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Kaspersky U, Levy R, Nashef A, Iraqi FA, Gabet Y. A study of the influence of genetic variance and sex on the density and thickness of the calvarial bone in collaborative cross mice. Animal Model Exp Med 2023; 6:355-361. [PMID: 37448168 PMCID: PMC10486330 DOI: 10.1002/ame2.12319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 03/13/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND Bone microarchitecture is affected by multiple genes, each having a small effect on the external appearance. It is thus challenging to characterize the genes and their specific effect on bone thickness and porosity. The purpose of this study was to assess the heritability and the genetic variation effect, as well as the sex effect on the calvarial bone thickness (Ca.Th) and calvarial porosity (%PoV) using the Collaborative Cross (CC) mouse population. METHODS In the study we examined the parietal bones of 56 mice from 9 lines of CC mice. Morphometric parameters were evaluated using microcomputed tomography (μCT) and included Ca.Th and %PoV. We then evaluated heritability, genetic versus environmental variance and the sex effect for these parameters. RESULTS Our morphometric analysis showed that Ca.Th and %PoV are both significantly different among the CC lines with a broad sense heritability of 0.78 and 0.90, respectively. The sex effect within the lines was significant in line IL111 and showed higher values of Ca.Th and %PoV in females compared to males. In line IL19 there was a borderline sex effect in Ca.Th in which males showed higher values than females. CONCLUSIONS These results stress the complexity of sex and genotype interactions controlling Ca.Th and %PoV, as the skeletal sexual dimorphism was dependent on the genetic background. This study also shows that the CC population is a powerful tool for establishing the genetic effect on these traits.
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Affiliation(s)
- Uriel Kaspersky
- Department of Anatomy and AnthropologyTel Aviv UniversityTel AvivIsrael
| | - Roei Levy
- Department of Anatomy and AnthropologyTel Aviv UniversityTel AvivIsrael
| | - Aysar Nashef
- Department of Clinical Microbiology and Immunology, Sackler Faculty of MedicineTel Aviv UniversityTel Aviv69978Israel
- Department of Oral and Maxillofacial SurgeryBaruch Padeh medical centerPoriyaIsrael
| | - Fuad A. Iraqi
- Department of Clinical Microbiology and Immunology, Sackler Faculty of MedicineTel Aviv UniversityTel Aviv69978Israel
| | - Yankel Gabet
- Department of Anatomy and AnthropologyTel Aviv UniversityTel AvivIsrael
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Page R, Huang S, Ronen M, Sela H, Sharon A, Shrestha S, Poland J, Steffenson BJ. Genome-wide association mapping of rust resistance in Aegilops longissima. Front Plant Sci 2023; 14:1196486. [PMID: 37575932 PMCID: PMC10413114 DOI: 10.3389/fpls.2023.1196486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/30/2023] [Indexed: 08/15/2023]
Abstract
The rust diseases, including leaf rust caused by Puccinia triticina (Pt), stem rust caused by P. graminis f. sp. tritici (Pgt), and stripe rust caused by P. striiformis f. sp. tritici (Pst), are major limiting factors in wheat production worldwide. Identification of novel sources of rust resistance genes is key to developing cultivars resistant to rapidly evolving pathogen populations. Aegilops longissima is a diploid wild grass native to the Levant and closely related to the modern bread wheat D subgenome. To explore resistance genes in the species, we evaluated a large panel of Ae. longissima for resistance to several races of Pt, Pgt, and Pst, and conducted a genome-wide association study (GWAS) to map rust resistance loci in the species. A panel of 404 Ae. longissima accessions, mostly collected from Israel, were screened for seedling-stage resistance to four races of Pt, four races of Pgt, and three races of Pst. Out of the 404 accessions screened, two were found that were resistant to all 11 races of the three rust pathogens screened. The percentage of all accessions screened that were resistant to a given rust pathogen race ranged from 18.5% to 99.7%. Genotyping-by-sequencing (GBS) was performed on 381 accessions of the Ae. longissima panel, wherein 125,343 single nucleotide polymorphisms (SNPs) were obtained after alignment to the Ae. longissima reference genome assembly and quality control filtering. Genetic diversity analysis revealed the presence of two distinct subpopulations, which followed a geographic pattern of a northern and a southern subpopulation. Association mapping was performed in the genotyped portion of the collection (n = 381) and in each subpopulation (n = 204 and 174) independently via a single-locus mixed-linear model, and two multi-locus models, FarmCPU, and BLINK. A large number (195) of markers were significantly associated with resistance to at least one of 10 rust pathogen races evaluated, nine of which are key candidate markers for further investigation due to their detection via multiple models and/or their association with resistance to more than one pathogen race. The novel resistance loci identified will provide additional diversity available for use in wheat breeding.
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Affiliation(s)
- Rae Page
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
| | - Shuyi Huang
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
| | - Moshe Ronen
- Institute for Cereal Crops Research, Tel Aviv University, Tel Aviv, Israel
| | - Hanan Sela
- Institute for Cereal Crops Research, Tel Aviv University, Tel Aviv, Israel
| | - Amir Sharon
- Institute for Cereal Crops Research, Tel Aviv University, Tel Aviv, Israel
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Sandesh Shrestha
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Jesse Poland
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- KAUST Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Brian J. Steffenson
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
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Avni R, Lux T, Minz‐Dub A, Millet E, Sela H, Distelfeld A, Deek J, Yu G, Steuernagel B, Pozniak C, Ens J, Gundlach H, Mayer KFX, Himmelbach A, Stein N, Mascher M, Spannagl M, Wulff BBH, Sharon A. Genome sequences of three Aegilops species of the section Sitopsis reveal phylogenetic relationships and provide resources for wheat improvement. Plant J 2022; 110:179-192. [PMID: 34997796 PMCID: PMC10138734 DOI: 10.1111/tpj.15664] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/21/2021] [Accepted: 01/03/2022] [Indexed: 05/20/2023]
Abstract
Aegilops is a close relative of wheat (Triticum spp.), and Aegilops species in the section Sitopsis represent a rich reservoir of genetic diversity for the improvement of wheat. To understand their diversity and advance their utilization, we produced whole-genome assemblies of Aegilops longissima and Aegilops speltoides. Whole-genome comparative analysis, along with the recently sequenced Aegilops sharonensis genome, showed that the Ae. longissima and Ae. sharonensis genomes are highly similar and are most closely related to the wheat D subgenome. By contrast, the Ae. speltoides genome is more closely related to the B subgenome. Haplotype block analysis supported the idea that Ae. speltoides genome is closest to the wheat B subgenome, and highlighted variable and similar genomic regions between the three Aegilops species and wheat. Genome-wide analysis of nucleotide-binding leucine-rich repeat (NLR) genes revealed species-specific and lineage-specific NLR genes and variants, demonstrating the potential of Aegilops genomes for wheat improvement.
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Affiliation(s)
- Raz Avni
- Wise Faculty of Life Sciences, Institute for Cereal Crops Improvement and School of Plant Sciences and Food SecurityTel Aviv UniversityTel Aviv6997801Israel
- Present address: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenCorrensstrasse 3Seeland06466Germany
| | - Thomas Lux
- Plant Genome and Systems Biology (PGSB)Helmholtz‐Center MunichIngolstädter Landstraße 1NeuherbergD‐85764Germany
| | - Anna Minz‐Dub
- Wise Faculty of Life Sciences, Institute for Cereal Crops ImprovementTel Aviv UniversityTel Aviv6997801Israel
| | - Eitan Millet
- Wise Faculty of Life Sciences, Institute for Cereal Crops ImprovementTel Aviv UniversityTel Aviv6997801Israel
| | - Hanan Sela
- Wise Faculty of Life Sciences, Institute for Cereal Crops Improvement and School of Plant Sciences and Food SecurityTel Aviv UniversityTel Aviv6997801Israel
- Present address: Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, Institute of EvolutionUniversity of Haifa199 Aba Khoushy Ave., Mount CarmelHaifa3498838Israel
| | - Assaf Distelfeld
- Wise Faculty of Life Sciences, Institute for Cereal Crops Improvement and School of Plant Sciences and Food SecurityTel Aviv UniversityTel Aviv6997801Israel
- Present address: Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, Institute of EvolutionUniversity of Haifa199 Aba Khoushy Ave., Mount CarmelHaifa3498838Israel
| | - Jasline Deek
- Wise Faculty of Life Sciences, Institute for Cereal Crops Improvement and School of Plant Sciences and Food SecurityTel Aviv UniversityTel Aviv6997801Israel
| | - Guotai Yu
- John Innes CentreNorwich Research ParkNorwichNR4 7UHUK
- Present address: Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)Thuwal23955‐6900Saudi Arabia
| | | | - Curtis Pozniak
- Department of Plant Sciences and Crop Development Centre, College of Agriculture and BioresourcesUniversity of SaskatchewanCampus Drive 51SaskatoonS7N 5A8Canada
| | - Jennifer Ens
- Department of Plant Sciences and Crop Development Centre, College of Agriculture and BioresourcesUniversity of SaskatchewanCampus Drive 51SaskatoonS7N 5A8Canada
| | - Heidrun Gundlach
- Plant Genome and Systems Biology (PGSB)Helmholtz‐Center MunichIngolstädter Landstraße 1NeuherbergD‐85764Germany
| | - Klaus F. X. Mayer
- Plant Genome and Systems Biology (PGSB)Helmholtz‐Center MunichIngolstädter Landstraße 1NeuherbergD‐85764Germany
- Faculty of Life SciencesTechnical University MunichWeihenstephanMunichD‐80333Germany
| | - Axel Himmelbach
- Center of Integrated Breeding Research (CiBreed), Department of Crop SciencesGeorg‐August‐UniversityVon Siebold Str. 8Göttingen37075Germany
| | - Nils Stein
- Center of Integrated Breeding Research (CiBreed), Department of Crop SciencesGeorg‐August‐UniversityVon Siebold Str. 8Göttingen37075Germany
- Leibniz‐Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenCorrensstrasse 3Seeland06466Germany
| | - Martin Mascher
- Leibniz‐Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenCorrensstrasse 3Seeland06466Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigPuschstrasse 4LeipzigD‐04103Germany
| | - Manuel Spannagl
- Plant Genome and Systems Biology (PGSB)Helmholtz‐Center MunichIngolstädter Landstraße 1NeuherbergD‐85764Germany
| | - Brande B. H. Wulff
- John Innes CentreNorwich Research ParkNorwichNR4 7UHUK
- Present address: Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)Thuwal23955‐6900Saudi Arabia
| | - Amir Sharon
- Wise Faculty of Life Sciences, Institute for Cereal Crops Improvement and School of Plant Sciences and Food SecurityTel Aviv UniversityTel Aviv6997801Israel
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