Abstract
Seed size/weight is a multigenic trait that is governed by complex transcriptional regulatory pathways. An understanding of the genetic basis of seed size is of great interest in the improvement of seed yield and quality in oilseed crops. A global transcriptome analysis was performed at the initial stages of seed development in two lines of Brassica juncea, small-seeded EH-2 and large-seeded PJ. The anatomical analyses revealed significant differences in cell number and cell size in the outer layer of the seed coat between EH-2 and PJ. Pairwise comparisons at each developmental stage identified 5,974 differentially expressed genes (DEGs) between the two lines, of which 954 genes belong to different families of transcription factors. Two modules were found to be significantly correlated with an increased seed size using weighted gene coexpression network analysis. The DEG and coexpression datasets were integrated with the thousand seed weight (Tsw) quantitative trait loci (QTL) mapped earlier in the EPJ (EH-2 × PJ) doubled haploid (DH) population, which identified forty potential key components controlling seed size. The candidate genes included genes regulating the cell cycle, cell wall biogenesis/modification, solute/sugar transport, and hormone signaling. The results provide a valuable resource to widen the current understanding of regulatory mechanisms underlying seed size in B. juncea.
Highlights
Seed size/weight is one of the most important traits from the evolutionary and breeding perspectives, as it is directly related to the overall yield of a crop
The maximum increase in seed size in EH-2 was observed at stages S0–S1 (1.17 ± 0.03 mm2) followed by stages S1–S2 (0.96 ± 0.03 mm2), and that in Pusa Jaikisan (PJ) was at stages S3–S4 (2.37 ± 0.09 mm2) followed by stages S1–S2 (1.7 ± 0.05 mm2) (Supplementary Table S1), indicating that the final seed size in B. juncea is mostly determined at the early stages of seed development
The average cell size and cell number of the outermost epidermal layer of seed coat in PJ seeds sampled at S5 were greater than in EH-2 (Supplementary Figure S2), showing that differential cell division and cell expansion in seed coat might partly contribute to the observed phenotypic differences in the seed size
Summary
Seed size/weight is one of the most important traits from the evolutionary and breeding perspectives, as it is directly related to the overall yield of a crop. Seed size is determined by coordinated cell proliferation and/or cell expansion in the triploid endosperm, the diploid maternal tissue of the ovule, and the diploid embryo and is controlled by both maternal and zygotic genetic factors (Chaudhury and Berger, 2001; Sun et al, 2010). The controlling mechanisms of seed size in plants have been extensively studied in A. thaliana and Oryza sativa (rice) and include maternally imprinted genes, IKU pathway, ubiquitin–proteasome pathway, mitogen-activated protein kinase (MAPK signaling), G-protein signaling, phytohormones, and transcriptional regulatory factors, which have been well described in some reviews (Li and Li, 2016; Savadi, 2018; Li et al, 2019). It has been shown that the time of cellularization of syncytial endosperm, mitotic activity at initial stages of seed development, and partitioning of carbohydrates and photoassimilates play a major role in the determination of seed size (Borrás et al, 2004; Zhou et al, 2009; Wang et al, 2010; Ruan et al, 2012). It has been suggested that transcriptional trajectories at the early stages of seed development are mostly responsible for the determination of final seed size via restricting cell numbers (Ruan et al, 2012; Du et al, 2017)
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