PeerJ Preprints: Plant Sciencehttps://peerj.com/preprints/index.atom?journal=peerj&subject=2400Plant Science articles published in PeerJ PreprintsA roadmap for gene functional characterisation in wheathttps://peerj.com/preprints/268772019-12-182019-12-18Nikolai M AdamskiPhilippa BorrillJemima BrintonSophie HarringtonClemence MarchalAlison R BentleyWiliam D BovillLuigi CattivelliJames CockramBruno Contreras-MoreiraBrett FordSreya GhoshWendy HarwoodKeywan Hassani-PakSadiye HaytaLee T HickeyKostya KanyukaJulie KingMarco MaccaferriGuy NaamatiCurtis J PozniakRicardo H Ramirez-GonzalezCarolina SansaloniBen TrevaskisLuzie U WingenBrande BH WulffCristobal Uauy
To adapt to the challenges of climate change and the growing world population, it is vital to increase global crop production. Understanding the function of genes within staple crops will accelerate crop improvement by allowing targeted breeding approaches. Despite the importance of wheat, which provides 20 % of the calories consumed by humankind, a lack of genomic information and resources has hindered the functional characterisation of genes in this species. The recent release of a high-quality reference sequence for wheat underpins a suite of genetic and genomic resources that support basic research and breeding. These include accurate gene model annotations, gene expression atlases and gene networks that provide background information about putative gene function. In parallel, sequenced mutation populations, improved transformation protocols and structured natural populations provide rapid methods to study gene function directly. We highlight a case study exemplifying how to integrate these resources to study gene function in wheat and thereby accelerate improvement in this important crop. We hope that this review provides a helpful guide for plant scientists, especially those expanding into wheat research for the first time, to capitalise on the discoveries made in Arabidopsis and other plants. This will accelerate the improvement of wheat, a complex polyploid crop, of vital importance for food and nutrition security.
To adapt to the challenges of climate change and the growing world population, it is vital to increase global crop production. Understanding the function of genes within staple crops will accelerate crop improvement by allowing targeted breeding approaches. Despite the importance of wheat, which provides 20 % of the calories consumed by humankind, a lack of genomic information and resources has hindered the functional characterisation of genes in this species. The recent release of a high-quality reference sequence for wheat underpins a suite of genetic and genomic resources that support basic research and breeding. These include accurate gene model annotations, gene expression atlases and gene networks that provide background information about putative gene function. In parallel, sequenced mutation populations, improved transformation protocols and structured natural populations provide rapid methods to study gene function directly. We highlight a case study exemplifying how to integrate these resources to study gene function in wheat and thereby accelerate improvement in this important crop. We hope that this review provides a helpful guide for plant scientists, especially those expanding into wheat research for the first time, to capitalise on the discoveries made in Arabidopsis and other plants. This will accelerate the improvement of wheat, a complex polyploid crop, of vital importance for food and nutrition security.Bacillus induced to biosynthesize VOCs & nitriles may benefit agriculture.https://peerj.com/preprints/26112019-09-302019-09-30Guenevere PerryDiane Perry
The scope of the project was to identify the possible agricultural applications for bacteria induced to synthesize nitriles and VOCs. The study was randomized. Cucurbit seeds and Bacillus licheniformis were selected as the plant and microbial models for two trial studies. In trial 1, 90 cucumber seeds were cultured with B.licheniformis induced to synthesize VOCs (including ethanol, 3-methyl-1-butanol, pentanol), esters (ethyl acetate), and acetonitriles. After 2 weeks the induced bacteria increased seed germination by 68% compared to control samples. Several seedlings were transferred to a small garden, infested with soil nematodes. Roots of control and induced samples appeared affected. Control samples appeared stunted in growth with decreased productivity, but cucumber plants initially planted with induced bacteria were noticeably larger in size with good productivity. Induced Bacillus increased the number of blossoms and cucumber per plant by 125% compared to control samples. Induced Bacillus did not increase solubility of nitrogen, phosphorous, or potassium in the soil, but appeared to increase plant health and defenses against pathogenic infections. Though the study findings are preliminary, soil microbes induced to synthesize VOCs and nitriles may improve plant health and productivity in cucurbit plants.
The scope of the project was to identify the possible agricultural applications for bacteria induced to synthesize nitriles and VOCs. The study was randomized. Cucurbit seeds and Bacillus licheniformis were selected as the plant and microbial models for two trial studies. In trial 1, 90 cucumber seeds were cultured with B.licheniformis induced to synthesize VOCs (including ethanol, 3-methyl-1-butanol, pentanol), esters (ethyl acetate), and acetonitriles. After 2 weeks the induced bacteria increased seed germination by 68% compared to control samples. Several seedlings were transferred to a small garden, infested with soil nematodes. Roots of control and induced samples appeared affected. Control samples appeared stunted in growth with decreased productivity, but cucumber plants initially planted with induced bacteria were noticeably larger in size with good productivity. Induced Bacillus increased the number of blossoms and cucumber per plant by 125% compared to control samples. Induced Bacillus did not increase solubility of nitrogen, phosphorous, or potassium in the soil, but appeared to increase plant health and defenses against pathogenic infections. Though the study findings are preliminary, soil microbes induced to synthesize VOCs and nitriles may improve plant health and productivity in cucurbit plants.Ethylene induced nitrile and VOC synthesis by soil microbes; Improved root elongation & reduced risk of fungal infection in plants.https://peerj.com/preprints/5432019-09-272019-09-27Guenevere PerryDiane Perry
The scope of the project was to develop a method to induce soil microbes to inhibit fungal infection and improve root elongation. The study was randomized. Gladiolus bulbs selected for the study were visibly inspected to for viability and visible signs of infection. Two trials were conducted from Aug. 5th – Sept. 5th 2014 with 4 replicates per condition over a 7-d period in damp outdoor conditions in late summer. A mixed culture of plant growth promoting rhizobacteria (PGPR) were collected from soil surrounding the roots of young fruit bearing trees. Microbes were mixed with minimal media (no-carbon source), and cultured with an ethylene and used as potting soil. Bulbs planted in ethylene induced soil displayed 0% visible fungal growth, while 38% of bulbs grown in control conditions displayed some form of fungal growth and/or infection. Ethylene induced soil increased root length by 225% in bulbs in 7-d period. GC Mass Spectrophotometry data suggest ethylene may induce soil microbes to synthesize several VOCs including (ethanol, 3-methyl-1-butanol, pentanol) and esters (ethyl acetate), that may have synergistic benefits to lower the risk of fungal infection by soil mold, while nitrile compounds improve root elongation. The findings are preliminary, additional studies are required to understand the mechanism.
The scope of the project was to develop a method to induce soil microbes to inhibit fungal infection and improve root elongation. The study was randomized. Gladiolus bulbs selected for the study were visibly inspected to for viability and visible signs of infection. Two trials were conducted from Aug. 5th – Sept. 5th 2014 with 4 replicates per condition over a 7-d period in damp outdoor conditions in late summer. A mixed culture of plant growth promoting rhizobacteria (PGPR) were collected from soil surrounding the roots of young fruit bearing trees. Microbes were mixed with minimal media (no-carbon source), and cultured with an ethylene and used as potting soil. Bulbs planted in ethylene induced soil displayed 0% visible fungal growth, while 38% of bulbs grown in control conditions displayed some form of fungal growth and/or infection. Ethylene induced soil increased root length by 225% in bulbs in 7-d period. GC Mass Spectrophotometry data suggest ethylene may induce soil microbes to synthesize several VOCs including (ethanol, 3-methyl-1-butanol, pentanol) and esters (ethyl acetate), that may have synergistic benefits to lower the risk of fungal infection by soil mold, while nitrile compounds improve root elongation. The findings are preliminary, additional studies are required to understand the mechanism.Functional characterization of a new maize heat shock transcription factor gene ZmHsf01 playing important roles in thermotolerancehttps://peerj.com/preprints/279872019-09-262019-09-26Huaning ZhangGuoliang LiYuanyuan ZhangYujie ZhangHongbo ShaoDong HuXiulin Guo
Background. The yield of maize crop is influenced seriously by heat waves. Plant heat shock transcription factors (Hsfs) play a key regulatory role in heat shock signal transduction pathway. Method. In this study, a new heat shock transcription factor gene, ZmHsf01 (accession number: MK888854) , was cloned from maize young leaves using homologous cloning method. The transcriptional level of ZmHsf01 were detected by qRT-PCR in different tissues or under heat shock, abscisic acid (ABA) and hydrogen peroxide (H2O2) treatment. The transgenic yeast and Arabidopsis were used to study the gene function of ZmHsf01. Result. The coding sequence (CDS) of ZmHsf01 was 1176 bp and encoded a protein that consisted of 391 amino acids. The homologous analysis result showed that ZmHsf01 and SbHsfA2d had the highest protein sequence identity. Subcellular localization experiments demonstrated that ZmHsf01 is localized to the nucleus. ZmHsf01 was expressed in many maize tissues and was up-regulated by heat stress. ZmHsf01 was up-regulated in roots and down-regulated in leaves by ABA and H2O2treatments. In yeast, ZmHsf01-overexpressing cells showed increased thermotolerance. In Arabidopsis seedlings, ZmHsf01 complemented the thermotolerance defects of athsfa2 mutant and ZmHsf01-overexpressing lines presented enhanced basal and acquired thermotolerance. Compared to wild type (WT) seedlings, ZmHsf01-overexpressing lines showed increased chlorophyll content after heat stress. The expression level of heat shock protein genes was up-regulated higher in ZmHsf01-overexpressing Arabidopsis seedlings than that in WT. These results suggested that ZmHsf01 plays a vital role in plant response to heat stress.
Background. The yield of maize crop is influenced seriously by heat waves. Plant heat shock transcription factors (Hsfs) play a key regulatory role in heat shock signal transduction pathway. Method. In this study, a new heat shock transcription factor gene, ZmHsf01 (accession number: MK888854), was cloned from maize young leaves using homologous cloning method. The transcriptional level of ZmHsf01 were detected by qRT-PCR in different tissues or under heat shock, abscisic acid (ABA) and hydrogen peroxide (H2O2) treatment. The transgenic yeast and Arabidopsis were used to study the gene function of ZmHsf01. Result. The coding sequence (CDS) of ZmHsf01 was 1176 bp and encoded a protein that consisted of 391 amino acids. The homologous analysis result showed that ZmHsf01 and SbHsfA2dhad the highest protein sequence identity. Subcellular localization experiments demonstrated that ZmHsf01 is localized to the nucleus. ZmHsf01 was expressed in many maize tissues and was up-regulated by heat stress. ZmHsf01 was up-regulated in roots and down-regulated in leaves by ABA and H2O2treatments. In yeast, ZmHsf01-overexpressing cells showed increased thermotolerance. In Arabidopsis seedlings, ZmHsf01 complemented the thermotolerance defects of athsfa2 mutant and ZmHsf01-overexpressing lines presented enhanced basal and acquired thermotolerance. Compared to wild type (WT) seedlings, ZmHsf01-overexpressing lines showed increased chlorophyll content after heat stress. The expression level of heat shock protein genes was up-regulated higher in ZmHsf01-overexpressing Arabidopsis seedlings than that in WT. These results suggested that ZmHsf01 plays a vital role in plant response to heat stress.Ethylene induced soil delays ripening in organic bananas.https://peerj.com/preprints/5062019-09-252019-09-25Guenevere PerryDiane Williams
The scope of the project was to develop a method to induce soil bacteria to biosynthesize compounds that retard the effects of ethylene induced ripening in climacteric fruits. The study was randomized. Organic bananas selected for the study were visibly inspected to ensure the fruit was unripen with no visible signs of bruising, spotting, or infection from a local distributor. Four trials were conducted from June 5th - August 5th 2014 with 3 replicates (3-4 bananas per experimental unit) in 4 trial studies for 3 days at room temperature. A mixed culture of plant growth promoting rhizobacteria (PGPR) were collected from soil surrounding the roots of young fruit bearing trees. Microbes were mixed with no-carbon source media, and cultured with an ethylene for 3 d at room temperature in a closed container. Induced soil was used to delay ripening. Microbes induced with media and ethylene delayed ripening 100% of the time in all experimental units compared to control samples, while microbes cultured with media (no ethylene) delayed ripening less than 10% of the time compared to the control. These cells also appeared to increase the incidence of fungal infection in the fruit. The findings suggest induced microbes may convert ethylene into ethanol then acetaldehyde. The two compounds may form an acetaldehyde/ethanol vapor that delays ripening, and a secondary nitrile compound that inhibits fungal growth.
The scope of the project was to develop a method to induce soil bacteria to biosynthesize compounds that retard the effects of ethylene induced ripening in climacteric fruits. Thestudy was randomized. Organic bananas selected for the study were visibly inspected to ensure the fruit was unripen with no visible signs of bruising, spotting, or infection from a local distributor. Four trials were conducted from June 5th - August 5th 2014 with 3 replicates (3-4 bananas per experimental unit) in 4 trial studies for 3 days at room temperature. A mixed culture of plant growth promoting rhizobacteria (PGPR) were collected from soil surrounding the roots of young fruit bearing trees. Microbes were mixed with no-carbon source media, and cultured with an ethylene for 3 d at room temperature in a closed container. Induced soil was used to delay ripening. Microbes induced with media and ethylene delayed ripening 100% of the time in all experimental units compared to control samples, while microbes cultured with media (no ethylene) delayed ripening less than 10% of the time compared to the control. These cells also appeared to increase the incidence of fungal infection in the fruit. The findings suggest induced microbes may convert ethylene into ethanol then acetaldehyde. The two compounds may form an acetaldehyde/ethanol vapor that delays ripening, and a secondary nitrile compound that inhibits fungal growth.Initial embedding of TRANSPARENT TESTA GLABRA 1 in the Arabidopsis thaliana flowering time regulatory pathwayhttps://peerj.com/preprints/279742019-09-202019-09-20Barbara A M PaffendorfRawan QassrawiAndrea M MeysLaura TrimbornAndrea Schrader
Pleiotropic regulatory factors mediate concerted responses of the plant’s trait network to endogenous and exogenous cues. TRANSPARENT TESTA GLABRA 1 (TTG1) is a pleiotropic regulator that has been predominantly described in its role as a regulator of early accessible developmental traits. Although its closest homologs LIGHT-REGULATED WD1 (LWD1) and LWD2 are regulators of photoperiodic flowering, a role of TTG1 in flowering time regulation has not been reported.
Here we reveal that TTG1 is a regulator of flowering time in Arabidopsis thaliana and changes transcription levels of different targets within the flowering time regulatory pathway. TTG1 mutants flower early and TTG1 overexpression lines flower late at long-day conditions. Consistently, TTG1 can suppress the transcript levels of the floral integrators FLOWERING LOCUS T and SUPPRESSOR OF OVEREXPRESSION OF CO1 and can act as an activator of circadian clock components. Moreover, TTG1 might form feedback loops at the protein level. The TTG1 protein interacts with PSEUDO RESPONSE REGULATOR (PRR)s and basic HELIX-LOOP-HELIX 92 (bHLH92) in yeast. In planta, the respective pairs exhibit interesting patterns of localization including a recruitment of TTG1 by PRR5 to subnuclear foci. This mechanism proposes additional layers of regulation by TTG1 and might aid to specify the function of bHLH92.
Within another branch of the pathway, TTG1 can elevate FLOWERING LOCUS C (FLC) transcript levels. FLC mediates signals from the vernalization, ambient temperature and autonomous pathway and the circadian clock is pivotal for the plant to synchronize with diurnal cycles of environmental stimuli like light and temperature. Our results suggest an unexpected positioning of TTG1 upstream of FLC and upstream of the circadian clock. In this light, this points to an adaptive value of the role of TTG1 in respect to flowering time regulation.
Pleiotropic regulatory factors mediate concerted responses of the plant’s trait network to endogenous and exogenous cues. TRANSPARENT TESTA GLABRA 1 (TTG1) is a pleiotropic regulator that has been predominantly described in its role as a regulator of early accessible developmental traits. Although its closest homologs LIGHT-REGULATED WD1 (LWD1) and LWD2 are regulators of photoperiodic flowering, a role of TTG1 in flowering time regulation has not been reported.Here we reveal that TTG1 is a regulator of flowering time in Arabidopsis thaliana and changes transcription levels of different targets within the flowering time regulatory pathway. TTG1 mutants flower early and TTG1 overexpression lines flower late at long-day conditions. Consistently, TTG1 can suppress the transcript levels of the floral integrators FLOWERING LOCUS T and SUPPRESSOR OF OVEREXPRESSION OF CO1 and can act as an activator of circadian clock components. Moreover, TTG1 might form feedback loops at the protein level. The TTG1 protein interacts with PSEUDO RESPONSE REGULATOR (PRR)s and basic HELIX-LOOP-HELIX 92 (bHLH92) in yeast. In planta, the respective pairs exhibit interesting patterns of localization including a recruitment of TTG1 by PRR5 to subnuclear foci. This mechanism proposes additional layers of regulation by TTG1 and might aid to specify the function of bHLH92.Within another branch of the pathway, TTG1 can elevate FLOWERING LOCUS C (FLC) transcript levels. FLC mediates signals from the vernalization, ambient temperature and autonomous pathway and the circadian clock is pivotal for the plant to synchronize with diurnal cycles of environmental stimuli like light and temperature. Our results suggest an unexpected positioning of TTG1 upstream of FLC and upstream of the circadian clock. In this light, this points to an adaptive value of the role of TTG1 in respect to flowering time regulation.Antibiosis effects of rice carrying Bph14 and Bph15 on the brown planthopper, Nilaparvata lugenshttps://peerj.com/preprints/279602019-09-142019-09-14Liangmiao QiuWuqi WangLongqing ShiQiquan LiuZhixiong Zhan
The brown planthopper (BPH), Nilaparvata lugens, is the most destructive insect pest in rice production worldwide. The development and cultivation of BPH-resistant varieties is the most economical and efficient strategy to overcome the destruction caused by BPH. In this study, the modified bulk seedling test method was used to identify the BPH resistance level and host feeding choice of rice lines of Liangyou8676 (Bph14/Bph15), Bph68S (Bph14/Bph15), RHT (Bph3), Fuhui676, and TN1 on BPH. Meanwhile, the population, survival and emergence rate, developmental duration, honeydew excretion, female ratio and brachyptery ratio of adults were used as indicators to detect the antibiosis effects of the different rice lines. The results showed that the resistance levels of Rathu Heenati (RHT), Bph68S, Liangyou8676, Fuhui676, and TN1 to BPH were HR, R, MR, S and HS, respectively. The host choice implied that BPH was more inclined to feeding on rice plants with a lower resistance. An analysis of the antibiosis activity of rice lines RHT, BPh68S, and Liangyou8676 carrying resistance genes indicated a significant reduction in the population growth rate, survival and emergence rate of BPH nymphs, significant delay in the developmental duration of nymphs, reduced honeydew excretion of females, decreased female ratio, and a decreased brachyptery ratio of females and males, when compared with rice carrying no BPH-resistant genes.
The brown planthopper (BPH), Nilaparvata lugens, is the most destructive insect pest in rice production worldwide. The development and cultivation of BPH-resistant varieties is the most economical and efficient strategy to overcome the destruction caused by BPH. In this study, the modified bulk seedling test method was used to identify the BPH resistance level and host feeding choice of rice lines of Liangyou8676 (Bph14/Bph15), Bph68S (Bph14/Bph15), RHT (Bph3), Fuhui676, and TN1 on BPH. Meanwhile, the population, survival and emergence rate, developmental duration, honeydew excretion, female ratio and brachyptery ratio of adults were used as indicators to detect the antibiosis effects of the different rice lines. The results showed that the resistance levels of Rathu Heenati (RHT), Bph68S, Liangyou8676, Fuhui676, and TN1 to BPH were HR, R, MR, S and HS, respectively. The host choice implied that BPH was more inclined to feeding on rice plants with a lower resistance. An analysis of the antibiosis activity of rice lines RHT, BPh68S, and Liangyou8676 carrying resistance genes indicated a significant reduction in the population growth rate, survival and emergence rate of BPH nymphs, significant delay in the developmental duration of nymphs, reduced honeydew excretion of females, decreased female ratio, and a decreased brachyptery ratio of females and males, when compared with rice carrying no BPH-resistant genes.Epiphytic fungi induced pathogen resistance of invasive plant Ipomoea cairica against Colletotrichum gloeosporioideshttps://peerj.com/preprints/279562019-09-112019-09-11Hua XuMinjie ZhuShaoshan LiWeibin RuanCan Xie
Background. Ipomoea cairica (L.) Sweet is a destructive invasive weed in South China but rarely infected with pathogens in nature. Its pathogen resistance mechanism is largely unknown at present. Some non-pathogenic isolates of Fusarium oxysporum and Fusarium fujikuroi are prevalent on many plant species and function as pathogen resistance inducers of host plants. The objective of the present research is to investigate whether the symbiosis between the both fungi and I. cairica is present, and thereby induce pathogen resistance of I. cairica. Methods. Through field investigation, we explored the occurrence rates of F. oxysporum and F. fujikuroi on leaf surfaces of I. cairica plants in natural habitats and compared their abundance between healthy leaves and leaves infected with Colletotrichum gloeosporioides, a natural pathogen. With artificial inoculation, we assessed their pathogencity to I. cairica and study their contribution of pathogen resistance to I. cairica against C. gloeosporioides. Results. We found that F. oxysporum and F. fujikuroi were widely epiphytic on healthy leaf surfaces of I. cairica in sunny non-saline, shady non-saline and sunny saline habitats. Their occurrence rates reached up to 100%. Moreover, we found that the abundance of F. oxysporum and F. fujikuroi on leaves infected with C. gloeosporioides were significantly lower than that of healthy leaves. With artificial inoculation, we empirically confirmed that F. oxysporum and F. fujikuroi were non-pathogenic to I. cairica. It was interesting that colonization by F. fujikuroi, F. oxysporum alone and a mixture of both fungi resulted in a reduction of C. gloeosporioides infection to I. cairica accompanied by lower lesion area to leaf surface area ratio, increased H2O2 concentration and salicylic acid (SA) level relative to the control. However, NPR1 expression, chitinase and β -1,3-glucanase activities as well as stem length and biomass of I. cairica plant only could be significantly improved by F. oxysporum and a mixture of both fungi but not by F. fujikuroi. In addition, as compared to colonization by F. oxysporum and a mixture of both fungi, F. fujikuroi induced significantly higher jasmonic acid (JA) level but significantly lower β -1,3-glucanase activity in leaves of I. cairica plants. Thus, our findings indicated the symbiosis of epiphytic fungi F. fujikuroi and F. oxysporum facilitated the fitness of I. cairica via the induced systemic resistance of host plant against C. gloeosporioides. F. oxysporum played a dominant role in inducing pathogen resistance of I. cairica. Its presence alleviated the antagonism of the JA signaling on SA-dependent β -1,3-glucanase activity and enabled I. cairica plants to maintain relatively higher level of resistance against C. gloeosporioides.
Background. Ipomoea cairica (L.) Sweet is a destructive invasive weed in South China but rarely infected with pathogens in nature. Its pathogen resistance mechanism is largely unknown at present. Some non-pathogenic isolates of Fusarium oxysporum and Fusarium fujikuroi are prevalent on many plant species and function as pathogen resistance inducers of host plants. The objective of the present research is to investigate whether the symbiosis between the both fungi and I. cairica is present, and thereby induce pathogen resistance of I. cairica.Methods. Through field investigation, we explored the occurrence rates of F. oxysporum and F. fujikuroi on leaf surfaces of I. cairica plants in natural habitats and compared their abundance between healthy leaves and leaves infected with Colletotrichum gloeosporioides, a natural pathogen. With artificial inoculation, we assessed their pathogencity to I. cairica and study their contribution of pathogen resistance to I. cairica against C. gloeosporioides.Results. We found that F. oxysporum and F. fujikuroi were widely epiphytic on healthy leaf surfaces of I. cairica in sunny non-saline, shady non-saline and sunny saline habitats. Their occurrence rates reached up to 100%. Moreover, we found that the abundance of F. oxysporum and F. fujikuroi on leaves infected with C. gloeosporioides were significantly lower than that of healthy leaves. With artificial inoculation, we empirically confirmed that F. oxysporum and F. fujikuroi were non-pathogenic to I. cairica. It was interesting that colonization by F. fujikuroi, F. oxysporum alone and a mixture of both fungi resulted in a reduction of C. gloeosporioides infection to I. cairica accompanied by lower lesion area to leaf surface area ratio, increased H2O2 concentration and salicylic acid (SA) level relative to the control. However, NPR1 expression, chitinase and β -1,3-glucanase activities as well as stem length and biomass of I. cairica plant only could be significantly improved by F. oxysporum and a mixture of both fungi but not by F. fujikuroi. In addition, as compared to colonization by F. oxysporum and a mixture of both fungi, F. fujikuroi induced significantly higher jasmonic acid (JA) level but significantly lower β -1,3-glucanase activity in leaves of I. cairica plants. Thus, our findings indicated the symbiosis of epiphytic fungiF. fujikuroi and F. oxysporum facilitated the fitness of I. cairicavia the induced systemic resistance of host plant against C. gloeosporioides. F. oxysporum played a dominant role in inducing pathogen resistance of I. cairica. Its presence alleviated the antagonism of the JA signaling on SA-dependentβ -1,3-glucanase activity and enabled I. cairica plantsto maintain relatively higher level of resistance against C. gloeosporioides.The complete chloroplast genomes of seventeen Aegilops tauschii: Genome characteristic and comparative analysishttps://peerj.com/preprints/279322019-08-312019-08-31Qing SuLuxian LiuMengyu ZhaoCancan ZhangDale ZhangYouyong LiSuoping Li
As the diploid progenitor of common wheat, Aegilops tauschii Cosson (DD, 2n = 2x = 14) is regarded to be a potential genetic resource for improving common wheat, which is naturally distributed in central Eurasia, spreading from northern Syria and Turkey to western China. In this work, the chloroplast genomes of seventeen Ae. tauschii accessions showed 135 551~ 136 009 bp in length and contained the typical quadripartite structure of angiosperms. Meanwhile, a total of 127 functional genes, including 78 protein-coding genes, 4 rRNAs, 26 tRNAs, and 19 duplicated genes were identified. Overall genomic structure including gene number, gene order were well conserved with identical IR/SC boundary regions, but few variations predominantly were detected in non-coding regions (intergenic spacer regions). IR expansion and contraction with identical structure among 17 Aegilops tauschii accessions were not influence chloroplast genomes in length. Four cpDNA markers including rpl32-trnL-UAG, ccsA-ndhD, rbcL-psaI and rps18-rpl20 showed high nucleotide polymorphisms,which may be used to study on inter- and intra-specific genetic structure and diversity of Ae. tauschii. The ndhF gene in AY46 accession appeared the highest ω value, which might be involved in the adaptation to high altitude ecological environment during the evolution of AY46 accession. The phylogenetic relationships constructed by the complete genome sequences strongly support that Ae. tauschii in the Yellow River region might be directly originated from Central Asia rather than Xinjiang. The specific spreading route of Ae. tauschii revealed in this work, reflects the frequent cultural exchange through the silk road from one point of view. We confirmed that Ae. tauschii derived from monophyletic speciation rather than hybrid speciation at the chloroplast genome level.
As the diploid progenitor of common wheat, Aegilops tauschii Cosson (DD, 2n = 2x = 14) is regarded to be a potential genetic resource for improving common wheat, which is naturally distributed in central Eurasia, spreading from northern Syria and Turkey to western China. In this work, the chloroplast genomes of seventeen Ae. tauschii accessions showed 135 551~ 136 009 bp in length and contained the typical quadripartite structure of angiosperms. Meanwhile, a total of 127 functional genes, including 78 protein-coding genes, 4 rRNAs, 26 tRNAs, and 19 duplicated genes were identified. Overall genomic structure including gene number, gene order were well conserved with identical IR/SC boundary regions, but few variations predominantly were detected in non-coding regions (intergenic spacer regions). IR expansion and contraction with identical structure among 17 Aegilops tauschii accessions were not influence chloroplast genomes in length. Four cpDNA markers including rpl32-trnL-UAG, ccsA-ndhD, rbcL-psaI and rps18-rpl20 showed high nucleotide polymorphisms,which may be used to study on inter- and intra-specific genetic structure and diversity of Ae. tauschii. The ndhF gene in AY46 accession appeared the highest ω value, which might be involved in the adaptation to high altitude ecological environment during the evolution of AY46 accession. The phylogenetic relationships constructed by the complete genome sequences strongly support that Ae. tauschii in the Yellow River region might be directly originated from Central Asia rather than Xinjiang. The specific spreading route of Ae. tauschii revealed in this work, reflects the frequent cultural exchange through the silk road from one point of view. We confirmed that Ae. tauschii derived from monophyletic speciation rather than hybrid speciation at the chloroplast genome level.Candidate genes in coffee (Coffea arabica L.) leaves associated with rust (Hemileia vastatrix Berk. & Br) stresshttps://peerj.com/preprints/279232019-08-282019-08-28Fabián Echeverría-BeiruteSeth C. MurrayBenoit BertrandPatricia E. Klein
Background. Coffee leaf rust (CLR) caused by Hemileia vastatrix Berk. & Br, is one of the most threatening diseases for Coffea arabica L. It is hypothesized that host tolerance to CLR relies on non-race-specific resistance genes.
Methods. This study evaluated gene expression in leaves of two susceptible coffee cultivars (one inbred and one F1 hybrid) under different stress conditions: rust control (fungicide and untreated) and fruit thinning (thinned and un-thinned) treatments. RNA-seq analysis focused on the association of differentially expressed genes (DEGs) with CLR and associated the effect of the most significant genes into the phenotype, using regression and prediction statistical models.
Results. Gene expression and gene ontology (GO) analysis allowed identification of 100 genes associated with quantitative traits. From these, 88 were correlated with rust incidence, rust severity, and rust sporulation. The expression of genes coding for pathogenesis-related proteins increased positively with rust incidence in the inbred, while genes involved in homoeostasis and broader cell wall structuring processes were upregulated in the F1 hybrid. The enriched gene functions and associations revealed that a possible hypersensitive response (HR) in the inbred and a systemic acquired resistance (SAR) in the F1 hybrid were involved in the tolerance mechanisms to CLR stress. This is the first study to demonstrate the specific interactions between CLR and host at a molecular level, useful for identifying control targets for breeding perennial species.
Background. Coffee leaf rust (CLR) caused by Hemileia vastatrix Berk. & Br, is one of the most threatening diseases for Coffea arabica L. It is hypothesized that host tolerance to CLR relies on non-race-specific resistance genes.Methods. This study evaluated gene expression in leaves of two susceptible coffee cultivars (one inbred and one F1 hybrid) under different stress conditions: rust control (fungicide and untreated) and fruit thinning (thinned and un-thinned) treatments. RNA-seq analysis focused on the association of differentially expressed genes (DEGs) with CLR and associated the effect of the most significant genes into the phenotype, using regression and prediction statistical models.Results. Gene expression and gene ontology (GO) analysis allowed identification of 100 genes associated with quantitative traits. From these, 88 were correlated with rust incidence, rust severity, and rust sporulation. The expression of genes coding for pathogenesis-related proteins increased positively with rust incidence in the inbred, while genes involved in homoeostasis and broader cell wall structuring processes were upregulated in the F1 hybrid. The enriched gene functions and associations revealed that a possible hypersensitive response (HR) in the inbred and a systemic acquired resistance (SAR) in the F1 hybrid were involved in the tolerance mechanisms to CLR stress. This is the first study to demonstrate the specific interactions between CLR and host at a molecular level, useful for identifying control targets for breeding perennial species.