D'Amico-Willman Katherine M, Sideli Gina M, Allen Brian J, Anderson Elizabeth S, Gradziel Thomas M, Fresnedo-Ramírez Jonathan
Center for Applied Plant Sciences, The Ohio State University, Wooster, OH, United States.
Department of Plant Sciences, University of California, Davis, Davis, CA, United States.
Front Plant Sci. 2022 Feb 14;13:804145. doi: 10.3389/fpls.2022.804145. eCollection 2022.
Almond [ (Mill.) D.A. Webb] is an economically important nut crop susceptible to the genetic disorder, Non-infectious Bud Failure (NBF). Despite the severity of exhibition in several prominent almond cultivars, no causal mechanism has been identified underlying NBF development. The disorder is hypothesized to be associated with differential DNA methylation patterns based on patterns of inheritance (i.e., via sexual reproduction and clonal propagation) and previous work profiling methylation in affected trees. Peach ( L. Batsch) is a closely related species that readily hybridizes with almond; however, peach is not known to exhibit NBF. A cross between an NBF-exhibiting 'Carmel' cultivar and early flowering peach ('40A17') produced an F where ∼50% of progeny showed signs of NBF, including canopy die-back, erratic branching patterns (known as "crazy-top"), and rough bark. In this study, whole-genome DNA methylation profiles were generated for three F progenies exhibiting NBF and three progenies considered NBF-free. Subsequent alignment to both the almond and peach reference genomes showed an increase in genome-wide methylation levels in NBF hybrids in CG and CHG contexts compared to no-NBF hybrids when aligned to the almond genome but no difference in methylation levels when aligned to the peach genome. Significantly differentially methylated regions (DMRs) were identified by comparing methylation levels across the genome between NBF- and no-NBF hybrids in each methylation context. In total, 115,635 DMRs were identified based on alignment to the almond reference genome, and 126,800 DMRs were identified based on alignment to the peach reference genome. Nearby genes were identified as associated with the 39 most significant DMRs occurring either in the almond or peach alignments alone or occurring in both the almond and peach alignments. These DMR-associated genes include several uncharacterized proteins and transposable elements. Quantitative PCR was also performed to analyze the gene expression patterns of these identified gene targets to determine patterns of differential expression associated with differential DNA methylation. These DMR-associated genes, particularly those showing corresponding patterns of differential gene expression, represent key targets for almond breeding for future cultivars and mitigating the effects of NBF-exhibition in currently affected cultivars.
杏仁[（Mill.）D.A. Webb]是一种具有重要经济价值的坚果作物，易患遗传性疾病——非传染性芽败育（NBF）。尽管在几个著名的杏仁品种中该病症表现严重，但尚未确定NBF发生的潜在因果机制。基于遗传模式（即通过有性繁殖和克隆繁殖）以及之前对受影响树木甲基化分析的工作，推测该病症与不同的DNA甲基化模式有关。桃（L. Batsch）是与杏仁亲缘关系密切的物种，很容易与杏仁杂交；然而，桃并未表现出NBF。表现出NBF的‘Carmel’品种与早花桃（‘40A17’）杂交产生了一个F代群体，其中约50%的后代表现出NBF的症状，包括树冠枯死、不规则的分枝模式（称为“疯顶”）和树皮粗糙。在本研究中，对三个表现出NBF的F代后代和三个被认为无NBF的后代进行了全基因组DNA甲基化谱分析。随后与杏仁和桃的参考基因组进行比对，结果显示，与无NBF的杂交种相比，当与杏仁基因组比对时，NBF杂交种在CG和CHG背景下全基因组甲基化水平有所增加，但与桃基因组比对时甲基化水平没有差异。通过比较每个甲基化背景下NBF和无NBF杂交种全基因组的甲基化水平，鉴定出了显著差异甲基化区域（DMR）。基于与杏仁参考基因组的比对，总共鉴定出115,635个DMR，基于与桃参考基因组的比对，鉴定出126,800个DMR。在仅出现在杏仁或桃比对中或同时出现在杏仁和桃比对中的39个最显著的DMR附近鉴定出了相关基因。这些与DMR相关的基因包括几种未表征的蛋白质和转座元件。还进行了定量PCR分析这些鉴定出的基因靶点的基因表达模式，以确定与DNA甲基化差异相关的差异表达模式。这些与DMR相关的基因，特别是那些表现出相应差异基因表达模式的基因，是未来杏仁品种育种以及减轻当前受影响品种中NBF表现影响的关键靶点。
