F1 hybrids in Arabidopsis and crops species are uniform and high yielding. The F2 generation loses much of the yield advantage and the plants have heterogeneous phenotypes. We generated pure breeding Hybrid Mimic lines by recurrent selection and also selected a pure breeding Small phenotype line. The Hybrid Mimics are almost completely homozygous with chromosome segments from each parent. Four particular chromosomal segments from C24 and eight from Ler were present in all of the Hybrid Mimic lines whereas in the F6 Small phenotype line the 12 segments were each derived from the alternative parent. Loci critical for promoting hybrid vigor may be contained in each of these 12 conserved segments. We have identified genes with similar altered expression in Hybrid Mimics and F1 plants but not in the Small phenotype line. These genes may be critical for the generation of hybrid vigour. Analysis of transcriptomes indicated that increased expression of the transcription factor PHYTOCHROME-INTERACTING FACTOR (PIF4) may contribute to hybrid vigor by targeting the auxin biosynthesis gene YUCCA8 and the auxin signalling gene IAA29. A number of auxin responsive genes promoting leaf growth were upregulated in the F1 hybrids and Hybrid Mimics suggesting increased auxin biosynthesis and signaling contribute to the hybrid phenotype. The Hybrid Mimic seeds had earlier germination as did the seeds of the F1 hybrids indicating co-segregation of the genes for rosette size and the germination trait. Early germination may be an indicator of vigorous hybrids. Overall design: For the transcriptomes of two parents C24 and Ler, F1 hybrids and F6 plant lines at 15 DAS. 30 samples were sequenced in total. C24 (three biological replicates), Ler (three biological replicates), C24xLer F1 hybrids (three biological replicates), LerxC24 F1 hybrids (three biological replicates) and three F6 siblings of each of six F6 lines (HM-W, HM-S, HM-G, Med-E, Med-F, Sml-D) were grown in one experiment under the same conditions. The library preparation and mRNA sequencing were completed by the Australian Genome Research Facility (AGRF).