Abstract
Soybean [Glycine max (L.) Merr.] is one of the most important legume crops abundant in edible protein and oil in the world. In recent years there has been increasingly more drastic weather caused by climate change, with flooding, drought, and unevenly distributed rainfall gradually increasing in terms of the frequency and intensity worldwide. Severe flooding has caused extensive losses to soybean production and there is an urgent need to breed strong soybean seeds with high flooding tolerance. The present study demonstrates bioinformatics big data mining and integration, meta-analysis, gene mapping, gene prioritization, and systems biology for identifying prioritized genes of flooding tolerance in soybean. A total of 83 flooding tolerance genes (FTgenes), according to the appropriate cut-off point, were prioritized from 36,705 test genes collected from multidimensional genomic features linking to soybean flooding tolerance. Several validation results using independent samples from SoyNet, genome-wide association study, SoyBase, GO database, and transcriptome databases all exhibited excellent agreement, suggesting these 83 FTgenes were significantly superior to others. These results provide valuable information and contribution to research on the varieties selection of soybean.
Highlights
Soybean [Glycine max (L.) Merr] is an important food crop worldwide that provides an essential source of anthocyanins and isoflavones for human beings (Cederroth and Nef, 2009)
We proposed a comprehensive framework that consists of bioinformatics big data mining, meta-analysis, and a gene prioritization algorithm to prioritize 83 flooding tolerance genes (FTgenes) from 36,705 test genes set collected from multidimensional data platforms
We introduced a comprehensive framework to integrate and prioritize diverse genetic data collected from multiple dimensional data sources to search for important genes that are highly connected to flooding tolerance or responding to stress
Summary
Soybean [Glycine max (L.) Merr] is an important food crop worldwide that provides an essential source of anthocyanins and isoflavones for human beings (Cederroth and Nef, 2009). Previous studies have shown that soybean isoflavones can decelerate at the apoptotic rate of the cerebral cortex of rats and minimize the occurrence of ischemic stroke (Schreihofer et al, 2005; Burguete et al, 2006; Lovekamp-Swan et al, 2007). Maintaining a stable supply of soybean is important for the treatment of complex diseases. Even though global soybean production has steadily risen in recent years (FAOstat, faostat.fao.org), there is still a shortage of food supply for human beings due to increases in natural disasters. Soybean is stress-sensitive and is affected by flooding (Hou and Thseng, 1991; VanToai et al, 2010), one of the major abiotic stresses that can cause enormous
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