Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content
Following the domestication of maize over the past approximately 10,000 years, breeders have exploited the extensive genetic diversity of this species to mold its phenotype to meet human needs. The extent of structural variation, including copy number variation (CNV) and presence/absence variation (...
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| creator | Springer, Nathan M Ying, Kai Fu, Yan Ji, Tieming Yeh, Cheng-Ting Jia, Yi Wu, Wei Richmond, Todd Kitzman, Jacob Rosenbaum, Heidi Iniguez, A Leonardo Barbazuk, W Brad Jeddeloh, Jeffrey A Nettleton, Daniel Schnable, Patrick S |
| description | Following the domestication of maize over the past approximately 10,000 years, breeders have exploited the extensive genetic diversity of this species to mold its phenotype to meet human needs. The extent of structural variation, including copy number variation (CNV) and presence/absence variation (PAV), which are thought to contribute to the extraordinary phenotypic diversity and plasticity of this important crop, have not been elucidated. Whole-genome, array-based, comparative genomic hybridization (CGH) revealed a level of structural diversity between the inbred lines B73 and Mo17 that is unprecedented among higher eukaryotes. A detailed analysis of altered segments of DNA conservatively estimates that there are several hundred CNV sequences among the two genotypes, as well as several thousand PAV sequences that are present in B73 but not Mo17. Haplotype-specific PAVs contain hundreds of single-copy, expressed genes that may contribute to heterosis and to the extraordinary phenotypic diversity of this important crop. |
| doi_str_mv | 10.1371/journal.pgen.1000734 |
| format | Article |
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The extent of structural variation, including copy number variation (CNV) and presence/absence variation (PAV), which are thought to contribute to the extraordinary phenotypic diversity and plasticity of this important crop, have not been elucidated. Whole-genome, array-based, comparative genomic hybridization (CGH) revealed a level of structural diversity between the inbred lines B73 and Mo17 that is unprecedented among higher eukaryotes. A detailed analysis of altered segments of DNA conservatively estimates that there are several hundred CNV sequences among the two genotypes, as well as several thousand PAV sequences that are present in B73 but not Mo17. Haplotype-specific PAVs contain hundreds of single-copy, expressed genes that may contribute to heterosis and to the extraordinary phenotypic diversity of this important crop.</description><identifier>ISSN: 1553-7404</identifier><identifier>ISSN: 1553-7390</identifier><identifier>EISSN: 1553-7404</identifier><identifier>DOI: 10.1371/journal.pgen.1000734</identifier><identifier>PMID: 19956538</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Base Sequence ; Corn ; Crops, Agricultural - genetics ; Cytogenetics ; Deoxyribonucleic acid ; DNA ; Exhibitions ; Gene Dosage ; Genes ; Genes, Plant ; Genetic diversity ; Genetic Variation ; Genetics and Genomics/Comparative Genomics ; Genetics and Genomics/Plant Genetics and Gene Expression ; Genetics and Genomics/Plant Genomes and Evolution ; Genome, Plant ; Genomics ; Genotype ; Haplotypes ; Inbreeding ; Sequence Deletion ; Single nucleotide polymorphisms ; Zea mays ; Zea mays - genetics</subject><ispartof>PLoS genetics, 2009-11, Vol.5 (11), p.e1000734-e1000734</ispartof><rights>COPYRIGHT 2009 Public Library of Science</rights><rights>Springer et al. 2009</rights><rights>2009 Springer et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Springer NM, Ying K, Fu Y, Ji T, Yeh C-T, et al. (2009) Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content. 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The extent of structural variation, including copy number variation (CNV) and presence/absence variation (PAV), which are thought to contribute to the extraordinary phenotypic diversity and plasticity of this important crop, have not been elucidated. Whole-genome, array-based, comparative genomic hybridization (CGH) revealed a level of structural diversity between the inbred lines B73 and Mo17 that is unprecedented among higher eukaryotes. A detailed analysis of altered segments of DNA conservatively estimates that there are several hundred CNV sequences among the two genotypes, as well as several thousand PAV sequences that are present in B73 but not Mo17. Haplotype-specific PAVs contain hundreds of single-copy, expressed genes that may contribute to heterosis and to the extraordinary phenotypic diversity of this important crop.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>19956538</pmid><doi>10.1371/journal.pgen.1000734</doi><oa>free_for_read</oa></addata></record> |
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| subjects | Base Sequence Corn Crops, Agricultural - genetics Cytogenetics Deoxyribonucleic acid DNA Exhibitions Gene Dosage Genes Genes, Plant Genetic diversity Genetic Variation Genetics and Genomics/Comparative Genomics Genetics and Genomics/Plant Genetics and Gene Expression Genetics and Genomics/Plant Genomes and Evolution Genome, Plant Genomics Genotype Haplotypes Inbreeding Sequence Deletion Single nucleotide polymorphisms Zea mays Zea mays - genetics |
| title | Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content |
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