The limited role of differential fractionation in genome content variation and function in maize (Zea mays L.) inbred lines.

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The Plant journal : for cell and molecular biology, ISSN: 1365-313X, Vol: 93, Issue: 1, Page: 131-141

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Alex B. Brohammer; Thomas J. Y. Kono; Nathan M. Springer; Suzanne E. McGaugh; Candice N. Hirsch
Biochemistry, Genetics and Molecular Biology; Agricultural and Biological Sciences
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article description
Maize is a diverse paleotetraploid species with considerable presence/absence variation and copy number variation. One mechanism through which presence/absence variation can arise is differential fractionation. Fractionation refers to the loss of duplicate gene pairs from one of the maize subgenomes during diploidization. Differential fractionation refers to non-shared gene loss events between individuals following a whole-genome duplication event. We investigated the prevalence of presence/absence variation resulting from differential fractionation in the syntenic portion of the genome using two whole-genome de novo assemblies of the inbred lines B73 and PH207. Between these two genomes, syntenic genes were highly conserved with less than 1% of syntenic genes being subject to differential fractionation. The few variably fractionated syntenic genes that were identified are unlikely to contribute to functional phenotypic variation, as there is a significant depletion of these genes in annotated gene sets. In further comparisons of 60 diverse inbred lines, non-syntenic genes were six times more likely to be variable than syntenic genes, suggesting that comparisons among additional genome assemblies are not likely to result in the discovery of large-scale presence/absence variation among syntenic genes.