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3. Integrating omics databases for enhanced crop breeding

Author

Chao Haoyu, Zhang Shilong, Hu Yueming, Ni Qingyang, Xin Saige, Zhao Liang, Ivanisenko Vladimir A., Orlov Yuriy L., and Chen Ming

Subjects
crop plant breeding, data integration, databases, omics, plant biology, Biotechnology, TP248.13-248.65
Abstract

Crop plant breeding involves selecting and developing new plant varieties with desirable traits such as increased yield, improved disease resistance, and enhanced nutritional value. With the development of high-throughput technologies, such as genomics, transcriptomics, and metabolomics, crop breeding has entered a new era. However, to effectively use these technologies, integration of multi-omics data from different databases is required. Integration of omics data provides a comprehensive understanding of the biological processes underlying plant traits and their interactions. This review highlights the importance of integrating omics databases in crop plant breeding, discusses available omics data and databases, describes integration challenges, and highlights recent developments and potential benefits. Taken together, the integration of omics databases is a critical step towards enhancing crop plant breeding and improving global food security.

Published
2023
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4. A chromosome-level genome assembly provides insights into Cornus wilsoniana evolution, oil biosynthesis and floral bud development

Author

He, Zhenxiang, primary, Chao, Haoyu, additional, Zhou, Xinkai, additional, Ni, Qingyang, additional, Hu, Yueming, additional, Yu, Ranran, additional, Wang, Minghuai, additional, Li, Changzhu, additional, Chen, Jingzhen, additional, Chen, Yunzhu, additional, Chen, Yong, additional, Cui, Chunyi, additional, Zhang, Liangbo, additional, Chen, Ming, additional, and Chen, Dijun, additional

Published
2023
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6. A chromosome-level genome assembly provides insights into Cornus wilsonianaevolution, oil biosynthesis, and floral bud development

Author

He, Zhenxiang, Chao, Haoyu, Zhou, Xinkai, Ni, Qingyang, Hu, Yueming, Yu, Ranran, Wang, Minghuai, Li, Changzhu, Chen, Jingzhen, Chen, Yunzhu, Chen, Yong, Cui, Chunyi, Zhang, Liangbo, Chen, Ming, and Chen, Dijun

Abstract

Cornus wilsonianaW. is a woody oil plant with high oil content and strong hypolipidemic effects, making it a valuable species for medicinal, landscaping, and ecological purposes in China. To advance genetic research on this species, we employed PacBio together with Hi-C data to create a draft genome assembly for C. wilsoniana. Based on an 11-chromosome anchored chromosome-level assembly, the estimated genome size was determined to be 843.51 Mb. The N50 contig size and N50 scaffold size were calculated to be 4.49 and 78.00 Mb, respectively. Furthermore, 30 474 protein-coding genes were annotated. Comparative genomics analysis revealed that C. wilsonianadiverged from its closest species ~12.46 million years ago (Mya). Furthermore, the divergence between Cornaceae and Nyssaceae occurred >62.22 Mya. We also found evidence of whole-genome duplication events and whole-genome triplication γ, occurring at ~44.90 and 115.86 Mya. We further inferred the origins of chromosomes, which sheds light on the complex evolutionary history of the karyotype of C. wilsoniana. Through transcriptional and metabolic analysis, we identified two FAD2homologous genes that may play a crucial role in controlling the oleic to linoleic acid ratio. We further investigated the correlation between metabolites and genes and identified 33 MADS-TF homologous genes that may affect flower morphology in C. wilsoniana. Overall, this study lays the groundwork for future research aimed at identifying the genetic basis of crucial traits in C. wilsoniana.

Published
2023
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