Prospects and challenges of epigenomics in crop improvement

doi:10.1007/s13258-021-01187-9

Review

. 2022 Mar;44(3):251-257.

doi: 10.1007/s13258-021-01187-9. Epub 2021 Nov 27.

Prospects and challenges of epigenomics in crop improvement

Yuhong Huang^{1

2}, Yang Liu¹, Chang Liu^{1

2}, James A Birchler³, Fangpu Han^{4

5}

Affiliations

¹ State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
² University of Chinese Academy of Sciences, Beijing, 100049, China.
³ Division of Biological Sciences, University of Missouri at Columbia, Columbia, MO, 65211, USA.
⁴ State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China. fphan@genetics.ac.cn.
⁵ University of Chinese Academy of Sciences, Beijing, 100049, China. fphan@genetics.ac.cn.

PMID: 34837632
DOI: 10.1007/s13258-021-01187-9

Review

Prospects and challenges of epigenomics in crop improvement

Yuhong Huang et al. Genes Genomics. 2022 Mar.

. 2022 Mar;44(3):251-257.

doi: 10.1007/s13258-021-01187-9. Epub 2021 Nov 27.

Authors

Yuhong Huang^{1

2}, Yang Liu¹, Chang Liu^{1

2}, James A Birchler³, Fangpu Han^{4

5}

Affiliations

¹ State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
² University of Chinese Academy of Sciences, Beijing, 100049, China.
³ Division of Biological Sciences, University of Missouri at Columbia, Columbia, MO, 65211, USA.
⁴ State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China. fphan@genetics.ac.cn.
⁵ University of Chinese Academy of Sciences, Beijing, 100049, China. fphan@genetics.ac.cn.

PMID: 34837632
DOI: 10.1007/s13258-021-01187-9

Abstract

Background: The advent of high-throughput epigenome mapping techniques has ushered in a new era of multiomics with powerful tools now available to map and record genomic output at different levels. Integrating the different components of the epigenome from these multiomics measures allows investigations of cis-regulatory elements on a genome-scale. Mapping of chromatin state, chromatin accessibility dynamics, and higher-order chromatin structure enables a new level of understanding of cell fate determination, identity and function in normal growth and development, disease resistance, and yield.

Objective: In this paper, the recent advances in epigenomics research of rice, maize, and wheat are reviewed, and the development trends of epigenomics of major crops in the coming years are projected.

Methods: We highlight the role of epigenomics in regulating growth and development and identifying potential distal cis-regulatory elements in three major crops, and discuss the prospects and challenges for new epigenetics-mediated breeding technologies in crop improvement.

Conclusion: In this review, we summarize and analyze recent epigenomic advances in three major crops epigenomics and discuss possibilities and challenges for future research in the field.

Keywords: Crop improvement; Epigenomics; Maize; Rice; Wheat.

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References

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1. Bayer PE, Golicz AA, Scheben A, Batley J, Edwards D (2020) Plant pan-genomes are the new reference. Nat Plants 6:914–920 - PubMed
1. Buenrostro JD, Wu B, Chang HY, Greenleaf WJ (2015) ATAC-seq: a method for assaying chromatin accessibility genome-wide. Curr Protoc Mol Biol 109:21.29.21-21.29.29
1. Concia L, Veluchamy A, Ramirez-Prado JS, Martin-Ramirez A, Huang Y, Perez M, Domenichini S, Rodriguez NY, Granados S, Kim T, Blein et al (2020) Wheat chromatin architecture is organized in genome territories and transcription factories. Genome Biol 21:104 - PubMed - PMC
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[1] Baum BR, Feldman M (2010) Elimination of 5S DNA unit classes in newly formed allopolyploids of the genera Aegilops and Triticum. Genome 53:430–438 - PubMed

[2] Baum BR, Feldman M (2010) Elimination of 5S DNA unit classes in newly formed allopolyploids of the genera Aegilops and Triticum. Genome 53:430–438 - PubMed

[3] Bayer PE, Golicz AA, Scheben A, Batley J, Edwards D (2020) Plant pan-genomes are the new reference. Nat Plants 6:914–920 - PubMed

[4] Bayer PE, Golicz AA, Scheben A, Batley J, Edwards D (2020) Plant pan-genomes are the new reference. Nat Plants 6:914–920 - PubMed

[5] Buenrostro JD, Wu B, Chang HY, Greenleaf WJ (2015) ATAC-seq: a method for assaying chromatin accessibility genome-wide. Curr Protoc Mol Biol 109:21.29.21-21.29.29

[6] Buenrostro JD, Wu B, Chang HY, Greenleaf WJ (2015) ATAC-seq: a method for assaying chromatin accessibility genome-wide. Curr Protoc Mol Biol 109:21.29.21-21.29.29

[7] Concia L, Veluchamy A, Ramirez-Prado JS, Martin-Ramirez A, Huang Y, Perez M, Domenichini S, Rodriguez NY, Granados S, Kim T, Blein et al (2020) Wheat chromatin architecture is organized in genome territories and transcription factories. Genome Biol 21:104 - PubMed - PMC

[8] Concia L, Veluchamy A, Ramirez-Prado JS, Martin-Ramirez A, Huang Y, Perez M, Domenichini S, Rodriguez NY, Granados S, Kim T, Blein et al (2020) Wheat chromatin architecture is organized in genome territories and transcription factories. Genome Biol 21:104 - PubMed - PMC

[9] Davis-Richardson AG, Russell JT, Dias R, McKinlay AJ, Canepa R, Fagen JR, Rusoff KT, Drew JC, Kolaczkowski B, Emerich DW et al (2016) Integrating DNA methylation and hene expression data in the development of the soybean-bradyrhizobium N2-fixing symbiosis. Front Microbiol 7:518 - PubMed - PMC

[10] Davis-Richardson AG, Russell JT, Dias R, McKinlay AJ, Canepa R, Fagen JR, Rusoff KT, Drew JC, Kolaczkowski B, Emerich DW et al (2016) Integrating DNA methylation and hene expression data in the development of the soybean-bradyrhizobium N2-fixing symbiosis. Front Microbiol 7:518 - PubMed - PMC

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Prospects and challenges of epigenomics in crop improvement

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Prospects and challenges of epigenomics in crop improvement

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