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Transcriptome profiling provides insights into molecular mechanism in Peanut semi-dwarf mutant.

ABSTRACT: BACKGROUND:Plant height, mainly decided by main stem height, is the major agronomic trait and closely correlated to crop yield. A number of studies had been conducted on model plants and crops to understand the molecular and genetic basis of plant height. However, little is known on the molecular mechanisms of peanut main stem height. RESULTS:In this study, a semi-dwarf peanut mutant was identified from 60Co ?-ray induced mutant population and designated as semi-dwarf mutant 2 (sdm2). The height of sdm2 was only 59.3% of its wild line Fenghua 1 (FH1) at the mature stage. The sdm2 has less internode number and short internode length to compare with FH1. Gene expression profiles of stem and leaf from both sdm2 and FH1 were analyzed using high throughput RNA sequencing. The differentially expressed genes (DEGs) were involved in hormone biosynthesis and signaling pathways, cell wall synthetic and metabolic pathways. BR, GA and IAA biosynthesis and signal transduction pathways were significantly enriched. The expression of several genes in BR biosynthesis and signaling were found to be significantly down-regulated in sdm2 as compared to FH1. Many transcription factors encoding genes were identified as DEGs. CONCLUSIONS:A large number of genes were found differentially expressed between sdm2 and FH1. These results provide useful information for uncovering the molecular mechanism regulating peanut stem height. It could facilitate identification of causal genes for breeding peanut varieties with semi-dwarf phenotype.

SUBMITTER: Guo F

PROVIDER: S-EPMC7059693 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature

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Transcriptome profiling provides insights into molecular mechanism in Peanut semi-dwarf mutant.

Guo Fengdan F Ma Junjie J Hou Lei L Shi Suhua S Sun Jinbo J Li Guanghui G Zhao Chuanzhi C Xia Han H Zhao Shuzhen S Wang Xingjun X Zhao Yanxiu Y

BMC genomics 20200305 1

<h4>Background</h4>Plant height, mainly decided by main stem height, is the major agronomic trait and closely correlated to crop yield. A number of studies had been conducted on model plants and crops to understand the molecular and genetic basis of plant height. However, little is known on the molecular mechanisms of peanut main stem height.<h4>Results</h4>In this study, a semi-dwarf peanut mutant was identified from <sup>60</sup>Co γ-ray induced mutant population and designated as semi-dwarf m ...[more]

PMID: 32138648

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Project description:BackgroundThe cultivated peanut (Arachis hypogaea) is one of the most important oilseed crops worldwide, and the generation of pegs and formation of subterranean pods are essential processes in peanut reproductive development. However, little information has been reported about alternative splicing (AS) in peanut peg formation and development.ResultsHerein, we presented a comprehensive full-length (FL) transcriptome profiling of AS isoforms during peanut peg and early pod development. We identified 1448, 1102, 832, and 902 specific spliced transcripts in aerial pegs, subterranean pegs, subterranean unswollen pegs, and early swelling pods, respectively. A total of 184 spliced transcripts related to gravity stimulation, light and mechanical response, hormone mediated signaling pathways, and calcium-dependent proteins were identified as possibly involved in peanut peg development. For aerial pegs, spliced transcripts we got were mainly involved in gravity stimulation and cell wall morphogenetic processes. The genes undergoing AS in subterranean peg were possibly involved in gravity stimulation, cell wall morphogenetic processes, and abiotic response. For subterranean unswollen pegs, spliced transcripts were predominantly related to the embryo development and root formation. The genes undergoing splice in early swelling pods were mainly related to ovule development, root hair cells enlargement, root apex division, and seed germination.ConclusionThis study provides evidence that multiple genes are related to gravity stimulation, light and mechanical response, hormone mediated signaling pathways, and calcium-dependent proteins undergoing AS express development-specific spliced isoforms or exhibit an obvious isoform switch during the peanut peg development. AS isoforms in subterranean pegs and pods provides valuable sources to further understand post-transcriptional regulatory mechanisms of AS in the generation of pegs and formation of subterranean pods.

Project description:IntroductionPeanut (Arachis hypogaea L.), also called groundnut is an important oil and cash crop grown widely in the world. The annual global production of groundnuts has increased to approximately 50 million tons, which provides a rich source of vegetable oils and proteins for humans. Low temperature (non-freezing) is one of the major factors restricting peanut growth, yield, and geographic distribution. Since the complexity of cold-resistance trait, the molecular mechanism of cold tolerance and related gene networks were largely unknown in peanut.MethodsIn this study, comparative transcriptomic analysis of two peanut cultivars (SLH vs. ZH12) with differential cold tolerance under low temperature (10°C) was performed using Oxford Nanopore Technology (ONT) platform.Results and discussionAs a result, we identified 8,949 novel gene loci and 95,291 new/novel isoforms compared with the reference database. More differentially expressed genes (DEGs) were discovered in cold-sensitive cultivar (ZH12) than cold-tolerant cultivar (SLH), while more alternative splicing events were found in SLH compared to ZH12. Gene Ontology (GO) analyses of the common DEGs showed that the "response to stress", "chloroplast part", and "transcription factor activity" were the most enriched GO terms, indicating that photosynthesis process and transcription factors play crucial roles in cold stress response in peanut. We also detected a total of 708 differential alternative splicing genes (DASGs) under cold stress compared to normal condition. Intron retention (IR) and exon skipping (ES) were the most prevalent alternative splicing (AS) events. In total, 4,993 transcription factors and 292 splicing factors were detected, many of them had differential expression levels and/or underwent AS events in response to cold stress. Overexpression of two candidate genes (encoding trehalose-6-phosphatephosphatases, AhTPPs) in yeast improves cold tolerance. This study not only provides valuable resources for the study of cold resistance in peanut but also lay a foundation for genetic modification of cold regulators to enhance stress tolerance in crops.

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Transcriptome profiling provides insights into molecular mechanism in Peanut semi-dwarf mutant.

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Transcriptome profiling provides insights into molecular mechanism in Peanut semi-dwarf mutant.

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