Prospects and challenges of epigenomics in crop improvement

다국어 초록 (Multilingual 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.

참고문헌 (Reference)

1 Zhang P, "eRice : a refined epigenomic platform for japonica and indica rice" 18 : 1642-1644, 2020

2 Huang C, "ZmCCT9 enhances maize adaptation to higher latitudes" 115 : E334-E341, 2017

3 Ricci WA, "Widespread long-range cis-regulatory elements in the maize genome" 5 : 1237-1249, 2019

4 Concia L, "Wheat chromatin architecture is organized in genome territories and transcription factories" 21 : 104-, 2020

5 Khush GS, "What it will take to feed 5. 0 billion rice consumers in 2030" 59 : 1-6, 2005

6 Ramírez-González RH, "The transcriptional landscape of polyploid wheat" 361 : eaar6089-, 2018

7 Lu Z, "The prevalence, evolution and chromatin signatures of plant regulatory elements" 5 : 1250-1259, 2019

8 International Rice Genome Sequencing, P, "The map-based sequence of the rice genome" 436 : 793-800, 2005

9 Van de Peer Y, "The evolutionary significance of polyploidy" 18 : 411-424, 2017

10 HenikoffS, "The centromere paradox stable inheritance with rapidly evolving DNA" 293 : 1098-1102, 2001

11 Li Z, "The bread wheat epigenomic map reveals distinct chromatin architectural and evolutionary features of functional genetic elements" 20 : 139-, 2019

12 Xu W, "The R-loop is a common chromatin feature of the Arabidopsis genome" 3 : 704-714, 2017

13 Schnable PS, "The B73 maize genome complexity, diversity, and dynamics" 326 : 1112-1116, 2009

14 Ha M, "Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids" 106 : 17835-17840, 2009

15 IWGSC, "Shifting the limits in wheat research and breeding using a fully annotated reference genome" 361 : eaar7191-, 2018

16 Xie L, "RiceENCODE : a comprehensive epigenomic database as a rice encyclopedia of DNA elements" 14 : 1604-1606, 2021

17 Han F, "Rapid and repeatable elimination of a parental genome-specific DNA repeat(pGc1R-1a)in newly synthesized wheat allopolyploids" 170 : 1239-1245, 2005

18 Zheng L, "Prolonged expression of the BX1 signature enzyme is associated with a recombination hotspot in the benzoxazinoid gene cluster in Zea mays" 66 : 3917-3930, 2015

19 de Souza LP, "Plant single-cell metabolomics-challenges and perspectives" 21 : 8987-, 2020

20 Ran X, "Plant regulomics : a data-driven interface for retrieving upstream regulators from plant multi-omics data" 101 : 237-248, 2020

21 Bayer PE, "Plant pan-genomes are the new reference" 6 : 914-920, 2020

22 Gu H, "PRIN : a predicted rice interactome network" 12 : 161-, 2011

23 Liu Y, "PCSD : a plant chromatin state database" 46 : D1157-D1167, 2018

24 Wang M, "Multi-omics maps of cotton fibre reveal epigenetic basis for staged single-cell differentiation" 44 : 4067-4079, 2016

25 van Dijk ADJ, "Machine learning in plant science and plant breeding" 24 : 101890-, 2021

26 Li E, "Long-range interactions between proximal and distal regulatory regions in maize" 10 : 2633-, 2019

27 Scott MF, "Limited haplotype diversity underlies polygenic trait architecture across 70 years of wheat breeding" 22 : 137-, 2021

28 Zhao L, "Integrative analysis of reference epigenomes in 20 rice varieties" 11 : 2658-, 2020

29 Davis-Richardson AG, "Integrating DNA methylation and hene expression data in the development of the soybean-bradyrhizobium N2-fixing symbiosis" 7 : 518-, 2016

30 Studer A, "Identification of a functional transposon insertion in the maize domestication gene tb1" 43 : 1160-1163, 2011

31 Thomas M, "Hybridization of RNA to double-stranded DNA_ formation of R-loops" 73 : 2294-2298, 1976

32 Jia J, "Homology-mediated inter-chromosomal interactions in hexaploid wheat lead to specific subgenome territories following polyploidization and introgression" 22 : 26-, 2021

33 Gaeta RT, "Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype" 19 : 3403-3417, 2007

34 Jackson S, "Genomic and expression plasticity of polyploidy" 13 : 153-159, 2010

35 Liu Y, "Genome-wide mapping reveals R-loops associated with centromeric repeats in maize" 31 : 1409-1418, 2021

36 Zhang Y, "Evolutionary rewiring of the wheat transcriptional regulatory network by lineage-specific transposable elements" 2021

37 Zhou Y, "Epigenomic reprogramming in cardiovascular disease" 9 : 149-163, 2019

38 Baum BR, "Elimination of 5S DNA unit classes in newly formed allopolyploids of the genera Aegilops and Triticum" 53 : 430-438, 2010

39 Liu W, "Ectopic targeting of CG DNA methylation in Arabidopsis with the bacterial SssI methyltransferase" 12 : 3130-, 2021

40 Wilkins O, "EGRINs(environmental gene regulatory influence networks)in rice that function in the response to water deficit, high temperature, and agricultural environments" 28 : 2365-2384, 2016

41 Yuan J, "Dynamic and reversible DNA methylation changes induced by genome separation and merger of polyploid wheat" 18 : 171-, 2020

42 Zhao Y, "Distinct nucleotide patterns among three subgenomes of bread wheat and their potential origins during domestication after allopolyploidization" 18 : 188-, 2020

43 Song B, "Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize" 31 : 1245-1257, 2021

44 Salvi S, "Conserved noncoding genomic sequences associated with a floweringtime quantitative trait locus in maize" 104 : 11376-11381, 2007

45 Pontes O, "Chromosomal locus rearrangements are a rapid response to formation of the allotetraploid Arabidopsis suecica genome" 101 : 18240-18245, 2004

46 Zhao L, "Chromatin loops associated with active genes and heterochromatin shape rice genome architecture for transcriptional regulation" 10 : 3640-, 2019

47 Peng Y, "Chromatin interaction maps reveal genetic regulation for quantitative traits in maize" 10 : 2632-, 2019

48 Fang Y, "Characterization of functional relationships of R-loops with gene transcription and epigenetic modifications in rice" 29 : 1287-1297, 2019

49 Topp CN, "Centromere-encoded RNAs are integral components of the maize kinetochore" 101 : 15986-15991, 2004

50 Ghoshal B, "CRISPRbased targeting of DNA methylation in Arabidopsis thaliana by a bacterial CG-specific DNA methyltransferase" 118 : e2125016118-, 2021

51 Pulecio J, "CRISPR/Cas9-based engineering of the epigenome" 21 : 431-447, 2017

52 Qi M, "CGT-seq : epigenome-guided de novo assembly of the core genome for divergent populations with large genome" 46 : e107-, 2018

53 Guo X, "Asymmetric epigenetic modification and elimination of rDNA sequences by polyploidization in wheat" 26 : 4311-4327, 2014

54 Fullwood MJ, "An oestrogen-receptoralpha-bound human chromatin interactome" 462 : 58-64, 2009

55 Wang M, "An atlas of wheat epigenetic regulatory elements reveals subgenome divergence in the regulation of development and stress responses" 33 : 865-881, 2021

56 Buenrostro JD, "ATAC-seq : a method for assaying chromatin accessibility genome-wide" 109 : 21.29.21-21.29.29, 2015

57 Marand AP, "A cisregulatory atlas in maize at single-cell resolution" 184 : 3041-3055, 2021