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%.

Deciphering resistance to Zymoseptoria tritici in the Tunisian durum wheat landrace accession ‘Agili39’

Background Septoria tritici blotch (STB), caused by Zymoseptoria tritici (Z. tritici), is an important biotic threat to durum wheat in the entire Mediterranean Basin. Although most durum wheat cultivars are susceptible to Z. tritici, research in STB resistance in durum wheat has been limited. Results In our study, we have identified resistance to a wide array of Z. tritici isolates in the Tunisian durum wheat landrace accession ‘Agili39’. Subsequently, a recombinant inbred population was developed and tested under greenhouse conditions at the seedling stage with eight Z. tritici isolates and for five years under field conditions with three Z. tritici isolates. Mapping of quantitative trait loci (QTL) resulted in the identification of two major QTL on chromosome 2B designated as Qstb2B_1 and Qstb2B_2. The Qstb2B_1 QTL was mapped at the seedling and the adult plant stage (highest LOD 33.9, explained variance 61.6 %), conferring an effective resistance against five Z. tritici isolates. The Qstb2B_2 conferred adult plant resistance (highest LOD 32.9, explained variance 42 %) and has been effective at the field trials against two Z. tritici isolates. The Qstb2B_1 QTL was mapped at the seedling and the adult plant stage (highest LOD 33.9, explained variance 61.6 %), conferring an effective resistance against five Z. tritici isolates. The Qstb2B_2 conferred adult plant resistance (highest LOD 32.9, explained variance 42 %) and has been effective at the field trials against two Z. tritici. The physical positions of the flanking markers linked to Qstb2B_1 and Qstb2B_2 indicate that these two QTL are 5Mb apart. In addition, we identified two minor QTL on chromosomes 1A (Qstb1A) and chromosome 7A (Qstb7A) (highest LODs 4.6 and 4.0, and explained variances of 16 % and 9%, respectively) that were specific to three and one Z. tritici isolates, respectively. All identified QTL were derived from the landrace accession Agili39 that represents a valuable source for STB resistance in durum wheat. Conclusion This study demonstrates that Z. tritici resistance in the ‘Agili39’ landrace accession is controlled by two minor and two major QTL acting in an additive mode.

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.

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.

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.

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 (Bgt) and Puccinia triticina (Pt), respectively, are widespread diseases of wheat worldwide. Utilizing resistant cultivars is considered as the most economical, environmental-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 (22.1%) wheat accessions were highly resistant to a widely prevalent Bgt isolate, E09, at the seedling stage, and 390 were consistently resistant to the mixture of Bgt isolates at the adult-plant stage. Meanwhile, 63 (2.1%) accessions were highly resistant to leaf rust at the adult-plant stage, of which 54 were resistant to a predominant and highly virulent Pt 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 Pm genes (Pm2, Pm4, Pm5, Pm6, Pm8, Pm21, and Pm24) and ten 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, while Pm24 was not detected. Besides, 139 accessions might contain unknown Pm genes different from those tested in this study. In the 63 accessions resistant leaf rust, four Lr genes (Lr1, Lr10, Lr26, and Lr34) were detected in 41 accessions either singly or in combination, while 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.

Identification of Resistance Sources and Genome-Wide Association Mapping of Septoria Tritici Blotch Resistance in Spring Bread Wheat Germplasm of ICARDA

Septoria tritici blotch (STB) of wheat, caused by the ascomycete Zymoseptoria tritici (formerly Mycosphaerella graminicola), is one of the most important foliar diseases of wheat. In Morocco, STB is a devastating disease in temperate wheat-growing regions, and the yield losses can exceed up to 50% under favorable conditions. The aims of this study were to identify sources of resistance to STB in Septoria Association Mapping Panel (SAMP), which is composed of 377 advanced breeding lines (ABLs) from spring bread wheat breeding program of ICARDA, and to identify loci associated with resistance to STB at seedling (SRT) as well as at the adult plant (APS) stages using genome-wide association mapping (GWAM). Seedling resistance was evaluated under controlled conditions with two virulent isolates of STB (SAT-2 and 71-R3) from Morocco, whereas adult plant resistance was assessed at two hot spot locations in Morocco (Sidi Allal Tazi, Marchouch) under artificial inoculation with a mixture of STB isolates. At seedling stage, 45 and 32 ABLs were found to be resistant to 71-R3 and SAT-2 isolates of STB, respectively. At adult plant stage, 50 ABLs were found to be resistant at hot spot locations in Morocco. Furthermore, 10 genotypes showed resistance in both locations during two cropping seasons. GWAM was conducted with 9,988 SNP markers using phenotypic data for seedling and the adult plant stage. MLM model was employed in TASSEL 5 (v 5.2.53) using principal component analysis and Kinship Matrix as covariates. The GWAM analysis indicated 14 quantitative trait loci (QTL) at the seedling stage (8 for isolate SAT-2 and 6 for isolate 71-R3), while 23 QTL were detected at the adult plant stage resistance (4 at MCH-17, 16 at SAT-17, and 3 at SAT-18). SRT QTL explained together 33.3% of the phenotypic variance for seedling resistance to STB isolate SAT-2 and 28.3% for 71-R3, respectively. QTL for adult plant stage resistance explained together 13.1, 68.6, and 11.9% of the phenotypic variance for MCH-17, SAT-17, and SAT-18, respectively. Identification of STB-resistant spring bread wheat germplasm in combination with QTL detected both at SRT and APS stage will serve as an important resource in STB resistance breeding efforts.

Disease Resistance and Genes in 146 Wheat Cultivars (Lines) from the Huang-Huai-Hai Region of China

Wheat stripe rust, powdery mildew, and Fusarium head blight (FHB) are the three most important diseases in wheat worldwide. Growing resistant cultivars is the most economic and effective method to control these diseases. To assess the disease resistance of commercial wheat cultivars and regional trial wheat lines in the Huang-Huai-Hai region of China, 146 wheat entries were inoculated with the Chinese prevalent Puccinia striiformis f. sp. tritici (Pst) races CYR32, CYR33, CYR34, and Blumeria graminis f. sp. tritici (Bgt) isolate E09 under controlled greenhouse conditions, respectively; these entries were also tested with the mixed Pst races, Bgt and FHB isolates at adult-plant stage in the field, respectively. The results showed that 108 (73.97%), 83 (56.85%), 99 (67.81%), and 22 (15.07%) entries were resistant to CYR32, CYR33, CYR34, and E09 at the seedling stage, respectively; 102 (69.86%), 24 (16.44%), and 2 (1.37%) entries were resistant to stripe rust, powdery mildew, and Fusarium head blight at the adult-plant stage, respectively. Additionally, the possible resistance gene(s) in these entries were postulated by the closely linked markers of stripe rust resistance genes Yr5, Yr9, Yr10, Yr15, Yr17, Yr18, Yr26, powdery mildew resistance gene Pm21, and Fusarium head blight resistance gene Fhb1. Combined with disease resistance and molecular markers tests, 62, nine, and three wheat entries were postulated to carry the Yr9, Yr17, Yr26 gene, respectively, and no entries contained Yr5, Yr10, Yr15, Yr18, Pm21, and Fhb1 gene. This study laid a theoretical foundation for rational utilization of these entries and gene in wheat breeding programs and disease control.

Isolation and characterization of yellow rust resistant mutants in wheat.

Stripe rust, also known as yellow rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a major threat to wheat production leading to yield losses up to 84%. Due to climate change, new races of the yellow rust pathogen are appearing for which no durable source of resistance has been observed in the present high-yielding varieties. A mutation breeding programme was initiated in two popular varieties, namely PBW343 and HD2967, using gamma-ray and electron beam irradiation. Gamma-ray doses of 250, 300 and 350 Gy and electron beam doses of 150, 200 and 250 Gy were used for seed irradiation. The M2 population was screened in the field from seedling to adult plant stage by spraying a mixture of urediniospores of Pst pathotypes. Disease severity was recorded as the percentage of leaf area covered by the rust pathogen following a modified Cobb's scale. A total of 52 putative yellow rust resistant mutants in HD2967 and 63 in PBW343 were isolated. The number of mutants was higher in the electron beam irradiated population compared with gamma-rays. The absence of sporulation and spore production of the rust pathogen on the mutants indicated resistance. Mutant plants showing seedling resistance also showed resistance at adult plant stage. Seed yield and its contributing characters were better in the mutants compared with the parents. These rust resistant mutants could be novel sources of stripe rust or yellow rust resistance. The plant-to-row progenies of these mutants were confirmed and characterized in the M3 generation.