Genome-wide identification and characterization of NB-ARC resistant genes in wheat (Triticum aestivum L.) and their expression during leaf rust infection

QTL mapping of downy mildew resistance in foxtail millet by SLAF‑seq and BSR-seq analysis

KEY MESSAGE

Key message Three major QTLs for resistance to downy mildew were located within an 0.78 Mb interval on chromosome 8 in foxtail millet. Downy mildew, a disease caused by Sclerospora graminicola, is a serious problem that jeopardizes the yield and quality of foxtail millet. Breeding resistant varieties represents one of the most economical and effective solutions, yet there is a lack of molecular markers related to the resistance. Here, a mapping population comprising of 158 F6:7 recombinant inbred lines (RILs) was constructed from the crossing of G1 and JG21. Based on the specific locus amplified fragment sequencing results, a high-density linkage map of foxtail millet with 1031 bin markers, spanning 1041.66 cM was constructed. Based on the high-density linkage map and the phenotype data in four environments, a total of nine quantitative trait loci (QTL) associated with resistance to downy mildew were identified. Further BSR-seq confirmed the genomic regions containing the potential candidate genes related to downy mildew resistance. Interestingly, a 0.78-Mb interval between C8M257 and C8M268 on chromosome 8 was highlighted because of its presence in three major QTL, qDM8_1, qDM8_2, and qDM8_4, which contains 10 NBS-LRR genes. Haplotype analysis in RILs and natural population suggest that 9 SNP loci on Seita8G.199800, Seita8G.195900, Seita8G.198300, and Seita.8G199300 genes were significantly correlated with disease resistance. Furthermore, we found that those genes were taxon-specific by collinearity analysis of pearl millet and foxtail millet genomes. The identification of these new resistance QTL and the prediction of resistance genes against downy mildew will be useful in breeding for resistant varieties and the study of genetic mechanisms of downy mildew disease resistance in foxtail millet.

Fine mapping of a major QTL, qKl-1BL controlling kernel length in common wheat

KEY MESSAGE

A major stable QTL, qKl-1BL, for kernel length of wheat was narrowed down to a 2.04-Mb interval on chromosome 1BL; the candidate genes were predicated and the genetic effects on yield-related traits were characterized. As a key factor influencing kernel weight, wheat kernel shape is closely related to yield formation, and in turn affects both wheat processing quality and market value. Fine mapping of the major quantitative trait loci (QTL) for kernel shape could provide genetic resources and a theoretical basis for the genetic improvement of wheat yield-related traits. In this study, a major QTL for kernel length (KL) on 1BL, named qKl-1BL, was identified from the recombinant inbred lines (RIL) in multiple environments based on the genetic map and physical map, with 4.76-21.15% of the phenotypic variation explained. To fine map qKl-1BL, the map-based cloning strategy was used. By using developed InDel markers, the near-isogenic line (NIL) pairs and eight key recombinants were identified from a segregating population containing 3621 individuals derived from residual heterozygous lines (RHLs) self-crossing. In combination with phenotype identification, qKl-1BL was finely positioned into a 2.04-Mb interval, KN1B:698.15-700.19 Mb, with eight differentially expressed genes enriched at the key period of kernel elongation. Based on transcriptome analysis and functional annotation information, two candidate genes for qKl-1BL controlling kernel elongation were identified. Additionally, genetic effect analysis showed that the superior allele of qKl-1BL from Jing411 could increase KL, thousand kernel weight (TKW), and yield per plant (YPP) significantly, as well as kernel bulk density and stability time. Taken together, this study identified a QTL interval for controlling kernel length with two possible candidate genes, which provides an important basis for qKl-1BL cloning, functional analysis, and application in molecular breeding programs.

Mapping of Candidate Genes for Nitrogen Uptake and Utilization in Japonica Rice at Seedling Stage

Nitrogen (N) is one of the essential nutrients for the growth and development of crops. The adequate application of N not only increases the yield of crops but also improves the quality of agricultural products, but the excessive application of N can cause many adverse effects on ecology and the environment. In this study, genome-wide association analysis (GWAS) was performed under low- and high-N conditions based on 788,396 SNPs and phenotypic traits relevant to N uptake and utilization (N content and N accumulation). A total of 75 QTLs were obtained using GWAS, which contained 811 genes. Of 811 genes, 281 genes showed different haplotypes, and 40 genes had significant phenotypic differences among different haplotypes. Of these 40 genes, 5 differentially expressed genes (Os01g0159250, Os02g0618200, Os02g0618400, Os02g0630300, and Os06g0619000) were finally identified as the more valuable candidate genes based on the transcriptome data sequenced from Longjing31 (low-N-tolerant variety) and Songjing 10 (low-N-sensitive variety) under low- and high-N treatments. These new findings enrich the genetic resources for N uptake and utilization in rice, as well as lay a theoretical foundation for improving the efficiency of N uptake and utilization in rice.

Stripe rust effector Pst21674 compromises wheat resistance by targeting transcription factor TaASR3

Pathogens compromise host defense responses by strategically secreting effector proteins. However, the molecular mechanisms by which effectors manipulate disease-resistance factors to evade host surveillance remain poorly understood. In this study, we characterized a Puccinia striiformis f. sp. tritici (Pst) effector Pst21674 with a signal peptide. Pst21674 was significantly upregulated during Pst infections in wheat (Triticum aestivum L.) and knocking down Pst21674 by host-induced gene silencing led to reduced Pst pathogenicity and restricted hyphal spread in wheat. Pst21674 interaction with the abscisic acid-, stress-, and ripening-induced protein TaASR3 was validated mainly in the nucleus. Size exclusion chromatography, bimolecular fluorescence complementation, and luciferase complementation imaging assays confirmed that TaASR3 could form a functional tetramer. Virus-induced gene silencing and overexpression demonstrated that TaASR3 contributes to wheat resistance to stripe rust by promoting accumulation of reactive oxygen species and cell death. Additionally, transcriptome analysis revealed that the expression of defense-related genes was regulated in transgenic wheat plants overexpressing TaASR3. Interaction between Pst21674 and TaASR3 interfered with the polymerization of TaASR3 and suppressed TaASR3-mediated transcriptional activation of defense-related genes. These results indicate that Pst21674 serves as an important virulence factor secreted into the host nucleus to impede wheat resistance to Pst, possibly by targeting and preventing polymerization of TaASR3.

Comparative transcriptome profiling of near isogenic lines PBW343 and FLW29 to unravel defense related genes and pathways contributing to stripe rust resistance in wheat

Stripe rust (Sr), caused by Puccinia striiformis f. sp. tritici (Pst), is the most devastating disease that poses serious threat to the wheat-growing nations across the globe. Developing resistant cultivars is the most challenging aspect in wheat breeding. The function of resistance genes (R genes) and the mechanisms by which they influence plant-host interactions are poorly understood. In the present investigation, comparative transcriptome analysis was carried out by involving two near-isogenic lines (NILs) PBW343 and FLW29. The seedlings of both the genotypes were inoculated with Pst pathotype 46S119. In total, 1106 differentially expressed genes (DEGs) were identified at early stage of infection (12 hpi), whereas expressions of 877 and 1737 DEGs were observed at later stages (48 and 72 hpi) in FLW29. The identified DEGs were comprised of defense-related genes including putative R genes, 7 WRKY transcriptional factors, calcium, and hormonal signaling associated genes. Moreover, pathways involved in signaling of receptor kinases, G protein, and light showed higher expression in resistant cultivar and were common across different time points. Quantitative real-time PCR was used to further confirm the transcriptional expression of eight critical genes involved in plant defense mechanism against stripe rust. The information about genes are likely to improve our knowledge of the genetic mechanism that controls the stripe rust resistance in wheat, and data on resistance response-linked genes and pathways will be a significant resource for future research.

Analysis of R Genes Related to Blackcurrant Reversion Virus Resistance in the Comparative Transcriptome of Ribes nigrum cv. Aldoniai

Blackcurrant reversion virus (BRV) is the most destructive mite-transmitted pathogen in blackcurrants. The understanding of the resistance to BRV is limited, hindering and delaying the selection process. To identify the resistance (R) gene for BRV resistance, a gene expression analysis based on de novo blackcurrant cv. Aldoniai comparative transcriptome analysis (mock- and BRV-inoculated samples at 2 and 4 days post-inoculation (dpi)) was performed. In this study, 111 annotated clusters associated with pathogenesis according to conservative R gene domains were identified. In virus-infected samples, only Cluster-12591.33361 showed significant expression at 4 dpi. The expression profiles of this cluster were significantly associated with the presence of BRV particles in plant tissues, making it a putative R gene in the dominant resistance strategy in the BRV-Ribes nigrum interaction. The newly identified gene R.nigrum_R belongs to the CC-NBS-LRR class and has 63.9% identity with RPM1 in Populus spp. This study provides new insights on dominant putative R genes related to resistance to BRV in R. nigrum, which could aid targeted research and genetic improvement in breeding programs of blackcurrants.

Sugar transporter TaSTP3 activation by TaWRKY19/61/82 enhances stripe rust susceptibility in wheat

Sugar efflux from host plants is essential for pathogen survival and proliferation. Sugar transporter-mediated redistribution of host sugar contributes to the outcomes of plant-pathogen interactions. However, few studies have focused on how sugar translocation is strategically manipulated during host colonization. To elucidate this question, the wheat sugar transport protein (STP) TaSTP3 responding to Puccinia striiformis f. sp. tritici (Pst) infection was characterized for sugar transport properties in Saccharomyces cerevisiae and its potential role during Pst infection by RNA interference and overexpression in wheat. In addition, the transcription factors regulating TaSTP3 expression were further determined. The results showed that TaSTP3 is localized to the plasma membrane and functions as a sugar transporter of hexose and sucrose. TaSTP3 confers enhanced wheat susceptibility to Pst, and overexpression of TaSTP3 resulted in increased sucrose accumulation and transcriptional suppression of defense-related genes. Furthermore, TaWRKY19, TaWRKY61 and TaWRKY82 were identified as positive transcriptional regulators of TaSTP3 expression. Our findings reveal that the Pst-induced sugar transporter TaSTP3 is transcriptionally activated by TaWRKY19/61/82 and facilitates wheat susceptibility to stripe rust possibly through elevated sucrose concentration, and suggest TaSTP3 as a strong target for engineering wheat resistance to stripe rust.

A pan-genome and chromosome-length reference genome of narrow-leafed lupin (Lupinus angustifolius) reveals genomic diversity and insights into key industry and biological traits

Narrow-leafed lupin (NLL; Lupinus angustifolius) is a key rotational crop for sustainable farming systems, whose grain is high in protein content. It is a gluten-free, non-genetically modified, alternative protein source to soybean (Glycine max) and as such has gained interest as a human food ingredient. Here, we present a chromosome-length reference genome for the species and a pan-genome assembly comprising 55 NLL lines, including Australian and European cultivars, breeding lines and wild accessions. We present the core and variable genes for the species and report on the absence of essential mycorrhizal associated genes. The genome and pan-genomes of NLL and its close relative white lupin (Lupinus albus) are compared. Furthermore, we provide additional evidence supporting LaRAP2-7 as the key alkaloid regulatory gene for NLL and demonstrate the NLL genome is underrepresented in classical NLR disease resistance genes compared to other sequenced legume species. The NLL genomic resources generated here coupled with previously generated RNA sequencing datasets provide new opportunities to fast-track lupin crop improvement.

Genome-Wide Association Analysis and Gene Mining of Resistance to China Race 1 of Frogeye Leaf Spot in Soybean

Soybean frogeye leaf spot (FLS) is a worldwide fungal disease. Its higher occurrence frequency and wider distribution range always led to severe yield losses of soybean, therefore, breeding new cultivars with FLS resistance has been an important breeding goal for soybean breeders. In this study, an association panel of 183 representative soybean accessions was used to evaluate their resistance to FLS race 1, and to identify quantitative trait nucleotides (QTNs) and candidate genes based on genome-wide association study (GWAS) and high-throughput single-nucleotide polymorphisms (SNPs). A total of 23,156 high-quality SNPs were developed using the specific locus-amplified fragment sequencing (SLAF-seq) approach. Finally, 13 novel association signals associated with FLS race 1 resistance were identified by the compressed mixed linear model (CMLM). In addition, 119 candidate genes were found within the 200-kb flanking genomic region of these 13 peak SNPs. Based on the gene-based association analysis, haplotype analysis, expression pattern analysis, and virus-induced gene silencing (VIGS) systems, four genes (Glyma.05G121100, Glyma.17G228300, Glyma.19G006900, and Glyma.19G008700) were preliminarily proved to play an important role in the soybean resistance to FLS race 1.

Systematic Analysis of NB-ARC Gene Family in Rice and Functional Characterization of GNP12

The NB-ARC (nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4) gene family plays a critical role in plant development. However, our understanding of the mechanisms of how NB-ARC genes regulate plant development in the plant panicle is still limited. Here, we subjected 258 NB-ARC genes in rice to genome-wide analysis to characterize their structure, function, and expression patterns. The NB-ARC genes were classified into three major groups, and group II included nine subgroups. Evolutionary analysis of NB-ARC genes in a dicotyledon plant (Arabidopsis thaliana) and two monocotyledonous plants (Oryza sativa L. and Triticum aestivum) indicated that homologous genome segments were conserved in monocotyledons and subjected to weak positive selective pressure during evolution. Dispersed and proximal replication events were detected. Expression analysis showed expression of most NB-ARC genes in roots, panicles, and leaves, and regulation at the panicle development stage in rice Ce253. The GNP12 gene encodes RGH1A protein, which regulates rice yield according to panicle length, grain number of panicle, and grain length, with eight major haplotypes. Most members of NB-ARC protein family are predicted to contain P-loop conserved domains and localize on the membrane. The results of this study will provide insight into the characteristics and evolution of NB-ARC family and suggest that GNP12 positively regulates panicle development.

Genome-Wide Analysis of the Auxin/Indoleacetic Acid Gene Family and Response to Indole-3-Acetic Acid Stress in Tartary Buckwheat (Fagopyrum tataricum)

Auxin/indoleacetic acid (Aux/IAA) family genes respond to the hormone auxin, which have been implicated in the regulation of multiple biological processes. In this study, all 25 Aux/IAA family genes were identified in Tartary buckwheat (Fagopyrum tataricum) by a reiterative database search and manual annotation. Our study provided comprehensive information of Aux/IAA family genes in buckwheat, including gene structures, chromosome locations, phylogenetic relationships, and expression patterns. Aux/IAA family genes were nonuniformly distributed in the buckwheat chromosomes and divided into seven groups by phylogenetic analysis. Aux/IAA family genes maintained a certain correlation and a certain species-specificity through evolutionary analysis with Arabidopsis and other grain crops. In addition, all Aux/IAA genes showed a complex response pattern under treatment of indole-3-acetic acid (IAA). These results provide valuable reference information for dissecting function and molecular mechanism of Aux/IAA family genes in buckwheat.

High-Throughput Sequencing-Based Identification of miRNAs and Their Target mRNAs in Wheat Variety Qing Mai 6 Under Salt Stress Condition

Soil salinization is one of the major abiotic stresses that adversely affect the yield and quality of crops such as wheat, a leading cereal crop worldwide. Excavating the salt-tolerant genes and exploring the salt tolerance mechanism can help breeding salt-tolerant wheat varieties. Thus, it is essential to identify salt-tolerant wheat germplasm resources. In this study, we carried out a salt stress experiment using Qing Mai 6 (QM6), a salt-tolerant wheat variety, and sequenced the miRNAs and mRNAs. The differentially expressed miRNAs and mRNAs in salt stress conditions were compared with the control. As results, a total of eight salt-tolerance-related miRNAs and their corresponding 11 target mRNAs were identified. Further analysis revealed that QM6 enhances salt tolerance through increasing the expression level of genes related to stress resistance, antioxidation, nutrient absorption, and lipid metabolism balance, and the expression of these genes was regulated by the identified miRNAs. The resulting data provides a theoretical basis for future research studies on miRNAs and novel genes related to salt tolerance in wheat in order to develop genetically improved salt-tolerant wheat varieties.

Genome-wide association mapping identifies novel loci underlying fire blight resistance in apple

Fire blight, caused by epiphytotic gram-negative bacteria Erwinia amylovora, is the most destructive bacterial disease of apple (Malus spp.). Genetic mechanisms of fire blight resistance have mainly been studied using traditional biparental quantitative trait loci (QTL) mapping approaches. Here, we use large-scale historic shoot and blossom fire blight data collected over multiple years and genotyping-by-sequencing (GBS) markers to identify significant marker-trait associations in a diverse set of 566 apple [Malus domestica (Suckow) Borkh.] accessions. There was large variation in fire blight resistance and susceptibility in these accessions. We identified 23 and 38 QTL significantly (p < .001) associated with shoot and blossom blight resistance, respectively. The QTL are distributed across all 17 chromosomes of apple. Four shoot blight and 19 blossom blight QTL identified in this study colocalized with previously identified QTL associated with resistance to fire blight or apple scab. Using transcriptomics data of two apple cultivars with contrasting fire blight responses, we also identified candidate genes for fire blight resistance that are differentially expressed between resistant and susceptible cultivars and located within QTL intervals for fire blight resistance. However, further experiments are needed to confirm and validate these marker-trait associations and develop diagnostic markers before use in marker-assisted breeding to develop apple cultivars with decreased fire blight susceptibility.

Comprehensive molecular dissection of TIFY Transcription factors reveal their dynamic responses to biotic and abiotic stress in wheat (Triticum aestivum L.)

The plant specific TIFY (previously known as ZIM) transcription factor (TF) family plays crucial roles in cross talk between Jasmonic Acid and other phytohormones like gibberellins, salicylic acid, abscisic acid, auxin, and ethylene signaling pathways. Wheat yield is severely affected by rust diseases and many abiotic stresses, where different phytohormone signaling pathways are involved. TIFYs have been studied in many plants yet reports describing their molecular structure and function in wheat are lacking. In the present study, we have identified 23 novel TIFY genes in wheat genome using in silico approaches. The identified proteins were characterized based on their conserved domains and phylogenetically classified into nine subfamilies. Chromosomal localization of the identified TIFY genes showed arbitrary distribution. Forty cis-acting elements including phytohormone, stress and light receptive elements were detected in the upstream regions of TIFY genes. Seventeen wheat microRNAs targeted the identified wheat TIFY genes. Gene ontological studies revealed their major contribution in defense response and phytohormone signaling. Secondary structure of TIFY proteins displayed the characteristic alpha-alpha-beta fold. Synteny analyses indicated all wheat TIFY genes had orthologous sequences in sorghum, rice, maize, barley and Brachypodium indicating presence of similar TIFY domains in monocot plants. Six TIFY genes had been cloned from wheat genomic and cDNA. Sequence characterization revealed similar characteristics as the in silico identified novel TIFY genes. Tertiary structures predicted the active sites in these proteins to play critical roles in DNA binding. Expression profiling of TIFY genes showed their contribution during incompatible and compatible leaf rust infestation. TIFY genes were also highly expressed during the initial hours of phytohormone induced stress. This study furnishes fundamental information on characterization and putative functions of TIFY genes in wheat.

Genetic dissection of soybean partial resistance to sclerotinia stem rot through genome wide association study and high throughout single nucleotide polymorphisms

Sclerotinia stem rot (SSR) is a disease of soybean [Glycine max (L.) Merr] that causes severe yield losses. We studied 185 representative soybean accessions to evaluate partial SSR resistance and sequenced these by the specific-locus amplified fragment sequencing method. In total, 22,048 single-nucleotide polymorphisms (SNPs), with minor allele frequencies (MAF) ≥5% and missing data <3%, were developed and applied to genome-wide association study of SSR responsiveness and assess linkage disequilibrium (LD) level for candidate gene selection. We identified 18 association signals related to SSR partial resistance. Among them, six overlapped the regions of previous quantitative trait loci, and twelve were novel. We identified 243 candidate genes located in the 200 kb genomic region of these peak SNPs. Based on quantitative real-time polymerase chain reaction and haplotype analysis, Glyma.03G196000 and Glyma.20G095100, encoding pentatricopeptide repeat proteins, might be important factors in the resistance response of soybean to SSR.

De novo transcriptome in roots of switchgrass (Panicum virgatum L.) reveals gene expression dynamic and act network under alkaline salt stress

Background

Soil salinization is a major limiting factor for crop cultivation. Switchgrass is a perennial rhizomatous bunchgrass that is considered an ideal plant for marginal lands, including sites with saline soil. Here we investigated the physiological responses and transcriptome changes in the roots of Alamo (alkaline-tolerant genotype) and AM-314/MS-155 (alkaline-sensitive genotype) under alkaline salt stress.

Results

Alkaline salt stress significantly affected the membrane, osmotic adjustment and antioxidant systems in switchgrass roots, and the ASTTI values between Alamo and AM-314/MS-155 were divergent at different time points. A total of 108,319 unigenes were obtained after reassembly, including 73,636 unigenes in AM-314/MS-155 and 65,492 unigenes in Alamo. A total of 10,219 DEGs were identified, and the number of upregulated genes in Alamo was much greater than that in AM-314/MS-155 in both the early and late stages of alkaline salt stress. The DEGs in AM-314/MS-155 were mainly concentrated in the early stage, while Alamo showed greater advantages in the late stage. These DEGs were mainly enriched in plant-pathogen interactions, ubiquitin-mediated proteolysis and glycolysis/gluconeogenesis pathways. We characterized 1480 TF genes into 64 TF families, and the most abundant TF family was the C2H2 family, followed by the bZIP and bHLH families. A total of 1718 PKs were predicted, including CaMK, CDPK, MAPK and RLK. WGCNA revealed that the DEGs in the blue, brown, dark magenta and light steel blue 1 modules were associated with the physiological changes in roots of switchgrass under alkaline salt stress. The consistency between the qRT-PCR and RNA-Seq results confirmed the reliability of the RNA-seq sequencing data. A molecular regulatory network of the switchgrass response to alkaline salt stress was preliminarily constructed on the basis of transcriptional regulation and functional genes.

Conclusions

Alkaline salt tolerance of switchgrass may be achieved by the regulation of ion homeostasis, transport proteins, detoxification, heat shock proteins, dehydration and sugar metabolism. These findings provide a comprehensive analysis of gene expression dynamic and act network induced by alkaline salt stress in two switchgrass genotypes and contribute to the understanding of the alkaline salt tolerance mechanism of switchgrass and the improvement of switchgrass germplasm.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07368-w.

Characterization of the leaf rust responsive ARF genes in wheat (Triticum aestivum L.)

Genome-wide identification, classification, functional characterization and expression analysis of Auxin Responsive Factor (ARF) gene family in wheat reveal their attributes and role during leaf rust infection. Auxins are important plant growth regulators that also impact plant-pathogen interaction. Auxin responsive factors (ARF) are plant specific transcription factors that control responses to auxins. Whole genome investigation of ARF gene family is limited in allohexaploid wheat (Triticum aestivum L.). Comprehensive study of this gene family was carried out by employing the currently available reference genome sequence of wheat. In total, 27 ARF genes were identified and located on the wheat genome as well as were positioned on wheat chromosome arms. Additionally, examination of the predicted genes unveiled a decent degree of relatedness within and among the phylogenetic clades. Leaf rust, caused by the obligate biotrophic fungal pathogen Puccinia triticina, is responsible for drastic loss of wheat crop worldwide reducing grain yield by 10-90%. Expression profiling of ARF genes in retort to leaf rust infection indicated their differential regulation during this plant-pathogen interaction. Highest expression of ARF genes were observed at 12 hpi that was maintained up to 72 hpi during incompatible interaction, whereas the high expression levels receded at 48 hpi during compatible interactions. Few of the identified ARF genes were likely to be post-transcriptionally regulated by microRNAs. Many light and stress responsive elements were detected in the promoter regions of ARF genes. Microsynteny analysis showed the conservation of ARF genes within the members of the Poaceae family. This study provides fundamental details for understanding the different types of ARF genes in wheat and there putative roles during leaf rust-wheat interaction.

QTL mapping of web blotch resistance in peanut by high-throughput genome-wide sequencing

BACKGROUND

Web blotch is one of the most important foliar diseases worldwide in peanut (Arachis hypogaea L.). The identification of quantitative trait loci (QTLs) for peanut web blotch resistance represents the basis for gene mining and the application of molecular breeding technologies.

RESULTS

In this study, a peanut recombinant inbred line (RIL) population was used to map QTLs for web blotch resistance based on high-throughput genome-wide sequencing. Frequency distributions of disease grade and disease index in five environments indicated wide phenotypic variations in response to web blotch among RILs. A high-density genetic map was constructed, containing 3634 bin markers distributed on 20 peanut linkage groups (LGs) with an average genetic distance of 0.5 cM. In total, eight QTLs were detected for peanut web blotch resistance in at least two environments, explaining from 2.8 to 15.1% of phenotypic variance. Two major QTLs qWBRA04 and qWBRA14 were detected in all five environments and were linked to 40 candidate genes encoding nucleotide-binding site leucine-rich repeat (NBS-LRR) or other proteins related to disease resistances.

CONCLUSIONS

The results of this study provide a basis for breeding peanut cultivars with web blotch resistance.

GWAS to Identify Genetic Loci for Resistance to Yellow Rust in Wheat Pre-Breeding Lines Derived From Diverse Exotic Crosses

Yellow rust (YR) or stripe rust, caused by Puccinia striformis f. sp tritici Eriks (Pst), is a major challenge to resistance breeding in wheat. A genome wide association study (GWAS) was performed using 22,415 single nucleotide polymorphism (SNP) markers and 591 haplotypes to identify genomic regions associated with resistance to YR in a subset panel of 419 pre-breeding lines (PBLs) developed at International Center for Maize and Wheat Improvement (CIMMYT). The 419 PBLs were derived from an initial set of 984 PBLs generated by a three-way crossing scheme (exotic/elite1//elite2) among 25 best elites and 244 exotics (synthetics, landraces) from CIMMYT's germplasm bank. For the study, 419 PBLs were characterized with 22,415 high-quality DArTseq-SNPs and phenotyped for severity of YR disease at five locations in Mexico. A population structure was evident in the panel with three distinct subpopulations, and a genome-wide linkage disequilibrium (LD) decay of 2.5 cM was obtained. Across all five locations, 14 SNPs and 7 haplotype blocks were significantly (P < 0.001) associated with the disease severity explaining 6.0 to 14.1% and 7.9 to 19.9% of variation, respectively. Based on average LD decay of 2.5 cM, identified 14 SNP-trait associations were delimited to seven quantitative trait loci in total. Seven SNPs were part of the two haplotype blocks on chromosome 2A identified in haplotypes-based GWAS. In silico analysis of the identified SNPs showed hits with interesting candidate genes, which are related to pathogenic process or known to regulate induction of genes related to pathogenesis such as those coding for glunolactone oxidase, quinate O-hydroxycinnamoyl transferase, or two-component histidine kinase. The two-component histidine kinase, for example, acts as a sensor in the perception of phytohormones ethylene and cytokinin. Ethylene plays a very important role in regulation of multiple metabolic processes of plants, including induction of defense mechanisms mediated by jasmonate. The SNPs linked to the promising genes identified in the study can be used for marker-assisted selection.

Exploring sources of resistance to brown rot in an interspecific almond × peach population

BACKGROUND

Monilinia spp. are responsible for brown rot, one of the most significant stone fruit diseases. Planting resistant cultivars seems a promising alternative, although most commercial cultivars are susceptible to brown rot. The aim of this study was to explore resistance to Monilinia fructicola over two seasons in a backcross one interspecific population between almond 'Texas' and peach 'Earlygold' (named T1E).

RESULTS

'Texas' almond was resistant to brown rot inoculation, whereas peach was highly susceptible. Phenotypic data from the T1E population indicated wide differences in response to M. fructicola. Additionally, several non-wounded individuals exhibited resistance to brown rot. Quantitative trait loci (QTLs) were identified in several linkage groups, but only two proximal QTLs in G4 were detected over both seasons and accounted for 11.3-16.2% of the phenotypic variation.

CONCLUSION

Analysis of the progeny allowed the identification of resistant genotypes that could serve as a source of resistance in peach breeding programs. The finding of loci associated with brown rot resistance would shed light on implementing a strategy based on marker-assisted selection (MAS) for introgression of this trait into elite peach materials. New peach cultivars resistant to brown rot may contribute to the implementation of more sustainable crop protection strategies. © 2019 Society of Chemical Industry.

Genome-Wide Characterization of NBS-Encoding Genes in Watermelon and Their Potential Association with Gummy Stem Blight Resistance

Watermelon (Citrullus lanatus) is a nutritionally rich and economically important horticultural crop of the Cucurbitaceae family. Gummy stem blight (GSB) is a major disease of watermelon, which is caused by the fungus Didymella bryoniae, and results in substantial economic losses in terms of yield and quality. However, only a few molecular studies have focused on GSB resistance in watermelon. Nucleotide binding site (NBS)-encoding resistance (R) genes play important roles in plant defense responses to several pathogens, but little is known about the role of NBS-encoding genes in disease resistance in watermelon. The analyzed NBS-encoding R genes comprises several domains, including Toll/interleukin-1 receptor(TIR), NBS, leucine-rich repeat (LRR), resistance to powdery mildew8(RPW8) and coiled coil (CC), which are known to be involved in disease resistance. We determined the expression patterns of these R genes in resistant and susceptible watermelon lines at different time points after D. bryoniae infection by quantitative RT-PCR. The R genes exhibited various expression patterns in the resistant watermelon compared to the susceptible watermelon. Only six R genes exhibited consistent expression patterns (Cla001821, Cla019863, Cla020705, Cla012430, Cla012433 and Cla012439), which were higher in the resistant line compared to the susceptible line. Our study provides fundamental insights into the NBS-LRR gene family in watermelon in response to D. bryoniae infection. Further functional studies of these six candidate resistance genes should help to advance breeding programs aimed at improving disease resistance in watermelons.

Genome-wide Analysis of the WRKY Gene Family and its Response to Abiotic Stress in Buckwheat (Fagopyrum Tataricum)

The WRKY gene family is an ancient plant transcription factor (TF) family with a vital role in plant growth and development, especially in response to biotic and abiotic stresses. Although many researchers have studied WRKY TFs in numerous plant species, little is known of them in Tartary buckwheat (Fagopyrum tataricum). Based on the recently reported genome sequence of Tartary buckwheat, we identified 78 FtWRKY proteins that could be classified into three major groups. All 77 WRKY genes were distributed unevenly across all eight chromosomes. Exon-intron analysis and motif composition prediction revealed the complexity and diversity of FtWRKYs, indicating that WRKY TFs may be of significance in plant growth regulation and stress response. Two separate pairs of tandem duplication genes were found, but no segmental duplications were identified. Overall, most orthologous gene-pairs between Tartary and common buckwheat evolved under strong purifying selection. qRT-PCR was used to analyze differences in expression among four FtWRKYs (FtWRKY6, 74, 31, and 7) under salt, drought, cold, and heat treatments. The results revealed that all four proteins are related to abiotic stress responses, although they exhibited various expression patterns. In particular, the relative expression levels of FtWRKY6, 74, and 31 were significantly upregulated under salt stress, while the highest expression of FtWRKY7 was observed from heat treatment. This study provides comprehensive insights into the WRKY gene family in Tartary buckwheat, and can support the screening of additional candidate genes for further functional characterization of WRKYs under various stresses.

Identification of NBS-encoding genes linked to black rot resistance in cabbage (Brassica oleracea var. capitata)

Heading cabbage is a nutritionally rich and economically important cruciferous vegetable. Black rot disease, caused by the bacterium Xanthomonas campestris pv. campestris, reduces both the yield and quality of the cabbage head. Nucleotide binding site (NBS)-encoding resistance (R) genes play a vital role in the plant immune response to various pathogens. In this study, we analyzed the expression and DNA sequence variation of 31 NBS-encoding genes in cabbage (Brassica oleracea var. capitata). These genes encoded TIR, NBS, LRR and RPW8 protein domains, all of which are known to be involved in disease resistance. RNA-seq revealed that these 31 genes were differentially expressed in leaf, root, silique, and stem tissues. Furthermore, qPCR analyses revealed that several of these genes were more highly expressed in resistant compared to susceptible cabbage lines, including Bol003711, Bol010135, Bol010559, Bol022784, Bol029866, Bol042121, Bol031422, Bol040045 and Bol042095. Further analysis of these genes promises to yield both practical benefits, such as molecular markers for marker-assisted breeding, and fundamental insights to the mechanisms of resistance to black rot in cabbage.