Genome-wide association mapping and gene expression analysis identify OsCPS1 as a new candidate gene controlling early seedling length in rice
Yamei Ma†, Jian Wang†, Tifeng Yang, Jingfang Dong,Wu Yang, Luo Chen, Lian Zhou, Jiansong Chen,Bin Liu, Shaohong Zhang*, David Edwards* and Junliang Zhao*
Frontiers in Plant Science
Abstract
High seedling vigor can
improve the ability to compete against weeds and flooding at the
seedling stage and is essential for the direct seeding of rice.
Early shoot length is an important performance index in seedling vigor
evaluation. However, information on the identity of rice germplasm with
high seedling vigor, and the genetic basis of seedling vigor are not
well understood. In this study, we have conducted a genome-wide
association study using 302 international diverse rice accessions from
the Rice Diversity Panel 2. Six quantitative trait loci (QTLs) were
found to associate with shoot length (SL). The locus qSL2 was further
analyzed for candidate gene characterization. We identified OsCPS1,
which encodes CDP synthase and functions in GA (Gibberellins)
biosynthesis in rice, exhibits differential expression between long and
short SL accessions. Using the Nipponbare genome sequence as the
reference, we identified a 36 bp deletion in the 5’ UTR of OsCPS1 in
long SL accessions, which is absent in short SL accessions. GA content
analysis showed that the levels of bioactive GA1 and GA4 are
considerably higher in long
SL accessions than in short SL accessions. Genome-wide gene expression
analysis indicated the expression of some photosynthesis
genes is higher in long SL accessions than in short SL accessions. In
contrast, genes involved in ABA (Abscisic Acid)-activated
signal pathway showed lower
expression in long SL accessions. Population analysis across wild rice,
indica and japonica, suggested that OsCPS1 may be under selection in
japonica during domestication. The results suggest that OsCPS1 is a
candidate gene underlying qSL2. These data provide a promising source
for candidate genetic variation associated with seedling vigor, with
practical applications in rice breeding.
Keyeords: rice, shoot length, genome-wide association study, OsCPS1, selection
