We describe a peculiar and often harmful budding disorder in soybean, leading to huge yield loss in India. To determine the prevalence of floral distortion in soybean, an extensive random roving survey was undertaken in the soybean-growing regions of Madhya Pradesh, Maharashtra and the adjoining part of Karnataka states during two successive seasons of kharif (monsoon-planted) crops -Oct 2010 and Sept 2011. The average rate of the disorder ranged from 8.0% to 14.6% and severity from 2.0 to 90.0% during 2010 and 2011, respectively. Affected plants were found to have either no or deformed pods and distorted flowers, and they remained green after maturity. All the soybean varieties grown in the surveyed region (i.e. JS 335, JS 93-05, JS 73-23, JS 95-60, AMS-MB-5-19, CO-2, Bragg, JS 10-44, Samrat) were affected by the disorder. The PCR-based diagnosis revealed the absence of phytoplasma in symptomatic soybean samples.

Molecular alterations of symptomatic and asymptomatic soybean plants in response to floral bud distortion (FBD) are not completely understood yet. Oilgo-dT anchoredcDNA-RAPD and cDNA-SCoT markers were exploited to determine differentially expressed genes in response to FBD. Differential transcriptome analysis using cDNA based oligo-decamer profiling was executed to identify differentially expressed TDFs. The TDFs were further analyzed using computational tools viz., BLAST homology, protein interactome, virtual karyotyping, sub-cellular localization, neighbor joining placement.The in-silico studies were used for annotation, structural, functional characterization and protein interaction of TDFs. Differential expression studies (cDNA-RAPD) produced transcript derived fragments (TDFs) in all tissues (leaf bud and node) of symptomatic and asymptomatic plant. Out of 197, only 26 TDFs were found differentially regulated. Amongst them 15 were found completely polymorphic and 11 showed differences in their amplicon intensity. Similarly cDNA-SCoTit revealed that total of 36 primers amplified 86 fragments between 200 bp to 1800 bp in length. Amongst them, nine differentially expressed fragments (DEFs) were re-amplified and sequenced. Sequence based studies of DEFs revealed their homology to five known genes; which were functionally involved in DNA repair mechanism, apoptopic, autophagy and pathogen responsive mechanisms in soybean. However, four fragments encode un-clarified proteins with unknown functions. The possible role of unknown genes, along with protein-protein interactome, physical karyotyping and cellular localization were predicted using in silico analysis. This study suggests that oligo-dT anchoredcDNA-RAPD, cDNA-SCoT differential display approach is a useful tool to serve as initial step for understanding alterations involved in upcoming malady and provide valuable information for further studies.