The B73 Maize Genome

-Complexity, Diversity, and Dynamics

Carlos
Carlos Linares,
Linares, Joshua
Joshua Garmizo,
Garmizo, Jauregui
Jauregui Lilibeth,
Lilibeth, Lauren
Lauren Sanborn,
Sanborn, Jovana
Jovana Obradovic
Obradovic

Diagrams

BACKGROUND
Maize
-Domesticated over approx. the past 10,000 years
-Originated in Central America
-Has undergone continuous cultivation and selection
-Hence, it a model organism for genetic studies

CONCLUSION/DISCUSSION
Maize B73 Reference Genome and Gene Families
Fig 3. Taken from Anderson et al.
2006 A Model depicting highest gene
density at the ends of chromosomes,
lowest surrounding the centromeres
supporting meiotic rates of
recombination

Maize as a Model Organism

-Inheritance & function of genes
-Physical linkage between genes and chromosomes
-Relationship between cytological crossover & recombination
-Origin of nucleolus -Telomeres -Epigenetic splicing
-Genomic Imprinting -Transposons

Whats the significance of this?

-Maize has been manipulated to maximize yield and cater to the
tastes of people in a given region, which is important from a
genetic standpoint
-Cultivating maize at such large quantities and actively
selecting favorable traits alters its genome
-Great genome expansion over the years
expanded dramatically (to 2.3 gigabases) over the last ~3
million years via a proliferation of long terminal repeat
retrotransposons
B73 RefGen_v1 Maize
-Almost 85% of the B73 genome consists of transposable elements
-Existence and high abundance of LTR retrotransposons in plants
originally discovered in maize
-Made up of 855 families of DNA transposable elements that make up
8.6% of the genome

METHODS

the human genome, the maize genome ( 2.3

gigabases) ranks among the largest plant
genomes that have been sequenced. The size of
the maize genome was achieved via a
proliferation of long terminal repeat(LTR)
retrotransposons over the last 3 million years.

Although TEs are a major component of all

studied plant genomes, and are the most
significant contributors to their genome structure
and evolution, their properties and reasons for
existence are not well understood. In this study,
over 32,000 genes were predicted, of which 99.8%
were placed on reference chromosomes.

Maize: A Staple Crop

In USA
-12 billion bushels of grain/yr
-86 million acres of land
-Value = $47 billion/yr

With a size approximating that of

Fig. 1.Reference chromosome showing

contigs, recombination rate, Mu insertions,
MF enrichment, repeat coverage and gene
density, along with rice and sorghum syntenies.

Comprehensive sequence analysis of the maize

RESULTS
Utilizing BACS and whole genome shotgun sequencing, B73 reference genome version 1
found to be 85% transposable elements consisting of 855 families
Majority LTR retrotransposons exhibiting family-specific, non uniform distributions along the
chromosome
Most complex is Mutator (Mu) family, insertion sites colocalize with gene rich regions that
have highest rates of meiotic recombination, also correlate with poorly methylated regions
8 families of Helitrons that are uniquely active within gene rich regions

Utilizing BACS and whole genome shotgun sequencing, B73 reference genome version 1
found to be 85% transposable elements consisting of 855 families
Majority LTR retrotransposons exhibiting family-specific, non uniform distributions along
the chromosome
Most complex is Mutator (Mu) family, insertion sites colocalize with gene rich regions that
have highest rates of
meiotic recombination, also correlate with poorly methylated
regions
8 families of Helitrons that are uniquely active within gene rich regions

Total of 32, 540 protein encoding genes and 150 microRNA genes predicted from assembled
BAC contig

Total of 32, 540 protein encoding genes and 150 microRNA genes predicted from
assembled BAC contig

Core set of 8,494 families shared between maize, rice, sorghum, and Arabidopsis
Exon sizes similar but maizes introns larger due to repeating units
Rice and sorghum genomes helped define maizes duplicate regions
Effective due to resemblance to maizes ancestral subgenomes and low numbers of
interchromosomal rearrangement since the lineage split
Genes retained as duplicates significantly enriched for transcription factors

Core set of 8,494 families shared between maize, rice, sorghum, and Arabidopsis
Exon sizes similar but maizes introns larger due to repeating units
Rice and sorghum genomes helped define maizes duplicate regions
Effective due to resemblance to maizes ancestral subgenomes and low numbers of
interchromosomal rearrangement since the lineage split
Genes retained as duplicates significantly enriched for transcription factors

Unlike most plant genomes, around 95% of genes are methylated and these regions are
heavily condensed during interphase, poorly methylated regions correlate with Mu insertions

Unlike most plant genomes, around 95% of genes are methylated and these regions are
heavily condensed during interphase, poorly methylated regions correlate with Mu
insertions
P < .007

P < .027

Maize centromeres, delineated on the basis of their centromere-specific histone H3,

contained variable amounts of tandem CentC satellite repeat and centromeric retrotransposon
elements (CRMS)
Regional centromeres are dynamic loci causing centromere-specific histone H3 domains shift
over time as a result of recombinants created by CRMs

Maize centromeres, delineated on the basis of their centromere-specific histone H3,

contained variable amounts of tandem CentC satellite repeat and centromeric
retrotransposon elements (CRMS)
Regional centromeres are dynamic loci causing centromere-specific histone H3 domains
shift over time as a result of recombinants created by CRMs

Epigenetic marks, such as hypomethylation and histone modifications, guide rates of meiotic
recombination
Rates highest at the ends of reference chromosomes and low in the regions surrounding the
centromere corresponding to pattern of gene density
Also key to the contribution of genomic imprinting on gene expression in maize hybrids

Epigenetic marks, such as hypomethylation and histone modifications, guide rates of

meiotic recombination
Rates highest at the ends of reference chromosomes and low in the regions surrounding
the centromere corresponding to pattern of gene density
Also key to the contribution of genomic imprinting on gene expression in maize hybrids

Uneven gene losses between duplicated regions, associated with many chromosomal breaks
and fusions, involved in returning to a diploid state from ancient allotetraploid

Uneven gene losses between duplicated regions, associated with many chromosomal
breaks and fusions, involved in returning to a diploid state from ancient allotetraploid

genome now permits detailed discovery and

description of transposable elements (TEs) in this
complex nuclear environment.

Regions of the genome with the highest LTR

retrotransposon density contained the lowest LTR
retrotransposon diversity. These results indicate
that the maize genome provides a great number
of different niches for the survival and
procreation of a great variety of retroelements
that have evolved to differentially occupy and
exploit this genomic diversity.

Furthermore, Helitrons in maize seem to

continually produce new nonautonomous
elements responsible for the duplicative insertion
of gene segments into new locations and for the
innovative genic diversity.

The finding that Mu insertions and meiotic

recombination sites both concentrate in genomic
regions marked with epigenetic marks of open
chromatin provides support for the hypothesis
that open chromatin enhances rates of
both Mu insertion and meiotic recombination.

The B73 maize reference sequence promises to

advance basic research and to facilitate efforts to
meet the worlds growing needs for food, feed,
energy, and industrial feed stocks in an era of
global climate change.
* References available upon request

1. L. K. Anderson, A. Lai, S. M. Stack, C.

Rizzon, B. S. Gaut, "Uneven distribution of
expressed sequence tag loci on maize
pachytene chromosomes," Genome
Research 16, 115 (2006).
2. P. S. Schnable et al., "The B73 Maize
Genome: Complexity, Diversity, and
Dynamics," Science 326, 1112 (2009).