Patterns of gene expression in developing embryos of Arabidopsis hybrids

• Published in: The Plant journal : for cell and molecular biology 2017-03, Vol.89 (5), p.927-939
• Main Authors: Alonso‐Peral, Maria M., Trigueros, Marina, Sherman, Bjorg, Ying, Hua, Taylor, Jennifer M., Peacock, William J., Dennis, Elizabeth S.
• Format: Article
• Language: English
• Subjects: Arabidopsis; Arabidopsis - embryology; Arabidopsis - genetics; Arabidopsis - metabolism; Arabidopsis Proteins - genetics; Arabidopsis Proteins - metabolism; Arabidopsis thaliana; Botany; Crop yield; Ecotypes; Embryos; Gene expression; Gene Expression Regulation, Plant - genetics; Gene Expression Regulation, Plant - physiology; Genes; Heterosis; Hybrids; Level (quantity); Loci; Nucleotides; Phenotypes; Plant tissues; Pollination; Seeds; Seeds - embryology; Seeds - genetics; Seeds - metabolism; Single-nucleotide polymorphism; Transcription; transcriptome; Transcriptome - genetics
• ISSN: 0960-7412; 1365-313X
• DOI: 10.1111/tpj.13432

Summary Hybrids between the Arabidopsis ecotypes C24 and Ler have high levels of hybrid vigour, or heterosis, in both biomass and seed yield. Heterosis can be detected throughout the development of the plant and in different tissues. We examined developing embryos and seeds of C24/Ler reciprocal hybrids with the aim of detecting the earliest time at which heterotic gene activity occurs. In the transcriptomes of 4‐dap (days after pollination; dermatogen to globular) and 6‐dap (heart) embryos from both parents and hybrids, 95% of expressed genes were at the mid parent value (MPV) and 95% of the genes with single nucleotide polymorphisms between C24 and Ler retained the same relative allelic expression levels in the hybrids as existed in the parents. This included loci that had equivalent levels of transcription in the two parents, together with loci which had different levels of expression in the parents. Amongst the genes which did not have MPV expression levels in the hybrids (non‐additively expressed genes), approximately 40 in the globular embryo stage and 89 in the heart embryo stage had altered levels of transcription in both reciprocal hybrids; these genes could contribute to the heterotic phenotype of the hybrid embryo. Many of the non‐additively expressed genes had expression levels that were shifted towards maternal levels of transcription, and these differed in the reciprocal hybrids. Allelic expression analysis indicated that most genes with altered allelic contributions in the hybrids had an increase in the expression level of the hybrid's maternal allele. Consistent with the maternal pattern of gene expression, embryo and seed also show maternally influenced phenotypes. Significance Statement Embryos of Arabidopsis hybrids between the C24 and Ler ecotypes show heterosis and also display a maternal effect on size. Here we used genome‐wide expression analyses of developing hybrid embryos to identify sets of genes that reflect these two behaviours: genes that are non‐additively expressed in both hybrids could explain the heterotic phenotype and non‐additively expressed genes that differ between reciprocal hybrids have expression levels shifted towards maternal expression levels, and could account for the maternal effect on phenotype.