Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content

Nathan M Springer,Patrick S Schnable,Heidi Rosenbaum,Dan Nettleton,Wei Wu,Yan Fu,Cheng-Ting Yeh,Jeffrey A Jeddeloh,Yi Jia,Tieming Ji,A Leonardo Iniguez,W Brad Barbazuk,Todd Richmond,Jacob Kitzman,Kai Ying

doi:10.1371/journal.pgen.1000734

Nathan M Springer, Patrick S Schnable + Show 13 more

Open Access

https://doi.org/10.1371/journal.pgen.1000734

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Abstract

Following the domestication of maize over the past ∼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.

Highlights

Many analyses of genetic variation have focused on single nucleotide polymorphisms (SNPs), there is a growing appreciation for the roles of structural variation as a cause for phenotypic variation [1,2,3,4,5,6,7]
The maize genome exhibits extraordinarily high levels of genetic diversity as assayed at the level of SNPs, InDel Polymorphisms (IDPs), and structural variation [9,12]
Probes range in sizes from 45–85 bp were selected using slightly relaxed criteria relative to those traditionally used for comparative genomic hybridization (CGH) probe design

Summary

Introduction

Many analyses of genetic variation have focused on single nucleotide polymorphisms (SNPs), there is a growing appreciation for the roles of structural variation as a cause for phenotypic variation [1,2,3,4,5,6,7]. The maize genome exhibits extraordinarily high levels of genetic diversity as assayed at the level of SNPs, InDel Polymorphisms (IDPs), and structural variation [9,12]. B73 and Mo17 contain an IDP every ,300 bp and SNPs every ,80 bp [13,14] and within transcripts SNPs are found between the inbred lines B73 and Mo17 on average every 300 bp [15] These levels of diversity are not limited to comparisons between B73 and Mo17. When comparing any two randomly chosen maize inbred lines, there is, on average, one polymorphism every 100 bp [16,17] These studies indicate that maize has relatively high levels of SNPs and IDPs as compared to many other species [9]

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