Re-sequencing and transcriptome analysis reveal rich DNA variations and differential expressions of fertility-related genes in neotetraploid rice
Re-sequencing and transcriptome analysis reveal rich DNA variations and differential expressions of fertility-related genes in neotetraploid rice
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重测序和转录组分析揭示了新四倍体水稻中丰富的DNA变异和育性相关基因的差异表达
DOI：
10.1371/journal.pone.0214953
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发表时间：
2019-04-05
期刊：
影响因子：
3.7
通讯作者：
Liu, Xiangdong
中科院分区：
文献类型：
--
作者：
Bei, Xuejun;Shahid, Muhammad Qasim;Liu, Xiangdong
同源四倍体水稻是多倍体水稻育种的有用种质，但结实率低是同源四倍体水稻商业化利用的主要障碍。本课题组育成了新四倍体水稻品系，与同源四倍体水稻杂交，具有丰产性和杂种优势的特点。本研究以三个新四倍体水稻品系为材料，分别采用重测序和RNA-SEQ技术检测减数分裂过程中的DNA变异和差异表达基因(Deg)。与参考基因组相比，新四倍体品系共检测到4109881个SNPs和640592个INDELs，在3个品系中检测到1805个特异性存在/缺失变异(PAV)。在三个品系中，约有12%的SNPs和0.5%的Indels位于基因区域。在这三个品系中共鉴定出28个基因，它们至少含有一个影响编码蛋白完整性的大效应SNP和/或Indel。与亲本相比，新四倍体水稻共检测到324个特异突变基因，包括52个减数分裂相关基因和8个表观遗传相关基因。在这324个基因中，5个与减数分裂相关的基因和3个与表观遗传相关的基因在减数分裂阶段表现出差异表达。值得注意的是，在新四倍体水稻中还检测到498个特异转录本、48个差异表达转座子和245个差异表达的ncRNAs。我们的结果表明，基因组结构重编程、DNA变异以及一些重要的减数分裂和表观遗传相关基因的差异表达可能与新四倍体水稻的高育性有关。
Autotetraploid rice is a useful germplasm for polyploid rice breeding, however, low seed setting is the major barrier in commercial utilization of autotetraploid rice. Our research group has developed neo-tetraploid rice lines, which have the characteristics of high fertility and heterosis when crossed with autotetraploid rice. In the present study, re-sequencing and RNA-seq were employed to detect global DNA variations and differentially expressed genes (DEGs) during meiosis stage in three neo-tetraploid rice lines compared to their parents, respectively. Here, a total of 4109881 SNPs and 640592 InDels were detected in neo-tetraploid lines compared to the reference genome, and 1805 specific presence/absence variations (PAVs) were detected in three lines. Approximately 12% and 0.5% of the total SNPs and InDels identified in three lines were located in genic regions, respectively. A total of 28 genes, harboring at least one of the large-effect SNP and/or InDel which affect the integrity of the encoded protein, were identified in the three lines. Together, 324 specific mutation genes, including 52 meiosis-related genes and 8 epigenetics-related genes were detected in neo-tetraploid rice compared to their parents. Of these 324 genes, five meiosis-related and three epigenetics-related genes displayed differential expressions during meiosis stage. Notably, 498 specific transcripts, 48 differentially expressed transposons and 245 differentially expressed ncRNAs were also detected in neo-tetraploid rice. Our results suggested that genomic structural reprogramming, DNA variations and differential expressions of some important meiosis and epigenetics-related genes might be associated with high fertility in neo-tetraploid rice.