Dataset Information

Nutraceutical potential of small chickpea grain associated with significant stress response revealed by proteomics and metabolomics

ABSTRACT: The main goal in cereal crops like chickpea is to improve yield due to the continually increasing demand for food. Therefore, there is a bias towards big seed genotypes in the grain marker because of the protein, lipid, and carbohydrate content. Although significant advance has been made in understanding the molecular foundation of grain size, limited efforts have focused on determining small grains nutraceutical values. This study carried out comparative proteomics and metabolomics of five chickpeas genotypes, including small and big commercial premium grains locally produced.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Cicer Arietinum (chickpea) (garbanzo)

TISSUE(S): Plant Cell, Cotyledon, Seed

SUBMITTER: Miguel Elizalde

LAB HEAD: Miguel elizalde

PROVIDER: PXD030279 | Pride | 2023-03-11

REPOSITORIES: Pride

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Publications

Proteometabolomic Analysis Reveals Molecular Features Associated with Grain Size and Antioxidant Properties amongst Chickpea (<i>Cicer arietinum</i> L.) Seeds Genotypes.

Quiroz-Figueroa Francisco R FR Monribot-Villanueva Juan L JL Bojórquez-Velázquez Esaú E Gómez-Peraza Rosa L RL Elizalde-Contreras José M JM Bautista-Valle Mirna V MV Guerrero-Analco José A JA Valdez-Morales Maribel M Singh Rupesh Kumar RK Ruiz-May Eliel E

Antioxidants (Basel, Switzerland) 20220920 10

Legumes are an essential source of nutrients that complement energy and protein requirements in the human diet. They also contribute to the intake of bioactive compounds such as polyphenols, whose content can vary depending on cultivars and genotypes. We conducted a comparative proteomics and metabolomics study to determine if there were significant variations in relevant nutraceutical compounds in the five genotypes of Kabuli-type chickpea grains. We performed an isobaric tandem mass tag (TMT) ...[more]

PMID: 36290573

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Project description:Transcriptomic analyses are particularly powerful in research when they are based on detailed underlying knowledge of developmental processes, morphological/anatomical features and biochemical/metabolic processes. Our work is based on our detailed knowledge of grain development and provides an invaluable resource for both Brachypodium grain development specifically and for comparative analyses to other species, including cereal crops. Grain development includes several transition points in addition to being preceded and succeeded by the fundamental developmental switches of fertilization and germination. Such complex process requires a larger sets of genes expressed in a highly-controlled manner. We have selected eight stages of developmental in Brachypodium distachyon encompassing these transitions and conducted comprehensive transcriptomic analyses to generate a valuable resource of the developmental transitions and the distinctive biological processes that are activated and/or repressed during grain development and germination. Comparison of the data generated in this project to other grasses, including the important crop species, and beyond will also shed light on the conservation and/or diversification in gene expression and function in an evolutionary context. Brachypodium distachyon grains (Bd-21 accession) were germinated on moist filter paper after stratification at 4°C for 48h. Five-day old seedlings were transferred to 9cm square pots with a 2:2:1 multipurpose compost: vermiculite: sand mix and grown under controlled environment conditions with a 18h photoperiod at 20°-22°C and light intensity of 180-200 umol/m/s. Tissue samples were collected from eight distinct developmental stages; pre-anthesis ovaries, young grains (1-3 DAA), middle length grains (3-8 DAA), full length grains (8-15 DAA), mature grains (15-20 DAA), mature grains without embryo, germinating grains and seedlings at 3-4 days after germination (Fig.1). Tissues were frozen in liquid nitrogen immediately after collection and were kept at -80°C until further analyses. Total RNA was isolated from frozen tissue samples using the Spectrum Plant Total RNA Kit (Sigma-Aldrich) following the manufacturer’s instructions. Three biological replicates were used for each stage of development. The RNA samples were treated with DNase I (New England Biolabs) in order to eliminate DNA contamination and their concentration was determined using a NanoDrop spectrophotometer (Thermo Fisher Scientific).

Project description:Endogenous small RNAs, including microRNAs (miRNAs) and short-interfering RNAs (siRNAs), function as posttranscriptional or transcriptional regulators in plants. miRNA function is essential for normal development and therefore likely to be important in the growth of the rice grain. To investigate the likely roles of miRNAs in rice grain development we carried out deep sequencing of the small RNA populations of rice grains. A total of 96,091 (including 23,867 reads from vegetative tissues) and 5,379,724 small RNA sequences that are longer than 17nt were generated. Approximately 94% of these small RNAs were 20-24nt in length. The majority of the small RNAs were singletons, indicating that rice genome has a very complex small RNA population, which is harder to be saturated. From these smal RNA sequences we found representatives of all 20 conserved plant miRNA families and evidence for changes in expression of miRNAs during rice grain development. Using an approach based on the presence of the miRNA and miRNA* sequences, we identified 51 novel, non-conserved rice miRNA families expressed in grains with functionally diverse predicted target genes. miRNA-guided cleavage was confirmed for a number of targets genes including ones with roles in sugar signalling and restoration of cytoplasmic male sterility. We identified a likely mirtron, indicating that plants can also use spliced introns as a source of miRNAs. Our sequencing results revealed four TAS3 loci; these all contain dual miR390 sites of which only the 3? site is cleaved. We also found a miRNA-like long hairpin generating phased 21nt small RNAs, strongly expressed in developing grains and show that these small RNAs act in trans to cleave target mRNAs. Keywords: high throughput pyrosequencing, small RNA, microRNA, grain development, rice Small RNA populations of shoots and roots of 7 days old seedlings, and 1-5 and 6-10 days after fertilization grains were determined using high throughput sequencing technology. The abundance of known miRNAs were compared based on the number of sequence reads. To give a whole picture of the rice small RNA populations and to reflect un-biasly the sequencing results, small RNAs that are longer than 17nt no matter whether or not they matched with the rice genome were included in this submitted dataset. The unmatched sequences may be derived from un-sequenced regions or sequencing errors.

Dataset Information

Nutraceutical potential of small chickpea grain associated with significant stress response revealed by proteomics and metabolomics

Publications

Proteometabolomic Analysis Reveals Molecular Features Associated with Grain Size and Antioxidant Properties amongst Chickpea (<i>Cicer arietinum</i> L.) Seeds Genotypes.

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