The seed coat is involved in the determination of seed quality traits such as seed size, seed composition, seed permeability, and hormonal regulation. Understanding seed coat structure is therefore a prerequisite to deciphering the genetic mechanisms that govern seed coat functions. By combining histological and transcriptomic data analyses, cellular and molecular events occurring during Medicago truncatula seed coat development were dissected in order to relate structure to function and pinpoint target genes potentially involved in seed coat traits controlling final seed quality traits. The analyses revealed the complexity of the seed coat transcriptome, which contains >30 000 genes. In parallel, a set of genes showing a preferential expression in seed coat that may be involved in more specific functions was identified. The study describes how seed coat anatomy and morphological changes affect final seed quality such as seed size, seed composition, seed permeability, and hormonal regulation. Putative regulator genes of different processes have been identified as potential candidates for further functional genomic studies to improve agronomical seed traits. The study also raises new questions concerning the implication of seed coat endopolyploidy in cell expansion and the participation of the seed coat in de novo abscisic acid biosynthesis at early seed filling.

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Genomic in situ hybridization (GISH) was used to investigate genomic relationships between different Setaria species of the foxtail millet gene pool (S. italica) and one interspecific F1 hybrid. The GISH patterns obtained on the two diploid species S. viridis (genome A) and S. adhaerans (genome B), and on their F1 hybrid showed clear differentiation between these two genomes except at the nucleolar organizing regions. Similar GISH patterns allowed differentiation of S. italica from S. adhaerans. However, GISH patterns did not distinguish between the genomes of S. italica and its putative wild ancestor S. viridis. GISH was also applied to polyploid Setaria species and enabled confirmation of the assumed allotetraploid nature of S. faberii and demonstration that both S. verticillata and S. verticillata var. ambigua were also allotetraploids. All these tetraploid species contained two sets of 18 chromosomes each, one from genome A and the other from genome B. Only one polyploid species, S. pumila, was shown to bear an unknown genomic composition that is not closely related either to genome A or to genome B.

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