Transcriptome analysis of immature seeds/seed coats of two NILs for seed size in Vicia faba

In many crop plants, seed size is one of the major yield related traits. In grain legumes seed size varies considerably between species but also within species, with an extreme case found in Vicia faba, where seed size between the minor and major groups can vary by a factor of about 15, making Vicia faba an ideal model to study the genetic control of seed size. To develop a plant material suitable for an analysis of seed size in Vicia faba, two Near Isogenic Lines (NILs), (HxP)2-2-4 (mean seed size 1.67 g) and (HxP)2-4-4 (mean seed size 0.86 g), were developed in a two-step crossing process from inbred lines 'Pietranera' (mean seed size >3 g) and 'HediLin' (mean seed size: 0.35 g). While the two inbred lines 'Pietranera' and 'HediLin' are very much different in morphology and development, the two NILs are quite similar phenotypically, except the about 2-fold difference in seed size. Marker analysis has shown that the two NILs are distinguished by 26 polymorphic segments that cover about 25 - 30% of the Vicia faba genome, in the rest they are identical by descent. For a differential transcriptome analysis, RNA was isolated from immature seeds/seed coats of the two NILs and 'HediLin' as well as 'Pietranera', harvested at 10, 14, 18, and 22 days after pollination. While three biological replicates were isolated for the NILs at all time points only single preparation were conducted for 'HediLin' and 'Pietranera', which were then pooled to form 2 bulked samples. Finally, RNAseq was conducted with all samples on the Illumina platform.