Dataset Information

Comparative transcriptome analysis of cultivated and wild seeds of Salvia hispanica (chia).

ABSTRACT: Salvia hispanica (chia) constituted an important crop for pre-Columbian civilizations and is considered a superfood for its rich content of essential fatty acids and proteins. In this study, we performed the first comprehensive comparative transcriptome analysis between seeds from cultivated varieties and from accessions collected from native wild populations in Mexico. From the 69,873 annotated transcripts assembled de novo, enriched functional categories and pathways revealed that the lipid metabolism was one of the most activated processes. Expression changes were detected among wild and cultivated groups and among growth conditions in transcripts responsible for triacylglycerol and fatty acid synthesis and degradation. We also quantified storage protein fractions that revealed variation concerning nutraceutical proteins such as albumin and glutelin. Genetic diversity estimated with 23,641 single nucleotide polymorphisms (SNPs) revealed that most of the variation remains in the wild populations, and that a wild-type cultivated variety is genetically related to wild accessions. Additionally, we reported 202 simple sequence repeat (SSRs) markers useful for population genetic studies. Overall, we provided transcript variation that can be used for breeding programs to further develop chia varieties with enhanced nutraceutical traits and tools to explore the genetic diversity and history of this rediscovered plant.

SUBMITTER: Pelaez P

PROVIDER: S-EPMC6611817 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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Comparative transcriptome analysis of cultivated and wild seeds of Salvia hispanica (chia).

Peláez Pablo P Orona-Tamayo Domancar D Montes-Hernández Salvador S Valverde María Elena ME Paredes-López Octavio O Cibrián-Jaramillo Angélica A

Scientific reports 20190705 1

Salvia hispanica (chia) constituted an important crop for pre-Columbian civilizations and is considered a superfood for its rich content of essential fatty acids and proteins. In this study, we performed the first comprehensive comparative transcriptome analysis between seeds from cultivated varieties and from accessions collected from native wild populations in Mexico. From the 69,873 annotated transcripts assembled de novo, enriched functional categories and pathways revealed that the lipid me ...[more]

PMID: 31278279

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Project description:Chia (Salvia hispanica L.), a member of the mint family (Lamiaceae), is a rediscovered crop with great importance in health and nutrition and is also the highest known terrestrial plant source of heart-healthy omega-3 fatty acid, alpha linolenic acid (ALA). At present, there is no public genomic information or database available for this crop, hindering research on its genetic improvement through genomics-assisted breeding programs. The first comprehensive analysis of the global transcriptome profile of developing Salvia hispanica L. seeds, with special reference to lipid biosynthesis is presented in this study. RNA from five different stages of seed development was extracted and sequenced separately using the Illumina GAIIx platform. De novo assembly of processed reads in the pooled transcriptome using Trinity yielded 76,014 transcripts. The total transcript length was 66,944,462 bases (66.9 Mb), with an average length of approximately 880 bases. In the molecular functions category of Gene Ontology (GO) terms, ATP binding and nucleotide binding were found to be the most abundant and in the biological processes category, the metabolic process and the regulation of transcription-DNA-dependent and oxidation-reduction process were abundant. From the EuKaryotic Orthologous Groups of proteins (KOG) classification, the major category was "Metabolism" (31.97%), of which the most prominent class was 'carbohydrate metabolism and transport' (5.81% of total KOG classifications) followed by 'secondary metabolite biosynthesis transport and catabolism' (5.34%) and 'lipid metabolism' (4.57%). A majority of the candidate genes involved in lipid biosynthesis and oil accumulation were identified. Furthermore, 5596 simple sequence repeats (SSRs) were identified. The transcriptome data was further validated through confirmative PCR and qRT-PCR for select lipid genes. Our study provides insight into the complex transcriptome and will contribute to further genome-wide research and understanding of chia. The identified novel UniGenes will facilitate gene discovery and creation of genomic resource for this crop.

Project description:Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] is an important vegetable crop world-wide. Watermelon fruit quality is a complex trait determined by various factors such as sugar content, flesh color and flesh texture. Fruit quality and developmental process of cultivated and wild watermelon are highly different. To systematically understand the molecular basis of these differences, we compared transcriptome profiles of fruit tissues of cultivated watermelon 97103 and wild watermelon PI296341-FR. We identified 2,452, 826 and 322 differentially expressed genes in cultivated flesh, cultivated mesocarp and wild flesh, respectively, during fruit development. Gene ontology enrichment analysis of these genes indicated that biological processes and metabolic pathways related to fruit quality such as sweetness and flavor were significantly changed only in the flesh of 97103 during fruit development, while those related to abiotic stress response were changed mainly in the flesh of PI296341-FR. Our comparative transcriptome profiling analysis identified critical genes potentially involved in controlling fruit quality traits including α-galactosidase, invertase, UDP-galactose/glucose pyrophosphorylase and sugar transporter genes involved in the determination of fruit sugar content, phytoene synthase, β-carotene hydroxylase, 9-cis-epoxycarotenoid dioxygenase and carotenoid cleavage dioxygenase genes involved in carotenoid metabolism, and 4-coumarate:coenzyme A ligase, cellulose synthase, pectinesterase, pectinesterase inhibitor, polygalacturonase inhibitor and α-mannosidase genes involved in the regulation of flesh texture. In addition, we found that genes in the ethylene biosynthesis and signaling pathway including ACC oxidase, ethylene receptor and ethylene responsive factor showed highly ripening-associated expression patterns, indicating a possible role of ethylene in fruit development and ripening of watermelon, a non-climacteric fruit. Our analysis provides novel insights into watermelon fruit quality and ripening biology. Furthermore, the comparative expression profile data we developed provides a valuable resource to accelerate functional studies in watermelon and facilitate watermelon crop improvement.

Dataset Information

Comparative transcriptome analysis of cultivated and wild seeds of Salvia hispanica (chia).

Publications

Comparative transcriptome analysis of cultivated and wild seeds of Salvia hispanica (chia).

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