West Lafayette, Indiana
January 23, 2009
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Purdue researcher Scott Jackson looks at an image of the
rice genome. He traced the evolutionary history of rice
in an effort to improve future varieties. (Purdue
Agricultural Communications photo/Tom Campbell) |
In an effort to improve rice
varieties, a Purdue University
researcher was part of a team that traced the evolutionary
history of domesticated rice by using a process that focuses on
one gene.
Scott A. Jackson, a professor of agronomy, said studying the
gene that decides how many shoots will form on a rice plant
allows researchers to better understand how the gene evolved
over time through natural selection and human interaction.
Understanding the variations could allow scientists to place
genes from wild rice species into domesticated rice to create
varieties with more branching, increased plant size or other
favorable characteristics.
By comparing the domesticated plant to other wild rice species,
they discovered a lot of genetic variation in rice over millions
of years.
"This is a way to find these valuable genes in non-domesticated
rice and bring them into cultivated rice," Jackson said. "We
need to grow more food to feed the human population, and it
needs to be done on less land and with less water. This could be
the way to do that."
Jackson worked with Rod A. Wing of the University of Arizona and
Mingsheng Chen of the Chinese Academy of Sciences in Beijing,
and they were the corresponding authors for the study. Their
findings are published in the
Proceedings of the National Academy of Sciences online
version this week.
The research team developed a tool to compare genes in different
species of Oryza, of which domesticated rice is a species.
Jackson said the comparisons showed how rice has changed from as
far back as 14 million years ago. As rice adapted to climate
changes and other natural circumstances, its genetic structure
changed, keeping some genes and losing others.
About 10,000 years ago, humans began making their own genetic
modifications, albeit unknowingly, by choosing plants that had
favorable traits. As they stopped growing plants with
unfavorable characteristics, genes responsible for those traits
disappeared.
"Humans knew that if the seeds stayed on the plant, or it had a
higher yield, they could save some of the seeds to plant next
year," Jackson said. "That was unintentional breeding."
Those favorable genes are still around in wild rice species
because they were valuable for plants in other climates or
situations, he said.
Jackson was involved with earlier research that looked at cell
structure in rice and also is studying the gene responsible for
flowering in rice plants. Once those genes are better
understood, scientists can match the best genes for particular
climates to give growers better yields.
One example can be found in a variety of rice that has genes
making it drought-resistant. Scientists could breed those genes
into domesticated rice in Africa where water shortages can
devastate crops.
National Science Foundation funding contributed to the
research in addition to other grants.
ABSTRACT
Comparative Sequence Analysis of MONOCULM1-orthologous
Regions in 14 Oryza Genomes
Fei Lu, Jetty S. S. Ammiraju, Abhijit Sanyal, Shengli Zhang,
Rentao Son, Jinfeng Chen, Gushing Li, Yi Sui, Xiang Song,
Zhukuan Chenga, Antonio Costa de Oliveirae, Jeffrey L.
Bennetzene, Scott A. Jackson, Rod A. Wing and Mingsheng Chen
Comparative genomics is a powerful tool to decipher gene and
genome evolution. Placing multiple genome comparisons in a
phylogenetic context improves the sensitivity of evolutionary
inferences. In the genus Oryza, this comparative approach can be
used to investigate gene function, genome evolution,
domestication, polyploidy, and ecological adaptation. A large
genomic region surrounding the MONOCULM1 (MOC1) locus was chosen
for study in 14 Oryza species, including 10 diploids and 4
allotetraploids. Sequencing and annotation of 18 bacterial
arti?cial chromosome clones for these species revealed highly
conserved gene colinearity and structure in the MOC1 region.
Since the Oryza radiation about 14 Mya, differences in
transposon ampli?cation appear to be responsible for the
different current sizes of the Oryza genomes. In the MOC1
region, transposons were only conserved between genomes of the
same type (e.g., AA or BB). In addition to the conserved gene
content, several apparent genes have been generated de novo or
uniquely retained in the AA lineage. Two different 3-gene
segments have been inserted into the MOC1 region of O. coarctata
(KK) or O. sativa by unknown mechanism(s). Large and apparently
noncoding sequences ?anking the MOC1 gene were observed to be
under strong purifying selection. The allotetraploids Oryza alta
and Oryza minuta were found to be products of recent
polyploidization, less than 1.6 and 0.4 Mya, respectively. In
allotetraploids, pseudogenization of duplicated genes was
common, caused by large deletions, small frame-shifting
insertions/deletions, or nonsense mutations. |
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