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Article

Bulk RNA-Seq Analysis Reveals Differentially Expressed Genes Associated with Lateral Branch Angle in Peanut

by
Naveed Ahmad
1,†,
Lei Hou
1,2,†,
Junjie Ma
1,
Ximeng Zhou
2,
Han Xia
1,
Mingxiao Wang
2,
Soraya Leal-Bertioli
3,4,
Shuzhen Zhao
1,
Ruizheng Tian
1,
Jiaowen Pan
1,
Changsheng Li
1,
Aiqin Li
1,
David Bertioli
3,5,
Xingjun Wang
1,2 and
Chuanzhi Zhao
1,2,*
1
Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, China
2
College of Life Sciences, Shandong Normal University, Jinan 250014, China
3
Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA
4
Department of Plant Pathology, University of Georgia, Athens, GA 31793, USA
5
Department of Crop and Soil Science, University of Georgia, Athens, GA 30602, USA
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Genes 2022, 13(5), 841; https://doi.org/10.3390/genes13050841
Submission received: 17 April 2022 / Revised: 1 May 2022 / Accepted: 5 May 2022 / Published: 8 May 2022
(This article belongs to the Special Issue Discovery and Exploration of Functional Genes in Oil Crops)
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Abstract

Lateral branch angle (LBA), or branch habit, is one of the most important agronomic traits in peanut. To date, the underlying molecular mechanisms of LBA have not been elucidated in peanut. To acquire the differentially expressed genes (DEGs) related to LBA, a TI population was constructed through the hybridization of a bunch-type peanut variety Tifrunner and prostrate-type Ipadur. We report the identification of DEGs related to LBA by sequencing two RNA pools, which were composed of 45 F3 lines showing an extreme opposite bunch and prostrate phenotype. We propose to name this approach Bulk RNA-sequencing (BR-seq) as applied to several plant species. Through BR-seq analysis, a total of 3083 differentially expressed genes (DEGs) were identified, including 13 gravitropism-related DEGs, 22 plant hormone-related DEGs, and 55 transcription factors-encoding DEGs. Furthermore, we also identified commonly expressed alternatively spliced (AS) transcripts, of which skipped exon (SE) and retained intron (RI) were most abundant in the prostrate and bunch-type peanut. AS isoforms between prostrate and bunch peanut highlighted important clues to further understand the post-transcriptional regulatory mechanisms of branch angle regulation. Our findings provide not only important insights into the landscape of the regulatory pathway involved in branch angle formation but also present practical information for peanut molecular breeding in the future.
Keywords: bulk RNA-sequencing (BR-seq); branch angle; gravitropism; plant hormones; alternative splicing; peanut bulk RNA-sequencing (BR-seq); branch angle; gravitropism; plant hormones; alternative splicing; peanut

Share and Cite

MDPI and ACS Style

Ahmad, N.; Hou, L.; Ma, J.; Zhou, X.; Xia, H.; Wang, M.; Leal-Bertioli, S.; Zhao, S.; Tian, R.; Pan, J.; et al. Bulk RNA-Seq Analysis Reveals Differentially Expressed Genes Associated with Lateral Branch Angle in Peanut. Genes 2022, 13, 841. https://doi.org/10.3390/genes13050841

AMA Style

Ahmad N, Hou L, Ma J, Zhou X, Xia H, Wang M, Leal-Bertioli S, Zhao S, Tian R, Pan J, et al. Bulk RNA-Seq Analysis Reveals Differentially Expressed Genes Associated with Lateral Branch Angle in Peanut. Genes. 2022; 13(5):841. https://doi.org/10.3390/genes13050841

Chicago/Turabian Style

Ahmad, Naveed, Lei Hou, Junjie Ma, Ximeng Zhou, Han Xia, Mingxiao Wang, Soraya Leal-Bertioli, Shuzhen Zhao, Ruizheng Tian, Jiaowen Pan, and et al. 2022. "Bulk RNA-Seq Analysis Reveals Differentially Expressed Genes Associated with Lateral Branch Angle in Peanut" Genes 13, no. 5: 841. https://doi.org/10.3390/genes13050841

APA Style

Ahmad, N., Hou, L., Ma, J., Zhou, X., Xia, H., Wang, M., Leal-Bertioli, S., Zhao, S., Tian, R., Pan, J., Li, C., Li, A., Bertioli, D., Wang, X., & Zhao, C. (2022). Bulk RNA-Seq Analysis Reveals Differentially Expressed Genes Associated with Lateral Branch Angle in Peanut. Genes, 13(5), 841. https://doi.org/10.3390/genes13050841

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