Physical and Genetic Structure of the Maize Genome Reflects Its Complex Evolutionary History

Abstract

Maize (Zea mays L.) is one of the most important cereal crops and a model for the study of genetics, evolution, and domestication. To better understand maize genome organization and to build a framework for genome sequencing, we constructed a sequence-ready fingerprinted contig-based physical map that covers 93.5% of the genome, of which 86.1% is aligned to the genetic map. The fingerprinted contig map contains 25,908 genic markers that enabled us to align nearly 73% of the anchored maize genome to the rice genome. The distribution pattern of expressed sequence tags correlates to that of recombination. In collinear regions, 1 kb in rice corresponds to an average of 3.2 kb in maize, yet maize has a 6-fold genome size expansion. This can be explained by the fact that most rice regions correspond to two regions in maize as a result of its recent polyploid origin. Inversions account for the majority of chromosome structural variations during subsequent maize diploidization. We also find clear evidence of ancient genome duplication predating the divergence of the progenitors of maize and rice. Reconstructing the paleoethnobotany of the maize genome indicates that the progenitors of modern maize contained ten chromosomes.

Paired-end sequencing of Fosmid libraries by Illumina

“…While Fosill appears to work for the extremely GC-rich (69%) genome of Rhodobacter sphaeroides (not shown), we expect cloning problems for extremely AT-rich DNA from organisms such as Dictyostelium discoideum or Plasmodium falciparum that proved recalcitrant to cloning as Fosmids or BACs in the past (Gardner et al 2002;Eichinger et al 2005). Nonetheless, we note that numerous large-insert clone libraries have been made that were sufficiently deep, unbiased, and comprehensive to support successful and high-profile genome projects (Osoegawa et al 2000(Osoegawa et al , 2001Wei et al 2007) and that sequencing libraries constructed without cloning have biases of their own (Dohm et al 2008;Kozarewa et al 2009;Aird et al 2011).…”

Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor

“…Many of the remaining CNV/PAV genes that did have annotations and/or orthologs are present in gene families that include members at syntenic positions or within paralogous clusters. The maize genome, which arose from an ancient allopolyploidization event (Gaut and Doebley 1997;Swigonova et al 2005;Wei et al 2007), has many gene families with a very high level of redundancy. Gene losses within these gene families may be tolerated if they result in only minor differences in phenotype or Figure 4.…”

“…The recent completion of a reference genome from one genotype, B73, affords the opportunity to assess structural variation and complexity within this species ). Detailed analyses of specific loci as well as genomic approaches have identified numerous duplications within the maize genome, many of which are located in colinear regions ) derived from an ancient allopolyploidization event (Gaut and Doebley 1997;Swigonova et al 2005;Wei et al 2007). There is also evidence for a high frequency of tandem duplicates within maize (Messing et al 2004;Emrich et al 2007;Schnable et al 2009), including several well-characterized genes affecting pigmentation such as R-r (Robbins et al 1991), P1 (Zhang and Peterson 2005), and A1-b (Yandeau- Nelson et al 2006).…”

The origin and evolution of maize and its introduction into South-Eastern Europe

“…U ovim studijama identifikovani su kandidati geni za određene osobine: tb1 -gen za razgranatost teozinte, tga1 -gen odgovoran za arhitekturu plevica teozinte. Wei et al (2007) navode da je kukuruz, kao gajena vrsta i kao model biološkog sistema za proučavanja genetike, evolucije i domestifikacije žitarica od najvećeg javnog interesa. Iako genom kukuruza u osnovi predstavlja jednostavan diploid sa 10 parova hromozoma, njegova organizacija je veoma kompleksna.…”