Adult Plant Stage Research Articles

Genome-Wide Association Analysis of Stable Stripe Rust Resistance Loci in a Chinese Wheat Landrace Panel Using the 660K SNP Array.

Stripe rust (caused by Puccinia striiformis f. sp. tritici) is one of the most severe diseases affecting wheat production. The disease is best controlled by developing and growing resistant cultivars. Chinese wheat (Triticum aestivum) landraces have excellent resistance to stripe rust. The objectives of this study were to identify wheat landraces with stable resistance and map quantitative trait loci (QTL) for resistance to stripe rust from 271 Chinese wheat landraces using a genome-wide association study (GWAS) approach. The landraces were phenotyped for stripe rust responses at the seedling stage with two predominant Chinese races of P. striiformis f. sp. tritici in a greenhouse and the adult-plant stage in four field environments and genotyped using the 660K wheat single-nucleotide polymorphism (SNP) array. Thirteen landraces with stable resistance were identified, and 17 QTL, including eight associated to all-stage resistance and nine to adult-plant resistance, were mapped on chromosomes 1A, 1B, 2A, 2D, 3A, 3B, 5A, 5B, 6D, and 7A. These QTL explained 6.06–16.46% of the phenotypic variation. Five of the QTL, QYrCL.sicau-3AL, QYrCL.sicau-3B.4, QYrCL.sicau-3B.5, QYrCL.sicau-5AL.1 and QYrCL.sicau-7AL, were likely new. Five Kompetitive allele specific PCR (KASP) markers for four of the QTL were converted from the significant SNP markers. The identified wheat landraces with stable resistance to stripe rust, significant QTL, and KASP markers should be useful for breeding wheat cultivars with durable resistance to stripe rust.

Root Trait Diversity in Field Grown Durum Wheat and Comparison with Seedlings

Roots are important for crop adaptation, particularly in dryland environments. We evaluated root development of 37 durum wheat genotypes (modern cultivars and landraces) in the field at the adult plant stage, through a shovelomics approach. Large genotypic variability was found for root traits. Differences between the landraces and modern cultivars were the main driver of this variation, with landraces showing higher plant vigor for roots and shoots. Nonetheless, genotypic variation within groups was also observed, related to different models of root growth, largely independent of total root length. These two models represented root growth were oriented either to occupy more soil volume, or to occupy less soil volume with increased density. The field results were then compared with root data previously collected in seedlings using a filter paper-based method, to assess whether early root anticipated adult root features. Field plants showed a narrower root angle than seedlings. In particular, landraces presented a narrower root angle than cultivars, but only at seedling stage. Potentially useful correlations were found between the two growth stages for root length and number.

Identification of Resistant Germplasm and Detection of Genes for Resistance to Powdery Mildew and Leaf Rust from 2,978 Wheat Accessions.

Powdery mildew and leaf rust, caused by Blumeria graminis f. sp. tritici and Puccinia triticina, respectively, are widespread diseases of wheat worldwide. The use of resistant cultivars is considered the most economical, environment-friendly, and effective method to control these diseases. In the present study, a collection of 2,978 wheat accessions consisting of 1,394 advanced breeding lines, 1,078 Chinese cultivars, 291 introduced cultivars, 132 lines containing alien chromosomes, and 83 landraces was tested for reactions to powdery mildew and leaf rust. The results indicated that 659 wheat accessions (22.1%) were highly resistant to a widely prevalent B. graminis f. sp. tritici isolate, E09, at the seedling stage, and 390 were consistently resistant to the mixture of B. graminis f. sp. tritici isolates at the adult plant stage. Meanwhile, 63 accessions (2.1%) were highly resistant to leaf rust at the adult plant stage, of which 54 were resistant to a predominant and highly virulent P. triticina race, THTT, at the seedling stage. Notably, 17 accessions were resistant to both powdery mildew and leaf rust. To detect known genes for resistance to powdery mildew and leaf rust, these accessions were tested with gene-specific or tightly linked markers for seven powdery mildew genes (Pm genes; Pm2, Pm4, Pm5, Pm6, Pm8, Pm21, and Pm24) and 10 Lr genes (Lr1, Lr9, Lr10, Lr19, Lr20, Lr24, Lr26, Lr34, Lr37, and Lr46). Of the 659 powdery mildew-resistant accessions, 328 might carry single Pm genes and 191 carry combined Pm genes. Pm2 was detected at the highest frequency of 59.6%, followed by Pm8, Pm6, Pm21, Pm4, and Pm5, whereas Pm24 was not detected. In addition, 139 accessions might contain unknown Pm genes different from those tested in this study. In the 63 accessions resistant to leaf rust, four leaf rust genes (Lr genes; Lr1, Lr10, Lr26, and Lr34) were detected in 41 accessions singly or in combination, whereas six genes (Lr9, Lr19, Lr20, Lr24, Lr37, and Lr46) were not detected. Twenty-two accessions might contain unknown Lr genes different from those tested in this study. This study not only provided important information for rationally distributing resistance genes in wheat breeding programs, but also identified resistant germplasm that might have novel genes to enrich the diversity of resistance sources.

Classification Method of Rape Root Swelling Disease Based on Convolution Neural Network

Both the seedling stage and the adult plant stage of rape can be infected with root edema, and the damaged roots swell to form tumors of different sizes and shapes. The incidence of rape root swelling at the seedling stage reached 17%, and the average incidence at the adult plant stage was 15%, resulting in a 10.2% reduction in rape production. The average plant height, number of siliques, number of kernels per horn, 1000-seed weight and yield per plant of healthy plants were significantly higher than those of diseased plants. Grading root lesions can help trace the root causes of root lesions. However, the method of grading is often performed manually by professionals at present, which has the problems of low speed and low efficiency. In order to solve this problem, a method for grading rape root swelling based on deep convolutional neural network is proposed in this paper. Firstly, a rape root swelling model based on convolutional neural network and regional candidate network was established, and then implement it on the deep learning Tensorflow framework Model, and finally compare and analyze the results. The rape root swelling model uses the VGG16 network to extract the characteristics of the rape root swelling image. The regional candidate network generates the preliminary position candidate frame of the rape root swelling, and Fast-RCNN realizes the classification and positioning of the candidate frame. The results show that this method can achieve rapid and accurate detection of healthy, first-level tumors, second-level tumors, and third-level tumors of four-level rape root swelling, with an average accuracy rate of 84.12%. The experimental results show that the accuracy rate can reach more than 90%.

Molecular Characterization of All-Stage and Adult-Plant Resistance Loci Against Powdery Mildew in Winter Wheat Cultivar Liangxing 99 Using BSR-Seq Technology.

Winter wheat cultivar Liangxing 99, which carries gene Pm52, is resistant to powdery mildew at both seedling and adult-plant stages. An F2:6 recombinant inbred line population from cross Liangxing 99 × Zhongzuo 9504 was phenotyped with Blumeria graminis f. sp. tritici isolate Bgt27 at the adult-plant stage in four field tests and the seedling stage in a greenhouse test. The analysis of bulk segregant RNA sequencing (BSR-Seq) identified a single-nucleotide polymorphism-enriched locus, Qaprpm.caas.2B, on chromosome 2BL in the same genomic interval of Pm52 associated with the all-stage resistance (ASR) and Qaprpm.caas.7A on chromosome 7AL associated with the adult-plant resistance (APR) against the disease. Qaprpm.caas.2B was detected in a 1.3 cM genetic interval between markers Xicscl726 and XicsK128 in which Pm52 was placed with a range of logarithm of odds (LOD) values from 28.1 to 34.6, and the phenotype variations explained in terms of maximum disease severity (MDS) ranged from 45 to 52%. The LOD peak of Qaprpm.caas.7A was localized in a 4.6 cM interval between markers XicsK7A8 and XicsK7A26 and explained the phenotypic variation of MDS ranging from 13 to 16%. The results of this study confirmed Pm52 for ASR and identified Qaprpm.caas.7A for APR to powdery mildew in Liangxing 99.

Identification of Fungal Species Associated with Crown and Root Rots of Wheat and Evaluation of Plant Reactions to the Pathogens in North Dakota

Common root rot (CRR) and crown rot (CR), caused by Bipolaris sorokiniana and Fusarium species, respectively, can cause significant yield losses in cereal crops. To assess the prevalence, incidence, and severity of these diseases in North Dakota, wheat samples were collected from spring wheat fields across the state in 2012, 2013, and 2014. Based on sub-crown internode symptoms, a greater incidence and severity of CRR was observed in 2012 (warm and dry year) than in 2013 and 2014. Also, the Northwestern Glaciated Plains and Northwestern Great Plains ecoregions showed greater CRR incidence and severity compared to the Northern Glaciated Plains and Lake Agassiz Plains ecoregions in the state. Bipolaris sorokiniana and Fusarium species including F. acuminatum, F. avenaceum, F. culmorum, F. graminearum, F. equiseti, F. pseudograminearum, F. oxysporum, F. redolens, F. sporotrichioides, and F. solani were isolated and identified from the root and crown tissues of the wheat samples. B. sorokiniana was isolated more frequently than other fungal species in all sampled years and ecoregions of North Dakota. F. acuminatum, F. avenaceum, F. culmorum, F. equiseti, F. graminearum, F. pseudograminearum, and F. redolens were pathogenic causing infections on seedlings of the two wheat genotypes (ND652 and Alsen), whereas isolates of F. oxysporum and F. solani were non-pathogenic and considered as secondary invaders associated with the root and crown rot diseases. Evaluation of some spring wheat genotypes for reactions to one B. sorokiniana isolate at seedling and adult plant stages, and one F. culmorum isolate at the seedling stage indicated that susceptibility to these pathogens varied among different wheat genotypes tested. This study provides useful information on fungal species associated with root and crown rots of wheat in North Dakota and on resistant/susceptible reactions of some spring wheat lines to the different fungal isolates evaluated.

Molecular Mapping and Analysis of an Excellent Quantitative Trait Loci Conferring Adult-Plant Resistance to Stripe Rust in Chinese Wheat Landrace Gaoxianguangtoumai.

The Chinese wheat landrace “Gaoxianguangtoumai” (GX) has exhibited a high level of adult-plant resistance (APR) to stripe rust in the field for more than a decade. To reveal the genetic background for APR to stripe rust in GX, a set of 249 F6:8 (F6, F7, and F8) recombinant inbred lines (RILs) was developed from a cross between GX and the susceptible cultivar “Taichung 29.” The parents and RILs were evaluated for disease severity at the adult-plant stage in the field by artificial inoculation with the currently predominant Chinese Puccinia striiformis f. sp. tritici races during three cropping seasons and genotyped using the Wheat 55K single-nucleotide polymorphism (SNP) array to construct a genetic map with 1,871 SNP markers finally. Two stable APR quantitative trait loci (QTL), QYr.GX-2AS and QYr.GX-7DS in GX, were detected on chromosomes 2AS and 7DS, which explained 15.5–27.0% and 11.5–13.5% of the total phenotypic variation, respectively. Compared with published Yr genes and QTL, QYr.GX-7DS and Yr18 may be the same, whereas QYr.GX-2AS is likely to be novel. Haplotype analysis revealed that QYr.GX-2AS is likely to be rare which presents in 5.3% of the 325 surveyed Chinese wheat landraces. By analyzing a heterogeneous inbred family (HIF) population from a residual heterozygous plant in an F8 generation of RIL, QYr.GX-2AS was further flanked by KP2A_36.85 and KP2A_38.22 with a physical distance of about 1.37Mb and co-segregated with the KP2A_37.09. Furthermore, three tightly linked Kompetitive allele-specific PCR (KASP) markers were highly polymorphic among 109 Chinese wheat cultivars. The results of this study can be used in wheat breeding for improving resistance to stripe rust.

Mining and predictive characterization of resistance to leaf rust (Puccinia hordei Otth) using two subsets of barley genetic resources

Sustainable barley (Hordeum vulgare L.) production will require access to diverse ex-situ conserved collections to develop varieties with high yields and capable of overcoming the challenges imposed by major abiotic and biotic stresses. This study aimed at searching efficient approaches for the identification of new sources of resistance to barley leaf rust (Puccinia hordei Otth). Two subsets, Generation Challenge Program Reference set (GCP) with 188 accessions and leaf rust subset constructed using the filtering approach of the Focused Identification of Germplasm Strategy (FIGS) with 86 accessions, were evaluated for the seedling as well as the adult plant stage resistance (APR) using two barley leaf rust (LR) isolates (ISO-SAT and ISO-MRC) and in four environments in Morocco, respectively. Both subsets yielded a high percent of accessions with a moderately resistant (MR) reaction to the two LR isolates at the seedling stage. For APR, more than 50% of the accessions showed resistant reactions in SAT2018 and GCH2018, while this rate was less than 20% in SAT2017 and SAT2019. Statistical analysis using chi-square test of independence revealed the dependency of LR reaction on subsets at the seedling (ISO-MRC), as well as at the APR (SAT2017 and SAT2018) stage. At seedling stage, the test of goodness of fit showed that GCP subset yielded higher percentages of resistant accessions than FIGS-LR in case of ISO-MRC isolate but the two subsets did not differ for ISO-SAT. At APR, FIGS approach performed better than GCP in yielding higher percentages of accessions in case of SAT2017 and SAT2018. Although some of the tested machine learning models had moderate to high accuracies, none of them was able to find a strong and significant relationship between the reaction to LR and the environmental conditions showing the needs for more fine tuning of approaches for efficient mining of genetic resources using machine learning.

No evidence of direct contribution of adult plant stages to climate adaptation in snapdragon plants

ABSTRACT Signatures of local adaptation have been found at all life stages in plants. Yet, the contribution of later plant stages is rarely disentangled from the influence of early-life stages. Here, we investigate the direct contribution of adult plant stages to climate adaptation in two subspecies of snapdragon plants (Antirrhinum majus), while growth conditions have been homogenized at early-life stages. We compared genetic variation in fitness proxies (i.e. flowering, number of flowers and survival) and phenotypic traits in adult plants of eight populations of A. m. pseudomajus and seven populations of A. m. striatum, in two common garden experiments at high and low elevations. We found no evidence of adaptation to elevation in adult plants in both subspecies. Populations of low-elevation habitats outperformed populations of high-elevation habitats in all gardens. The effects of phenotypic traits on fitness components were similar at high and low elevation, suggesting no divergent selection along elevation. Different traits had an effect on fitness proxies in A. m. striatum and A. m. pseudomajus, suggesting that different mechanisms are at play in these two subspecies. Our findings suggest that there is no direct contribution of adult plant stages to climate adaptation in snapdragon plants and that adaptive processes potentially differ at the scale of A. majus subspecies.

Evaluations of Genomic Prediction and Identification of New Loci for Resistance to Stripe Rust Disease in Wheat (Triticum aestivum L.).

Stripe rust is one of the most destructive diseases of wheat (Triticum aestivum L.), caused by Puccinia striiformis f. sp. tritici (Pst), and responsible for significant yield losses worldwide. Single-nucleotide polymorphism (SNP) diagnostic markers were used to identify new sources of resistance at adult plant stage to wheat stripe rust (YR) in 141 CIMMYT advanced bread wheat lines over 3 years in replicated trials at Borlaug Institute for South Asia (BISA), Ludhiana. We performed a genome-wide association study and genomic prediction to aid the genetic gain by accumulating disease resistance alleles. The responses to YR in 141 advanced wheat breeding lines at adult plant stage were used to generate G × E (genotype × environment)-dependent rust scores for prediction and genome-wide association study (GWAS), eliminating variation due to climate and disease pressure changes. The lowest mean prediction accuracies were 0.59 for genomic best linear unbiased prediction (GBLUP) and ridge-regression BLUP (RRBLUP), while the highest mean was 0.63 for extended GBLUP (EGBLUP) and random forest (RF), using 14,563 SNPs and the G × E rust score results. RF and EGBLUP predicted higher accuracies (∼3%) than did GBLUP and RRBLUP. Promising genomic prediction demonstrates the viability and efficacy of improving quantitative rust tolerance. The resistance to YR in these lines was attributed to eight quantitative trait loci (QTLs) using the FarmCPU algorithm. Four (Q.Yr.bisa-2A.1, Q.Yr.bisa-2D, Q.Yr.bisa-5B.2, and Q.Yr.bisa-7A) of eight QTLs linked to the diagnostic markers were mapped at unique loci (previously unidentified for Pst resistance) and possibly new loci. The statistical evidence of effectiveness and distribution of the new diagnostic markers for the resistance loci would help to develop new stripe rust resistance sources. These diagnostic markers along with previously established markers would be used to create novel DNA biosensor-based microarrays for rapid detection of the resistance loci on large panels upon functional validation of the candidate genes identified in the present study to aid in rapid genetic gain in the future breeding programs.

Leaf tip necrosis and seedling leaf rust resistance conditioned by Lr34 in wheat grown at low temperatures

Wheat leaf rust, caused by Puccinia triticina Eriks., is a common and destructive disease of wheat worldwide. The durable leaf rust-resistance gene Lr34 is typically described as an adult plant resistance gene, which is not expressed at the seedling stage at normal greenhouse temperatures. However, Lr34 is expressed at the seedling stage when plants with Lr34 are grown at low temperatures, i.e. approximately 8°C. Lines and cultivars with Lr34 demonstrate a range of responses from near immunity to intermediate reactions on the primary leaf. The Thatcher-Lr34 near isogenic lines ‘RL6058ʹ (Thatcher*6/PI58548) and ‘RL6091ʹ (Tc*6/Chinese Spring) were resistant to a number of P. triticina virulence phenotypes at the seedling stage when grown under these cool conditions, but were susceptible at typical greenhouse temperatures. A double haploid population from a cross between ‘Thatcher’ and ‘RL6058ʹ, previously genotyped for Lr34, was grown at 8°C and screened for leaf rust response at the seedling stage. The population is segregated by a seedling resistance gene that corresponds to the presence of a resistance allele of Lr34. After extended incubation at cold temperatures, the seedling progeny lines with Lr34 also developed distinct leaf tip necrosis; this phenotype was absent in susceptible plants, similar to their reaction as adult plants. When uninfected plants from this population were grown to the adult plant stage at 10°C, those with the Lr34 resistance allele had extensive leaf necrosis and shrunken, sometimes sterile, spikes.

Powdery mildew resistance of barley accessions from Dagestan.

Powdery mildew caused by the parasitic fungus Blumeria graminis (DC.) Golovin ex Speer f. sp. hordei Marchal is one of the most common diseases of barley. Growing resistant varieties can signif icantly minimize harmful effects of the pathogen. The specif icity in the interaction between the fungus and its host plant requires a continuous search for new donors of the resistance trait. The powdery mildew resistance of 264 barley accessions from Dagestan and genetic control of the trait in resistant forms were studied under f ield and laboratory conditions. Forty-seven barley lines carrying previously identif ied powdery mildew resistance genes were also examined. During three years, the experimental material was evaluated under severe infection pressure at the Dagestan Experiment Station of VIR (North Caucasus, Derbent). Juvenile resistance against the Northwest (St. Petersburg, Pushkin) pathogen population was evaluated in a climatic chamber. The genetic control of B. graminis resistance in the selected accessions was studied with the application of hybridological and molecular analyses. The level of genetic diversity of Dagestan barley for effective resistance to powdery mildew is very low. Only two accessions, VIR-23787 and VIR-28212, are resistant against B. graminis at both seedling and adult plant stages. The high-level resistance of breeding line VIR-28212 originating from barley landrace VIR-17554 (Ep-80 Abyssinien) from Ethiopia is controlled by the recessive gene mlo11. Accession VIR-17554 is heterogeneous for the studied trait, with the powdery mildew resistant genotypes belonging to two varieties, dupliatrum (an awnless phenotype) and nigrinudum (an awned phenotype). In accession VIR-23787, a recessive resistance gene distinct from the mlo11 allele was identif ied. This accession is supposed to be protected by a new, effective pathogen resistance gene.

A Stable Quantitative Trait Locus on Chromosome 5BL Combined with Yr18 Conferring High-Level Adult Plant Resistance to Stripe Rust in Chinese Wheat Landrace Anyuehong

Chinese wheat landrace Anyuehong (AYH) has displayed high levels of stable adult-plant resistance (APR) to stripe rust for more than 15 years. To identify QTL for stripe rust resistance in AYH, a set of 110 recombinant inbred lines (RILs) was developed from a cross between AYH and susceptible cultivar Taichung 29. The parents and RILs were evaluated for final disease severity (FDS) in six field tests with a mixture of predominant Pst races at the adult-plant stage and genotyped using the wheat 55K SNP array to construct a genetic map with 1,143 SNP markers. Three QTL, designated as QYr.AYH-1AS, QYr.AYH-5BL and QYr.AYH-7DS, were mapped on chromosome 1AS, 5BL and 7DS, respectively. RILs combining three QTL showed significantly reduced FDS compared with the lines in other combinations. Of them, QYr.AYH-5BL and QYr.AYH-7DS were stably detected in all environments, explaining 13.6-21.4% and 17.6-33.6% of phenotypic variation, respectively. Compared with previous studies, QYr.AYH-5BL may be a new QTL, while QYr.AYH-7DS may be Yr18. Haplotype analysis revealed that QYr.AYH-5BL is likely present in 6.2% of the 323 surveyed Chinese wheat landraces. The Kompetitive allele specific PCR (KASP) markers for QYr.AYH-5BL were developed by the linked SNP markers to successfully confirm the effects of the QTL in a validation population derived from a residual heterozygous line, and were further assessed in 38 Chinese wheat landraces and 92 cultivars. Our results indicated that QYr.AYH-5BL with linked KASP markers should have potential value for marker-assisted selection to improve stripe rust resistance in breeding programs.

Assessment and modeling using machine learning of resistance to scald (Rhynchosporium commune) in two specific barley genetic resources subsets

Barley production worldwide is limited by several abiotic and biotic stresses and breeding of highly productive and adapted varieties is key to overcome these challenges. Leaf scald, caused by Rhynchosporium commune is a major disease of barley that requires the identification of novel sources of resistance. In this study two subsets of genebank accessions were used: one extracted from the Reference set developed within the Generation Challenge Program (GCP) with 191 accessions, and the other with 101 accessions selected using the filtering approach of the Focused Identification of Germplasm Strategy (FIGS). These subsets were evaluated for resistance to scald at the seedling stage under controlled conditions using two Moroccan isolates, and at the adult plant stage in Ethiopia and Morocco. The results showed that both GCP and FIGS subsets were able to identify sources of resistance to leaf scald at both plant growth stages. In addition, the test of independence and goodness of fit showed that FIGS filtering approach was able to capture higher percentages of resistant accessions compared to GCP subset at the seedling stage against two Moroccan scald isolates, and at the adult plant stage against four field populations of Morocco and Ethiopia, with the exception of Holetta nursery 2017. Furthermore, four machine learning models were tuned on training sets to predict scald reactions on the test sets based on diverse metrics (accuracy, specificity, and Kappa). All models efficiently identified resistant accessions with specificities higher than 0.88 but showed different performances between isolates at the seedling and to field populations at the adult plant stage. The findings of our study will help in fine-tuning FIGS approach using machine learning for the selection of best-bet subsets for resistance to scald disease from the large number of genebank accessions.

English

Global wheat production is constantly threatened by rust diseases. Identifying resistant genes is a useful tactic to control wheat rust pathogen. Twenty-six wheat varieties were screened with twelve Simple Sequence Repeats (SSR) markers to detect rust resistant genes and the efficacy of genes was validated through field testing. The alleles Lr32, Lr39, Lr50, SrCad and SrWeb were not amplified in the varieties included in this study. The SSR markers indicated that the varieties viz., Chakwal-97, Bakhar-2002 and Lasani-2008 had a combination of 02 slow rusting alleles (Lr46/Yr29 and Yr18/Lr34). The adult plant resistance (APR) allele Yr17 was less prevalent and found only in BWL-97. However, Noshera-96 had a slow rusting combination of Lr67/Yr46 and Lr46/Yr46 alleles. The Lr46/Yr29 identified in 50% of the varieties, Yr18/Lr34 in 19.23%, Lr32 in 11.54%, and multiple APR alleles in 19.32%. Their resistance was validated through a field trap nursery for 3 consecutive seasons. The slow rusting combination of Lr46/Yr29 and Yr18/Lr34 was comparatively more effective than Lr67/Yr46 and Lr46/Yr29 alleles under field conditions. The varieties Yecora-70, Lylpure-73 and Tandojam-83 showed highly susceptible phenotype. The varieties Chakwal-86, Pirsabak-2005, Fareed-2006, and Sehar-2006 showed resistant to moderately resistant phenotype at high-temperature adult-plant stage. The cluster diagram divided the varieties into two distinct clades. The clade II depicted the abundance of APR allele Lr46/Yr29. The varieties contain valuable sources of durable rust resistant alleles that can be exploited to deploy rust resistance in future wheat cultivars. It has been observed that the varieties approved for commercial cultivation after 1990s and onwards contain APR alleles. © 2021 Friends Science Publishers

Evaluation of Wheat Germplasm for Resistance to Leaf Rust (Puccinia triticina) and Identification of the Sources of Lr Resistance Genes Using Molecular Markers.

Leaf rust, caused by Puccinia triticina (Ptr), is a significant disease of spring wheat spread in Kazakhstan. The development of resistant cultivars importantly requires the effective use of leaf rust resistance genes. This study aims to: (i) determine variation in Ptr population using races from the East Kazakhstan, Akmola, and Almaty regions of Kazakhstan; (ii) examine resistance during seedling and adult plant stages; and (iii) identify the sources of Lr resistance genes among the spring wheat collection using molecular markers. Analysis of a mixed population of Ptr identified 25 distinct pathotypes. Analysis of these pathotypes using 16 Thatcher lines that are near-isogenic for leaf rust resistance genes (Lr) showed different virulence patterns, ranging from least virulent “CJF/B” and “JCL/G” to highly virulent “TKT/Q”. Most of the pathotypes were avirulent to Lr9, Lr19, Lr24, and Lr25 and virulent to Lr1, Lr2a, Lr3ka, Lr11, and Lr30. The Ptr population in Kazakhstan is diverse, as indicated by the range of virulence observed in five different races analyzed in this study. The number of genotypes showed high levels of seedling resistance to each of the five Ptr races, thus confirming genotypic diversity. Two genotypes, Stepnaya 62 and Omskaya 37, were highly resistant to almost all five tested Ptr pathotypes. Stepnaya 62, Omskaya 37, Avangard, Kazakhstanskaya rannespelaya, and Kazakhstanskaya 25 were identified as the most stable genotypes for seedling resistance. However, most of the varieties from Kazakhstan were susceptible in the seedling stage. Molecular screening of these genotypes showed contrasting differences in the genes frequencies. Among the 30 entries, 22 carried leaf rust resistance gene Lr1, and two had Lr9 and Lr68. Lr10 and Lr28 were found in three and four cultivars, respectively. Lr19 was detected in Omskaya 37. Two single cultivars separately carried Lr26 and Lr34, while Lr37 was not detected in any genotypes within this study. Field evaluation demonstrated that the most frequent Lr1 gene is ineffective. Kazakhstanskaya 19 and Omskaya 37 had the highest number of resistance genes: three and four Lr genes, respectively. Two gene combinations (Lr1, Lr68) were detected in Erythrospermum 35 and Astana. The result obtained may assist breeders in incorporating effective Lr genes into new cultivars and developing cultivars resistant to leaf rust.

Control of stripe rust of wheat using indigenous endophytic bacteria at seedling and adult plant stage

Stripe rust (caused by Puccinia striiformis tritici) is one of the most devastating diseases of wheat. The most effective ways to control stripe rust are the use of resistant cultivars and the timely use of an appropriate dose of fungicide. However, the changing nature of rust pathogen outwits the use of resistant cultivars, and the use of a fungicide is associated with environmental problems. To control the disease without sacrificing the environment, we screened 16 endophytic bacteria, which were isolated from stripe rust-resistant wheat cultivars in our previous study, for their biocontrol potential. A total of 5 bacterial strains Serratia marcescens 3A, Bacillus megaterium 6A, Paneibacillus xylanexedens 7A, Bacillus subtilis 11A, and Staphyloccus agentis 15A showed significant inhibition of Puccinia striiformis f. sp. tritici (Pst) urediniospores germination. Two formulations i.e., fermented liquid with bacterial cell (FLBC) and fermented liquid without bacterial cells (FL) of each bacterial strain, were evaluated against the urediniospores germination. Formulations of five selected endophytic bacteria strains significantly inhibited the uredinioospores germination in the lab experiments. It was further confirmed on seedlings of Pakistani susceptible wheat cultivar Inqilab-91 in the greenhouse, as well as in semi-field conditions. FLBC and FL formulations applied 24 h before Pst inoculation (hbi) displayed a protective mode. The efficacy of FLBC was between 34.45 and 87.77%, while the efficacy of FL was between 39.27 and 85.16% when applied 24 hbi. The inoculated wheat cultivar Inqilab-91 was also tested under semi-field conditions during the 2017–2018 cropping season at the adult plant stage. The strains Bacillus megaterium 6A and Paneibacillus xylanexedens 7A alone significantly reduced the disease severity of stripe rust with the efficacy of 65.16% and 61.11% for the FLBC in protective effect, while 46.07% and 44.47% in curative effect, respectively. Inoculated seedlings of Inqilab-91 showed higher activities of antioxidant enzymes, superoxide dismutase (SOD), peroxidase (POD), polyphenol oxidase (PPO), and phenylalanine ammonia-lyase (PAL). The treated seedlings also showed higher expressions of pathogenesis-related (PR) protein genes, antifungal protein (PR-1), β-1,3-endoglucanases (PR-2), endochitinases (PR-4), peroxidase (PR-9), and ribonuclease-like proteins (PR-10). These results indicated that endophytic bacteria have the biocontrol potential, which can be used to manage stripe rust disease. High production antioxidant enzymes, as well as high expression of PR protein genes, might be crucial in triggering the host defense mechanism against Pst.

Mining of Leaf Rust Resistance Genes Content in Egyptian Bread Wheat Collection.

Wheat is a major nutritional cereal crop that has economic and strategic value worldwide. The sustainability of this extraordinary crop is facing critical challenges globally, particularly leaf rust disease, which causes endless problems for wheat farmers and countries and negatively affects humanity’s food security. Developing effective marker-assisted selection programs for leaf rust resistance in wheat mainly depends on the availability of deep mining of resistance genes within the germplasm collections. This is the first study that evaluated the leaf rust resistance of 50 Egyptian wheat varieties at the adult plant stage for two successive seasons and identified the absence/presence of 28 leaf rust resistance (Lr) genes within the studied wheat collection. The field evaluation results indicated that most of these varieties demonstrated high to moderate leaf rust resistance levels except Gemmeiza 1, Gemmeiza 9, Giza162, Giza 163, Giza 164, Giza 165, Sids 1, Sids 2, Sids 3, Sakha 62, Sakha 69, Sohag 3 and Bany Swif 4, which showed fast rusting behavior. On the other hand, out of these 28 Lr genes tested against the wheat collection, 21 Lr genes were successfully identified. Out of 15 Lr genes reported conferring the adult plant resistant or slow rusting behavior in wheat, only five genes (Lr13, Lr22a, Lr34, Lr37, and Lr67) were detected within the Egyptian collection. Remarkedly, the genes Lr13, Lr19, Lr20, Lr22a, Lr28, Lr29, Lr32, Lr34, Lr36, Lr47, and Lr60, were found to be the most predominant Lr genes across the 50 Egyptian wheat varieties. The molecular phylogeny results also inferred the same classification of field evaluation, through grouping genotypes characterized by high to moderate leaf rust resistance in one cluster while being highly susceptible in a separate cluster, with few exceptions.

Identification of salt-tolerant barley genotypes using multiple-traits index and yield performance at the early growth and maturity stages

BackgroundSalinity is one of the major limiting abiotic stresses that decrease crop production worldwide. To recommend genotypes for cultivation under saline stress conditions, a comprehensive understanding of the genetic basis and plant responses to this stress is needed. In the present study, a total of 20 barley genotypes were investigated to identify potential salt-tolerant genotypes, both at the early growth stage using a hydroponic system, and in adult plants under field conditions. For these purposes, the multi-trait genotype-ideotype distance index (MGIDI) was used to identify salt-tolerant barley genotypes at the seedling stage, and the weighted average of absolute scores (WAASB) index was used to identify the high-yielding and stable genotypes in adult plant stage. At the early growth stage, barley seedlings were treated with two salinity levels: 0 mM NaCl (as control conditions) and 200 mM NaCl (as stress conditions) for 30 days, and during this period different growth and physiological traits were measured. Besides, the yield performance and stability of the investigated barley genotypes were evaluated across five environments during the 2018–2020 cropping seasons.ResultsSalinity stress significantly decreased growth and physiological traits in all seedling plants; however, some salt-tolerant genotypes showed minimal reduction in the measured traits. Multivariate analysis grouped the measured traits and genotypes into different clusters. In the early growth stage, the G12, G14, G6, G7, and G16 were selected as the most salt-tolerant genotypes using MGIDI index. In the multi-environment trials experiment, AMMI analysis showed that grain yields of the tested barley genotypes were influenced by the environment (E), genotype (G), and GE interaction. Based on the weighted average of absolute scores of the genotype index (WAASB) and other stability statistics, G7, G8, G14, and G16 were selected as superior genotypes.ConclusionTogether the MGIDI and WAASB indices revealed that three genotypes—G7, G14 and G16—can be recommended as new genetic resources for improving and stabilizing grain yield in barley programs for the moderate climate and saline regions of Iran. Our results suggest that using the MGIDI index in the early growth stage can accelerate screening nurseries in barley breeding programs. Besides, the WAASB index can be used as a useful stability measurement for identify high-yielding and stable genotypes in multi-environment trials.

English

Stripe (yellow) rust caused by Puccinia striiformis f.sp. tritici, is one of the major diseases of wheat in the world. Development and use of resistant wheat cultivars is the most economical and environmentally friendly solution in combating wheat stripe rust. Field experiments were carried out at two sites in Ethiopia (Kulumsa and Meraro) and seedling tests were conducted at KARC greenhouse during the 2015 cropping season to evaluate the response 192 elite spring bread wheat genotypes and eight checks to the prevailing races of stripe rust at adult plant stage and seedling stage. About 72.5 and 42.5% of the lines exhibited resistance to stripe rust during the field screening at Kulumsa and Meraro, respectively. Disease was more severe at the cooler site Meraro than Kulumsa. Eighteen genotypes at Kulumsa and 16 genotypes at Merao were almost immune to the disease (severity and AUDPC of zero). Seventy-two genotypes (36%) showed resistant reaction at both locations in field condition for adult plant stage (CI < 20). For seedling, 47% for mixed isolates and 31% for kubsa isolates showed resistance reaction responses to stripe rust disease based on coefficient of infection (CI). Key words: Puccinia striiformis, resistance, susceptible, Triticum aestivum, genotypes.