Comparative Genomics and Transcriptomics Analyses Reveal a Unique Environmental Adaptability of Vibrio fujianensis

The genus Vibrio is ubiquitous in marine environments and uses numerous evolutionary characteristics and survival strategies in order to occupy its niche. Here, a newly identified species, Vibrio fujianensis, was deeply explored to reveal a unique environmental adaptability. V. fujianensis type strain FJ201301T shared 817 core genes with the Vibrio species in the population genomic analysis, but possessed unique genes of its own. In addition, V. fujianensis FJ201301T was predicated to carry 106 virulence-related factors, several of which were mostly found in other pathogenic Vibrio species. Moreover, a comparative transcriptome analysis between the low-salt (1% NaCl) and high-salt (8% NaCl) condition was conducted to identify the genes involved in salt tolerance. A total of 913 unigenes were found to be differentially expressed. In a high-salt condition, 577 genes were significantly upregulated, whereas 336 unigenes were significantly downregulated. Notably, differentially expressed genes have a significant association with ribosome structural component and ribosome metabolism, which may play a role in salt tolerance. Transcriptional changes in ribosome genes indicate that V. fujianensis may have gained a predominant advantage in order to adapt to the changing environment. In conclusion, to survive in adversity, V. fujianensis has enhanced its environmental adaptability and developed various strategies to fill its niche.

Genome-wide association study reveals genetic variation and candidate genes of lint yield components under salt field conditions in cotton (Gossypium hirsutum L.)

Background Salinity is one of the most decisive environmental factors limiting the productivity of cotton. However, the key genetic components leading to the reduction of cotton yield in saline-alkali soils are still unclear. Results Here, we evaluated three main components of lint yield across 316 G. hirsutum accessions, including single boll weight (SBW), lint percentage (LP) and boll number per plant (BNPP), under four salt conditions for two years. Phenotypic analysis indicated that LP showed no change under different salt conditions, however BNPP decreased significantly while SBW increased slightly under high salt condition. Based on 57,413 high-quality single nucleotide polymorphisms (SNPs) and genome-wide association studies (GWAS) analysis, a total of 42, 91 and 25 stable quantitative trait loci (QTLs) were identified for SBW, LP and BNPP, respectively. Few overlapped QTLs and no significant phenotypic correlation among the three traits was observed. Gene Ontology (GO) analysis indicated that their regulatory mechanisms were also quite different. There were 8 overlapped QTLs for LP while fewer for SBW and BNPP identified by comparing different salt conditions. We detected that 10 genes from the 8 stable LP QTLs were predominantly expressed during fiber development. Further, haplotype analyses found that a MYB gene ( GhMYB103 ) with the two SNP variations in cis-regulatory and coding regions, was significantly correlated with lint percentage, implying the crucial role in lint yield. With transcriptome analysis, we identified that 40 candidate genes from BNPP QTLs were salt-inducible. However, these genes exhibited different regulation pattern. Genes related to carbohydrate metabolism and cell structure maintenance were rich in high salt condition, while genes related to ion transport were active in low salt condition. Conclusions This study provides a foundation for elucidating cotton salt tolerance mechanism and contributes gene resources for developing varieties with high yield and salt stress tolerance in upland cotton.

Overexpression of BnaAOX1b Confers Tolerance to Osmotic and Salt Stress in Rapeseed

Alternative oxidases (AOXs) are the terminal oxidase in the cyanide-resistant respiration pathway in plant mitochondria, which play an important role in abiotic stress and are proposed as a functional marker for high tolerant breeding. In this study, ten AOX genes (BnaAOXs) were identified, and CysI and CysII of AOX isoforms were highly conserved in rapeseed. Among them, Bna.AOX1b was mainly expressed in the ovule and displayed varying expression between rapeseed cultivars which showed different salt resistance in seed germination. We identified its mitochondrial localization of this gene. To investigate the function of BnaAOX1b in rapeseed, transgenic rapeseed lines with overexpressed BnaAOX1b were created and seed germination and seedling establishment assays were performed under osmotic, salt, and ABA treatment. The results indicated that overexpression of BnaAOX1b significantly improved seed germination under osmotic and salt stress and weakened ABA sensitivity. In addition, post-germination seedling growth was improved under high salt condition, but showed hypersensitivity to ABA. RNA-sequencing analysis indicated that the genes involved in electron transport or energy pathway were induced and a number of gene responses to salt stress and ABA were regulated in Bna.AOX1b overexpressing seeds. Taken together, our results imply that Bna.AOX1b confers tolerance to osmotic and salt stress in terms of seed germination and seedling establishment by regulating stress responsive genes and the response to ABA, and could be utilized as a candidate gene in transgenic breeding.

Expression Patterns of ERF Genes Underlying Abiotic Stresses in Di-HaploidPopulus simonii×P. nigra

176 ERF genes fromPopuluswere identified by bioinformatics analysis, 13 of these in di-haploidPopulus simonii×P. nigrawere investigate by real-time RT-PCR, the results demonstrated that 13 ERF genes were highly responsive to salt stress, drought stress and ABA treatment, and all were expressed in root, stem, and leaf tissues, whereas their expression levels were markedly different in the various tissues. In roots,PthERF99,110,119, and168were primarily downregulated under drought and ABA treatment but were specifically upregulated under high salt condition. Interestingly, in poplar stems, all ERF genes showed the similar trends in expression in response to NaCl stress, drought stress, and ABA treatment, indicating that they may not play either specific or unique roles in stems in abiotic stress responses. In poplar leaves,PthERF168was highly induced by ABA treatment, but was suppressed by high salinity and drought stresses, implying thatPthERF168participated in the ABA signaling pathway. The results of this study indicated that ERF genes could play essential but distinct roles in various plant tissues in response to different environment cues and hormonal treatment.