144 prioritized genes of flooding-tolerance (FTgenes) in soybean

Soybean [Glycine max (L.) Merr.] is one of the most important legume crops
abundant in edible protein and oil in the world. Due to the drastic
climate change, flooding, drought and unevenly distributed rainfall have
gradually increased in terms of the frequency and intensity worldwide. In
particular, severe flooding has caused extensive losses to soybean
production. In light of the harsh situation, there has been an urge to
breed strong soybean seeds with high flooding tolerance. We collected and
integrated genetic data that relevant to flooding-tolerant responses in
soybean from multiple dimensional data sources. A step-function adjusted
factor prioritization algorithm was proposed to prioritize these
integrated genetic data. A total of 144 candidate genes of
flooding-tolerance (FTgenes) in soybean were prioritized, using a
cut-off threshold of combined score of 42, from 36,705 test genes
that collected from multidimensional genomic features linking to soybean
flooding tolerance. Several validation results using independent
samples from SoyNet, GWAS, SoyBase, GO database and transcriptome
databases all exhibited excellent agreement, suggesting these 144 FTgenes
were significantly superior than others. Our results provide valuable
information, meaningful insight, and contribution to varieties selection
of soybean. The FTgenes demonstrated the potential for uncovering
important insights underlying flooding-tolerant response in soybean in
systems biology stuydies.