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Zhou J, Cui R, Lin L. A Systematic Review of the Application of Computational Technology in Microtia. J Craniofac Surg 2024; 35:1214-1218. [PMID: 38710037 DOI: 10.1097/scs.0000000000010210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 03/11/2024] [Indexed: 05/08/2024] Open
Abstract
Microtia is a congenital and morphological anomaly of one or both ears, which results from a confluence of genetic and external environmental factors. Up to now, extensive research has explored the potential utilization of computational methodologies in microtia and has obtained promising results. Thus, the authors reviewed the achievements and shortcomings of the research mentioned previously, from the aspects of artificial intelligence, computer-aided design and surgery, computed tomography, medical and biological data mining, and reality-related technology, including virtual reality and augmented reality. Hoping to offer novel concepts and inspire further studies within this field.
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Affiliation(s)
- Jingyang Zhou
- Ear Reconstruction Center, Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
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Zhang L, Liang L, Kasimu H, Li W, Liu M, Li H, He S. A 76-base pair duplication within the enhancer region of the HMX1 gene causes sheep microtia. Gene 2024; 909:148307. [PMID: 38395239 DOI: 10.1016/j.gene.2024.148307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 02/01/2024] [Accepted: 02/20/2024] [Indexed: 02/25/2024]
Abstract
Sheep congenital microtia is characterized by underdeveloped ears and provides an ideal basis for studying human microtia. This study identified the causal mutation and regulatory mechanisms underlying this disorder. Whole-genome association analysis was conducted using 23 ear tissue samples from sheep with microtia and 28 samples from normal-eared sheep. A significant correlation was found between microtia and a 76-base pair duplication in the enhancer region of the HMX1 gene. Further analysis of offspring phenotypes confirmed an autosomal dominant inheritance pattern. Genotypic analysis showed that individuals that are homozygous for this duplication were earless, heterozygous individuals exhibited shortened ears, and wild-type individuals had normal ears. Moreover, luciferase assays confirmed that this duplication increased HMX1 gene expression, and duplication knock-in mice also exhibited shorter and narrower external ears compared to wild-type mice. Transcriptomic analysis further demonstrated that this duplication enhanced HMX1 gene expression in animal models. This study characterized the causal regulatory mutation underlying sheep microtia.
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Affiliation(s)
- Lihua Zhang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, 830052, China; Key Laboratory of Ruminant Genetics, Breeding & Reproduction, Ministry of Agriculture, Key Laboratory of Animal Biotechnology of Xinjiang, Institute of Biotechnology, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, 830011, China
| | - Long Liang
- Key Laboratory of Ruminant Genetics, Breeding & Reproduction, Ministry of Agriculture, Key Laboratory of Animal Biotechnology of Xinjiang, Institute of Biotechnology, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, 830011, China
| | - Hailati Kasimu
- Key Laboratory of Ruminant Genetics, Breeding & Reproduction, Ministry of Agriculture, Key Laboratory of Animal Biotechnology of Xinjiang, Institute of Biotechnology, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, 830011, China
| | - Wenrong Li
- Key Laboratory of Ruminant Genetics, Breeding & Reproduction, Ministry of Agriculture, Key Laboratory of Animal Biotechnology of Xinjiang, Institute of Biotechnology, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, 830011, China
| | - Mingjun Liu
- Key Laboratory of Ruminant Genetics, Breeding & Reproduction, Ministry of Agriculture, Key Laboratory of Animal Biotechnology of Xinjiang, Institute of Biotechnology, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, 830011, China
| | - Haiying Li
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, 830052, China.
| | - Sangang He
- Key Laboratory of Ruminant Genetics, Breeding & Reproduction, Ministry of Agriculture, Key Laboratory of Animal Biotechnology of Xinjiang, Institute of Biotechnology, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, 830011, China.
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Klawatsch J, Papachristou D, Koutsouli P, Upadhyay M, Seichter D, Russ I, Mioč B, Simčič M, Bizelis I, Medugorac I. Genetic basis of ear length in sheep breeds sampled across the region from the Middle East to the Alps. Anim Genet 2024; 55:123-133. [PMID: 38069488 DOI: 10.1111/age.13387] [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: 11/28/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 01/04/2024]
Abstract
Ear length in sheep (Ovis aries) shows a wide range of natural variation, from the absence of an outer ear structure (anotia), to small outer ears (microtia), to regular ear length. Up until now, the underlying genetics of this phenotype has been studied in four sheep breeds from China, Jordan and Italy. These studies revealed a broad range of genes significantly associated with ear length, potentially indicating genetic heterogeneity across breeds or geographic regions. In the current study, we performed genome-wide SNP genotyping and haplotype-based mapping, in a population of 340 individuals, to identify loci influencing ear length variation in additional sheep breeds from Slovenia, Croatia, Cyprus and Greece. Additionally, two previously described candidate variants were also genotyped in our mapping population. The mapping model without candidate variant genotypes revealed only one genome-wide significant signal, which was located next to HMX1 on OAR6. This region was previously described as being associated with ear length variation in the Altay and Awassi sheep breeds. The mapping model including the candidate duplication genotype near HMX1 as a fixed effect explained the phenotypic variance on OAR6 and revealed an additional genome-wide significant locus on OAR13 associated with ear length. Our results, combined with published evidence, suggest that a duplication in the evolutionarily conserved region near HMX1 is the major regulator of ear length in sheep breeds descended from a larger region from Central Asia, to the Middle East, Cyprus, Greece and to the Alps. This distribution suggests an ancient origin of the derived allele.
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Affiliation(s)
- Jürgen Klawatsch
- Population Genomics Group, Department of Veterinary Sciences, Ludwig Maximillians University Munich, Munich, Germany
- Tierzuchtforschung e.V. Munich, Grub, Germany
| | | | - Panagiota Koutsouli
- Department of Animal Science, Agricultural University of Athens, Athens, Greece
| | - Maulik Upadhyay
- Population Genomics Group, Department of Veterinary Sciences, Ludwig Maximillians University Munich, Munich, Germany
| | | | - Ingolf Russ
- Tierzuchtforschung e.V. Munich, Grub, Germany
| | - Boro Mioč
- Department of Animal Science and Technology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Mojca Simčič
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Iosif Bizelis
- Department of Animal Science, Agricultural University of Athens, Athens, Greece
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, Ludwig Maximillians University Munich, Munich, Germany
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Kalds P, Zhou S, Gao Y, Cai B, Huang S, Chen Y, Wang X. Genetics of the phenotypic evolution in sheep: a molecular look at diversity-driving genes. Genet Sel Evol 2022; 54:61. [PMID: 36085023 PMCID: PMC9463822 DOI: 10.1186/s12711-022-00753-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/29/2022] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND After domestication, the evolution of phenotypically-varied sheep breeds has generated rich biodiversity. This wide phenotypic variation arises as a result of hidden genomic changes that range from a single nucleotide to several thousands of nucleotides. Thus, it is of interest and significance to reveal and understand the genomic changes underlying the phenotypic variation of sheep breeds in order to drive selection towards economically important traits. REVIEW Various traits contribute to the emergence of variation in sheep phenotypic characteristics, including coat color, horns, tail, wool, ears, udder, vertebrae, among others. The genes that determine most of these phenotypic traits have been investigated, which has generated knowledge regarding the genetic determinism of several agriculturally-relevant traits in sheep. In this review, we discuss the genomic knowledge that has emerged in the past few decades regarding the phenotypic traits in sheep, and our ultimate aim is to encourage its practical application in sheep breeding. In addition, in order to expand the current understanding of the sheep genome, we shed light on research gaps that require further investigation. CONCLUSIONS Although significant research efforts have been conducted in the past few decades, several aspects of the sheep genome remain unexplored. For the full utilization of the current knowledge of the sheep genome, a wide practical application is still required in order to boost sheep productive performance and contribute to the generation of improved sheep breeds. The accumulated knowledge on the sheep genome will help advance and strengthen sheep breeding programs to face future challenges in the sector, such as climate change, global human population growth, and the increasing demand for products of animal origin.
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Affiliation(s)
- Peter Kalds
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- Department of Animal and Poultry Production, Faculty of Environmental Agricultural Sciences, Arish University, El-Arish, 45511 Egypt
| | - Shiwei Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100 China
| | - Yawei Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Bei Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Shuhong Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Yulin Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs, Yangling, 712100 China
| | - Xiaolong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs, Yangling, 712100 China
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Tingaud-Sequeira A, Trimouille A, Sagardoy T, Lacombe D, Rooryck-Thambo C. Oculo-auriculo-vertebral spectrum: new genes and literature review on a complex disease. J Med Genet 2022; 59:417-427. [PMID: 35110414 DOI: 10.1136/jmedgenet-2021-108219] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 12/30/2021] [Indexed: 12/23/2022]
Abstract
Oculo-auriculo-vertebral spectrum (OAVS) or Goldenhar syndrome is due to an abnormal development of first and second branchial arches derivatives during embryogenesis and is characterised by hemifacial microsomia associated with auricular, ocular and vertebral malformations. The clinical and genetic heterogeneity of this spectrum with incomplete penetrance and variable expressivity, render its molecular diagnosis difficult. Only a few recurrent CNVs and genes have been identified as causatives in this complex disorder so far. Prenatal environmental causal factors have also been hypothesised. However, most of the patients remain without aetiology. In this review, we aim at updating clinical diagnostic criteria and describing genetic and non-genetic aetiologies, animal models as well as novel diagnostic tools and surgical management, in order to help and improve clinical care and genetic counselling of these patients and their families.
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Affiliation(s)
- Angèle Tingaud-Sequeira
- Univ. Bordeaux, Maladies Rares: Génétique et Métabolisme (MRGM), U 1211 INSERM, F-33000 Bordeaux, France
| | - Aurélien Trimouille
- Univ. Bordeaux, Maladies Rares: Génétique et Métabolisme (MRGM), U 1211 INSERM, F-33000 Bordeaux, France.,CHU de Bordeaux, Service de Génétique Médicale, Centre de Référence Anomalies du Développement et Syndromes Malformatifs, F-33076, Bordeaux, France
| | - Thomas Sagardoy
- CHU de Bordeaux, Service d'oto-rhino-laryngologie, de chirurgie cervico-faciale et d'ORL pédiatrique, 33076 Bordeaux, France
| | - Didier Lacombe
- Univ. Bordeaux, Maladies Rares: Génétique et Métabolisme (MRGM), U 1211 INSERM, F-33000 Bordeaux, France.,CHU de Bordeaux, Service de Génétique Médicale, Centre de Référence Anomalies du Développement et Syndromes Malformatifs, F-33076, Bordeaux, France
| | - Caroline Rooryck-Thambo
- Univ. Bordeaux, Maladies Rares: Génétique et Métabolisme (MRGM), U 1211 INSERM, F-33000 Bordeaux, France .,CHU de Bordeaux, Service de Génétique Médicale, Centre de Référence Anomalies du Développement et Syndromes Malformatifs, F-33076, Bordeaux, France
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Ilie DE, Mizeranschi AE, Mihali CV, Neamț RI, Goilean GV, Georgescu OI, Zaharie D, Carabaș M, Huțu I. Genome-Wide Association Studies for Milk Somatic Cell Score in Romanian Dairy Cattle. Genes (Basel) 2021; 12:genes12101495. [PMID: 34680890 PMCID: PMC8535694 DOI: 10.3390/genes12101495] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/22/2021] [Accepted: 09/22/2021] [Indexed: 02/07/2023] Open
Abstract
Mastitis is one of the most frequently encountered diseases in dairy cattle, negatively affecting animal welfare and milk production. For this reason, contributions to understanding its genomic architecture are of great interest. Genome-wide association studies (GWAS) have identified multiple loci associated with somatic cell score (SCS) and mastitis in cattle. However, most of the studies have been conducted in different parts of the world on various breeds, and none of the investigations have studied the genetic architecture of mastitis in Romanian dairy cattle breeds up to this point in time. In this study, we report the first GWAS for SCS in dairy cattle breeds from Romania. For GWAS, we used an Axiom Bovine v3 SNP-chip (>63,000 Single Nucleotide Polymorphism -SNPs) and 33,330 records from 690 cows belonging to Romanian Spotted (RS) and Romanian Brown (RB) cattle. The results found one SNP significantly associated with SCS in the RS breed and 40 suggestive SNPs with -log10 (p) from 4 to 4.9 for RS and from 4 to 5.4 in RB. From these, 14 markers were located near 12 known genes (AKAP8, CLHC1, MEGF10, SATB2, GATA6, SPATA6, COL12A1, EPS8, LUZP2, RAMAC, IL12A and ANKRD55) in RB cattle, 3 markers were close to ZDHHC19, DAPK1 and MMP7 genes, while one SNP overlapped the HERC3 gene in RS cattle. Four genes (HERC3, LUZP2, AKAP8 and MEGF10) associated with SCS in this study were previously reported in different studies. The most significant SNP (rs110749552) associated with SCS was located within the HERC3 gene. In both breeds, the SNPs and position of association signals were distinct among the three parities, denoting that mastitis is controlled by different genes that are dependent according to parity. The current results contribute to an expansion in the body of knowledge regarding the proportion of genetic variability explained by SNPs for SCS in dairy cattle.
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Affiliation(s)
- Daniela Elena Ilie
- The Molecular Research Department, Research and Development Station for Bovine Arad, Bodrogului Street, No. 32, 310059 Arad, Romania; (A.E.M.); (C.V.M.); (R.I.N.); (G.V.G.)
- Faculty of Veterinary Medicine, Banat’s University of Agricultural Sciences and Veterinary Medicine “King Michael I of Romania” from Timisoara, Calea Aradului No. 119, 300645 Timisoara, Romania; (O.I.G.); (I.H.)
- Correspondence:
| | - Alexandru Eugeniu Mizeranschi
- The Molecular Research Department, Research and Development Station for Bovine Arad, Bodrogului Street, No. 32, 310059 Arad, Romania; (A.E.M.); (C.V.M.); (R.I.N.); (G.V.G.)
| | - Ciprian Valentin Mihali
- The Molecular Research Department, Research and Development Station for Bovine Arad, Bodrogului Street, No. 32, 310059 Arad, Romania; (A.E.M.); (C.V.M.); (R.I.N.); (G.V.G.)
| | - Radu Ionel Neamț
- The Molecular Research Department, Research and Development Station for Bovine Arad, Bodrogului Street, No. 32, 310059 Arad, Romania; (A.E.M.); (C.V.M.); (R.I.N.); (G.V.G.)
| | - George Vlad Goilean
- The Molecular Research Department, Research and Development Station for Bovine Arad, Bodrogului Street, No. 32, 310059 Arad, Romania; (A.E.M.); (C.V.M.); (R.I.N.); (G.V.G.)
| | - Ovidiu Ionuț Georgescu
- Faculty of Veterinary Medicine, Banat’s University of Agricultural Sciences and Veterinary Medicine “King Michael I of Romania” from Timisoara, Calea Aradului No. 119, 300645 Timisoara, Romania; (O.I.G.); (I.H.)
| | - Daniela Zaharie
- Faculty of Mathematics and Computer Science, West University of Timișoara, 300223 Timisoara, Romania;
| | - Mihai Carabaș
- Faculty of Automatic Control and Computer Science, Politehnica University of Bucharest, 060042 București, Romania;
| | - Ioan Huțu
- Faculty of Veterinary Medicine, Banat’s University of Agricultural Sciences and Veterinary Medicine “King Michael I of Romania” from Timisoara, Calea Aradului No. 119, 300645 Timisoara, Romania; (O.I.G.); (I.H.)
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