Dynamic proteomic changes in soft wheat seeds during accelerated ageing

Previous research demonstrated that soft wheat cultivars have better post-harvest storage tolerance than harder cultivars during accelerated ageing. To better understand this phenomenon, a tandem mass tag-based quantitative proteomic analysis of soft wheat seeds was performed at different storage times during accelerated ageing (germination ratios of 97%, 45%, 28%, and 6%). A total of 1,010 proteins were differentially regulated, of which 519 and 491 were up- and downregulated, respectively. Most of the differentially expressed proteins were predicted to be involved in nutrient reservoir, enzyme activity and regulation, energy and metabolism, and response to stimulus functions, consistent with processes occurring in hard wheat during artificial ageing. Notably, defense-associated proteins including wheatwin-2, pathogenesis-related proteins protecting against fungal invasion, and glutathione S-transferase and glutathione synthetase participating in reactive oxygen species (ROS) detoxification, were upregulated compared to levels in hard wheat during accelerated ageing. These upregulated proteins might be responsible for the superior post-harvest storage-tolerance of soft wheat cultivars during accelerated ageing compared with hard wheat. Although accelerated ageing could not fully mimic natural ageing, our findings provided novel dynamic proteomic insight into soft wheat seeds during seed deterioration

Genetic analysis and QTL mapping of traits related to head shape in cabbage (Brassica oleracea var. capitata L.)

AbstractTraits related to head shape, including Hvd (head vertical diameter), Htd (head transverse diameter), and Hsi (head shape index, the ratio of Hvd/Htd), are very important agronomic traits associated with both yield and quality in cabbage (Brassica oleracea var. capitata L.). However, reports of inheritance analysis and quantitative trait locus (QTL) mapping of these traits remain rare. In this study, a double haploid (DH) population with 130 lines constructed from a cross between 24-5 (inbred line, oblate head)×01-88 (inbred line, round head) was used to analyze inheritance and to detect QTLs related to Htd and Hsi using major gene plus polygene mixed inheritance analysis and inclusive composite interval mapping (ICIM). The results indicated that Htd was controlled by two independent major genes and polygenes with recessive-epistatic effects. Hsi was controlled by two linkage major genes and polygenes with cumulative effects. A genetic linkage map with 48 insertions or deletions (InDel) and 149 simple sequence repeat (SSR) markers was constructed based on the DH population, with a total length of 866.2cM and an average interval length of 4.40cM. Fourteen QTLs for Htd and Hsi were identified on six chromosomes based on two years of phenotypic data with ICIM. Ten of the QTLs explained greater than 10.0% of the phenotypic variance, and five QTLs could be repeatedly detected in two years. For Htd, two major QTLs, Htd 3.1 and Htd 8.1, explained 19.16–24.56% and 11.25–21.55% of the phenotypic variation in the two years, respectively. For Hsi, two major QTLs, Hsi 7.1 and Hsi 7.2, explained 22.30–24.93% and 14.85–16.79% of phenotypic variation in the two years, respectively. The results from QTL mapping and genetic analysis in both years were partially consistent and complemented each other. Our results provide a foundation for further research on genetic regulation, gene cloning and molecular marker-assisted selection (MAS) for head shape in cabbage

Genome-wide identification and characterization of non-specific lipid transfer proteins in cabbage

Plant non-specific lipid transfer proteins (nsLTPs) are a group of small, secreted proteins that can reversibly bind and transport hydrophobic molecules. NsLTPs play an important role in plant development and resistance to stress. To date, little is known about the nsLTP family in cabbage. In this study, a total of 89 nsLTP genes were identified via comprehensive research on the cabbage genome. These cabbage nsLTPs were classified into six types (1, 2, C, D, E and G). The gene structure, physical and chemical characteristics, homology, conserved motifs, subcellular localization, tertiary structure and phylogeny of the cabbage nsLTPs were comprehensively investigated. Spatial expression analysis revealed that most of the identified nsLTP genes were positively expressed in cabbage, and many of them exhibited patterns of differential and tissue-specific expression. The expression patterns of the nsLTP genes in response to biotic and abiotic stresses were also investigated. Numerous nsLTP genes in cabbage were found to be related to the resistance to stress. Moreover, the expression patterns of some nsLTP paralogs in cabbage showed evident divergence. This study promotes the understanding of nsLTPs characteristics in cabbage and lays the foundation for further functional studies investigating cabbage nsLTPs

Overcoming Cabbage Crossing Incompatibility by the Development and Application of Self-Compatibility-QTL- Specific Markers and Genome-Wide Background Analysis

Cabbage hybrids, which clearly present heterosis vigor, are widely used in agricultural production. We compared two S5 haplotype (Class II) cabbage inbred-lines 87–534 and 94–182: the former is highly SC while the latter is highly SI; sequence analysis of SI-related genes including SCR, SRK, ARC1, THL1, and MLPK indicates the some SNPs in ARC1 and SRK of 87–534; semi-quantitative analysis indicated that the SI-related genes were transcribed normally from DNA to mRNA. To unravel the genetic basis of SC, we performed whole-genome mapping of the quantitative trait loci (QTLs) governing self-compatibility using an F2 population derived from 87–534 × 96–100. Eight QTLs were detected, and high contribution rates (CRs) were observed for three QTLs: qSC7.2 (54.8%), qSC9.1 (14.1%) and qSC5.1 (11.2%). 06–88 (CB201 × 96–100) yielded an excellent hybrid. However, F1 seeds cannot be produced at the anthesis stage because the parents share the same S-haplotype (S57, class I). To overcome crossing incompatibility, we performed rapid introgression of the self-compatibility trait from 87–534 to 96–100 using two self-compatibility-QTL-specific markers, BoID0709 and BoID0992, as well as 36 genome-wide markers that were evenly distributed along nine chromosomes for background analysis in recurrent back-crossing (BC). The transfer process showed that the proportion of recurrent parent genome (PRPG) in BC4F1 was greater than 94%, and the ratio of individual SC plants in BC4F1 reached 100%. The newly created line, which was designated SC96–100 and exhibited both agronomic traits that were similar to those of 96–100 and a compatibility index (CI) greater than 5.0, was successfully used in the production of the commercial hybrid 06–88. The study herein provides new insight into the genetic basis of self-compatibility in cabbage and facilitates cabbage breeding using SC lines in the male-sterile (MS) system

Proteome-wide profiling of protein lysine acetylation in <i>Aspergillus flavus</i> - Fig 3

<p><b>(A)</b> GO, <b>(B)</b> subcellular-localization analysis, and <b>(C)</b> KEGG-pathway enrichment of the identified Kac proteins. (<b>D</b>) Comparison analysis of enriched pathways between <i>Aspergillus flavus</i>, <i>Phytophthora sojae</i>, <i>Botrytis cinerea</i>, and <i>Bacillus amyloliquefaciens</i>.</p

Motif analysis of Kac peptides.

<p>(<b>A</b>) Acetylation motifs and conservation of acetylation sites. The height of each letter corresponds to the frequency with which that amino acid residue is found at that position. (<b>B</b>) Heat map representing the amino acid composition of the Kac sites, showing the frequency of the different types of amino acids surrounding Kac sites. (<b>C</b>) Cellular distribution of acetylated proteins and sites. (<b>D</b>) Sequence logo plots of normalized amino acid frequencies ±10 amino acids from the lysine acetylation site in cellular compartments. (<b>E</b>) Comparison analysis of acetylation motifs between <i>Aspergillus flavus</i>, <i>Phytophthora sojae</i>, <i>Botrytis cinerea</i>, and <i>Bacillus amyloliquefaciens</i>.</p

Protein information involved in synthesis of aflatoxin in <i>A</i>. <i>flavus</i>.

<p>Protein information involved in synthesis of aflatoxin in <i>A</i>. <i>flavus</i>.</p

Acetylation of metabolic enzymes identified as involved in glycolysis/gluconeogenesis and the citric acid cycle.

<p>The identified numbers of lysine-acetylated enzymes and proteins are shown in red. The identified Kac proteins found in mammalian cells are marked with●, those in <i>Escherichia coli</i> with ★, and those in <i>Saccharopolyspora erythraea</i> with▲.</p

Lysine acetylation status is analyzed by using SDS-PAGE and western blotting.

<p>(<b>A</b>) Confirmation of acetylated proteins present in <i>A</i>. <i>flavus</i>. 15μg protein samples were loaded for SDS-PAGE analysis. Acetylated Lys antibody (PTM Biolabs) was used in a 1:1000 dilution. (<b>B</b>) Distribution of lysine-acetylated peptides based on the number of acetylation sites.</p