Project description:We present results from deep sequencing of small RNA populations from several genotypes of soybean and demonstrate that the CHS siRNAs accumulated only in the seed coats of the yellow varieties having either the dominant I or i-i alleles and not in the pigmented seed coats with homozygous recessive i genotypes. However, the diagnostic CHS siRNAs did not accumulate in the cotyledons of genotypes with the dominant I or i-i alleles thus demonstrating the novelty of an endogenous inverted repeat region of CHS genes driving RNA silencing in trans of non-linked CHS family members in a tissue-specific manner. The phenomenon results in inhibition of a metabolic pathway by siRNAs in one tissue allowing expression of the flavonoid pathway and synthesis of secondary metabolites in other organs as the chalcone synthase small RNAs are found in the seed coats of yellow seeded soybean varieties but not in the cotyledons of the same genotype. In order to compare the population of chalcone synthase related small RNAs, we sequenced 3 to 6 million small RNAs using the Illumina Genome Analyzer from the following four soybean cultivars and tissues with specific genotypes at the I locus: Richland immature seed coats (homozygous for the dominant I allele that specifies yellow seed coat); Williams immature seed coats (homozygous for the dominant i-i allele that specifies yellow seed coat with pigmented hilum) Williams (i-i/i-i yellow) immature cotyledons (homozygous for the dominant i-i allele that specifies yellow seed coat with pigmented hilum); Williams 55 immature seed coats (a Williams isogenic line homozygous for the recessive i allele that specifics pigmented seed coats. All seed coats and cotyledons were dissected from green stage immature seeds within the fresh weight range of 50-75 mg.
Project description:We profiled the global gene and miRNA expression in soybean following infections by three different Soybean mosaic virus (SMV) isolates, L (G2 strain), LRB (G2 strain) and G7 (G7 strain) by small RNA (sRNA)-seq, degradome-seq and as well as a genome-wide transcriptome analysis.
Project description:Transcriptional changes in soybean plants infected with Soybean mosaic virus (SMV) was assessed at 7, 14 and 21 days post inoculation (dpi). Keywords: Time course
Project description:We present results from deep sequencing of small RNA populations from several genotypes of soybean and demonstrate that the CHS siRNAs accumulated only in the seed coats of the yellow varieties having either the dominant I or i-i alleles and not in the pigmented seed coats with homozygous recessive i genotypes. However, the diagnostic CHS siRNAs did not accumulate in the cotyledons of genotypes with the dominant I or i-i alleles thus demonstrating the novelty of an endogenous inverted repeat region of CHS genes driving RNA silencing in trans of non-linked CHS family members in a tissue-specific manner. The phenomenon results in inhibition of a metabolic pathway by siRNAs in one tissue allowing expression of the flavonoid pathway and synthesis of secondary metabolites in other organs as the chalcone synthase small RNAs are found in the seed coats of yellow seeded soybean varieties but not in the cotyledons of the same genotype.
Project description:Seed coat color in soybean (Glycine max) is determined by the accumulation of flavonoid-derived pigments. However, to date the molecular mechanisms driving natural variation remain poorly defined. This study integrated data from RNA sequencing (RNA-seq) with metabolite profiling via high-performance liquid chromatography (HPLC) to investigate genetic and metabolic differences between black and yellow seed coat soybean lines that share an identical genetic background. Transcriptomic analysis revealed that key anthocyanin biosynthesis genes, including flavanone 3-hydroxylase (F3H-3), anthocyanidin synthase (ANS), UDP-glucose:flavonoid 3-O-glucosyltransferase (UF3GT), UDP-glycosyltransferase (UGT79B6), and glutathione S-transferase (GSTF11), were more highly expressed in black seed coats, where we also observed increased anthocyanin and proanthocyanidin (PA) accumulation and antioxidant activity. In contrast, leucoanthocyanidin reductase (LAR) was strongly expressed in yellow seed coats but did not correspond to PA levels, likely due to the specific expression of laccase (LAC5) in black seeds, which facilitates PA polymerization. Elevated expression of cytochrome P450 enzymes (i.e., CYP73A5, cinnamate 4-hydroxylase; CYP82C4) in yellow seed coats suggested activation of the isoflavone biosynthesis pathway. Further transcriptional profiling also indicated that black-seed-specific MYB transcription factors (i.e., MYB111, MYB113, and MYB17) promoted anthocyanin production. This study is the first to provide evidence that small heat shock proteins (sHSPs) are implicated in the regulation of seed coat pigmentation and stress adaptation. Together, these findings elucidate the genetic and metabolic regulation of seed coat color in soybean and identify candidate genes relevant to functional breeding and genomics research.
Project description:Millet is a dangerous weed in Hungary. Lack of seed dormancy helps it to spread easily and be present at maize, wheat and other crop fields. Our previous report revealed the possibility that millet can also play a role as a virus reservoir. In that study we detected the presence of several viruses in millet using DAS ELISA. Because serological methods can only detect the presence of the investigated particular pathogens, we suspected that other, previously unknown viruses can also be present in this weed. To investigate this theory, we randomly sampled two locations and collected millets showing stunting, chlorosis, and striped leaves and investigated the presence of viruses using small RNA HTS as a diagnostic method. Our result confirmed the widespread presence of wheat streak mosaic virus at both locations. Moreover, barley yellow striate mosaic virus and barley virus G were also identified, which have not been described from Hungary before. As these viruses can cause severe diseases on wheat, their presence on a weed mean a potential infection risk. Our study indicates that the presence of millets on the fields needs a special control in order to prevent emergence of new diseases at crop fields.
Project description:To dissect the gene regulatory networks operating during soybean seed development, we identified the binding sites genome-wide for transcription factor in soybean seeds during seed development using ChIP-seq
Project description:To dissect the gene regulatory networks operating during soybean seed development, we identified the binding sites genome-wide for transcription factor in soybean seeds during seed development using ChIP-seq