Title:
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A molecular analysis of weedy rice from South East Asia
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To meet demographic demand, global rice production will have to increase by
about 2% per year despite losses of land and water supply to industrialisation and
urbanisation, and the reduction of availability of farm labour. In Asia, the traditional
transplanting of rice is increasingly being replaced by direct seeding that reduces labour
costs and saves water. However, yield in direct seeded rice is threatened by weed
competition due to the absence of weed suppression through early flooding. Moreover
the appearance of "weedy" rice has notably been associated with the use of direct
seeding. Weedy rice are plants that appear in and around rice fields and exhibit
unwanted wild traits that reduce the quality and the quantity of the harvest. Little is
known of the evolutionary origin of weedy rice. The aims of this project were to
examine the phylogenetic relationships between weedy rice, cultivars, and wild rice to
investigate the origins of weedy rice and to develop molecular diagnostics that would
identify weedy rice contamination of seed sources.
Using 19 microsatellite markers, individual plants of weedy rice, and cultivars
from field samples in Malaysia and the Philippines were genetically characterised
together with populations of Oryza niwlra and 0. rlljipogon, rice wild relatives. from
different geographical locations in south east Asia, and reference 0. saliva accessions.
Genetic differentiation between weedy rice and crop cultivars was evident. Weedy rice
populations were more closely related to companion crop cultivars in Malaysia than in
the Philippines. In the Philippines, weedy rice appeared to be genetically intermediate
between crop cultivars and certain wild rice accessions, suggesting the presence of wild
rice genes in their genomes.
There are three main hypotheses for weedy rice: the invasion and persistence of
preadapted annual wild rice in cultivated fields; the introgression and segregation of
genes from annual or perennial wild rice surrounding fields into the sown cultivars; the
segregation and expression of weedy traits introgressed during cultivar production. The
data presented in this study demonstrated that weedy rice appears to be cultivars with
introgressed wild traits. This excludes the first hypothesis. The fact that there is little or
no evidence of 0. nivara and 0. rujipogon around the fields in the sampled regions also
suggests that the second hypothesis is unlikely unless the source is cryptic. The
conclusion of this study therefore has to be that weedy rice plants are "hybrids",
carrying cultivar and wild traits. However, the use of 0. nivara in the breeding program
of modern varieties to produce lines resistant to diseases may have accidentally
introduced genes for unwanted wild traits (e.g. seed shattering, red peri carps, awns) to
genomes of cultivars. These traits were subsequently selected against during the
development of elite lines, but the release of highly inbred but not completely isogenic
lines may allow the segregation and selection of these traits and hence produce weedy
rice plants.
The distant relationship between the weedy rice and the cultivars in the
Philippines, allowed the identification of two genetic regions (one insertion in the
microsatellite RM009, and one in the intron 2 of the catalase, CatA, gene) specific to
weedy rice. These regions were used to design two PCR based molecular diagnostics
that showed nearly 100% correlation between a PCR amplification and the presence of a
weedy phenotype. The close genetic relationship between cultivars and the weedy rice
samples in Malaysia prevented the identification of such regions.
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