Alternative Splicing (AS) Dynamics in Dwarf Soybean Derived from Cross of <i<Glycine max</i< and <i<Glycine soja</i<

Short crop height is the preferred breeding trait since there is a positive correlation between lodging resistance and a crop yield increase. Alternative splicing can alter transcriptome diversity and contribute to plant adaptation to environmental stress. We characterized the transcriptomes obtaine...
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Autor*in:	Neha Samir Roy [verfasserIn] Prakash Basnet [verfasserIn] Rahul Vasudeo Ramekar [verfasserIn] Taeyoung Um [verfasserIn] Ju-Kyung Yu [verfasserIn] Kyong-Cheul Park [verfasserIn] Ik-Young Choi [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2022

Schlagwörter:	alternative splicing dwarf isoforms soybean splice junctions

Übergeordnetes Werk:	In: Agronomy - MDPI AG, 2012, 12(2022), 7, p 1685
Übergeordnetes Werk:	volume:12 ; year:2022 ; number:7, p 1685

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.3390/agronomy12071685

Katalog-ID:	DOAJ040844854

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language	English
source	In Agronomy 12(2022), 7, p 1685 volume:12 year:2022 number:7, p 1685
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author	Neha Samir Roy
spellingShingle	Neha Samir Roy misc alternative splicing misc dwarf misc isoforms misc soybean misc splice junctions misc Agriculture misc S Alternative Splicing (AS) Dynamics in Dwarf Soybean Derived from Cross of <i<Glycine max</i< and <i<Glycine soja</i<
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topic_title	Alternative Splicing (AS) Dynamics in Dwarf Soybean Derived from Cross of <i<Glycine max</i< and <i<Glycine soja</i< alternative splicing dwarf isoforms soybean splice junctions
topic	misc alternative splicing misc dwarf misc isoforms misc soybean misc splice junctions misc Agriculture misc S
topic_unstemmed	misc alternative splicing misc dwarf misc isoforms misc soybean misc splice junctions misc Agriculture misc S
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title	Alternative Splicing (AS) Dynamics in Dwarf Soybean Derived from Cross of <i<Glycine max</i< and <i<Glycine soja</i<
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title_full	Alternative Splicing (AS) Dynamics in Dwarf Soybean Derived from Cross of <i<Glycine max</i< and <i<Glycine soja</i<
author_sort	Neha Samir Roy
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author_browse	Neha Samir Roy Prakash Basnet Rahul Vasudeo Ramekar Taeyoung Um Ju-Kyung Yu Kyong-Cheul Park Ik-Young Choi
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title_sort	alternative splicing (as) dynamics in dwarf soybean derived from cross of <i<glycine max</i< and <i<glycine soja</i<
title_auth	Alternative Splicing (AS) Dynamics in Dwarf Soybean Derived from Cross of <i<Glycine max</i< and <i<Glycine soja</i<
abstract	Short crop height is the preferred breeding trait since there is a positive correlation between lodging resistance and a crop yield increase. Alternative splicing can alter transcriptome diversity and contribute to plant adaptation to environmental stress. We characterized the transcriptomes obtained from dwarf and normal soybean lines derived from a cross of <i<Glycine max</i< var. Peking (<i<G. max</i<) and <i<G. soja</i< var. IT182936 in an F7 RIL population to study the differences between the isoforms. Full-length mRNA derived from leaf tissues was sequenced using the PacBio RSII platform, generating 904,474 circular consensus sequence (CCS) reads. Using the Structural and Quality Annotation of Novel Transcript Isoforms (SQANTI) process, 42,582 and 44,762 high-quality isoforms, and 91 and 179 polished low-quality isoforms were obtained in dwarf and normal cells, respectively. As a result, 832 and 36,772 nonredundant transcripts were generated. Approximately 30% of the identified genes were estimated to produce two or more isoforms. We detected an average of 166,171 splice junctions (SJs), of which 93.8% were canonical SJs. We identified that novel isoforms accounted for 19% of all isoforms, among which 12% fell within coding regions. The dwarf soybean demonstrated a greater number of isoforms in most of the annotated genes, particularly in genes related to growth hormones and defense responses. Our study provides comprehensive isoform and gene information that may accelerate transcriptome research in <i<G. max</i< and provide a basis to further study the impact of these isoforms on plant growth.
abstractGer	Short crop height is the preferred breeding trait since there is a positive correlation between lodging resistance and a crop yield increase. Alternative splicing can alter transcriptome diversity and contribute to plant adaptation to environmental stress. We characterized the transcriptomes obtained from dwarf and normal soybean lines derived from a cross of <i<Glycine max</i< var. Peking (<i<G. max</i<) and <i<G. soja</i< var. IT182936 in an F7 RIL population to study the differences between the isoforms. Full-length mRNA derived from leaf tissues was sequenced using the PacBio RSII platform, generating 904,474 circular consensus sequence (CCS) reads. Using the Structural and Quality Annotation of Novel Transcript Isoforms (SQANTI) process, 42,582 and 44,762 high-quality isoforms, and 91 and 179 polished low-quality isoforms were obtained in dwarf and normal cells, respectively. As a result, 832 and 36,772 nonredundant transcripts were generated. Approximately 30% of the identified genes were estimated to produce two or more isoforms. We detected an average of 166,171 splice junctions (SJs), of which 93.8% were canonical SJs. We identified that novel isoforms accounted for 19% of all isoforms, among which 12% fell within coding regions. The dwarf soybean demonstrated a greater number of isoforms in most of the annotated genes, particularly in genes related to growth hormones and defense responses. Our study provides comprehensive isoform and gene information that may accelerate transcriptome research in <i<G. max</i< and provide a basis to further study the impact of these isoforms on plant growth.
abstract_unstemmed	Short crop height is the preferred breeding trait since there is a positive correlation between lodging resistance and a crop yield increase. Alternative splicing can alter transcriptome diversity and contribute to plant adaptation to environmental stress. We characterized the transcriptomes obtained from dwarf and normal soybean lines derived from a cross of <i<Glycine max</i< var. Peking (<i<G. max</i<) and <i<G. soja</i< var. IT182936 in an F7 RIL population to study the differences between the isoforms. Full-length mRNA derived from leaf tissues was sequenced using the PacBio RSII platform, generating 904,474 circular consensus sequence (CCS) reads. Using the Structural and Quality Annotation of Novel Transcript Isoforms (SQANTI) process, 42,582 and 44,762 high-quality isoforms, and 91 and 179 polished low-quality isoforms were obtained in dwarf and normal cells, respectively. As a result, 832 and 36,772 nonredundant transcripts were generated. Approximately 30% of the identified genes were estimated to produce two or more isoforms. We detected an average of 166,171 splice junctions (SJs), of which 93.8% were canonical SJs. We identified that novel isoforms accounted for 19% of all isoforms, among which 12% fell within coding regions. The dwarf soybean demonstrated a greater number of isoforms in most of the annotated genes, particularly in genes related to growth hormones and defense responses. Our study provides comprehensive isoform and gene information that may accelerate transcriptome research in <i<G. max</i< and provide a basis to further study the impact of these isoforms on plant growth.
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title_short	Alternative Splicing (AS) Dynamics in Dwarf Soybean Derived from Cross of <i<Glycine max</i< and <i<Glycine soja</i<
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Alternative Splicing (AS) Dynamics in Dwarf Soybean Derived from Cross of <i<Glycine max</i< and <i<Glycine soja</i<

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