Discovery of QTL for root traits and water use efficiency in rice (Oryza sativa L.) and their validation - A combined approach of association analysis and linkage mapping
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Date
2013-08-24
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University of Agricultural Sciences, Bengaluru
Abstract
Introgression of water mining and water use efficiency (WUE) traits on to a
single elite genetic background is needed while developing aerobic worthy rice
cultivars. Considering the complexity of inheritance of these traits, a focused
molecular breeding is a promising approach.
A set of 173 diverse indica rice accessions were phenotyped for these traits and
significant variability was noticed which was consistent across seasons, indicating a
strong genetic control. Assessment of molecular diversity using 291 SSR markers
detected a total of 2,615 alleles with an average of 8.95 allele per locus and an
average PIC value of 0.6. Population structure analysis identified six main subgroups
which corresponded to the diversity analysis derived from neighbour joining method.
Of the 108 significant marker-trait associations (MTAs) identified using mixed linear
model, 51 were highly significant (P<0.01). There were 24 associations for Root traits
and 1 for 13C and 16 for other physiological traits. Many of these markers were
found to be located in QTL regions previously reported for similar traits. A trait
specific mapping population was characterized for root traits and WUE under aerobic
conditions validating the associated markers. Significant phenotypic variations with
transgressive segregants were found for all the traits and 30 QTLs were detected. The
combined approach of association and linkage mapping lead to the identification of
several common markers viz., RM1235, RM8020, RM4477, RM163 and RM307
linked with the traits of interest. These markers can significantly enhance breeding
efficiency in introgressing complex traits. This novel two pronged strategy lead to the
discovery of 13 robust QTLs which on in-silico analysis revealed the presence of
genes that govern variability in cellular metabolism, transport and signal transduction,
transcription and hormonal regulation under abiotic stress adaptation and yield
improvement in rice.
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Keywords
vegetative propagation, grain, rice, yields, irrigation, developmental stages, biological phenomena, planting, genetics, weather hazards