A Novel Soybean Diacylglycerol Acyltransferase 1b Variant with Three Amino Acid Substitutions Increases Seed Oil Content.

Improving soybean (Glycine max) seed composition by increasing the protein and oil components will add significant value to the crop and enhance environmental sustainability. Diacylglycerol acyltransferase (DGAT) catalyzes the final rate-limiting step in triacylglycerol biosynthesis and has a major impact on seed oil accumulation. We previously identified a soybean DGAT1b variant modified with 14 amino acid substitutions (GmDGAT1b-MOD) that increases total oil content by 3 percentage points when overexpressed in soybean seeds.

Genome-Wide Analysis of Alternative Splicing during Development and Drought Stress in Maize.

Alternative splicing plays a crucial role in plant development as well as stress responses. Although alternative splicing has been studied during development and in response to stress, the interplay between these two factors remains an open question. To assess the effects of drought stress on developmentally regulated splicing in maize (Zea mays), 94 RNA-seq libraries from ear, tassel, and leaf of the B73 public inbred line were constructed at four developmental stages under both well-watered and drought conditions.

Genome-wide analysis of alternative splicing in Zea mays: landscape and genetic regulation.

Alternative splicing enhances transcriptome diversity in all eukaryotes and plays a role in plant tissue identity and stress adaptation. To catalog new maize (Zea mays) transcripts and identify genomic loci that regulate alternative splicing, we analyzed over 90 RNA-seq libraries from maize inbred lines B73 and Mo17, as well as Syn10 doubled haploid lines (progenies from B73 × Mo17). Transcript discovery was augmented with publicly available data from 14 maize tissues, expanding the maize transcriptome by more than 30,000 and increasing the percentage of intron-containing genes that undergo alternative splicing to 40%.

Differential expression of miRNAs and their target genes in senescing leaves and siliques: insights from deep sequencing of small RNAs and cleaved target RNAs.

MicroRNAs (miRNAs) are a class of small RNAs, which typically function by guiding cleavage of target mRNAs. They are known to play roles in a variety of plant processes including development, responses to environmental stresses and senescence. To identify senescence regulation of miRNAs in Arabidopsis thaliana, eight small RNA libraries were constructed and sequenced at four different stages of development and senescence from both leaves and siliques, resulting in more than 200 million genome-matched sequences.

Comprehensive investigation of microRNAs enhanced by analysis of sequence variants, expression patterns, ARGONAUTE loading, and target cleavage.

MicroRNAs (miRNAs) are a class of small RNAs that typically function by guiding the cleavage of target messenger RNAs. They have been shown to play major roles in a variety of plant processes, including development, and responses to pathogens and environmental stresses. To identify new miRNAs and regulation in Arabidopsis (Arabidopsis thaliana), 27 small RNA libraries were constructed and sequenced from various tissues, stresses, and small RNA biogenesis mutants, resulting in 95 million genome-matched sequences.

Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs.

Deep sequencing technologies such as Illumina, SOLiD, and 454 platforms have become very powerful tools in discovering and quantifying small RNAs in diverse organisms. Sequencing small RNA fractions always identifies RNAs derived from abundant RNA species such as rRNAs, tRNAs, snRNA, and snoRNA, and they are widely considered to be random degradation products. We carried out bioinformatic analysis of deep sequenced HeLa RNA and after quality filtering, identified highly abundant small RNA fragments, derived from mature tRNAs that are likely produced by specific processing rather than from random degradation.

Abiotic stress-associated miRNAs: detection and functional analysis.

MicroRNAs (miRNAs) are small regulatory noncoding RNAs varying in length between 20 and 24 nucleotides. They play a key role during plant development by negatively regulating gene expression at the posttranscriptional level. Moreover, recent studies reported several miRNAs associated with abiotic stress responses.

Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs).

Small RNAs (21-24 nt) are involved in gene regulation through translation inhibition, mRNA cleavage, or directing chromatin modifications. In rice, currently approximately 240 microRNAs (miRNAs) have been annotated. We sequenced more than four million small RNAs from rice and identified another 24 miRNA genes.