Gene And Small RNA Expression Changes In The Endosperm Of Artificially Synthesized Wheat Allotetraploids S~1S~1AA And AADD

Although whole genome duplication is common in plants,the consequences of polyploidization on the development and speciation of polyploids are largely unknown,partly because their exact progenitors are extinct in nature.As one of the most important food crops in the world,the allohexaploid common wheat(Triticum aestivum,AABBDD)was generated from two rounds of hybridization and polyploidization of three diploid progenitors.In theory,the random hybridization and polyploidization of the different diploid wheat progenitors should generate allotetraploid wheats with various genome constitutions.However,only allotetraploid wheats generated from S(S～B)or closely related species and A genome combinations were diverged into new species,including T.timopheevi and T.turgidum.The artificially synthesized allotetraploid wheats S1S1AA and AADD using T.urartu(AA),Aegilops longissima(S1S1)and Ae.tauschii(DD)as progenitors showed different genome stabilities.S1S1AA is stable,whereas AADD is instable,they showed great differences in genetic and epigenetic modification changes relative to progenitors.Using diploids and the newly synthesized allotetraploid wheats S1S1AA and AADD,genome-wide RNA-seq and sRNA-seq were performed with the endosperm at six days after pollination,the gene and small interfering RNA(siRNA)expression changes in S1S1AA and AADD relative to their progenitors were investigated,the gene expression dynamics among different tissues of AADD were also compared between the endosperm and root.Major results are listed as follows.1)Seed size and morphological changes in allotetraploids relative to their progenitors:S1S1AA and AADD showed different morphological changes in seeds relative to progenitors,the thousand kernel weight of S1S1AA and AADD were significantly increased,but S1S1AA showed greater level of heterosis relative to the middle parent value.2)Additive and nonadditive expression of homoeologous genes in allotetraploids:There were more nonadditively expressed homoeologous genes in S1S1AA than in AADD in the endosperm,and these nonadditively expressed genes showed great species specifity among the two allotetraploids.The nonadditively expressed homoeologs were developmentally regulated in the endosperm and root of AADD,the homoeologous gene expression divergences between different tissues were reduced in AADD relative to progenitors.More genes were downregulated in the endosperm and root of AADD than in the endosperm of S1S1AA,and the repressed genes in AADD originated from those genes that were differentially expressed between the parents.There was an expression dominance of S1 over A homoeologs in the endosperm of S1S1AA,and many genes similarly expressed between progenitors were activated(70%).3)The nonadditively expressed genes in the endosperm of S1S1AA and AADD were enriched in different functions:The biological processes of post-embryonic development and multicellular organismal development were enriched in the downregulated genes in S1S1AA but in the upregulated genes in AADD;on the contrary,the processes of cell communication and transport were enriched in the upregulated genes in S1S1AA but in the downregulated genes in AADD.4)Differential regulation of histone H3K9 methyltransferases and transponsable elements(TEs)between S1S1AA and AADD:The histone H3K9 methyltransferase homologs were mainly additively expressed in the endosperm of S1S1AA,but downregulated in the endosperm and root of AADD.TEs were activated in the endosperm and root of AADD,but not in the endosperm of S1S1 AA.5)Activation of siRNAs in the endosperm of S1S1AA and AADD relative to AA:S1S1AA and AADD activated different 24-nt siRNA loci along the A genome,and more 24-nt siRNAs were activated in AADD than in S1S1AA,which might be associated with the expression changes of A genome homoeologs.The results could help explain the different genome stabilities and evolutionary trajectories of wheat allotetraploids formed by different progenitors.These findings could help us utilize wild relatives for breeding and improvement of tetraploid and hexaploid wheat crops.