近日，Genome biology在线发表了南京农业大学张天真教授课题组与德克萨斯大学杰夫瑞·陈的课题组合作的题为“Epigenomic and functional analyses reveal roles of epialleles in the loss of photoperiod sensitivity during domestication of allotetraploid cottons”研究论文，论文报道了首次绘制出棉花表观遗传基因的“甲基化基因图谱”，即野生棉和种植棉之间500多种表观遗传基因的差异，为通过表观修饰育种培育出高产优质棉花提供了重要依据。
Fig. 6Repression of COL2 delayed flowering of cultivated cotton (TM-1).
几十年来，科学家们发现，许多动植物的表观特征，既可用基于DNA序列改变的遗传学方法调控，也能用不改变DNA序列的表观遗传学方法进行可遗传性修饰。这些研究成果为动植物育种开启了全新路径，特别是利用表观遗传学技术，不需改变基因，就能创造出全新品种，可规避人们对转基因技术的质疑和争论。
在该研究中通过将美国陆地棉与野生棉对比，识别出500多种与DNA甲基化过程有关的基因开关列表，从而绘制出了这份棉花的“甲基化基因图谱”。DNA甲基化是一种重要的表观遗传修饰过程，新图谱信息可提供棉花在100多万年进化过程中的表观基因变化，帮助研究人员选育出拥有某些新特征的新品种，提高棉花的产量，改善其抗旱性、耐热性或抗虫性。研究人员发现，野生棉花内的一种甲基化基因能阻止棉花开花，而种植棉中的这种基因已去甲基化，导致了棉花从热带植物变成在世界多数地区“安家”的普适性农作物，这种关键性突变不是遗传变异，而是表观遗传变异。
另外，作者表示参照这一最新“甲基化基因图谱”，育种专家可通过化学方法或CRISPR-Cas9等技术进行基因甲基化修饰，靶向培育出改良品种，同样的方法也可用于小麦、咖啡、土豆和玉米等主要农作物育种。
Polyploidy is a pervasive evolutionary feature of all flowering plants and some animals, leading to genetic and epigenetic changes that affect gene expressionand morphology. DNA methylation changes can produce meiotically stable epialleles, which are transmissible through selection and breeding. However, the relationship between DNA methylation and polyploid plant domestication remains elusive.
We report comprehensive epigenomic and functional analyses, including ~12 million differentially methylated cytosines in domesticated allotetraploid cottons and their tetraploid and diploid relatives. Methylated genes evolve faster than unmethylated genes; DNA methylation changes between homoeologous loci are associated with homoeolog-expression bias in the allotetraploids. Significantly, methylation changes induced in the interspecific hybrids are largely maintained in the allotetraploids. Among 519 differentially methylated genes identified between wild and cultivated cottons, some contribute to domestication traits, including flowering time and seed dormancy. CONSTANS (CO) andCO-LIKE (COL) genes regulate photoperiodicity in Arabidopsis. COL2 is an epiallele in allotetraploid cottons. COL2Ais hypermethylated and silenced, while COL2D is repressed in wild cottons but highly expressed due to methylation loss in all domesticated cottons tested. Inhibiting DNA methylation activates COL2 expression, and repressing COL2 in cultivated cotton delays flowering.
We uncover epigenomic signatures of domestication traits during cotton evolution. Demethylation of COL2 increases its expression, inducing photoperiodic flowering, which could have contributed to the suitability of cotton for cultivation worldwide. These resources should facilitate epigenetic engineering, breeding, and improvement of polyploid crops.
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