteristics, as well as in production, reproductive and health traits. To identify major genes associated with the formation of the Afec-Assaf strain, we genotyped 41 Awassi and 141 Afec-Assaf sheep using the Illumina Ovine SNP50 BeadChip array, and analyzed the results with PLINK and EMMAX software. The detected variable genomic regions that differed between Awassi and Afec-Assaf sheep (variable genomic regions; VGR) were compared to selection signatures that were reported in 48 published genome-wide association studies in sheep. Because the Afec-Assaf strain, but not the Awassi breed, carries the Booroola mutation, association analysis of BMPR1B used as the test gene was performed to evaluate the ability of this study to identify a VGR that includes such a major gene. RESULTS Of the 20 detected VGR, 12 were novel to this study. A ~7-Mb VGR was identified on Ovies aries chromosome OAR6 where the Booroola mutation is located. Similar to other studies, the most significant VGR was detected on OAR10, in a region that contains candidate genes affecting horn type (RXFP2), climate adaptation (ALOX5AP), fiber diameter (KATNAl1), coat pigmentation (FRY) and genes associated with fat distribution. The VGR on OAR2 included BNC2, which is also involved in controlling coat pigmentation in sheep. Six other VGR contained genes that were shown to be involved in coat pigmentation by analyzing their mammalian orthologues. Genes associated with fat distribution in humans, including GRB14 and COBLL1, were located in additional VGR. Sequencing DNA from Awassi and Afec-Assaf individuals revealed non-synonymous mutations in some of these candidate genes. CONCLUSIONS Our results highlight VGR that differentiate the Awassi breed from the Afec-Assaf strain, some of which may include genes that confer an advantage to Afec-Assaf and Assaf over Awassi sheep with respect to intensive sheep production under Mediterranean conditions.
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Affiliation(s)
- Eyal Seroussi
- Institute of Animal Science, ARO, The Volcani Center, PO Box 15159, 7528809 Rishon LeZion, Israel
| | - Alexander Rosov
- Institute of Animal Science, ARO, The Volcani Center, PO Box 15159, 7528809 Rishon LeZion, Israel
| | - Andrey Shirak
- Institute of Animal Science, ARO, The Volcani Center, PO Box 15159, 7528809 Rishon LeZion, Israel
| | - Alon Lam
- Institute of Animal Science, ARO, The Volcani Center, PO Box 15159, 7528809 Rishon LeZion, Israel
| | - Elisha Gootwine
- Institute of Animal Science, ARO, The Volcani Center, PO Box 15159, 7528809 Rishon LeZion, Israel
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Peled A, Sarig O, Samuelov L, Bertolini M, Ziv L, Weissglas-Volkov D, Eskin-Schwartz M, Adase CA, Malchin N, Bochner R, Fainberg G, Goldberg I, Sugawara K, Baniel A, Tsuruta D, Luxenburg C, Adir N, Duverger O, Morasso M, Shalev S, Gallo RL, Shomron N, Paus R, Sprecher E. Mutations in TSPEAR, Encoding a Regulator of Notch Signaling, Affect Tooth and Hair Follicle Morphogenesis. PLoS Genet 2016; 12:e1006369. [PMID: 27736875 PMCID: PMC5065119 DOI: 10.1371/journal.pgen.1006369] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 09/16/2016] [Indexed: 11/19/2022] Open
Abstract
Despite recent advances in our understanding of the pathogenesis of ectodermal dysplasias (EDs), the molecular basis of many of these disorders remains unknown. In the present study, we aimed at elucidating the genetic basis of a new form of ED featuring facial dysmorphism, scalp hypotrichosis and hypodontia. Using whole exome sequencing, we identified 2 frameshift and 2 missense mutations in TSPEAR segregating with the disease phenotype in 3 families. TSPEAR encodes the thrombospondin-type laminin G domain and EAR repeats (TSPEAR) protein, whose function is poorly understood. TSPEAR knock-down resulted in altered expression of genes known to be regulated by NOTCH and to be involved in murine hair and tooth development. Pathway analysis confirmed that down-regulation of TSPEAR in keratinocytes is likely to affect Notch signaling. Accordingly, using a luciferase-based reporter assay, we showed that TSPEAR knock-down is associated with decreased Notch signaling. In addition, NOTCH1 protein expression was reduced in patient scalp skin. Moreover, TSPEAR silencing in mouse hair follicle organ cultures was found to induce apoptosis in follicular epithelial cells, resulting in decreased hair bulb diameter. Collectively, these observations indicate that TSPEAR plays a critical, previously unrecognized role in human tooth and hair follicle morphogenesis through regulation of the Notch signaling pathway. Ectodermal dysplasias refer to a large group of inherited disorders characterized by developmental defects in tissues of ectodermal origin. The study of these conditions has been instrumental in the discovery of biological pathways involved in the regulation of epithelial tissue morphogenesis. In this report, through the delineation of the molecular basis of a novel form of autosomal recessive ectodermal dysplasia, we identified a new key player in ectodermal development. We detected a number of mutations in TSPEAR co-segregating with abnormal hair and tooth development in three families. TSPEAR encodes the thrombospondin-type laminin G domain and EAR repeats (TSPEAR) protein, whose function is poorly understood. TSPEAR was found to be strongly expressed in murine hair and tooth. Using a reporter assay, we showed that it regulates Notch activity. Accordingly, NOTCH1 expression was altered in patient skin, and NOTCH1, as well as many of its known targets, was down-regulated in TSPEAR deficient keratinocytes. Moreover, Tspear silencing in mouse hair follicle organ cultures was found to induce apoptosis in follicular epithelial cells, resulting in decreased hair bulb diameter. Collectively, these observations indicate that TSPEAR plays a critical, previously unrecognized role in human tooth and hair follicle morphogenesis through regulation of the Notch pathway. As such, these new data are likely to lead to further investigations aimed at characterizing the role of Notch signaling pathway in other forms of ectodermal dysplasias as well as acquired hair and tooth pathologies.
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Affiliation(s)
- Alon Peled
- Department of Dermatology, Tel Aviv Medical Center, Tel Aviv, Israel
- Department of Human Molecular Genetics and Biochemistry, Tel-Aviv University, Tel Aviv, Israel
| | - Ofer Sarig
- Department of Dermatology, Tel Aviv Medical Center, Tel Aviv, Israel
| | - Liat Samuelov
- Department of Dermatology, Tel Aviv Medical Center, Tel Aviv, Israel
- Division of Dermatology, University of California, San Diego, San Diego, California, United States of America
| | - Marta Bertolini
- Department of Dermatology, University of Münster, Münster, Germany
| | - Limor Ziv
- Sheba Medical Center, Ramat Gan, Israel
| | | | - Marina Eskin-Schwartz
- Department of Dermatology, Tel Aviv Medical Center, Tel Aviv, Israel
- Department of Human Molecular Genetics and Biochemistry, Tel-Aviv University, Tel Aviv, Israel
| | - Christopher A. Adase
- Division of Dermatology, University of California, San Diego, San Diego, California, United States of America
| | - Natalia Malchin
- Department of Dermatology, Tel Aviv Medical Center, Tel Aviv, Israel
| | - Ron Bochner
- Department of Dermatology, Tel Aviv Medical Center, Tel Aviv, Israel
| | - Gilad Fainberg
- Department of Dermatology, Tel Aviv Medical Center, Tel Aviv, Israel
| | - Ilan Goldberg
- Department of Dermatology, Tel Aviv Medical Center, Tel Aviv, Israel
| | - Koji Sugawara
- Department of Dermatology, Osaka City University, Osaka, Japan
| | - Avital Baniel
- Department of Dermatology, Tel Aviv Medical Center, Tel Aviv, Israel
| | - Daisuke Tsuruta
- Department of Dermatology, Osaka City University, Osaka, Japan
| | - Chen Luxenburg
- Department of Cell and Developmental Biology, Tel Aviv University, Tel Aviv, Israel
| | - Noam Adir
- Faculty of Chemistry, Technion, Haifa, Israel
| | - Olivier Duverger
- Laboratory of Skin Biology, National Institute of Health, Bethesda, Maryland, United States of America
| | - Maria Morasso
- Laboratory of Skin Biology, National Institute of Health, Bethesda, Maryland, United States of America
| | - Stavit Shalev
- Institute of Human Genetics, Haemek Medical Center, Afula, Israel
- Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Richard L. Gallo
- Division of Dermatology, University of California, San Diego, San Diego, California, United States of America
| | - Noam Shomron
- Department of Cell and Developmental Biology, Tel Aviv University, Tel Aviv, Israel
| | - Ralf Paus
- Department of Dermatology, University of Münster, Münster, Germany
- Centre for Dermatology Research, Institute of Inflammation and Repair, University of Manchester, Manchester, United Kingdom
| | - Eli Sprecher
- Department of Dermatology, Tel Aviv Medical Center, Tel Aviv, Israel
- Department of Human Molecular Genetics and Biochemistry, Tel-Aviv University, Tel Aviv, Israel
- * E-mail:
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Rong EG, Yang H, Zhang ZW, Wang ZP, Yan XH, Li H, Wang N. Association of methionine synthase gene polymorphisms with wool production and quality traits in Chinese Merino population. J Anim Sci 2016; 93:4601-9. [PMID: 26523551 DOI: 10.2527/jas.2015-8963] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Methionine synthase (MTR) plays a crucial role in maintaining homeostasis of intracellular methionine, folate, and homocysteine, and its activity correlates with DNA methylation in many mammalian tissues. Our previous genomewide association study identified that 1 SNP located in the gene was associated with several wool production and quality traits in Chinese Merino. To confirm the potential involvement of the gene in sheep wool production and quality traits, we performed sheep tissue expression profiling, SNP detection, and association analysis with sheep wool production and quality traits. The semiquantitative reverse transcription PCR analysis showed that the gene was differentially expressed in skin from Merino and Kazak sheep. The sequencing analysis identified a total of 13 SNP in the gene from Chinese Merino sheep. Comparison of the allele frequencies revealed that these 13 identified SNP were significantly different among the 6 tested Chinese Merino strains ( < 0.001). Linkage disequilibrium analysis showed that SNP 3 to 11 were strongly linked in a single haplotype block in the tested population. Association analysis showed that SNP 2 to 11 were significantly associated with the average wool fiber diameter and the fineness SD and that SNP 4 to 11 were significantly associated with the CV of fiber diameter trait ( < 0.05). Single nucleotide polymorphism 2 and SNP 5 to 12 were weakly associated with wool crimp. Similarly, the haplotypes derived from these 13 identified SNP were also significantly associated with the average wool fiber diameter, fineness SD, and the CV of fiber diameter ( < 0.05). Our results suggest that is a candidate gene for sheep wool production and quality traits, and the identified SNP might be used in sheep breeding.
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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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64
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Wang H, Zhang L, Cao J, Wu M, Ma X, Liu Z, Liu R, Zhao F, Wei C, Du L. Genome-Wide Specific Selection in Three Domestic Sheep Breeds. PLoS One 2015; 10:e0128688. [PMID: 26083354 PMCID: PMC4471085 DOI: 10.1371/journal.pone.0128688] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 04/29/2015] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Commercial sheep raised for mutton grow faster than traditional Chinese sheep breeds. Here, we aimed to evaluate genetic selection among three different types of sheep breed: two well-known commercial mutton breeds and one indigenous Chinese breed. RESULTS We first combined locus-specific branch lengths and di statistical methods to detect candidate regions targeted by selection in the three different populations. The results showed that the genetic distances reached at least medium divergence for each pairwise combination. We found these two methods were highly correlated, and identified many growth-related candidate genes undergoing artificial selection. For production traits, APOBR and FTO are associated with body mass index. For meat traits, ALDOA, STK32B and FAM190A are related to marbling. For reproduction traits, CCNB2 and SLC8A3 affect oocyte development. We also found two well-known genes, GHR (which affects meat production and quality) and EDAR (associated with hair thickness) were associated with German mutton merino sheep. Furthermore, four genes (POL, RPL7, MSL1 and SHISA9) were associated with pre-weaning gain in our previous genome-wide association study. CONCLUSIONS Our results indicated that combine locus-specific branch lengths and di statistical approaches can reduce the searching ranges for specific selection. And we got many credible candidate genes which not only confirm the results of previous reports, but also provide a suite of novel candidate genes in defined breeds to guide hybridization breeding.
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Affiliation(s)
- Huihua Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China, Beijing, China
| | - Li Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China, Beijing, China
| | - Jiaxve Cao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China, Beijing, China
| | - Mingming Wu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China, Beijing, China
| | - Xiaomeng Ma
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China, Beijing, China
| | - Zhen Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China, Beijing, China
| | - Ruizao Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China, Beijing, China
| | - Fuping Zhao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China, Beijing, China
| | - Caihong Wei
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China, Beijing, China
| | - Lixin Du
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China, Beijing, China
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