Sources Of Genetic Resistance Research Articles

Potential of the Colombian Coffee Collection as a Source of Genetic Resistance to Colletotrichum kahawae JM Waller PD Bridge

Coffee berry disease (CBD) is not present in the Americas and presents a potential risk for growing coffee. Therefore, Colombia, which has been in scientific cooperation with the Centro de Investigação de Ferrugens do Cafeeiro (CIFC) of Portugal for more than 30 years, has been evaluating the genetic resistance of nine populations of C. arabica to 13 isolates of Colletotrichum kahawae JM Waller and PD Bridge, which are diverse in terms of aggressiveness and geographical origin. The phenotypes observed in the interaction between C. arabica and C. kahawae were used to develop a statistically reliable scale (p-value ≥ 0.001) to categorize resistance in C. arabica into five classes, and this scale was used to classify the nine populations of C. arabica evaluated. The results allowed us to corroborate the potential of Timor Hybrid CIFC 1343 (TH CIFC 1343) as a source of genetic resistance to CBD and to identify new genetic sources not yet explored for the development of varieties in Colombia that may eventually mitigate the effects of CBD in the face of increasing rainfall events and minimum temperatures due to climate change, which can favor disease development. Additionally, the results suggest that the existence of races in the C. arabica–C. kahawae complex is probable, and a selection of genotypes was identified as a possible differential series of races in C. kahawae.

Identification and Screening of Leaf Rust Resistance Genes in Wheat Cultivars Through Microsatellites

Wheat is one of the important staple food being grown worldwide and in Pakistan. The wheat rust-causing fungi are very eco-adaptive and evolve rapidly to overcome genetic resistance of wheat varieties. Among all rust-causing fungi, Puccinia triticina causes leaf rust in wheat, and inflicts heavy yield losses. Deploying resistant varieties against leaf rust is the most effective, environmentally-friendly and economic way to control the disease. Therefore, new sources of genetic resistance are continually sought to develop rust resistance in wheat varieties, and nowadays rust resistant varieties have been developed through the accumulation of slow rusting or minor genes that would perform better in fields. Hence, the purpose of this study is to screen a few of the available leaf rust-resistant germplasm in field and evaluate their field response on genetic basis. For this purpose, minor genes were detected through the amplification of simple sequence repeat (SSR) in the selected wheat genotypes through screened primers. Field experiment was conducted. Molecular studies to identify the minor genes were performed. Meteorological data was recorded at the observatory laboratory of the same area. All the epidemiological factors (Temperature (maximum, minimum), Relative Humidity, and Pan Evaporation) showed significant correlation in tested 5 varieties ZARDANA89, ZARLASHTA99, RASKOH 05, BHAKKAR-2000, GA-2002 which were conducive for disease development except rainfall. PCR amplification of Xgwm118, and Xgwm165, showed the range of alleles in 14 genotypes. It was observed that 22 verities showed resistance, 3 were moderately resistant, 3 varieties were moderately susceptible, 8 varieties were moderately susceptible, and 5 varieties were moderately susceptible against leaf rust pathogen.

Identification of Pathogen-Specific Novel Sources of Genetic Resistance Against Ascochyta Blight and Identification of Their Underlying Genetic Control.

Global chickpea production is restricted by Ascochyta blight caused by the necrotrophic fungi Ascochyta rabiei. Developing locally adapted disease-resistant cultivars is an economically and environmentally sustainable approach to combat this disease. However, the lack of genetic variability in cultivated chickpeas and breeder-friendly markers poses a significant challenge to Ascochyta blight-resistant breeding efforts in chickpeas. In this study, we screened the mini-core germplasm of Cicer reticulatum against a local pathotype of A. rabiei. A modified mini-dome screening approach resulted in the identification of five accessions showing a high level of resistance. The mean disease score of resistant accessions ranged between 1.75 ± 0.3 and 2.88 ± 0.4 compared to susceptible accessions, where the mean disease score ranged between 3.59 ± 0.62 and 8.86 ± 0.14. Genome-wide association study revealed a strong association on chromosome 5, explaining ∼58% of the phenotypic variance. The underlying region contained two candidate genes (Cr_14190.1_v2 and Cr_14189.1_v2), the characterization of which showed the presence of a DNA-binding domain (cl28899 and cd18793) in Cr_14190.1_v2 and its orthologs in C. arietinum, whereas Cr_14190.1_v2 carried an additional N-terminal domain (cl31759). qPCR expression analysis in resistant and susceptible accessions revealed ∼3- and ∼110-fold higher transcript abundance for Cr_14189.1 and Cr_14190.1, respectively.

Reshaping the Primary Cell Wall: Dual Effects on Plant Resistance to Ralstonia solanacearum and Heat Stress Response.

Temperature elevation drastically affects plant defense responses to Ralstonia solanacearum and inhibits the major source of resistance in Arabidopsis thaliana, which is mediated by the receptor pair RRS1-R/RPS4. In this study, we refined a previous genome-wide association (GWA) mapping analysis by using a local score approach and detected the primary cell wall CESA3 gene as a major gene involved in plant response toR. solanacearumat both 27°C and an elevated temperature, 30°C. We functionally validatedCESA3as a susceptibility gene involved in resistance toR. solanacearumat both 27 and 30°C through a reverse genetic approach. We provide evidence that thecesa3mre1mutant enhances resistance to bacterial disease and that resistance is associated with an alteration of root cell morphology conserved at elevated temperatures. However, even by forcing the entry of the bacterium to bypass the primary cell wall barrier, thecesa3mre1mutant still showed enhanced resistance toR. solanacearumwith delayed onset of bacterial wilt symptoms. We demonstrated that thecesa3mre1mutant had constitutive expression of the defense-related geneVSP1, which is upregulated at elevated temperatures, and that during infection, its expression level is maintained higher than in the wild-type Col-0. In conclusion, this study reveals that alteration of the primary cell wall by mutating the cellulose synthase subunit CESA3 contributes to enhanced resistanceto R. solanacearum,remaining effective under heat stress. We expect that these results will help to identify robust genetic sources of resistance toR. solanacearumin the context of global warming. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Unraveling the genetic basis of quantitative resistance to diseases in tomato: a meta-QTL analysis and mining of transcript profiles.

Whole-genome QTL mining and meta-analysis in tomato for resistance to bacterial and fungal diseases identified 73 meta-QTL regions with significantly refined/reduced confidence intervals. Tomato production is affected by a range of biotic stressors, causing yield losses and quality reductions. While sources of genetic resistance to many tomato diseases have been identified and characterized, stability of the resistance genes or quantitative trait loci (QTLs) across the resources has not been determined. Here, we examined 491 QTLs previously reported for resistance to tomato diseases in 40 independent studies and 54 unique mapping populations. We identified 29 meta-QTLs (MQTLs) for resistance to bacterial pathogens and 44 MQTLs for resistance to fungal pathogens, and were able to reduce the average confidence interval (CI) of the QTLs by 4.1-fold and 6.7-fold, respectively, compared to the average CI of the original QTLs. The corresponding physical length of the CIs of MQTLs ranged from 56kb to 6.37Mb, with a median of 921 kb, of which 27% had a CI lower than 500kb and 53% had a CI lower than 1Mb. Comparison of defense responses between tomato and Arabidopsis highlighted 73 orthologous genes in the MQTL regions, which were putatively determined to be involved in defense against bacterial and fungal diseases. Intriguingly, multiple genes were identified in some MQTL regions that are implicated in plant defense responses, including PR-P2, NDR1, PDF1.2, Pip1, SNI1, PTI5, NSL1, DND1, CAD1, SlACO, DAD1, SlPAL, Ph-3, EDS5/SID1, CHI-B/PR-3, Ph-5, ETR1, WRKY29, and WRKY25. Further, we identified a number of candidate resistance genes in the MQTL regions that can be useful for both marker/gene-assisted breeding as well as cloning and genetic transformation.

A comprehensive review of soybean RNL and TIR domain proteins.

Both prokaryotic and eukaryotic organisms use the nucleotide-binding domain/leucine-rich repeat (NBD/LRR)-triggered immunity (NLR-triggered immunity) signaling pathway to defend against pathogens. Plant NLRs are intracellular immune receptors that can bind to effector proteins secreted by pathogens. Dicotyledonous plants express a type of NLR known as TIR domain-containing NLRs (TNLs). TIR domains are enzymes that catalyze the production of small molecules that are essential for immune signaling and lead to plant cell death. The activation of downstream TNL signaling components, such as enhanced disease susceptibility 1 (EDS1), phytoalexin deficient 4 (PAD4), and senescence-associated gene 101 (SAG101), is facilitated by these small molecules. Helper NLRs (hNLRs) and the EDS1-PAD4/SAG101 complex associate after activation, causing the hNLRs to oligomerize, translocate to the plasma membrane (PM), and produce cation-selective channels. According to a recent theory, cations enter cells through pores created by oligomeric hNLRs and trigger cell death. Occasionally, TNLs can self-associate to create higher-order oligomers. Here, we categorized soybean TNLs based on the protein domains that they possess. We believe that TNLs may help soybean plants effectively fight pathogens by acting as a source of genetic resistance. In summary, the purpose of this review is to elucidate the range of TNLs that are expressed in soybean.

Study on submergence tolerance of rice (Oryza sativa L.) in a core panel of North-East India using GWAS

Rice (Oryza sativa L.) being the major food crop of the north-eastern region, combating floods in rice fields for higher economic yield is a major challenge. A core panel, consisting of local rice landraces that have been cultivated in the flood-prone areas of this region for years, was used for this GWAS study to uncover possible genetic resistance sources to submergence. A study on GWAS was conducted to understand the mechanism of resistance of rice under water-submerged conditions through higher expression of genes. The GWAS analysis of a core panel of 400 rice landraces generated 38,723 filtered SNPs. The result showcased nine loci across the 12 rice chromosomes, one locus each in chromosome 2 and 4, five loci in chromosome 6, and two loci in chromosome 9. The two promising loci among these nine identified loci codes for zinc fingers, C3HC4 type domain-containing proteins, with FDR adjusted p-values of 0.04 each and allele effect of 4.60 and 4.57, respectively. These GWAS-identified association signals are a valuable source for allele mining and can be validated and introgressed into elite germplasms to decipher submergence tolerance in future breeding programs.

Jasmonate ZIM Domain Protein (JAZ) Gene SLJAZ15 Increases Resistance to Orobanche aegyptiaca in Tomato.

Orobanche aegyptiaca Pers. is a holoparasitic plant that severely reduces tomato (Solanum lycopersicum L.) production in China. However, there is a lack of effective control methods and few known sources of genetic resistance. In this study, we focused on key genes in the JAZ family, comparing the JAZ family in Arabidopsis thaliana (L. Heynh.) to the tomato genome. After identifying the JAZ family members in S. lycopersicum, we performed chromosomal localization and linear analysis with phylogenetic relationship analysis of the JAZ family. We also analyzed the gene structure of the JAZ gene family members in tomato and the homology of the JAZ genes among the different species to study their relatedness. The key genes for O. aegyptiaca resistance were identified using VIGS (virus-induced gene silencing), and the parasitization rate of silenced tomato plants against O. aegyptiaca increased by 47.23-91.13%. The genes were localized in the nucleus by subcellular localization. Heterologous overexpression in A. thaliana showed that the key gene had a strong effect on the parasitization process of O. aegyptiaca, and the overexpression of the key gene reduced the parasitization rate of O. aegyptiaca 1.69-fold. Finally, it was found that the SLJAZ15 gene can positively regulate the hormone content in tomato plants and affect plant growth and development, further elucidating the function of this gene.

Identification of new genetic sources of resistance to bacterial blight race 18 in diploid Asiatic cotton and resistance transfer to tetraploid Upland cotton (Gossypium hirsutum)

Identification of new genetic sources of resistance to bacterial blight race 18 in diploid Asiatic cotton and resistance transfer to tetraploid Upland cotton (Gossypium hirsutum)

Phytoparasitic Nematodes of Musa spp. with Emphasis on Sources of Genetic Resistance: A Systematic Review.

Bananas are a staple food that considerably contributes to both food security and income generation, especially in countries of Africa, Asia, and Central and South America. The banana plant (Musa spp.) is affected by various pathogens, of main concern being the plant-parasitic nematodes associated with the rhizosphere, the most important of which are Radopholus similis (burrowing nematode), Helicotylenchus sp. (spiral nematode), Pratylenchus sp. (root lesion nematode), and Meloidogyne sp. (gall nematode). Infected plants reduce their ability to absorb water and nutrients, which can lead to delayed flowering, fewer bunches, and lower fruit mass. Obtaining nematode-resistant banana cultivars through genetic improvement is an effective and sustainable option compared with chemical control with nematicides. Here, we provide the first systematic review of existing banana sources of resistance to nematodes to aid the management and control of nematodes in banana and plantain crops. Articles selected from different databases were evaluated, and searches were conducted using pre-established inclusion and exclusion criteria. We found 69 studies dealing with genetic improvement for nematode resistance in banana cultivation. Our findings revealed that sources of resistance are currently under investigation to combat the diseases caused by different nematode species in banana plants.

Registration of the “Woodies” multi–rust‐resistant barley germplasm

AbstractSelection for resistance to plant diseases is a continuous effort on the part of plant breeders. Sources of genetic resistance are often limited, despite considerable discovery efforts. Stem rust and stripe rust are two diseases of particular importance in barley (Hordeum vulgare L.) production. The present work aims to develop and deploy genotypes with resistance to these diseases that can be used in future breeding efforts. The Woodies, Woody‐1 (DH160733; Reg. no. GP‐218, PI 704479) and Woody‐2 (DH160754; Reg. no. GP‐219, PI 704480), are two doubled‐haploid genotypes produced via F1 anther culture named in honor of the late Lynn “Woody” Gallagher. These two‐row spring habit barley germplasm accessions were released by the Oregon Agricultural Experiment Station in 2023. These genotypes have demonstrated resistance to both stem and stripe rust at the seedling and adult plant stage in trials conducted between 2018 and 2023. The genetic basis of this resistance appears to be a novel quantitative trait locus conferring resistance to both diseases on chromosome 5H that is different from the known rpg4/Rpg5 complex for stem rust resistance found on the same chromosome. Seed can be requested from the Oregon State University Barley Breeding Program or from the NLGRP Germplasm repository.

Non-destructive SPE-UPLC-based Quantification of Aflatoxins and Stilbenoid Phytoalexins in Single Peanut (Arachis spp.) Seeds.

Aflatoxins are highly carcinogenic secondary metabolites of some fungal species, particularly Aspergillus flavus. Aflatoxins often contaminate economically important agricultural commodities, including peanuts, posing a high risk to human and animal health. Due to the narrow genetic base, peanut cultivars demonstrate limited resistance to fungal pathogens. Therefore, numerous wild peanut species with tolerance to Aspergillus have received substantial consideration by scientists as sources of disease resistance. Exploring plant germplasm for resistance to aflatoxins is difficult since aflatoxin accumulation does not follow a normal distribution, which dictates the need for the analyses of thousands of single peanut seeds. Sufficiently hydrated peanut (Arachis spp.) seeds, when infected by Aspergillus species, are capable of producing biologically active stilbenes(stilbenoids) that are considered defensive phytoalexins. Peanut stilbenes inhibit fungal development and aflatoxin production. Therefore, it is crucial to analyze the same seeds for peanut stilbenoids to explain the nature of seed resistance/susceptibility to the Aspergillus invasion. None of the published methods offer single-seed analyses for aflatoxins and/or stilbene phytoalexins. We attempted to fulfill the demand for such a method that is environment-friendly, uses inexpensive consumables, and is sensitive and selective. In addition, the method is non-destructive since it uses only half of the seed and leaves the other half containing the embryonic axis intact. Such a technique allows germination and growth of the peanut plant to full maturity from the same seed used for the aflatoxin and stilbenoid analysis. The integrated part of this method, the manual challenging of the seeds with Aspergillus, is a limiting step that requires more time and labor compared to other steps in the method. The method has been used for the exploration of wild Arachis germplasm to identify species resistant to Aspergillus and to determine and characterize novel sources of genetic resistance to this fungal pathogen.

Reproducible Quantitative Trait Loci for Resistance to Soft Rot Caused by Dickeya dianthicola Derived from the Wild Potato Solanum microdontum (PI 458355) Are Located on Chromosomes 1, 3, and 5.

The potato wild relative Solanum microdontum is a breeder-friendly source of genetic resistance to soft rot. Our objectives were to (i) identify loci associated with soft rot resistance in S. microdontum germplasm and (ii) develop bi-parental populations in a self-compatible S. tuberosum genetic background to recover segregating F2 progenies, construct a linkage map, and identify quantitative trait loci (QTLs). Under objective (i), tubers from 103 S. microdontum genotypes from the United States Potato Genebank were inoculated with a high virulence strain of Dickeya dianthicola, and lesion size was measured after a 24-h incubation period at 30°C. Association analysis using 3,490 polymorphic Infinium array SNP markers identified soft rot resistance loci on chromosomes 1, 2, 3, 5, 7, 8, 11, and 12. Under objective (ii), a resistant S. microdontum accession PI 458355 was crossed with a highly fertile, self-compatible, diploid S. tuberosum pollen parent (PI 654351) to generate segregating F2 populations. Composite interval mapping was conducted using a genetic linkage map with 970 GBS-based SNP markers. Reproducible QTLs were detected on chromosomes 1, 3, and 5, explaining 11, 13, and 23% of the phenotypic variation, respectively. Homozygous S. microdontum alleles at the QTL on chromosome 5 and heterozygous or homozygous S. microdontum alleles at QTLs on chromosomes 1 and 3 significantly decrease lesion size compared with the homozygous S. tuberosum parent. The germplasm created in these studies provides a resource for studying traits from S. microdontum, and we can use the advanced F2 selections for future potato improvement. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Evaluation of lettuce germplasm for resistance to impatiens necrotic spot virus

Recently, impatiens necrotic spot virus (INSV) has emerged as a major pathogen of lettuce in the Salinas Valley of California. The virus is a member of the genus Orthotospovirus, and under natural conditions, is transmitted by the tiny insect, western flower thrips. Due to the high efficiency of virus transmission, chemical management of thrips vectors is often ineffective in preventing the spread of the disease. Utilization of genetic resistance will be a critical component for managing the disease; however, little is known about genetic sources of resistance in lettuce. Here, we evaluated 189 lettuce lines under natural disease pressure in four field experiments to identify INSV resistant germplasm. The stability of resistance was also evaluated using different inoculation methods under controlled conditions. Our results showed a significant variation (p < 0.0001) among lettuce cultivars for both INSV severity and incidence. We identified INSV resistant germplasm that belongs to different horticultural types and leaf color, including a red-leaf cultivar ‘Eruption’ with a high degree of genetic stability. Moreover, we characterized several factors influencing thrips and host plant relationships, including horticultural type, leaf color, and polyphenol concentration. Overall, INSV resistant germplasm identified in this study provide valuable resources for breeding of INSV resistant lettuce cultivars.

Occurrence of the &lt;i&gt;FBF&lt;/i&gt;7 fire blight resistance locus in accessions of apple wild species (&lt;i&gt;Malus&lt;/i&gt; Mill.)

Background. Fire blight (Erwinia amylovora (Burill) Winslow et al.) is a dangerous disease of fruit crops. In the Russian Federation, fire blight is one of the quarantine diseases. Apple resistance to fire blight is controlled polygenically. However, the data on the genotypes of Malus Mill. wild species and varieties in the context of individual resistance loci are scarce. The purpose of the research was studying the genetic collection of apple wild species according to the FBF7 fire blight resistance locus to identify promising sources of resistance to E. amylovora.Materials and methods. The materials of this study included 23 wild and two cultivated apple-tree species (50 accessions) from the genetic collection of the I.V. Michurin FSC. The FBF7 QTL for fire blight resistance was identified with the flanking SCAR-markers AE10-375 and GE-8019, and SSR-marker CH-F7-Fb1.Results and conclusion. The GE-8019 marker was identified in 50.0% of the apple accessions, AE10-375 in 76.0% of the accessions, and CH-F7-Fb1 in 30.0%. Inter- and intraspecific polymorphism of the Malus genus was revealed for the analyzed resistance locus, as well as for individual DNA markers linked to the FBF7 QTL. The GE-8019 and AE10-375 markers flanking the FBF7 QTL were found in 42.0% of the studied genotypes. Meanwhile, three diagnostic markers (GE-8019, AE10-375, and CH-F7-Fb1) were identified only in 7 accessions: M. × robusta var. persicifolia (Carr.) Rehd. (к-41279), M. × cerasifera var. hiemalis Spach. (к-2342) (Ser. Baccatae), M. sylvestris (L.) Mill. (k-73 and k-123), M. × spectabilis var. albi plena (Ait.) Borkh. (к-2416) (Ser. Malus), M. × sargentii (Rehd.) Langenf. (k-2428) (Ser. Toringonae), and M. coronaria (L.) Mill. (к-2336) (Ser. Coronariae). These forms are promising genetic sources of resistance to E. amylovora.

Dissecting the effect of heat stress on durum wheat under field conditions.

Heat stress negatively affects wheat production in several ways, mainly by reducing growth rate, photosynthetic capacity and reducing spike fertility. Modeling stress response means analyzing simultaneous relationships among traits affecting the whole plant response and determinants of grain yield. The aim of this study was to dissect the diverse impacts of heat stress on key yield traits and to identify the most promising sources of alleles for heat tolerance. We evaluated a diverse durum wheat panel of 183 cultivars and breeding lines from worldwide, for their response to long-term heat stress under field conditions (HS) with respect to non stress conditions (NS), considering phenological traits, grain yield (GY) and its components as a function of the timing of heat stress and climatic covariates. We investigated the relationships among plant and environmental variables by means of a structural equation model (SEM) and Genetic SEM (GSEM). Over two years of experiments at CENEB, CIMMYT, the effects of HS were particularly pronounced for the normalized difference vegetation index, NDVI (-51.3%), kernel weight per spike, KWS (-40.5%), grain filling period, GFP (-38.7%), and GY (-56.6%). Average temperatures around anthesis were negatively correlated with GY, thousand kernel weight TKW and test weight TWT, but also with spike density, a trait determined before heading/anthesis. Under HS, the correlation between the three major determinants of GY, i.e., fertile spike density, spike fertility and kernel size, were of noticeable magnitude. NDVI measured at medium milk-soft dough stage under HS was correlated with both spike fertility and grain weight while under NS it was less predictive of grain weight but still highly correlated with spike fertility. GSEM modeling suggested that the causal model of performance under HS directly involves genetic effects on GY, NDVI, KWS and HD. We identified consistently suitable sources of genetic resistance to heat stress to be used in different durum wheat pre-breeding programs. Among those, Desert Durums and CIMMYT'80 germplasm showed the highest degree of adaptation and capacity to yield under high temperatures and can be considered as a valuable source of alleles for adaptation to breed new HS resilient cultivars.

An emergent plant‐parasitic nematode in Brazil: Aphelenchoides besseyi. Current status and research perspectives

AbstractAphelenchoides besseyi is an emerging and yet overlooked plant parasite of many economically important crops, including cotton, soybean and common bean. It presents an economic risk to these crops in several countries, notably in Brazil. Although first reported infecting strawberries in the United States as early as 1942, it was only identified to be the causal agent of green stem and foliar retention (GSFR) disease in Brazil in 2017. Currently, there are no chemical nematicides registered in Brazil against A. besseyi, and no known sources of genetic resistance. Here, we review the biology of A. besseyi, its spread across Brazil, its relevance to the country's current and future agriculture and the limited control measures. We describe control measures that have been successfully used to manage infestations of other plant‐parasitic nematodes and could potentially be extended to use in the control of A. besseyi. We also review and discuss potential future control measures, such as RNA interference and genome editing, for the development of crops with enhanced resistance to A. besseyi.

HaploCatcher: An R package for prediction of haplotypes.

Wheat (Triticum aestivum L.) is crucial to global food security but is often threatened by diseases, pests, and environmental stresses. Wheat-stem sawfly (Cephus cinctus Norton) poses a major threat to food security in the United States, and solid-stem varieties, which carry the stem-solidness locus (Sst1), are the main source of genetic resistance against sawfly. Marker-assisted selection uses molecular markers to identify lines possessing beneficial haplotypes, like that of the Sst1 locus. In this study, an R package titled "HaploCatcher" was developed to predict specific haplotypes of interest in genome-wide genotyped lines. A training population of 1056 lines genotyped for the Sst1 locus, known to confer stem solidness, and genome-wide markers was curated to make predictions of the Sst1 haplotypes for 292 lines from the Colorado State University wheat breeding program. Predicted Sst1 haplotypes were compared to marker-derived haplotypes. Our results indicated that the training set was substantially predictive, with kappa scores of 0.83 for k-nearest neighbors and 0.88 for random forest models. Forward validation on newly developed breeding lines demonstrated that a random forest model, trained on the total available training data, had comparable accuracy between forward and cross-validation. Estimated group means of lines classified by haplotypes from PCR-derived markers and predictive modeling did not significantly differ. The HaploCatcher package is freely available and may be utilized by breeding programs, using their own training populations, to predict haplotypes for whole-genome sequenced early generation material.

Molecular, phenotypic and histological analysis reveals a multi-tiered immune response and callose deposition in stone fruit rootstocks (Prunus spp.) against Pseudomonas syringae pv. syringae (Pss) infection

Bacterial canker, caused by Pseudomonas syringae pv syringae (Pss), is a serious disease of stone fruit orchards causing severe yield reductions and the death of entire trees. To analyze the response and to identify novel sources of Pss resistance in our rootstock breeding program, we used a novel, rapid and reliable leaf disk pathogenicity test to screen pre-breeding material constituted by interspecific hybrids of plum/peach/almond (‘AGAF’/‘ADAGAF’) or sweet cherry (‘PACIR’) species and commercial rootstocks with two Pss strains. Some ‘AGAF’/ ‘ADAGAF’ and all ‘PACIR’ rootstocks showed lower susceptibility than commercial rootstocks to Pss strains used. The reduced symptoms displayed by the ‘PACIR’ hybrids with Prunus lannesiana and P. incisa as genomic background suggest that these species could be novel sources of genetic resistance to Pss within the Cerasus subgenus. Histological and candidate gene expression analysis suggest a multi-tiered immune response of Prunus species to Pss attack with a higher callose deposition and activation of molecular mechanisms that would restrict the bacteria infection and help to maintain a better redox homeostasis and performance of ‘Marianna 2624′, a plum resistant genotype. Identification of Prunus species with resistance to Pss and the analysis of their immune response are the first step towards characterizing the underlying genetic mechanisms of resistance and introducing these traits into commercial germplasm.

Combined Omics Approaches Reveal Distinct Mechanisms of Resistance and/or Susceptibility in Sugar Beet Double Haploid Genotypes at Early Stages of Beet Curly Top Virus Infection.

Sugar beet is susceptible to Beet curly top virus (BCTV), which significantly reduces yield and sugar production in the semi-arid growing regions worldwide. Sources of genetic resistance to BCTV is limited and control depends upon insecticide seed treatments with neonicotinoids. Through double haploid production and genetic selection, BCTV resistant breeding lines have been developed. Using BCTV resistant (R) [KDH13; Line 13 and KDH4-9; Line 4] and susceptible (S) [KDH19-17; Line 19] lines, beet leafhopper mediated natural infection, mRNA/sRNA sequencing, and metabolite analyses, potential mechanisms of resistance against the virus and vector were identified. At early infection stages (2- and 6-days post inoculation), examples of differentially expressed genes highly up-regulated in the 'R' lines (vs. 'S') included EL10Ac5g10437 (inhibitor of trypsin and hageman factor), EL10Ac6g14635 (jasmonate-induced protein), EL10Ac3g06016 (ribosome related), EL10Ac2g02812 (probable prolyl 4-hydroxylase 10), etc. Pathway enrichment analysis showed differentially expressed genes were predominantly involved with peroxisome, amino acids metabolism, fatty acid degradation, amino/nucleotide sugar metabolism, etc. Metabolite analysis revealed significantly higher amounts of specific isoflavonoid O-glycosides, flavonoid 8-C glycosides, triterpenoid, and iridoid-O-glycosides in the leaves of the 'R' lines (vs. 'S'). These data suggest that a combination of transcriptional regulation and production of putative antiviral metabolites might contribute to BCTV resistance. In addition, genome divergence among BCTV strains differentially affects the production of small non-coding RNAs (sncRNAs) and small peptides which may potentially affect pathogenicity and disease symptom development.