Uncloaking lncRNA-meditated gene expression as a potential regulator of CMS in cotton (Gossypium hirsutum L.)

Abeyawardana

et al. 2020

Cells

Cytoplasmic male sterility (CMS), encoded by the interacting mitochondrial and nuclear genes, causes pollen abortion or non-viability. CMS is widely used in agriculture and extensively studied in crops. Much less is known about CMS in wild species. We performed a comparative transcriptomic analysis of male sterile and fertile individuals of Silene vulgaris, a model plant for the study of gynodioecy, to reveal the genes responsible for pollen abortion in this species. We used RNA-seq datasets previously employed for the analysis of mitochondrial and plastid transcriptomes of female and hermaphrodite flower buds, making it possible to compare the transcriptomes derived from three genomes in the same RNA specimen. We assembled de novo transcriptomes for two haplotypes of S. vulgaris and identified differentially expressed genes between the females and hermaphrodites, associated with stress response or pollen development. The gene for alternative oxidase was downregulated in females. The genetic pathways controlling CMS in S. vulgaris are similar to those in crops. The high number of the differentially expressed nuclear genes contrasts with the uniformity of organellar transcriptomes across genders, which suggests these pathways are evolutionarily conserved and that selective mechanisms may shield organellar transcription against changes in the cytoplasmic transcriptome.

Section: Aox1 Gene Was Downregulated In Female Flower Buds In S Vulgsupporting

confidence: 83%

Differentially Expressed Genes Shared by Two Distinct Cytoplasmic Male Sterility (CMS) Types of Silene vulgaris Suggest the Importance of Oxidative Stress in Pollen Abortion

Abeyawardana

et al. 2020

Cells

“…For cDNA library preparation, purified mRNA randomly fragmented into short fragments (~ 200 bp) by RNaseIII enzyme then subjected to Ion adapter v2 hybridization, ligation and cDNA was synthesized and amplified as per manufacturer’s guidelines. After amplification, cDNA libraries were selected for target fragments of ~ 200 bp on 2% Agarose EGelTM (Thermo Fisher Scientific) and stored at − 20 °C until used 10 , 28 . The selected ~ 200 bp cDNA library was subjected to emulsion PCR (Ion OneTouch™ 2 System, Thermofisher Scientific, USA), followed by enrichment of template positive bead recovery.…”

Section: Methodsmentioning

confidence: 99%

Genic microsatellite marker characterization and development in little millet (Panicum sumatrense) using transcriptome sequencing

Desai

Hamid

Ghorbanzadeh

et al. 2021

Sci Rep

Self Cite

Little millet is a climate-resilient and high-nutrient value plant. The lack of molecular markers severely limits the adoption of modern genomic approaches in millet breeding studies. Here the transcriptome of three samples were sequenced. A total of 4443 genic-SSR motifs were identified in 30,220 unigene sequences. SSRs were found at a rate of 12.25 percent, with an average of one SSR locus per 10 kb. Among different repeat motifs, tri-nucleotide repeat (66.67) was the most abundant one, followed by di- (27.39P), and tetra- (3.83P) repeats. CDS contained fewer motifs with the majority of tri-nucleotides, while 3′ and 5′ UTR carry more motifs but have shorter repeats. Functional annotation of unigenes containing microsatellites, revealed that most of them were linked to metabolism, gene expression regulation, and response to environmental stresses. Fifty primers were randomly chosen and validated in five little millet and 20 minor millet genotypes; 48% showed polymorphism, with a high transferability (70%) rate. Identified microsatellites can be a noteworthy resource for future research into QTL-based breeding, genetic resource conservation, MAS selection, and evolutionary genetics.

“…RNA sequencing (RNA-Seq) is widely used among the different transcriptome analysis methods as it can e ciently detect unknown genes and novel transcripts and has much potential to study gene expression and their regulating pathways [55]. This approach has been successfully applied in many important crops, including sesame [56], chickpea [57], nger millet [58], foxtail millet [59], peanut [60], maize [61] and cotton [62,63].…”

Section: Discussionmentioning

confidence: 99%

Stage Specific Comparative Transcriptomic Analysis To Reveal Gene Networks Regulating Iron And Zinc Content In Pearl Millet [Pennisetum glaucum (L.) R. Br.]

Satyavathi¹,

Tomar²,

Ambawat³

et al. 2021

Preprint

Self Cite

Pearl millet is an important staple food crop of poor people which is rich in micronutrients like iron and zinc and amenable for focused breeding for these micronutrients along with high yield. Transcriptome sequencing using ION S5 Next Generation Sequencer generated 43.5 million sequence reads resulting in 83,721 transcripts with N50 of 597 bp and 84.35% of transcripts matched with the pearl millet genome assembly. The genotypes having high Fe and Zn showed differential gene expression during different stages. Of which, 155 were up-regulated and 251were down-regulated while during flowering stage and milking stage 349 and 378 transcripts were differentially expressed, respectively. Gene annotation and GO term showed the presence of transcripts involved in metabolic activities associated with uptake and transport of iron and zinc. In the present study, the 83,721 transcripts were also examined for identification of SSRs. A total of 4,327 SSRs were identified with dominance of tri-nucleotide SSRs in comparison to di-nucleotide SSRs. These EST-SSRs can be used in molecular breeding, genetic diversity analysis and determination of heterozygosity of the allelic loci. Information generated will help in gaining insights into iron and zinc metabolism and develop genotypes with high yield, grain iron and zinc content.