A Combined Comparative Transcriptomic, Metabolomic, and Anatomical Analyses of Two Key Domestication Traits: Pod Dehiscence and Seed Dormancy in Pea (Pisum sp.)

Abstract

The origin of the agriculture was one of the turning points in human history, and a central part of this was the evolution of new plant forms, domesticated crops. Seed dispersal and germination are two key traits which have been selected to facilitate cultivation and harvesting of crops. The objective of this study was to analyze anatomical structure of seed coat and pod, identify metabolic compounds associated with water-impermeable seed coat and differentially expressed genes involved in pea seed dormancy and pod dehiscence. Comparative anatomical, metabolomics, and transcriptomic analyses were carried out on wild dormant, dehiscent Pisum elatius (JI64, VIR320) and cultivated, indehiscent Pisum sativum non-dormant (JI92, Cameor) and recombinant inbred lines (RILs). Considerable differences were found in texture of testa surface, length of macrosclereids, and seed coat thickness. Histochemical and biochemical analyses indicated genotype related variation in composition and heterogeneity of seed coat cell walls within macrosclereids. Liquid chromatography–electrospray ionization/mass spectrometry and Laser desorption/ionization–mass spectrometry of separated seed coats revealed significantly higher contents of proanthocyanidins (dimer and trimer of gallocatechin), quercetin, and myricetin rhamnosides and hydroxylated fatty acids in dormant compared to non-dormant genotypes. Bulk Segregant Analysis coupled to high throughput RNA sequencing resulted in identification of 770 and 148 differentially expressed genes between dormant and non-dormant seeds or dehiscent and indehiscent pods, respectively. The expression of 14 selected dormancy-related genes was studied by qRT-PCR. Of these, expression pattern of four genes: porin (MACE-S082), peroxisomal membrane PEX14-like protein (MACE-S108), 4-coumarate CoA ligase (MACE-S131), and UDP-glucosyl transferase (MACE-S139) was in agreement in all four genotypes with Massive analysis of cDNA Ends (MACE) data. In case of pod dehiscence, the analysis of two candidate genes (SHATTERING and SHATTERPROOF) and three out of 20 MACE identified genes (MACE-P004, MACE-P013, MACE-P015) showed down-expression in dorsal and ventral pod suture of indehiscent genotypes. Moreover, MACE-P015, the homolog of peptidoglycan-binding domain or proline-rich extensin-like protein mapped correctly to predicted Dpo1 locus on PsLGIII. This integrated analysis of the seed coat in wild and cultivated pea provides new insight as well as raises new questions associated with domestication and seed dormancy and pod dehiscence.

Interaction of roses with a biotrophic and a hemibiotrophic leaf pathogen leads to differences in defense transcriptome activation

“…Significant changes in gene expression are marked with thicker lines. Enzyme names are abbreviated as follows: PAL phenylalanine ammonia-lyase, C4H cinnamate-4-hy-droxylase, 4CL 4-coumaroyl-CoA-ligase, HCT hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase, C3H p-coumarate 3-hydroxylase, CCoAOMT caffeoyl-CoA O-methyltransferase, CCR cinnamoyl-CoA reductase, F5H ferulate 5-hydroxylase, COMT caffeic acid O-methyltransferase, and CAD cinnamyl alcohol dehydrogenase are comparable to those of other studies that applied this technique, e.g., Hradilová et al (2017), applied the MACE technique to pea with an output of 8 to 15 million reads per library, and 12.3-21.7 million reads per library were generated from the RNA of apple roots (Weiß et al 2017).…”

Genomic dissection of pod shattering in common bean: mutations at non‐orthologous loci at the basis of convergent phenotypic evolution under domestication of leguminous species

“…Moreover, we have shown that the pod shattering phenotype depends not only on the single effects of the genes, but also on their epistatic interactions. We also discuss our findings for P. vulgaris in comparison with V. unguiculata (Suanum et al ., ; Lo et al ., ), G. max (Dong et al ., ; Funatsuki et al ., ), M. truncatula (Fourquin et al ., ; Ferrándiz and Fourquin, ) and P. sativum (Hradilová et al ., ), to shed light on the genetic mechanisms of convergent evolution under parallel selection and domestication.…”

“…Hradilová et al . () suggested that in P. sativum the main candidate gene responsible for pod shattering and localized on linkage group III is a homolog of peptidoglycan‐binding domain protein (PGDB) of Medicago truncatula . These proteins might have a general peptidoglycan‐binding function, and this motif is found at the N‐ or C‐terminus of a variety of enzymes involved in bacterial cell‐wall degradation.…”

Physical Dormancy Release in Medicago truncatula Seeds Is Related to Environmental Variations

“…The β-1,3-Glucanase (EC 3.2.1.39) plays roles in the regulation of seed germination, dormancy, and in the defense against pathogens. The β-1,3-glucan layer is in the seed coat of cucurbitaceous species and confers seed semi-permeability [64]. In tobacco seeds, β-1,3-Glucanase was shown to be at the micropylar part of the endosperm prior to radicle protrusion, and seems to play a role in cell wall loosening [65].…”