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Hu H, Scheben A, Wang J, Li F, Li C, Edwards D, Zhao J. Unravelling inversions: Technological advances, challenges, and potential impact on crop breeding. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:544-554. [PMID: 37961986 PMCID: PMC10893937 DOI: 10.1111/pbi.14224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/11/2023] [Accepted: 10/22/2023] [Indexed: 11/15/2023]
Abstract
Inversions, a type of chromosomal structural variation, significantly influence plant adaptation and gene functions by impacting gene expression and recombination rates. However, compared with other structural variations, their roles in functional biology and crop improvement remain largely unexplored. In this review, we highlight technological and methodological advancements that have allowed a comprehensive understanding of inversion variants through the pangenome framework and machine learning algorithms. Genome editing is an efficient method for inducing or reversing inversion mutations in plants, providing an effective mechanism to modify local recombination rates. Given the potential of inversions in crop breeding, we anticipate increasing attention on inversions from the scientific community in future research and breeding applications.
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Affiliation(s)
- Haifei Hu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co‐construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering LaboratoryGuangzhouChina
| | - Armin Scheben
- Simons Center for Quantitative Biology, Cold Spring Harbor LaboratoryCold Spring HarborNew YorkUSA
| | - Jian Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co‐construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering LaboratoryGuangzhouChina
| | - Fangping Li
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
| | - Chengdao Li
- Western Crop Genetics Alliance, Centre for Crop & Food Innovation, Food Futures Institute, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - David Edwards
- School of Biological SciencesUniversity of Western AustraliaPerthWestern AustraliaAustralia
- Australia & Centre for Applied BioinformaticsUniversity of Western AustraliaPerthWestern AustraliaAustralia
| | - Junliang Zhao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co‐construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering LaboratoryGuangzhouChina
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Kasper E, Coutant S, Manase S, Vasseur S, Macquère P, Bougeard G, Faivre L, Ingster O, Baert-Desurmont S, Houdayer C. Detecting inversions in routine molecular diagnosis in MMR genes. Fam Cancer 2022; 21:423-428. [PMID: 34997397 DOI: 10.1007/s10689-021-00287-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/27/2021] [Indexed: 01/07/2023]
Abstract
Inversions, i.e. a change in orientation of a segment of DNA, are a recognized cause of human diseases which remain overlooked due to their balanced nature. Inversions can have severe or more subtle impacts on gene expression. We describe two families that exemplify these aspects and underline the need for inversion detection in routine diagnosis. The first family (F1) displayed a sibship with two constitutional mismatch repair deficiency patients and a family history of colon cancer in the paternal branch. The second family (F2) displayed a severe history of Lynch syndrome. These families were analyzed using a whole gene panel (WGP) strategy i.e. including colon cancer genes with their intronic and flanking genomic regions. In F1, a PMS2 inversion encompassing the promoter region to intron 1 and a PMS2 splice variant were found in the maternal and paternal branch, respectively. In F2, we described the first MSH6 inversion, involving the 5' part of MSH6 and the 3' part of the nearby gene ANXA4. Inversion detection mandates genomic sequencing, but makes a valuable contribution to the diagnostic rate. WGP is an attractive strategy as it maximizes the detection power on validated genes and keeps sufficient depth to detect de novo events.
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Affiliation(s)
- Edwige Kasper
- Department of Genetics, Normandy Center for Genomic and Personalized Medicine, UNIROUEN, Inserm U1245 and Rouen University Hospital, CHU Rouen, Normandie University, 76000, Rouen, France.
| | - Sophie Coutant
- Department of Genetics, Normandy Center for Genomic and Personalized Medicine, UNIROUEN, Inserm U1245 and Rouen University Hospital, CHU Rouen, Normandie University, 76000, Rouen, France
| | - Sandrine Manase
- Department of Genetics, Normandy Center for Genomic and Personalized Medicine, UNIROUEN, Inserm U1245 and Rouen University Hospital, CHU Rouen, Normandie University, 76000, Rouen, France
| | - Stéphanie Vasseur
- Department of Genetics, Normandy Center for Genomic and Personalized Medicine, UNIROUEN, Inserm U1245 and Rouen University Hospital, CHU Rouen, Normandie University, 76000, Rouen, France
| | - Pierre Macquère
- Department of Genetics, Normandy Center for Genomic and Personalized Medicine, UNIROUEN, Inserm U1245 and Rouen University Hospital, CHU Rouen, Normandie University, 76000, Rouen, France
| | - Gaëlle Bougeard
- Department of Genetics, Normandy Center for Genomic and Personalized Medicine, UNIROUEN, Inserm U1245 and Rouen University Hospital, CHU Rouen, Normandie University, 76000, Rouen, France
| | - Laurence Faivre
- Centre de Référence Maladies Rares, «Anomalies du Développement ET Syndromes Malformatifs», Centre de Génétique, FHU-TRANSLAD et Institut GIMI, 77908, Dijon, France.,UMR 1231 GAD, Inserm - Université Bourgogne-Franche Comté, 77908, Dijon, France
| | - Olivier Ingster
- Department of Genetics, University Hospital Centre Angers, Angers, Pays de la Loire, France
| | - Stéphanie Baert-Desurmont
- Department of Genetics, Normandy Center for Genomic and Personalized Medicine, UNIROUEN, Inserm U1245 and Rouen University Hospital, CHU Rouen, Normandie University, 76000, Rouen, France
| | - Claude Houdayer
- Department of Genetics, Normandy Center for Genomic and Personalized Medicine, UNIROUEN, Inserm U1245 and Rouen University Hospital, CHU Rouen, Normandie University, 76000, Rouen, France
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Damián A, Ionescu RO, Rodríguez de Alba M, Tamayo A, Trujillo-Tiebas MJ, Cotarelo-Pérez MC, Pérez Rodríguez O, Villaverde C, de la Fuente L, Romero R, Núñez-Moreno G, Mínguez P, Ayuso C, Cortón M. Fine Breakpoint Mapping by Genome Sequencing Reveals the First Large X Inversion Disrupting the NHS Gene in a Patient with Syndromic Cataracts. Int J Mol Sci 2021; 22:ijms222312713. [PMID: 34884523 PMCID: PMC8657747 DOI: 10.3390/ijms222312713] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/17/2021] [Accepted: 11/19/2021] [Indexed: 11/16/2022] Open
Abstract
Inversions are structural variants that are generally balanced. However, they could lead to gene disruptions or have positional effects leading to diseases. Mutations in the NHS gene cause Nance-Horan syndrome, an X-linked disorder characterised by congenital cataracts and dental anomalies. Here, we aimed to characterise a balanced pericentric inversion X(p22q27), maternally inherited, in a child with syndromic bilateral cataracts by breakpoint mapping using whole-genome sequencing (WGS). 30× Illumina paired-end WGS was performed in the proband, and breakpoints were confirmed by Sanger sequencing. EdU assays and FISH analysis were used to assess skewed X-inactivation patterns. RNA expression of involved genes in the breakpoint boundaries was evaluated by droplet-digital PCR. We defined the breakpoint position of the inversion at Xp22.13, with a 15 bp deletion, disrupting the unusually large intron 1 of the canonical NHS isoform, and also perturbing topologically-associated domains (TADs). Moreover, a microhomology region of 5 bp was found on both sides. RNA analysis confirmed null and reduced NHS expression in the proband and his unaffected mother, respectively. In conclusion, we report the first chromosomal inversion disrupting NHS, fine-mapped by WGS. Our data expand the clinical spectrum and the pathogenic mechanisms underlying the NHS defects.
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Affiliation(s)
- Alejandra Damián
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (A.D.); (M.R.d.A.); (A.T.); (M.J.T.-T); (C.V.); (L.d.l.F.); (R.R.); (G.N.-M); (P.M.); (C.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 28290 Madrid, Spain
| | - Raluca Oancea Ionescu
- Department of Medical Genetics, University Hospital Clínico San Carlos, 28040 Madrid, Spain; (R.O.I.); (M.C.C.P.)
| | - Marta Rodríguez de Alba
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (A.D.); (M.R.d.A.); (A.T.); (M.J.T.-T); (C.V.); (L.d.l.F.); (R.R.); (G.N.-M); (P.M.); (C.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 28290 Madrid, Spain
| | - Alejandra Tamayo
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (A.D.); (M.R.d.A.); (A.T.); (M.J.T.-T); (C.V.); (L.d.l.F.); (R.R.); (G.N.-M); (P.M.); (C.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 28290 Madrid, Spain
| | - María José Trujillo-Tiebas
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (A.D.); (M.R.d.A.); (A.T.); (M.J.T.-T); (C.V.); (L.d.l.F.); (R.R.); (G.N.-M); (P.M.); (C.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 28290 Madrid, Spain
| | - María Carmen Cotarelo-Pérez
- Department of Medical Genetics, University Hospital Clínico San Carlos, 28040 Madrid, Spain; (R.O.I.); (M.C.C.P.)
| | - Olga Pérez Rodríguez
- Department of Pediatrics, University Hospital Clínico San Carlos, 28040 Madrid, Spain;
| | - Cristina Villaverde
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (A.D.); (M.R.d.A.); (A.T.); (M.J.T.-T); (C.V.); (L.d.l.F.); (R.R.); (G.N.-M); (P.M.); (C.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 28290 Madrid, Spain
| | - Lorena de la Fuente
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (A.D.); (M.R.d.A.); (A.T.); (M.J.T.-T); (C.V.); (L.d.l.F.); (R.R.); (G.N.-M); (P.M.); (C.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 28290 Madrid, Spain
- Bioinformatics Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040, Madrid, Spain
| | - Raquel Romero
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (A.D.); (M.R.d.A.); (A.T.); (M.J.T.-T); (C.V.); (L.d.l.F.); (R.R.); (G.N.-M); (P.M.); (C.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 28290 Madrid, Spain
| | - Gonzalo Núñez-Moreno
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (A.D.); (M.R.d.A.); (A.T.); (M.J.T.-T); (C.V.); (L.d.l.F.); (R.R.); (G.N.-M); (P.M.); (C.A.)
- Bioinformatics Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040, Madrid, Spain
| | - Pablo Mínguez
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (A.D.); (M.R.d.A.); (A.T.); (M.J.T.-T); (C.V.); (L.d.l.F.); (R.R.); (G.N.-M); (P.M.); (C.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 28290 Madrid, Spain
- Bioinformatics Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040, Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (A.D.); (M.R.d.A.); (A.T.); (M.J.T.-T); (C.V.); (L.d.l.F.); (R.R.); (G.N.-M); (P.M.); (C.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 28290 Madrid, Spain
| | - Marta Cortón
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (A.D.); (M.R.d.A.); (A.T.); (M.J.T.-T); (C.V.); (L.d.l.F.); (R.R.); (G.N.-M); (P.M.); (C.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 28290 Madrid, Spain
- Correspondence:
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