c o rresp o n de n ce
sequence information (e.g., epitopes,
© 2011 Nature America, Inc. All rights reserved.
Even so, as Peccoud et al. point out, full
functional domains, genetic markers
or haplotypes) and their surrounding
sequence information as well as any RNA
interference, antisense or morpholino
probes used in a paper (http://www.
nature.com/authors/editorial_policies/
availability.html); there is no consensus
as yet that the sequence of every plasmid
used in every paper should be lodged
with GenBank or that such a policy would
be beneficial to the wider community.
Is transgenic maize what Mexico
really needs?
To the Editor:
In the past three years, substantial progress
has been made in updating knowledge on
the present diversity of maize landraces and
where these are still being grown within
the Mexican territory. Here, we summarize
some of these findings and briefly discuss
their implications in relation to maize
production and use in Mexico.
The term landrace was first described by
Anderson and Cutler1 as “a group of related
individuals with enough characteristics
in common to permit their recognition
as a group.” It refers to the varieties and
populations of native maize in Mexico
and has helped in the study of the genetic
diversity of the crop.
As part of the implementation of the
Biosafety Law—legislation that passed in
March 2005 requiring the definition of
both the areas of origin for crops native to
Mexico and their genetic diversity—the
Mexican government has been carrying out
a survey of maize landraces since 2006. The
program was financed with $1.5 million
from the Ministry of Agriculture,
Livestock, Rural Development, Fishery
and Food (SAGARPA), the Ministry of
Environment and Natural Resources
(SEMARNAT) and the Inter-Ministerial
Commission for Biosafety of Genetically
Modified Organisms (CIBIOGEM).
Some of the key findings of this survey
are as follows (for one of the results already
published in Spanish, see http://www.
biodiversidad.gob.mx/genes/origenDiv.html
and ref. 2): first, a large number of maize
landraces are currently being cultivated
very widely in Mexico; second, diversity
in maize landraces under cultivation is
superior to what was originally believed to
nature biotechnology volume 29 number 1 JANAURY 2011 23
genetic diversity that has been revealed
sequence information is often essential
to reproduce the findings reported in
papers in the area of synthetic biology.
As such, on a case-by-case basis, Nature
Biotechnology will encourage authors of
such papers to lodge the sequences of the
constructs used in a paper in GenBank
together with the corresponding accession
numbers.
1. Kemmer, C. et al. Nat. Biotechnol. 28, 355–360
(2010).
exist before the study started (in particular
for the northern states of Mexico); and
third, probable new maize landraces have
been identified, diversity is higher than
previously appreciated within landraces
(such as Tuxpeño, which is the number-one
provider of germplasm to most of the maize
known in commercial breeding), and new
teocintle (the most probable progenitor of
maize) populations have been identified.
Maize genetic diversity exists as a result
of the activities of small farm-holders
(their plots currently represent 86% of the
area where maize is cultivated in Mexico),
who generally plant maize for subsistence3
and depending on rainfall, permanently
experiment and exchange seeds, and have
designated many uses for the different
variants cultivated4,5. It is because of these
traditional agricultural practices that
Mexico preserves and enhances the many
different maize landraces we now know6,7.
The new data acquired about the
present number and distribution of maize
landraces underline, on the one hand, the
richness of genetic diversity of cultivars
and, on the other, the reasons Mexico
has for valuing and maintaining that
diversity for future breeding needs. It is
thus important that the very process by
which those landraces are generated and
maintained (that is, the practices of the
small farmers) is preserved.
Currently there is no commercial
production of transgenic maize in
Mexico; only experimental trials have
been approved. The question has been
raised as to how Mexico will manage the
commercialization of transgenic maize
together with meeting its responsability
of safeguarding the characteristics of the
in the recent study. Much debate, some
of it scientifically based, has taken place
about the risks and benefits of allowing
experimental trials of transgenic maize in
a center of genetic diversity for the same
crop. It is our opinion that some relevant
questions about the potential impacts of
transgenic maize on landraces have not
been addressed either in these discussions
or by experiments. For example, further
experimental work is required to establish
the potential for gene flow from transgenic
maize to landraces, measures for managing
this gene flow and the potential long-term
impact of gene flow on landraces.
If gene flow from transgenic maize to
landraces occurs, several other questions
arise. How will intellectual property
issues interact with the biological, social
and economic reality of small-farmer
agricultural practices that maintain and
keep generating new variability in maize
landraces in Mexico? What are the practical
consequences for a small subsistence
farmer cultivating native landraces of
maize and finding his crops contain genes
from transgenic plants? What is the legal
position of such a farmer and is he/she
likely to be infringing patents by cultivating
or exchanging (knowingly or not) seeds
that contain transgenes? What would be the
stance of agbiotech companies in pursuing
their intellectual property and licenses
in such situations? Such questions need
to be considered both at the small rural
community level and nationally.
There is also the broader issue of the
extent to which introduction of transgenic
maize will provide solutions to existing
problems for Mexican agriculture, such as
the migration of male peasants (especially
young people) to cities and abroad, an
increasingly older rural population, the
absence of effective mechanisms and
incentives to cultivate maize landraces in
a certified manner, weak market and grain
distribution arrangements, and increasingly
dominant patterns of food consumption
based on foreign models of fast foods.
Mexico does not yet have in place a working
and efficient mechanism for monitoring
cross-pollination and gene flow under local
agricultural conditions, despite claims that
this is being instituted8. Information is lacking
on the value that transgenic maize has for
Mexican farming systems and its management
requirements. Meanwhile, illegal transgenic
maize introductions have been documented,
and in some cases prosecuted, in Mexico.
Moreover, there are concerns about the
 c o rresp o n de n ce
introduction of transgenic maize developed
for pharmaceutical or other non-food
purposes, and its impact on landraces9,10.
Mexico needs to be able to define what kind
of transgenic materials (for maize and any
other relevant crop) it needs for its ecological,
social and economic requirements. This
responsibility must be carefully analyzed in
order to provide farmers with adequate and
necessary elements to help achieve a level of
food security for the present and future of
Mexican society, while conserving genetic
diversity and helping develop adequately the
social structures of the rural economy and
society.
COMPETING FINANCIAL INTERESTS
The authors declare no competing financial interests.
Disclaimer
The manuscript reflects only the opinion of the
© 2011 Nature America, Inc. All rights reserved.
authors and not the institution they represent.
Francisca Acevedo, Elleli Huerta,
Caroline Burgeff, Patricia Koleff &
José Sarukhán
Integrative genomics viewer
To the Editor:
Rapid improvements in sequencing
and array-based platforms are resulting
in a flood of diverse genome-wide
data, including data from exome and
whole-genome sequencing, epigenetic
surveys, expression profiling of coding
and noncoding RNAs, single nucleotide
polymorphism (SNP) and copy number
profiling, and functional assays. Analysis
Figure 1 Copy number, expression and mutation
data grouped by tumor subtype. This figure
illustrates an integrated, multi-modal view of
202 glioblastoma multiforme samples from The
Cancer Genome Atlas (TCGA). Copy number data
are segmented values from Affymetrix (Santa
Clara, CA, USA) SNP6.0 arrays. Expression
data are limited to genes represented on all
TCGA-employed platforms and displayed across
the entire gene locus. Red shading indicates
relative upregulation of a gene and the degree
of copy gain of a region; blue shading indicates
relative downregulation and copy loss. Small
black squares indicate the position of point
missense mutations. Samples are grouped by
tumor subtype (2nd annotation column) and data
type (1st sample annotation column) and sorted
by copy number of the EGFR locus. Linking
by sample attributes ensures that the order of
sample tracks is consistent across data types
within their respective tumor subtypes.
24 volume 29 number 1 JANAURY 2011 nature biotechnology
Comisión Nacional para el Conocimiento y Uso
de la Biodiversidad, México D.F., México.
e-mail: facevedo@conabio.gob.mx
1. Anderson, E. & Cutler, H.C. Ann. Mo. Bot. Gard. 29,
69–86 (1942).
2. Kato, T.A., Mapes, L.M., Mera, L.M., Serratos, J.A. &
Bye, R.A. Origen y Diversificación del Maíz: una Revisión
Analítica (Universidad Autónoma de México, Comisión
Nacional para el Conocimiento y Uso de la Biodiversidad,
México, D.F. (2009).
3. Bellón, M.R. & Brush, S.B. Econ. Bot. 48, 196–209
(1994).
4. Bellón, M.R. et al. Diversidad y Conservación de Recursos
Genéticos en Plantas Cultivadas, en Capital Natural de
México, vol. II: Estado de la Conservación y Tendencias
de Cambio. (CONABIO, México, 2009).
5. Bourges, H. in La Alimentación de los Mexicanos (eds.
Alarcón-Segovia, D. & Bourges, H.) 97–134 (El Colegio
Nacional, México D.F., 2002).
6. Hernández-Xolocotzi, E. Econ. Bot. 39, 416–430
(1985).
7. Pressoir, G. & Berthaud, J. Heredity 92, 88–94
(2004).
8. Dalton, R. Nature 462, 404 (2009).
9. Acevedo, F. Nat. Biotechnol. 22, 803 (2004).
10. Acevedo G.F. et al. La Bioseguridad en México y los
Organismos Genéticamente Modificados: Como Enfrentar
un Nuevo Desafío, en Capital Natural de México, vol.
II: Estado de la Conservación y Tendencias de Cambio
(CONABIO, México, 2009).
of these large, diverse data sets holds
the promise of a more comprehensive
understanding of the genome and its
relation to human disease. Experienced
and knowledgeable human review is
an essential component of this process,
complementing computational approaches.
This calls for efficient and intuitive
visualization tools able to scale to very
large data sets and to flexibly integrate
Classical
Neural
Proneural
Mesen-
chymal
multiple data types, including clinical data.
However, the sheer volume and scope of
data pose a significant challenge to the
development of such tools.
To address this challenge, we have
developed the Integrative Genomics
Viewer (IGV), a lightweight visualization
tool that enables intuitive real-time
exploration of diverse, large-scale genomic
data sets on standard desktop computers.
It supports flexible integration of a wide
range of genomic data types including
aligned sequence reads, mutations, copy
number, RNA interference screens, gene
expression, methylation and genomic
annotations (Supplementary Fig. 1).
The IGV makes use of efficient, multi-
resolution file formats to enable real-time
exploration of arbitrarily large data sets
over all resolution scales, while consuming
minimal resources on the client computer
(Supplementary Notes). Navigation
through a data set is similar to that of
Google Maps, allowing the user to zoom
and pan seamlessly across the genome
at any level of detail from whole genome
to base pair (Supplementary Fig. 2).
Data sets can be loaded from local or
remote sources, including cloud-based
resources, enabling investigators to view
their own genomic data sets alongside
publicly available data from, for example,
The Cancer Genome Atlas1, 1000
Genomes2 (http://www.1000genomes.
org/) and ENCODE3 (http://www.genome.
gov/10005107) projects. In addition, IGV
allows collaborators to load and share data
locally or remotely over the internet.
IGV supports concurrent visualization
of diverse data types across hundreds,