Working Paper Article Version 1 This version is not peer-reviewed

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

Version 1 : Received: 19 July 2021 / Approved: 20 July 2021 / Online: 20 July 2021 (15:30:47 CEST)

How to cite: Kumar, S.; Ruggles, A.; Logan, S.; Mazarakis, A.; Thomas, T.; Bates, M.; Reed, D.; Grosse, C.; Li, Z.; Grimwood, J.; Schmutz, J.; Saski, C.A. Comparative Transcriptomics of Non-Embryogenic and Embryogenic Callus in Semi-Recalcitrant and Non-Recalcitrant Upland Cotton Lines. Preprints 2021, 2021070459 Kumar, S.; Ruggles, A.; Logan, S.; Mazarakis, A.; Thomas, T.; Bates, M.; Reed, D.; Grosse, C.; Li, Z.; Grimwood, J.; Schmutz, J.; Saski, C.A. Comparative Transcriptomics of Non-Embryogenic and Embryogenic Callus in Semi-Recalcitrant and Non-Recalcitrant Upland Cotton Lines. Preprints 2021, 2021070459

Abstract

Somatic embryogenesis-mediated plant regeneration is essential for 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 includes non-embryogenic callus (NEC) and embryogenic callus (EC) cells, and the results compared to a non-recalcitrant genotype ‘Jin668’. We discovered of 305 differentially expressed genes in Coker312, whereas, in Jin668, about 6-fold more genes (2,155) were differentially expressed. A total of 154 differentially expressed genes were common between the two genotypes. Gene enrichment analysis of upregulated genes identified functional categories such as lipid transport, embryo development, regulation of transcription, sugar transport, 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 expression of the above genes between Coker312 and Jin668 may be a critical factor affecting the regenerative ability of these genotypes.

Subject Areas

callus; genotype-specific recalcitrance; reprogramming; somatic embryogenesis; transcriptomics; upland cotton

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