Genome Diversity in Maize

Abstract

Zea mays (maize) has historically been used as a model species for genetics, development, physiology and more recently, genome structure. The maize genome is complex with striking intraspecific variation in gene order, repetitive DNA content, and allelic content exceeding the levels observed between primate species. Maize genome complexity is primarily driven by polyploidization and explosive amplification of LTR retrotransposons, with the counteracting effect of unequal and illegitimate crossover. Transposable elements have been shown to capture genic content, create chimeras, and amplify those sequences via transposition. New sequencing platforms and hybridization-based strategies have appeared over the past decade which are being applied to maize and providing the first genome-wide comprehensive view of structural variation and will provide the basis for investigating the interplay between repeats and genes as well as the amount of species level diversity within maize.

Evolutionary analysis of plant jacalin-related lectins (JRLs) family and expression of rice JRLs in response to Magnaporthe oryzae

“…For rice and maize, both of which have polyploid origin, whole-genome duplication occurred in the common rice and maize ancestor (at 70-80mya) followed by genome diploidization (including some loss of duplicated genes) before the divergence of rice-maize (at 50 mya) from the polyploid ancestor (Gaut et al 1997;Paterson et al 2004;Wang et al 2005b;Llaca et al 2011). The genome contraction most probably has continued further in the maize line and removed more duplicated genes, during at least two more polyploidization-contraction events (Paterson et al 2004;Llaca et al 2011), while in rice more of the originally duplicated genes were retained instead of diversifying to gain new functions. Ancient polyploidization and subsequent diploidization (loss) of many duplicated gene copies have shaped the genomes of all Poaceae cereal, forage, and biomass crops.…”

Strategies for Sequence Assembly of Plant Genomes

“…Finally, most plant genomes are characterized by elevated proportions of highly repetitive DNA and by the presence of segmental duplications or full genome duplications due to polyploidization events [38], which can be problematic during assembly. The 1C genome content in Maize, for example, is smaller than in humans but it consists of higher proportions and larger tracks of high-copy elements such as retrotransposable elements [29,38]. At least some of the differences between the assembled and estimated genomes of the Maize line B73 could be attributed to the assembly-based collapse of highly similar long terminal repeats (LTRs) at the end of retrotransposons.…”

Genotyping-by-Sequencing in Plants

“…Furthermore, the significant sequence diversity and the high structural polymorphism observed in important plant models such as maize imposes a challenge to these knowledge-based platforms. Structural genome differences, including translocations, copy number variation and presence-absence variation are observed in landraces and lines in the same species and correspond to differences in repetitive, non-coding DNA and gene content [ 48 , 49 ]. There is an inherent bias towards cultivars used as reference in genome projects.…”