Comprehensive evaluation of the response to aluminum stress in olive tree (Olea europaea L.)

Olive (Olea europaea L.) is an ancient tree species in the Mediterranean, but the lack of knowledge about aluminum-resistant varieties limits its introduction to acidic soil. The objective of this study was to have a comprehensive evaluation of the response to aluminum stress in olive tree at germplasm, metabolome, and transcriptome levels. In this experiment, seedlings of 97 olive germplasm with 1.0–3.0 cm roots and two leaves were treated with 50 μM Al3+ (pH = 5.0). By factor analysis of the traits of defoliation rate, rooting rate, length of extended root, and length of new root, 97 germplasm were classified into five different groups according to their diverse responses to aluminum stress: 5 highly resistant (5.15%), 30 moderately resistant (30.93%), 31 general (31.96%), 23 moderately sensitive (23.71%), and 8 highly sensitive (8.25%) germplasm. The three most sensitive and three most resistant germplasm were further used for metabolome and transcriptome analysis. Exposed to aluminum stress, 96 differentially accumulated metabolites (DAMs)/4,845 differentially expressed genes (DEGs) and 66 DAMs/2,752 DEGs were identified in highly sensitive and resistant germplasm, respectively. Using multi-omics technology, the pathways and related DAMs/DEGs involved in cell wall/cytoplasm receptors, reactive oxygen species balance, hormone induction, synthesis of organic acids, Al3+ transport, and synthesis of metabolites were identified to mainly regulate the response to aluminum stress in olive. This study provides a theoretical guide and prior germplasm and genes for further genetic improvement of aluminum tolerance in the olive tree

Genome-Wide Association Studies Reveal Genetic Variation and Candidate Genes of Drought Stress Related Traits in Cotton (Gossypium hirsutum L.)

Cotton is an important industrial crop worldwide and upland cotton (Gossypium hirsutum L.) is most widely cultivated in the world. Due to ever-increasing water deficit, drought stress brings a major threat to cotton production. Thus, it is important to reveal the genetic basis under drought stress and develop drought tolerant cotton cultivars. To address this issue, in present study, 319 upland cotton accessions were genotyped by 55,060 single nucleotide polymorphisms (SNPs) from high-density CottonSNP80K array and phenotyped nine drought tolerance related traits. The two datasets were used to identify quantitative trait nucleotides (QTNs) for the above nine traits using multi-locus random-SNP-effect mixed linear model method. As a result, a total of 20 QTNs distributed on 16 chromosomes were found to be significantly associated with six drought tolerance related traits. Of the 1,326 genes around the 20 QTNs, 205 were induced after drought stress treatment, and 46 were further mapped to Gene ontology (GO) term “response to stress.” Taken genome-wide association study (GWAS) analysis, RNA-seq data and qRT-PCR verification, four genes, RD2 encoding a response to desiccation 2 protein, HAT22 encoding a homeobox-leucine zipper protein, PIP2 encoding a plasma membrane intrinsic protein 2, and PP2C encoding a protein phosphatase 2C, were proposed to be potentially important for drought tolerance in cotton. These results will deepen our understanding of the genetic basis of drought stress tolerance in cotton and provide candidate markers to accelerate the development of drought-tolerant cotton cultivars

Chloroplast Genome Variation and Evolutionary Analysis of Olea europaea L.

Olive (Olea europaea L.) is a very important woody tree and favored by consumers because of the fruit’s high-quality olive oil. Chloroplast genome analysis will provide insights into the chloroplast variation and genetic evolution of olives. The complete chloroplast genomes of three accessions (O. europaea subsp. cuspidata isolate Yunnan, O. europaea subsp. europaea var. sylvestris, and O. europaea subsp. europaea var. frantoio) were obtained by next-generation sequencing technology. A total of 133 coding regions were identified in the three chloroplast genomes without rearrangement. O. europaea subsp. europaea var. sylvestris and O. europaea subsp. europaea var. frantoio had the same sequences (155,886 bp), while O. europaea subsp. cuspidata isolate Yunnan (155,531 bp) presented a large gap between rps16 and trnQ-UUG genes with six small gaps and fewer microsatellites. The whole chloroplast genomes of 11 O. europaea were divided into two main groups by a phylogenetic tree and O. europaea subsp. cuspidata formed a separate group (Cuspidata group) with the other subspecies (Mediterranean/North African group). Identification of consistency and diversity among O. europaea subspecies will benefit the exploration of domestication events and facilitate molecular-assisted breeding for O. europaea

Genome-wide analysis of the WRKY transcription factor gene family in Gossypium raimondii and the expression of orthologs in cultivated tetraploid cotton

WRKY proteins are members of a family of transcription factors in higher plants that function in plant responses to various physiological processes. We identified 120 candidate WRKY genes from Gossypium raimondii with corresponding expressed sequence tags in at least one of four cotton species, Gossypium hirsutum, Gossypium barbadense, Gossypium arboreum, and G. raimondii. These WRKY members were anchored on 13 chromosomes in G. raimondii with uneven distribution. Phylogenetic analysis showed that WRKY candidate genes can be classified into three groups, with 20 members in group I, 88 in group II, and 12 in group III. The 88 genes in group II were further classified into five subgroups, groups IIa–e, containing 7, 16, 37, 15, and 13 members, respectively. We characterized diversity in amino acid residues in the WRKY domain and/or other zinc finger motif regions in the WRKY proteins. The expression patterns of WRKY genes revealed their important roles in diverse functions in cotton developmental stages of vegetative and reproductive growth and stress response. Structural and expression analyses show that WRKY proteins are a class of important regulators of growth and development and play key roles in response to stresses in cotton

Genome-Wide Identification and Functional Differentiation of Fatty Acid Desaturase Genes in Olea europaea L.

Olive (Olea europaea L.) is a world-famous woody oil tree and popular for redundant unsaturated fatty acids. Fatty acid desaturase (FAD) genes are responsible for fatty acid desaturation and stress regulation but have not yet been identified in olive at the whole genome level. This study identified 40 and 27 FAD genes in the cultivated olive O. europaea cv. Farga and the wild olive O. europaea var. Sylvestris, respectively. Phylogenetic analysis showed that all the FAD genes could be classified into the soluble FAB2/SAD clade and membrane-bound clade, including ADS/FAD5, DES, FAD4, SLD, ω-6 and ω-3, with the high consistency of subcellular localization, motif composition and exon-intron organization in each group. FAD genes in olive showed the diverse functional differentiation in morphology of different tissues, fruit development and stress responses. Among them, OeFAB2.8 and OeFAD2.3 were up-regulated and OeADS.1, OeFAD4.1 and OeFAD8.2 were down-regulated under the wound, Verticillium dahliae and cold stresses. This study presents a comprehensive analysis of the FAD genes at the whole-genome level in olives and will provide guidance for the improvement of oil quality or stress tolerance of olive trees

Comparative Evaluation of the Phytochemical Profiles and Antioxidant Potentials of Olive Leaves from 32 Cultivars Grown in China

Olives (Olea europaea L.) are a significant part of the agroindustry in China. Olive leaves, the most abundant by-products of the olive and olive oil industry, contain bioactive compounds that are beneficial to human health. The purpose of this study was to evaluate the phytochemical profiles and antioxidant capacities of olive leaves from 32 cultivars grown in China. A total of 32 phytochemical compounds were identified using high-performance liquid chromatography–electrospray ionization–tandem mass spectrometry, including 17 flavonoids, five iridoids, two hydroxycinnamic acids, six triterpenic acids, one simple phenol, and one coumarin. Specifically, olive leaves were found to be excellent sources of flavonoids (4.92–18.29 mg/g dw), iridoids (5.75–33.73 mg/g dw), and triterpenic acids (15.72–35.75 mg/g dw), and considerable variations in phytochemical content were detected among the different cultivars. All tested cultivars were classified into three categories according to their oil contents for further comparative phytochemicals assessment. Principal component analysis indicated that the investigated olive cultivars could be distinguished based upon their phytochemical profiles and antioxidant capacities. The olive leaves obtained from the low-oil-content (20%) cultivars contained mainly triterpenic acids in their compositions. Correspondingly, the low-oil-content cultivars (OL3, Frantoio selection and OL14, Huaou 5) exhibited the highest ABTS antioxidant activities (758.01 ± 16.54 and 710.64 ± 14.58 mg TE/g dw, respectively), and OL9 (Olea europaea subsp. Cuspidata isolate Yunnan) and OL3 exhibited the highest ferric reducing/antioxidant power assay values (1228.29 ± 23.95 mg TE/g dw and 1099.99 ± 14.30 mg TE/g dw, respectively). The results from this study may be beneficial to the comprehensive evaluation and utilization of bioactive compounds in olive leaves

GC-MS/LC-MS and transcriptome analyses revealed the metabolisms of fatty acid and flavonoid in olive fruits (Olea europaea L.)

Olive (Olea europaea L.) is an economical fruit tree for the usage of oil extraction and table olives. It is favored by consumers because of abundant unsaturated fatty acids and flavonoids, but little known about the genetic mechanisms. This study identifies the fruit traits of three olive cultivars ‘Arbequina’, ‘Frantoio selection’ and ‘Nikitskii Ⅰ’, first planted in the conditions of acid soil and rainy summer and further elucidates the fatty acid and flavonoid biosynthesis mechanism by multi-omics analysis. ‘Arbequina’ and ‘Frantoio selection’ had medium flesh/pit ratios (3.94, 3.53) and oil contents (15.95%, 12.95%) and were suitable for oil extraction. ‘Nikitskii Ⅰ’ had a big flesh/pit ratio (6.25) and medium oil content (13.13%) and could be used both for table olives and oil purpose. Totally, 37 fatty acid and 35 flavonoid compounds were detected by gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry technologies with the average Pearson correlation indexes of 0.985 and 0.971 among different cultivars, respectively. Transcriptome analysis identified 14,684 differentially expressed genes with 1008 common differential genes. Furthermore, enrichment analysis showed 15 and 8 pathways involved in fatty acid and flavonoid metabolism with 44 and 32 prior transcripts tested, respectively. Overall, among the three cultivars, ‘Frantoio selection’ and ‘Nikitskii Ⅰ’ displayed a larger difference and they showed the high ratios of unsaturated fatty acids/fatty acids and oleic acid/fatty acids, respectively. While ‘Arbequina’ presented a big advantage in flavonoid compounds and expressions of related genes. The study provides the excellent materials and candidate genes for genetically improving of the quality of olive oil.info:eu-repo/semantics/publishedVersio

Comprehensive Analysis of the COBRA-Like (COBL) Gene Family in Gossypium Identifies Two COBLs Potentially Associated with Fiber Quality.

COBRA-Like (COBL) genes, which encode a plant-specific glycosylphosphatidylinositol (GPI) anchored protein, have been proven to be key regulators in the orientation of cell expansion and cellulose crystallinity status. Genome-wide analysis has been performed in A. thaliana, O. sativa, Z. mays and S. lycopersicum, but little in Gossypium. Here we identified 19, 18 and 33 candidate COBL genes from three sequenced cotton species, diploid cotton G. raimondii, G. arboreum and tetraploid cotton G. hirsutum acc. TM-1, respectively. These COBL members were anchored onto 10 chromosomes in G. raimondii and could be divided into two subgroups. Expression patterns of COBL genes showed highly developmental and spatial regulation in G. hirsutum acc. TM-1. Of them, GhCOBL9 and GhCOBL13 were preferentially expressed at the secondary cell wall stage of fiber development and had significantly co-upregulated expression with cellulose synthase genes GhCESA4, GhCESA7 and GhCESA8. Besides, GhCOBL9 Dt and GhCOBL13 Dt were co-localized with previously reported cotton fiber quality quantitative trait loci (QTLs) and the favorable allele types of GhCOBL9 Dt had significantly positive correlations with fiber quality traits, indicating that these two genes might play an important role in fiber development

Table_1_Alterations of phenotype, physiology, and functional substances reveal the chilling-tolerant mechanism in two common Olea Europaea cultivars.xlsx

Olive suffers from cold damage when introduced to high-latitude regions from its native warm climes. Therefore, this study aims to improve the adaption of olive to climates in which it is cold for part of the year. The phenotype, physiological performance, nutrient content, and gene expression of olive leaves (from two widely planted cultivars) were examined after cultivation in normal and cold stress conditions. The results showed that the cold-tolerant cultivar possessed stronger photosynthesis efficiency and higher anti-oxidase activity after cold treatment than the cold-sensitive cultivar. Alteration of gene expression and metabolites in the amino acid metabolism, glycerolipid metabolism, diterpenoid biosynthesis, and oleuropein metabolism pathways played an important role in the cold responses of olive. Furthermore, the construction of the network of genes for ubiquitination and metabolites suggested that polyubiquitination contributes most to the stable physiology of olive under cold stress. Altogether, the results of this study can play an important role in helping us to understand the cold hardiness of olive and screen cold-resistant varieties for excellent quality and yield.</p