Abstract
The rice gene seed dormancy 4 (OsSdr4) functions in seed dormancy and is a major factor associated with pre-harvest sprouting (PHS). Although previous studies of this protein family were reported for rice and other species, knowledge of the evolution of genes homologous to OsSdr4 in plants remains inadequate. Fifty four Sdr4-like (hereafter designated Sdr4L) genes were identified in nine plant lineages including 36 species. Phylogenetic analysis placed these genes in eight subfamilies (I-VIII). Genes from the same lineage clustered together, supported by analysis of conserved motifs and exon-intron patterns. Segmental duplications were present in both dicot and monocot clusters, while tandemly duplicated genes occurred only in monocot clusters indicating that both tandem and segmental duplications contributed to expansion of the grass I and II subfamilies. Estimation of the approximate ages of the duplication events indicated that ancestral Sdr4 genes evolved from a common angiosperm ancestor, about 160 million years ago (MYA). Moreover, diversification of Sdr4L genes in mono and dicot plants was mainly associated with genome-wide duplication and speciation events. Functional divergence was observed in all subfamily pairs, except IV/VIIIa. Further analysis indicated that functional constraints between subfamily pairs I/II, I/VIIIb, II/VI, II/VIIIb, II/IV, and VI/VIIIb were statistically significant. Site and branch-site model analyses of positive selection suggested that these genes were under strong adaptive selection pressure. Critical amino acids detected for both functional divergence and positive selection were mostly located in the loops, pointing to functional importance of these regions in this protein family. In addition, differential expression studies by transcriptome atlas of 11 Sdr4L genes showed that the duplicated genes may have undergone divergence in expression between plant species. Our findings showed that Sdr4L genes are functionally divergent and positively selected. These may contribute to further functional analysis and molecular evolution of Sdr4L gene families in land plants.
Highlights
Seed dormancy can be defined as the process by which viable seeds lack the capacity to germinate even in the presence of favorable environmental conditions [1]
To investigate the origin and evolutionary history of the Seed dormancy 4 (Sdr4) gene family, we first retrieved the available Sdr4 or Sdr4L sequences from currently sequenced and unfinished genomes; 54 Sdr4 homologues were identified from 38 plant species representing both monocotyledonous and dicotyledonous plants using the Phytozome, JGI, TAIR, RAP, and BRAD databases (S1 Table)
Two Sdr4L gene copies were identified in monocots Sorghum bicolor and Brachypodium distachyon and dicot species Populous trichocarpa, Linum usitatissimum, Gossypium raimondii, Brassica rapa, Glycine max, and Malus domestica
Summary
Seed dormancy can be defined as the process by which viable seeds lack the capacity to germinate even in the presence of favorable environmental conditions [1]. It is considered to be a way of regulating the distribution of seed germination in time, and to enable them to adapt in a diversity of habitats or in unfavorable conditions. Seed dormancy is an important component of plant fitness and an agronomically significant physiological trait [2, 3]. Pre-harvest sprouting (PHS) is a phenomenon in which seeds germinate within the spike caused by inappropriate level of dormancy under the prevailing wet weather conditions. Seed dormancy is been considered a main component of PHS, and is an important quality trait. PHS affects grain yield and quality, and reduces the market value of the grains, the improvement of PHS is an important objective for the cereal breeding programs across the world [4]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
