Evidence map›Paper›PMID 39404887›Full record

ArticleFunctional & integrative genomics2024

Identification of lncRNAs regulating seed traits in Brassica juncea and development of a comprehensive seed omics database.

Pinky Yadav, Prachi Priyam, Garima Yadav, Abhinandan Yadav, Rubi Jain, Satyam Sunderam, Manoj Kumar Sharma, Inderjeet Kaur, Namrata Dhaka

Abstract read
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In one paragraph

Article in Functional & integrative genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Pinky YadavDepartment of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India.
Prachi PriyamDepartment of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India.
Garima YadavDepartment of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India.
Abhinandan YadavDepartment of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India.
Rubi JainSchool of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
Satyam SunderamAmity Institute of Information Technology, Noida, Uttar Pradesh, India.
Manoj Kumar SharmaSchool of Biotechnology, Jawaharlal Nehru University, New Delhi, India.
Inderjeet KaurDepartment of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India.
Namrata DhakaDepartment of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India. namratadhaka@gmail.com.

Funding

Department of Science and Technology, Ministry of Science and Technology, India DST INSPIRE research grant IFA17-LSPA90Science and Engineering Research Board (SERB), Government of India CRG research grant CRG/2019/001695
6 · The paper itself

Abstract

Brassica juncea is a crucial oilseed crop, and its seeds possess high economic value as they are a source of edible oil. In order to understand the role of long non coding RNAs (lncRNAs) in the regulation of seed development, we carried out computational analysis using transcriptome data of developing seeds of two contrasting genotypes of B. juncea, Pusajaikisan (PJK) and Early Heera 2 (EH2). The seeds were sampled at three stages, 15, 30, and 45 days after pollination. We identified 1,539 lncRNAs, of which 809 were differentially expressed. We also carried out extensive characterization and functional analysis of seed lncRNAome. The expression patterns were analysed using k-means clustering, and the targets were analysed using pathway, transcription factor, and GO enrichment, as well as ortholog information. We shortlisted a total of 25 robust lncRNA candidates for seed size, oil content, and seed coat color. We also identified 4 lncRNAs as putative precursors of miRNAs regulating seed development. Moreover, a total of 28 miRNA-lncRNA-mRNA regulatory networks regulating seed traits were identified. We also developed a comprehensive database, (BrassIca juncea database or "BIJ" ( https://bij.cuh.ac.in/ ), which provides seed omics as well as other functional genomics and genetics data in an easily accessible form. These candidate lncRNAs are suitable for including in crop improvement programs through molecular breeding, as well as for future validations through genome editing. Together, the knowledge of these candidate lncRNAs and availability of BIJ database shall leverage the crop improvement efforts in B. juncea.

Indexed as

MicroRNAsMustard PlantRNA, Long NoncodingSeedsDatabases, GeneticGene Expression Regulation, PlantGene Regulatory NetworksTranscriptomeMicroRNAsRNA, Long NoncodingBrassica databaseBrassica junceaLong non coding RNAs (lncRNAs)Oil contentSeed coat colorSeed size

Identifiers

PMID39404887

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.