Phenotypic and DNA Marker-Assisted Characterization of Russian Potato Cultivars for Resistance to Potato Cyst Nematodes

Potato is one of the most important food crops in the world and also in the Russian Federation. Among harmful organisms reducing potato yield potential, the potato cyst nematodes (PCN) are considered to be ones of the most damaging pests. Information on PCN resistant cultivars is important for potato breeding and production. Russian potato cultivars are characterized in the state-bio-test program for resistance to only one PCN species Globodera rostochiensis and one pathotype Ro1 which is reported to be present in the country. This study aimed to find domestic cultivars with multiple resistances to different PCN species and different pathotypes using phenotyping coupled with molecular marker analysis due to the risk of the occasional introduction of new pests. The phenotypic response was determined by the inoculation of plants with pathotypes Ro5 of G. rostochiensis and Pa3 of G. pallida. The obtained results were supplemented by the state-bio-test data on resistance to Ro1 of G. rostochiensis. Nine of 26 Russian cultivars were resistant both to Ro5 and Ro1 pathotypes and two cultivars possess multiple resistances to both PCN species. Most tested molecular markers associated with the Gpa2, GpaVvrn, GpaVsspl, Grp1 loci showed discrepancies with phenotyping. However, a predictive haplotype and epistatic effect were detected

The In-Silico Development of DNA Markers for Breeding of Spring Barley Varieties That Are Resistant to Spot Blotch in Russia

The fungal pathogen Cochliobolus sativus Drechs. Ex Dastur, anamorph Bipolaris sorokiniana (Sacc.) Shoemaker is one of the most common barley pathogens worldwide and causes spot blotch and root rot in barley. Spot blotch is considered to be the major biotic stress hampering the commercial production of barley. During high disease severity, which occurs in the northwestern region of Russia once every three to four years, yield losses for barley may reach 40%. An increase in common root rot severity results in yield losses that can reach 80%. The goal of the current study was to identify significant markers that can be employed as diagnostic DNA markers to breed C. sativus pathogen-resistant varieties of barley. In 94 spring barley cultivars and lines, the resistance of seedlings and adult plants to the impact of C. sativus on their leaves and roots was investigated. Five genomic regions associated with resistance to Spot blotch were identified (on chromosome 1H (50–61.2 cM), 2H (68.7–69.68 cM), 3H (18.72–26.18 cM), 7H (7.52–15.44 cM)). No significant loci were determined to be associated with root rot. According to obtained data, 11 significant SNPs were converted into KASP markers and 6 markers located on chromosome 3H were determined to possess good accuracy and the potential to be employed in marker-assisted selection

Identification of 50 K Illumina-chip SNPs associated with resistance to spot blotch in barley

Abstract Background Spot blotch, caused by Cochliobolus sativus, is one of the most widespread and harmful diseases in barley. Identification of genetic loci associated with resistance to C. sativus is of importance for future marker-assisted selection. The goal of the current study was to identify loci conferring seedling resistance to two different pathotypes of C. sativus in the Siberian spring barley core collection. Results A total of 96 spring barley cultivars and lines were phenotyped at the seedling stage with two C. sativus isolates (Kr2 and Ch3). According to the Fetch-Steffenson rating scale 16%/17% of genotypes were resistant and 26%/30% were moderate-resistant to the Kr2/Ch3 isolates respectively. A total of 94 genotypes were analyzed with the barley 50 K Illumina Infinium iSELECT assay. From 44,040 SNPs, 40,703 were scorable, from which 39,140 were polymorphic. 27,319 SNPs passed filtering threshold and were used for association mapping. Data analysis by GLM revealed 48 and 41 SNPs for Kr2 and Ch3 isolates, respectively. After application of 5% Bonferroni multiple test correction, only 3 and 27 SNPs were identified, respectively. A total of three genomic regions were associated with the resistance. The region on chromosome 3H associated with Ch3-resistance was expanded between markers SCRI_RS_97417 and JHI-Hv50k-2016-158003 and included 11 SNPs, from which JHI-Hv50k-2016-157070, JHI-Hv50k-2016-156842 had the lowest p-values. These two SNPs were also significant in case of Kr2 isolate. The region on chromosome 2H included 16 loci (7 of them with the lowest p-values were tightly linked to BOPA2_12_11504). Three loci corresponding to this region had suggestive p-values in case of Kr2 tests, so the locus on chromosome 2H may also contribute to resistance to Kr2 isolate. The third region with significant p-value in case of Kr2 tests was identified on chromosome 1H at the locus JHI-Hv50k-2016-33568. Conclusions Three genomic regions associated with the resistance to one or both isolates of C. sativus were identified via screening of the Siberian spring barley core collection. Comparison of their location with QTLs revealed previously either with biparental mapping populations studies or with GWAS of distinct germplasm and other isolates, demonstrated that resistance to isolates Kr2 and Ch3 is conferred by known spot blotch resistance loci. Information on SNPs related can be used further for development of DNA-markers convenient for diagnostics of resistance-associated alleles in barley breeding programs

Evaluation of Responses of Potato Cultivars to Potato Spindle Tuber Viroid and to Mixed Viroid/Viral Infection

Potato spindle tuber viroid (PSTVd) is a harmful quarantine disease with wide geographic distribution. To date, experimentally proved resistance or tolerance of potato cultivars to PSTVd has not been reported. The aim of this study was to evaluate responses to four PSTVd strains of 39 modern potato cultivars of different origin. Four PSTVd strains of different origin, the intermediate VP35, VP87, and two sever strains FP10-13 and NicTr-3, deposited in GenBank, were used. Transcripts of these strains were used to inoculate tomato plants of the cv. Rutgers. Before PSTVd inoculation with tomato sap, all plants were tested for viral infection by ELISA. The presence of PSTVd in infected plants was verified by RT-PCR as well as by RT-qPCR at sixty days post-inoculation (dpi). The strain-specificity in the response of cultivars to viroid infection was revealed. Five cultivars were identified in which, after the first inoculation of plants with all PSTVd strains, normal in shape tubers were formed. All plants of the next generation derived from infected but normally shaped tubers showed strong symptoms of disease. PSTVd and mixed viroid/viral infection (PVY + PSTVd, PVM + PSTVd, and PVY + PVS + PSTVd) led to a significant decrease in the number and weight of tubers in most of the cultivars studied

NLR Genes Related Transcript Sets in Potato Cultivars Bearing Genetic Material of Wild Mexican Solanum Species

The long history of potato breeding includes the numerous introgressions of resistance genes from many wild species of South and Central America as well as from cultivated species into the breeding genepool. Most R genes belong to the NLR family with nucleotide-binding site–leucine-rich repeat. The aim of this research concerns an evaluation of NLR genes expression in transcriptomes of three potato cultivars (Evraziya, Siverskij, Sudarynya), which combine genetic material from wild and cultivated potato species, and each bears intragenic markers of RB/Rpi-blb1/Rpi-sto1 genes conferring broad-range resistance to late blight. The transcriptomes of the cultivars were compared before and 24 h after the Phytophthora infestans inoculation. The induction of RB/Rpi-blb1/Rpi-sto1 transcript after 24 h of inoculation was detected in the resistant cultivars Siverskij and Sudarynya but not in susceptible cv. Evraziya. This demonstrates the importance of transcriptomic assay for understanding the results of marker-assisted selection and phenotyping. Interestingly, assembling the transcriptomes de novo and analysis with NLR-parser tool revealed significant fractions of novel NLR genes with no homology to the reference genome from 103 (cv. Siverskij) to 160 (S. stoloniferum, 30514/15). Comparison of novel NLRs demonstrated a relatively small intersection between the genotypes that coincided with their complex pedigrees with several interspecific hybridization events. These novel NLRs may facilitate the discovery of new efficient R genes

Unlocking new alleles for leaf rust resistance in the Vavilov wheat collection

Thirteen potentially new leaf rust resistance loci were identified in a Vavilov wheat diversity panel. We demonstrated the potential of allele stacking to strengthen resistance against this important pathogen