RES complex modulates pre-mRNA splicing and embryo development. A and B, RT-PCR analysis of defective splicing of randomly selected genes in RNA-Seq data. Wiggle plots of RNA-Seq data (A) with gene diagrams showing intron retentions in atbud13-1/+ compared to wild-type (Col-0) siliques (Xiong et al., 2019a). The red boxes indicate introns which are differentially spliced in atbud13-1/+ compared to wild-type. The intron retentions (red arrows) were detected by RT-PCR with primers designed on exons flanking the introns under analysis (B). Total RNA was isolated from siliques at 1–3 DAP from wild-type Col-0, atbud13-1/+, atbud13-2−/+, atbud13-1/+ rescued line (atbud13-1/+ AtBUD13g-GFP), gds1-2, gds1-3, gds1-2 rescued line (gds1-2 GDS1g-GFP), wild-type WS, ddl-1 and ddl-2 plants. C and D, RES complex-mediated pre-mRNA splicing of genes required for embryo development. Intron retention of pre-mRNAs of ATML1 and AGO10/ZLL was detected by RNA-Seq (upper). Wiggle plots of RNA-Seq data with gene diagrams showing retention of ATML1 introns 3 and AGO10/ZLL intron 6 (Xiong et al., 2019a). The red boxes indicate introns which are differentially spliced between atbud13-1/+ compared and wild-type siliques. RT-qPCR analysis (below) to determine the retention of ATML1 intron 3 and AGO10/ZLL intron 6 in wild-type, atbud13-1/+, gds1-2 and ddl-1 mutants. Total RNA was extracted from siliques at 1–3 DAP. Error bars indicate the se of three biological replicates. Student’s t test showing the significant differences (*P < 0.05; **P < 0.01) compared with wild-type Col-0 or WS. E and F, Splicing efficiency of ATML1 intron 3 and AGO10/ZLL intron 6 in wild-type, atbud13-1/+, gds1-2 and ddl-1 mutants. Significant differences were evaluated using Student’s t test (*P < 0.05; **P < 0.01).