Importance of parental genome balance in the generation of novel yet heritable epigenetic and transcriptional states during doubled haploid breeding
Importance of parental genome balance in the generation of novel yet heritable epigenetic and transcriptional states during doubled haploid breeding
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双单倍体育种过程中亲本基因组平衡在新型但可遗传的表观遗传和转录状态生成中的重要性
DOI：
10.1101/812347
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发表时间：
2019
期刊：
影响因子：
--
通讯作者：
Price J
中科院分区：
文献类型：
--
作者：
Price J
背景单倍体植物的基因组贡献加倍加速了大多数栽培作物物种的育种。尽管植物双单倍体本质上是同基因的，但它们经常表现出不可预测的表型，从而限制了该技术的潜力。因此，能够预测与这种表型变异相关的因素可以加速所需基因组组合的产生并最终加速植物育种。结果我们使用计算分析来评估甘蓝基因组中双单倍体生成过程中发生的转录和表观遗传动态。我们观察到双单倍体系显示出意想不到的转录和表观遗传变异水平，并且这种变异很大程度上是由于亲本基因组的不平衡贡献造成的。我们揭示了 DH 育种过程中转座子相关序列的表观遗传修饰有助于产生不可预测但可遗传的转录状态。使用 dCas9-hsTET3 对这些元件进行靶向表观遗传操作，证实了它们在转录调控中的作用。我们发现了亲本基因组平衡在双单倍体转录和表观遗传稳定性中迄今未知的作用。结论这是第一项证明亲本基因组平衡在双单倍体转录和表观遗传稳定性中重要性的研究，从而使预测模型能够改善双单倍体辅助植物育种。
BackgroundDoubling the genome contribution of haploid plants has accelerated breeding in most cultivated crop species. Although plant doubled haploids are isogenic in nature, they frequently display unpredictable phenotypes, thus limiting the potential of this technology. Therefore, being able to predict the factors implicated in this phenotypic variability could accelerate the generation of desirable genomic combinations and ultimately plant breeding.ResultsWe use computational analysis to assess the transcriptional and epigenetic dynamics taking place during doubled haploids generation in the genome ofBrassica oleracea. We observe that doubled haploid lines display unexpected levels of transcriptional and epigenetic variation, and that this variation is largely due to imbalanced contribution of parental genomes. We reveal that epigenetic modification of transposon-related sequences during DH breeding contributes to the generation of unpredictable yet heritable transcriptional states. Targeted epigenetic manipulation of these elements using dCas9-hsTET3 confirms their role in transcriptional regulation. We have uncovered a hitherto unknown role for parental genome balance in the transcriptional and epigenetic stability of doubled haploids.ConclusionsThis is the first study that demonstrates the importance of parental genome balance in the transcriptional and epigenetic stability of doubled haploids, thus enabling predictive models to improve doubled haploid-assisted plant breeding.
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DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
拟南芥 DNA 甲基化遗传学
DOI：
--
发表时间：
2009
期刊：
影响因子：
--
作者：
Y. Tamaura;H. Kaneko;他3名;N. Hasegawa;田中和夫;Kaktani T.
通讯作者：
Kaktani T.
DOI：
10.1016/j.tig.2013.04.004
发表时间：
2013-07
期刊：
Trends in genetics : TIG
影响因子：
--
作者：
R. Veitia;S. Bottani;J. Birchler
通讯作者：
R. Veitia;S. Bottani;J. Birchler
影响因子：
4.6
作者：
Matveeva NM;Fishman VS;Zakharova IS;Shevchenko AI;Pristyazhnyuk IE;Menzorov AG;Serov OL
通讯作者：
Serov OL
影响因子：
12.3
作者：
Parkin IA;Koh C;Tang H;Robinson SJ;Kagale S;Clarke WE;Town CD;Nixon J;Krishnakumar V;Bidwell SL;Denoeud F;Belcram H;Links MG;Just J;Clarke C;Bender T;Huebert T;Mason AS;Pires JC;Barker G;Moore J;Walley PG;Manoli S;Batley J;Edwards D;Nelson MN;Wang X;Paterson AH;King G;Bancroft I;Chalhoub B;Sharpe AG
通讯作者：
Sharpe AG