Loss of chromatin remodeler DDM1 causes segregation distortion in Arabidopsis thaliana
Loss of chromatin remodeler DDM1 causes segregation distortion in Arabidopsis thaliana
复制标题
拟南芥中染色质重塑蛋白 DDM1 的缺失导致分离扭曲
DOI：
10.1007/s00425-021-03763-5
复制
发表时间：
2021-11-01
期刊：
影响因子：
4.3
通讯作者：
Zhang, Qingzhu
中科院分区：
文献类型：
--
作者：
Ali, Shahid;Zhang, Tianxu;Zhang, Qingzhu
在ddm 1突变体中，DNA甲基化主要在染色体的异染色质区域受到影响，这与SNP在F2后代中的分离畸变有关。分离畸变（SD）在大多数遗传作图实验中是常见的，并且是确定基因位点如何引起偏差的有价值的资源。减数分裂DNA交换和SD是在几种类型的表观遗传修饰的控制下。DNA甲基化是一种重要的调节性表观遗传修饰，可以代代遗传。在本研究中，我们调查了SD和DNA甲基化之间的关系。以生态型Col-0/C24和染色质重塑突变体ddm 1 -10/Col和ddm 1 -15/C24为亲本，进行正反交，获得F2代。对F2代中每株双杂交植物的总共300株植物进行下一代测序，以检测作为DNA标记的单核苷酸多态性（SNP）。采用卡方检验方法对所有SNP进行分析，以确定其在F2代中的分离率。根据分离率将全基因组SNP分为16类。在第10类中，野生型正反交中的SNPs显示出预期的孟德尔比率1：2：1，而ddm 1突变体正反交中的SNPs显示出失真。相比之下，第16类中的所有SNP显示正常的1：2：1比率，并且第1类显示SD，无论野生型或突变体，如使用CAPS（切割扩增多态性序列）标记分析所评估的，以确认下一代测序。在ddm 1突变体中，DNA甲基化在整个基因组中高度降低，在染色体的异染色质区域中更显着。我们的研究结果表明，ddm 1突变体表现出低水平的DNA甲基化，这有利于主要位于染色体异染色质区的SNP的SD通过降低杂合率。本研究为进一步研究DNA甲基化对性状分离和植物进化的影响奠定了基础。
In ddm1 mutants, the DNA methylation is primarily affected in the heterochromatic region of the chromosomes, which is associated with the segregation distortion of SNPs in the F2 progenies. Segregation distortion (SD) is common in most genetic mapping experiments and a valuable resource to determine how gene loci induce deviation. Meiotic DNA crossing over and SD are under the control of several types of epigenetic modifications. DNA methylation is an important regulatory epigenetic modification that is inherited across generations. In the present study, we investigated the relationship between SD and DNA methylation. The ecotypes Col-0/C24 and chromatin remodeler mutants ddm1-10/Col and ddm1-15/C24 were reciprocally crossed to obtain F2 generations. A total of 300 plants for each reciprocally crossed plant in the F2 generations were subjected to next-generation sequencing to detect the single-nucleotide polymorphisms (SNPs) as DNA markers. All SNPs were analyzed using the Chi-square test method to determine their segregation ratio in F2 generations. Through the segregation ratio, whole-genome SNPs were classified into 16 classes. In class 10, the SNPs in the reciprocal crosses of wild type showed the expected Mendelian ratio of 1:2:1, while those in the reciprocal crosses of ddm1 mutants showed distortion. In contrast, all SNPs in class 16 displayed a normal 1:2:1 ratio, and class 1 showed SD, regardless of wild type or mutants, as assessed using CAPS (cleaved amplified polymorphic sequences) marker analysis to confirm the next-generation sequencing. In ddm1 mutants, the DNA methylation is highly reduced throughout the whole genome and more significantly in the heterochromatic regions of chromosomes. Our results showed that the ddm1 mutants exhibit low levels of DNA methylation, which facilitates the SD of SNPs primarily located in the heterochromatic region of chromosomes by reducing the heterozygous ratio. The present study will provide a strong base for future research focusing on the impact of DNA methylation on trait segregation and plant evolution.