Asymmetrical changes of gene expression, small RNAs and chromatin in two resynthesized wheat allotetraploids

Polyploidy occurs in some animals and all flowering plants including important crops such as wheat. The consequences of polyploidy on crops remain elusive partly because their progenitors are unknown. Using two resynthesized wheat allotetraploids SSAA and AADD with known diploid progenitors, we analyzed mRNA and small RNA transcriptomes in the endosperm, compared transcriptomes between endosperm and root in AADD, and examined chromatin changes in the allotetraploids. In the endosperm, there were more nonadditively expressed genes in SSAA than in AADD. In AADD, nonadditively expressed genes were developmentally regulated, and the majority (62-70%) were repressed. The repressed genes in AADD included a group of histone methyltransferase gene homologs, which correlated with reduced histone H3K9me2 levels and activation of various transposable elements in AADD. In SSAA, there was a tendency of expression dominance of S over A homoeologs, but the histone methyltransferase gene homologs were additively expressed, correlating with insignificant changes in histone H3K9me2 levels. Moreover, more 24-nt small inferring RNAs (siRNAs) in the A subgenome were disrupted in AADD than in SSAA, which were associated with expression changes of siRNA-associated genes. Our results indicate that asymmetrical changes in siRNAs, chromatin modifications, transposons, and gene expression coincide with unstable AADD genomes and stable SSAA genomes, which could help explain evolutionary trajectories of wheat allotetraploids formed by different progenitors. We have submitted RNA-seq and small RNA-seq libraries of the endosperm of two synthetic wheats SSAA and AADD, and their diploid progenitors, RNA-seq libraries of the seedling root of AADD and its progenitors AA and DD. Tetraploid AT2 (AADD) was resynthesized by pollinating T. urartu (AA, accession TMU38) with pollen of Ae. tauschii (DD, accession TQ27), while TLTU (SSAA) was derived from the pollination of Ae. longissima (SS, accession TL05) with pollen of T. urartu (AA, accession TMU06).

多倍体现象存在于部分动物及所有显花植物中，涵盖小麦这类重要农作物。多倍体对农作物的影响仍有待厘清，部分原因在于其祖先物种尚未被明确鉴定。
本研究利用两个拥有已知二倍体祖先的人工合成小麦异源四倍体SSAA与AADD，对胚乳中的mRNA与小RNA转录组开展分析，比较了AADD胚乳与根系的转录组差异，并检测了异源四倍体的染色质变化情况。
在胚乳中，SSAA品系的非加性表达基因数量显著多于AADD品系。在AADD品系中，非加性表达基因受发育进程调控，其中多数（62%~70%）呈现表达抑制状态。
AADD品系中被抑制的基因包含一类组蛋白甲基转移酶基因同源物，其表达水平与该品系中组蛋白H3K9me2修饰水平的降低以及多种转座因子的激活呈显著相关。
而在SSAA品系中，S亚基因组同源基因相较于A亚基因组同源基因呈现表达优势的趋势，但组蛋白甲基转移酶基因同源物的表达则符合加性模式，这与组蛋白H3K9me2修饰水平无显著变化的结果相契合。
此外，相较于SSAA品系，AADD品系中A亚基因组内更多的24 nt小干扰RNA（small interfering RNAs，siRNAs）出现表达紊乱现象，该现象与siRNA相关基因的表达变化存在密切关联。
本研究结果表明，siRNA、染色质修饰、转座因子以及基因表达的不对称变化，与AADD基因组的不稳定性及SSAA基因组的稳定性相契合，这或有助于阐释不同祖先起源的小麦异源四倍体的演化轨迹。
本研究已提交两个人工合成小麦SSAA、AADD及其二倍体祖先的胚乳RNA测序（RNA-seq）与小RNA测序（small RNA-seq）文库，同时提交了AADD及其祖先AA、DD的幼苗根系RNA-seq文库。
异源四倍体AT2（AADD）通过以节节麦（Ae. tauschii，种质编号TQ27）的花粉授粉乌拉尔图小麦（T. urartu，种质编号TMU38）人工合成获得；而TLTU（SSAA）则通过以乌拉尔图小麦（T. urartu，种质编号TMU06）的花粉授粉长穗山羊草（Ae. longissima，种质编号TL05）得到。