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Article

The Integrated Analysis of miRNome and Degradome Sequencing Reveals the Regulatory Mechanisms of Seed Development and Oil Biosynthesis in Pecan (Carya illinoinensis)

by
Kaikai Zhu
1,
Lu Wei
1,
Wenjuan Ma
1,
Juan Zhao
1,
Mengyun Chen
1,
Guo Wei
2,
Hui Liu
3,
Pengpeng Tan
1 and
Fangren Peng
1,*
1
Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
2
College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
3
State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
*
Author to whom correspondence should be addressed.
Foods 2024, 13(18), 2934; https://doi.org/10.3390/foods13182934
Submission received: 29 July 2024 / Revised: 8 September 2024 / Accepted: 15 September 2024 / Published: 16 September 2024
(This article belongs to the Section Foodomics)
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Abstract

Pecan seed oil is a valuable source of essential fatty acids and various bioactive compounds; however, the functions of microRNAs and their targets in oil biosynthesis during seed development are still unknown. Here, we found that the oil content increased rapidly in the three early stages in three cultivars, and that oleic acid was the predominant fatty acid component in the mature pecan embryos. We identified, analyzed, and validated the expression levels of miRNAs related to seed development and oil biosynthesis, as well as their potential target genes, using small RNA sequencing data from three stages (120, 135, and 150 days after flowering). During the seed development process, 365 known and 321 novel miRNAs were discovered. In total, 91 known and 181 novel miRNAs were found to be differentially expressed, and 633 target genes were further investigated. The expression trend analysis revealed that the 91 known miRNAs were classified into eight groups, approximately two-thirds of which were up-regulated, whereas most novel miRNAs were down-regulated. The qRT–PCR and degradome sequencing data were used to identify five miRNA- target pairs. Overall, our study provides valuable insights into the molecular regulation of oil biosynthesis in pecan seeds.
Keywords: Carya illinoinensis; expression patterns; microRNA; oil biosynthesis; seed development Carya illinoinensis; expression patterns; microRNA; oil biosynthesis; seed development

Share and Cite

MDPI and ACS Style

Zhu, K.; Wei, L.; Ma, W.; Zhao, J.; Chen, M.; Wei, G.; Liu, H.; Tan, P.; Peng, F. The Integrated Analysis of miRNome and Degradome Sequencing Reveals the Regulatory Mechanisms of Seed Development and Oil Biosynthesis in Pecan (Carya illinoinensis). Foods 2024, 13, 2934. https://doi.org/10.3390/foods13182934

AMA Style

Zhu K, Wei L, Ma W, Zhao J, Chen M, Wei G, Liu H, Tan P, Peng F. The Integrated Analysis of miRNome and Degradome Sequencing Reveals the Regulatory Mechanisms of Seed Development and Oil Biosynthesis in Pecan (Carya illinoinensis). Foods. 2024; 13(18):2934. https://doi.org/10.3390/foods13182934

Chicago/Turabian Style

Zhu, Kaikai, Lu Wei, Wenjuan Ma, Juan Zhao, Mengyun Chen, Guo Wei, Hui Liu, Pengpeng Tan, and Fangren Peng. 2024. "The Integrated Analysis of miRNome and Degradome Sequencing Reveals the Regulatory Mechanisms of Seed Development and Oil Biosynthesis in Pecan (Carya illinoinensis)" Foods 13, no. 18: 2934. https://doi.org/10.3390/foods13182934

APA Style

Zhu, K., Wei, L., Ma, W., Zhao, J., Chen, M., Wei, G., Liu, H., Tan, P., & Peng, F. (2024). The Integrated Analysis of miRNome and Degradome Sequencing Reveals the Regulatory Mechanisms of Seed Development and Oil Biosynthesis in Pecan (Carya illinoinensis). Foods, 13(18), 2934. https://doi.org/10.3390/foods13182934

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