Comparative Transcriptomics of Non-Embryogenic and Embryogenic Callus in Semi-Recalcitrant and Non-Recalcitrant Upland Cotton Lines

Somatic embryogenesis-mediated plant regeneration is essential for the genetic manipulation of agronomically important traits in upland cotton. Genotype specific recalcitrance to regeneration is a primary challenge in deploying genome editing and incorporating useful transgenes into elite cotton ger...

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Autores principales: Kumar, Sonika, Ruggles, Ashleigh, Logan, Sam, Mazarakis, Alora, Tyson, Thomas, Bates, Matthew, Grosse, Clayton, Reed, David, Li, Zhigang, Grimwood, Jane, Schmutz, Jeremy, Saski, Christopher
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8472754/
https://www.ncbi.nlm.nih.gov/pubmed/34579308
http://dx.doi.org/10.3390/plants10091775
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author Kumar, Sonika
Ruggles, Ashleigh
Logan, Sam
Mazarakis, Alora
Tyson, Thomas
Bates, Matthew
Grosse, Clayton
Reed, David
Li, Zhigang
Grimwood, Jane
Schmutz, Jeremy
Saski, Christopher
author_facet Kumar, Sonika
Ruggles, Ashleigh
Logan, Sam
Mazarakis, Alora
Tyson, Thomas
Bates, Matthew
Grosse, Clayton
Reed, David
Li, Zhigang
Grimwood, Jane
Schmutz, Jeremy
Saski, Christopher
author_sort Kumar, Sonika
collection PubMed
description Somatic embryogenesis-mediated plant regeneration is essential for the genetic manipulation of agronomically important traits in upland cotton. Genotype specific recalcitrance to regeneration is a primary challenge in deploying genome editing and incorporating useful transgenes into elite cotton germplasm. In this study, transcriptomes of a semi-recalcitrant cotton (Gossypium hirsutum L.) genotype ‘Coker312’ were analyzed at two critical stages of somatic embryogenesis that include non-embryogenic callus (NEC) and embryogenic callus (EC) cells, and the results were compared to a non-recalcitrant genotype ‘Jin668’. We discovered 305 differentially expressed genes in Coker312, whereas, in Jin668, about 6-fold more genes (2155) were differentially expressed. A total of 154 differentially expressed genes were common between the two genotypes. Gene enrichment analysis of the upregulated genes identified functional categories, such as lipid transport, embryo development, regulation of transcription, sugar transport, and vitamin biosynthesis, among others. In Coker312 EC cells, five major transcription factors were highly upregulated: LEAFY COTYLEDON 1 (LEC1), WUS-related homeobox 5 (WOX5), ABSCISIC ACID INSENSITIVE3 (ABI3), FUSCA3 (FUS3), and WRKY2. In Jin668, LEC1, BABY BOOM (BBM), FUS3, and AGAMOUS-LIKE15 (AGL15) were highly expressed in EC cells. We also found that gene expression of these embryogenesis genes was typically higher in Jin668 when compared to Coker312. We conclude that significant differences in the expression of the above genes between Coker312 and Jin668 may be a critical factor affecting the regenerative ability of these genotypes.
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spelling pubmed-84727542021-09-28 Comparative Transcriptomics of Non-Embryogenic and Embryogenic Callus in Semi-Recalcitrant and Non-Recalcitrant Upland Cotton Lines Kumar, Sonika Ruggles, Ashleigh Logan, Sam Mazarakis, Alora Tyson, Thomas Bates, Matthew Grosse, Clayton Reed, David Li, Zhigang Grimwood, Jane Schmutz, Jeremy Saski, Christopher Plants (Basel) Article Somatic embryogenesis-mediated plant regeneration is essential for the genetic manipulation of agronomically important traits in upland cotton. Genotype specific recalcitrance to regeneration is a primary challenge in deploying genome editing and incorporating useful transgenes into elite cotton germplasm. In this study, transcriptomes of a semi-recalcitrant cotton (Gossypium hirsutum L.) genotype ‘Coker312’ were analyzed at two critical stages of somatic embryogenesis that include non-embryogenic callus (NEC) and embryogenic callus (EC) cells, and the results were compared to a non-recalcitrant genotype ‘Jin668’. We discovered 305 differentially expressed genes in Coker312, whereas, in Jin668, about 6-fold more genes (2155) were differentially expressed. A total of 154 differentially expressed genes were common between the two genotypes. Gene enrichment analysis of the upregulated genes identified functional categories, such as lipid transport, embryo development, regulation of transcription, sugar transport, and vitamin biosynthesis, among others. In Coker312 EC cells, five major transcription factors were highly upregulated: LEAFY COTYLEDON 1 (LEC1), WUS-related homeobox 5 (WOX5), ABSCISIC ACID INSENSITIVE3 (ABI3), FUSCA3 (FUS3), and WRKY2. In Jin668, LEC1, BABY BOOM (BBM), FUS3, and AGAMOUS-LIKE15 (AGL15) were highly expressed in EC cells. We also found that gene expression of these embryogenesis genes was typically higher in Jin668 when compared to Coker312. We conclude that significant differences in the expression of the above genes between Coker312 and Jin668 may be a critical factor affecting the regenerative ability of these genotypes. MDPI 2021-08-26 /pmc/articles/PMC8472754/ /pubmed/34579308 http://dx.doi.org/10.3390/plants10091775 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Kumar, Sonika
Ruggles, Ashleigh
Logan, Sam
Mazarakis, Alora
Tyson, Thomas
Bates, Matthew
Grosse, Clayton
Reed, David
Li, Zhigang
Grimwood, Jane
Schmutz, Jeremy
Saski, Christopher
Comparative Transcriptomics of Non-Embryogenic and Embryogenic Callus in Semi-Recalcitrant and Non-Recalcitrant Upland Cotton Lines
title Comparative Transcriptomics of Non-Embryogenic and Embryogenic Callus in Semi-Recalcitrant and Non-Recalcitrant Upland Cotton Lines
title_full Comparative Transcriptomics of Non-Embryogenic and Embryogenic Callus in Semi-Recalcitrant and Non-Recalcitrant Upland Cotton Lines
title_fullStr Comparative Transcriptomics of Non-Embryogenic and Embryogenic Callus in Semi-Recalcitrant and Non-Recalcitrant Upland Cotton Lines
title_full_unstemmed Comparative Transcriptomics of Non-Embryogenic and Embryogenic Callus in Semi-Recalcitrant and Non-Recalcitrant Upland Cotton Lines
title_short Comparative Transcriptomics of Non-Embryogenic and Embryogenic Callus in Semi-Recalcitrant and Non-Recalcitrant Upland Cotton Lines
title_sort comparative transcriptomics of non-embryogenic and embryogenic callus in semi-recalcitrant and non-recalcitrant upland cotton lines
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8472754/
https://www.ncbi.nlm.nih.gov/pubmed/34579308
http://dx.doi.org/10.3390/plants10091775
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