Suppr超能文献

跨基因型的印记表达保守性与玉米胚乳发育过程中印记的一致性相关。

Conservation of imprinted expression across genotypes is correlated with consistency of imprinting across endosperm development in maize.

作者信息

Higgins Kaitlin, Nyabashi Vital, Anderson Sarah

机构信息

Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50010, USA.

出版信息

G3 (Bethesda). 2025 Apr 17;15(4). doi: 10.1093/g3journal/jkaf028.

Abstract

Imprinted expression is an essential process for seed viability affecting hundreds of genes in Zea mays endosperm; however, most studies have examined just one time point for analysis. The focus on single time points can limit our ability to identify imprinted genes and our ability to draw conclusions for the role of imprinting in endosperm. In this study, we examine imprinted expression across 4 time points ranging from the transition to endoreduplication from mitotic division through the beginning of programmed cell death. Additionally, we assessed imprinting variation across 8 diverse maize lines, 6 of which have never before been assessed for imprinting. Through this analysis, we identify over 700 imprinted genes with varying consistency across time points including 255 genes imprinted at every time point and 105 genes displaying transient imprinting. We find a correlation between high consistency of imprinting across time and high conservation of parental bias across 8 diverse maize lines reciprocally crossed with B73. Additionally, we identify evidence of imprinting for 3 zein genes that are critical for nutrient accumulation in the endosperm, suggesting that imprinting may play a more important role in seed composition than previously thought. Taken together, this study provides a more holistic view of imprinting variation across time and across genotypes in maize and enables us to more thoroughly investigate the complex imprinting landscape.

摘要

印记表达是影响玉米胚乳中数百个基因种子活力的一个重要过程;然而,大多数研究仅考察了一个时间点进行分析。对单个时间点的关注可能会限制我们识别印记基因的能力以及我们就印记在胚乳中的作用得出结论的能力。在本研究中,我们考察了从有丝分裂向核内复制转变直至程序性细胞死亡开始这4个时间点的印记表达。此外,我们评估了8个不同玉米品系的印记变异,其中6个品系此前从未进行过印记评估。通过该分析,我们鉴定出700多个在不同时间点具有不同一致性的印记基因,包括在每个时间点都有印记的255个基因和显示瞬时印记的105个基因。我们发现,在与B73相互杂交的8个不同玉米品系中,印记在时间上的高一致性与亲本偏向的高保守性之间存在相关性。此外,我们鉴定出3个对胚乳营养积累至关重要的醇溶蛋白基因的印记证据,这表明印记在种子组成中可能比之前认为的发挥更重要的作用。综上所述,本研究提供了一个关于玉米中印记变异在时间和基因型上的更全面的观点,并使我们能够更彻底地研究复杂的印记格局。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fe05/12005164/90c91b5995f5/jkaf028f1.jpg

相似文献

2
Sequential gene activation and gene imprinting during early embryo development in maize.
Plant J. 2018 Feb;93(3):445-459. doi: 10.1111/tpj.13786. Epub 2018 Jan 7.
3
The conservation of allelic DNA methylation and its relationship with imprinting in maize.
J Exp Bot. 2024 Feb 28;75(5):1376-1389. doi: 10.1093/jxb/erad440.
4
Widespread imprinting of transposable elements and variable genes in the maize endosperm.
PLoS Genet. 2021 Apr 8;17(4):e1009491. doi: 10.1371/journal.pgen.1009491. eCollection 2021 Apr.
5
Imprinted gene expression in maize starchy endosperm and aleurone tissues of reciprocal F1 hybrids at a defined developmental stage.
Genes Genomics. 2018 Jan;40(1):99-107. doi: 10.1007/s13258-017-0613-9. Epub 2017 Sep 30.
7
Parent-of-origin effects on gene expression and DNA methylation in the maize endosperm.
Plant Cell. 2011 Dec;23(12):4221-33. doi: 10.1105/tpc.111.092668. Epub 2011 Dec 23.
8
Extensive, clustered parental imprinting of protein-coding and noncoding RNAs in developing maize endosperm.
Proc Natl Acad Sci U S A. 2011 Dec 13;108(50):20042-7. doi: 10.1073/pnas.1112186108. Epub 2011 Nov 23.
9
Comprehensive analysis of imprinted genes in maize reveals allelic variation for imprinting and limited conservation with other species.
Proc Natl Acad Sci U S A. 2013 Nov 26;110(48):19639-44. doi: 10.1073/pnas.1309182110. Epub 2013 Nov 11.
10
Conservation Study of Imprinted Genes in Maize Triparental Heterozygotic Kernels.
Int J Mol Sci. 2022 Dec 6;23(23):15424. doi: 10.3390/ijms232315424.

本文引用的文献

2
A pan-genomic approach to genome databases using maize as a model system.
BMC Plant Biol. 2021 Aug 20;21(1):385. doi: 10.1186/s12870-021-03173-5.
3
Widespread imprinting of transposable elements and variable genes in the maize endosperm.
PLoS Genet. 2021 Apr 8;17(4):e1009491. doi: 10.1371/journal.pgen.1009491. eCollection 2021 Apr.
4
Maize endosperm development.
J Integr Plant Biol. 2021 Apr;63(4):613-627. doi: 10.1111/jipb.13069. Epub 2021 Mar 8.
5
Using multiple reference genomes to identify and resolve annotation inconsistencies.
BMC Genomics. 2020 Apr 8;21(1):281. doi: 10.1186/s12864-020-6696-8.
6
The regulation of zein biosynthesis in maize endosperm.
Theor Appl Genet. 2020 May;133(5):1443-1453. doi: 10.1007/s00122-019-03520-z. Epub 2020 Jan 2.
7
Genomic imprinting in plants-revisiting existing models.
Genes Dev. 2020 Jan 1;34(1-2):24-36. doi: 10.1101/gad.332924.119.
8
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype.
Nat Biotechnol. 2019 Aug;37(8):907-915. doi: 10.1038/s41587-019-0201-4. Epub 2019 Aug 2.
9
Differences in Effective Ploidy Drive Genome-Wide Endosperm Expression Polarization and Seed Failure in Wild Tomato Hybrids.
Genetics. 2019 May;212(1):141-152. doi: 10.1534/genetics.119.302056. Epub 2019 Mar 22.
10
The maize W22 genome provides a foundation for functional genomics and transposon biology.
Nat Genet. 2018 Sep;50(9):1282-1288. doi: 10.1038/s41588-018-0158-0. Epub 2018 Jul 30.

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验