Late Blight Resistance Genes Research Articles

Evaluating tomato lines resistance to Late Blight and molecular genetic screening with the use of molecular markers

Relevance. Tomato late blight caused by Phytophthora infestans can cause almost 100% yield loss in open ground in cool and humid conditions. At the same time, the genetic characteristics of P. infestans allow it to overcome the genetic resistance of host plants over time, which requires breeders to look for new genes for resistance to late blight and to obtain new varieties that have several resistance genes at once.Material and methods. 12 tomato lines, or a total of 335 plants, were obtained from the N.N. Timofeev breeding station collection and planted in an artificially infected background. For molecular genetic screening, 12 plants from the Kr6 line were used. The markers linked to the late blight resistance genes Ph-3, R1, and R3a were utilized.Results. On an artificial infectious background, phenotypic evaluation of tomato resistance to late blight showed 1 line of plants free of pathogen damage, 5 lines of plants fully afflicted by late blight, and 6 lines with only partial plant damage. According to molecular genetic investigation the resistant plants were heterozygotes for the Ph-3 gene. Furthermore, the R1 gene was present in most of the plants under study; but, without the Ph-3 gene, this gene did not provide plant resistance against late blight.Conclusions. The results of this research led to the selection of tomato plants for further breeding that were resistant to late blight. It was shown that markers linked to the Ph-3 and R1 genes might be used for marker-mediated selection. Furthermore, it has been established that tomato plants are more effectively protected against P. infestans when several resistance genes are present.

A search for tomato disease resistance genes using molecular markers to create new genotypes

Background. The creation of tomato cultivars and hybrids with a complex of resistance genes is the main task of a breeder. This process can be accelerated through the use of molecular markers at the stages of initial forms selection and the offspring analysis. There is a large amount of information in the literature about DNA markers of resistance genes. Their significant part was recommended for the use in marker-assisted breeding. The purpose of our work was to screen a collection of tomato varieties and hybrids using molecular markers of genes for resistance to the most common diseases of open-ground tomato (late blight, root nematodes, tomato bronzing virus (TSWV)) and to identify gene sources for breeding work. The following markers were selected for research: Sw-5-2 (Sw-5b gene of resistance to TSWV), Mi23 (Mi1.2 gene of resistance to the root-knot nematode), 2 markers NC-LB-9-78 and NC-LB-9-79 (late blight resistance gene Ph-3). During the work, a collection of 46 accessions of tomato cultivars and hybrids was analyzed. Results. The molecular genetic analysis has yielded clear, reproducible fragments that corresponded to the expected ones. All the used markers were codominant. Analysis of the studied collection accessions found the analyzed genes to be polymorphic. The cultivars and hybrids F1 of tomato identified as promising for the use in breeding have resistance to root nematodes (F1 hybrids: A-01, ‘Imitator’, ‘Manon’, cultivars ‘Elegiya’ and ‘Buoy-Tur’), to tomato spotted wilt virus (TSWV) (F1 hybrids: A-01, ‘Manon’ and cultivar ‘Buoy-Tur’), and also to late blight (hybrids F1: А-01, ‘Azhur’, ‘Barin’, ‘Vlastelin stepej’, ‘Zhirdyaj’, Luchshij SeDeK, ‘Manon’ and cultivars: ‘Buoy-Tur’, ‘Zefir v shokolade’, ‘Zolotaya kaplya’, ‘Krasavec’, ‘Lodochka’, ‘Metelitsa’, ‘Alice's Dream’, ‘Sibirskij tigr’, ‘Slavyanskij shedevr’, ‘Elegiya’). It is advisable to use these accessions as sources of resistance genes. Based on the obtained data, five initial forms were selected for breeding and assessed for the intracultivar polymorphism of the studied genes. Cultivars ‘Krasavec’ and ‘Sibirskij tigr’ were used as parent forms. Their hybridization was carried out and hybrid forms homozygous for the dominant allele of the Ph-3 gene were obtained. Conclusions. The use of molecular markers in the conducted study allowed screening the collection of tomato varieties and hybrids for the presence of resistance genes to the most common diseases. Based on the obtained data, parental pairs were selected, hybridization carried out, and hybrid forms with the late blight resistance gene obtained.

Transcriptome, hormonal, and secondary metabolite changes in leaves of DEFENSE NO DEATH 1 (DND1) silenced potato plants

DEFENSE NO DEATH 1 (DND1) is a cyclic nucleotide-gated ion channel protein. Earlier, it was shown that the silencing of DND1 in the potato (Solanum tuberosum L.) leads to resistance to late blight, powdery mildew, and gray mold diseases. At the same time, however, it can reduce plant growth and cause leaf necrosis. To obtain knowledge of the molecular events behind the pleiotropic effect of DND1 downregulation in the potato, metabolite and transcriptome analyses were performed on three DND1 silenced lines of the cultivar ‘Désirée.’ A massive increase in the salicylic acid content of leaves was detected. Concentrations of jasmonic acid and chlorogenic acid and their derivatives were also elevated. Expression of 1866 genes was altered in the same way in all three DND1 silenced lines, including those related to the synthesis of secondary metabolites. The activation of several alleles of leaf rust, late blight, and other disease resistance genes, as well as the induction of pathogenesis-related genes, was detected. WRKY and NAC transcription factor families were upregulated, whereas bHLHs were downregulated, indicating their central role in transcriptome changes. These results suggest that the maintenance of the constitutive defense state leads to the reduced growth of DND1 silenced potato plants.

The use of <i>in vitro</i> androgenesis for the involvement of interspecific hybrids between <i>Solanum tuberosum</i> L. and wild allotetraploid potato species <i>Solanum stoloniferum</i> Schltdl. et Bouché into breeding

Wild allotetraploid potato species Solanum stoloniferum Schltdl. & Bouché from Mexico is regarded as a valuable source of resistance genes for use in breeding. However, introgression of its resistance genes into breeding material is hampered by a set of reproductive barriers. The genomic difference between S. stoloniferum (genome ААВВ) and S. tuberosum L. (AAAA) is one of them. This makes questionable the possibility of transferring a variety of valuable genes of the wild species localized on the chromosomes of its genome B into the genome of cultivated potatoes. It is proposed to produce tetraploid (4x, AAAB) interspecific hybrids of S. stoloniferum, which are regarded as more promising for homoeological recombination than pentaploid (5x, ААААВ) hybrids commonly used in the introgression schemes. However, the effective ploidy of tetraploid hybrids (3EBN) hinders their backcrossing to cultivated potatoes (4 EBN). For instance, our attempts to involve the tetraploid hybrid of S. stoloniferum IGC16/36.1 obtained by us into hybridization with potato varieties were unsuccessful for a number of years. To solve this problem, we suggested a technique based on the production of 4x plants obtained in anther culture of this hybrid. The present research was aimed at assessing the efficiency of this approach.Thirty-one plants were obtained in anther culture (androgenic clones, androclones) of the hybrid IGC16/36.1 in 2018. Most of them exceeded the initial hybrid in habitus strength and flowering intensity. As a result of crosses made in 2019, 1039 hybrid seeds were obtained from crossing 21 androclones with the ‘Lemhi Russet’ variety (8.7 seeds/pollination), 1017 seeds (7.5 seeds/pollination) from crosses of 23 androclones with the ‘Quarta’ variety, and 716 seeds (12.3 seeds/pollination) from crosses of 11 androclones and a diploid potato line IGC 17n8 capable of producing fertile unreduced (2n) pollen. The hybrid seeds had good germination rate of 70-90%. Among the androclones that gave progeny in crosses with potato varieties, we identified genotypes carrying DNA markers of late blight (LB) resistance genes Rpi-sto1, R2 and R3b, PVY resistance genes Ryadg, Rysto and Rychc, and potato wart disease resistance gene Sen2 (these markers were found in the initial accession of S. stoloniferum PI 205522 and in the IGC 16/36.1 hybrid). Despite the complex nature of inheritance of the analyzed markers in progenies of backcrosses of androclones, a number of isolated hybrids carried several markers, including those of the Rpi-sto1, a broad-spectrum gene for high resistance to late blight. Hybrids with relatively high tuber productivity, features of cultivated potatoes such as regularly shaped tubers with small eyes, and high field resistance to late blight were selected.The prospects for using androclones of the tetraploid interspecific hybrid IGC 16/36.1 for increasing the frequency of homoeologous A/B recombination of chromosomes are discussed.

Оценка устойчивости перспективных гибридов цветного картофеля к фитофторозу

Abstract. Potatoes with pigmented tubers contain anthocyanins and other phenolic compounds that demonstrate antioxidant activity and have a beneficial effect on human health. The nutritional value and other consumer qualities of available potato varieties must be combined with resistance to various infections, primarily late blight, which leads to significant yield losses and considerable costs for chemical protection. The purpose of this work was to assess late blight resistance of 46 promising potato hybrids with different pigmentation patterns, both in the field and by laboratory methods, including molecular screening. The objectives of this study included obtaining promising hybrids of colored potatoes characterized by a set of economically importatnt traits, laboratory and field assessment of the resistance of leaves and tubers to the late blight pathogen Phytophthora infestans, as well as molecular screening of late blight resistance gene markers (Rpi genes). The production, cultivation and evaluation of the hybrid material was carried out using standard methods. Field and laboratory resistance of leaves and tubers was assessed on a 9-point scale. Molecular screening was carried out using PCR analysis. The scientific novelty of the work lies in the fact that for the first time a comprehensive assessment of the resistance to late blight of hybrid material of colored potatoes obtained on the territory of Russian Federation was carried out. According to the results obtained, the studied samples demonstrated a high level of resistance of tubers and leaves in field conditions and laboratory tests. However, the results of the study did not reveal a relationship between laboratory or field resistance and the presence of Rpi gene markers, which may be due to the influence of many independent factors that determine horizontal resistance.

Peculiarities of Transfer of DNA Markers of Wild Allotetraploid Potato Species <i>Solanum stoloniferum</i> to Backcross Progenies Depending on Their Subgenomic Location and Used Schemes of Introgression

Genomic difference between wild allotetraploid potato species Solanum stoloniferum Schltdl et Bouchet (genome AABB) and S. tuberosum L. (AAAA) is one of the factors hampering its use in breeding. However, there is practically no information on valuable genes of this species located in the subgenome B and on the way of their transfer into the genome A of cultivated potatoes. The objectives of this research were to identify subgenomic location of a set of S. stoloniferum genes using an original approach based on a difference of inheritance of DNA markers of the genes in backcross BC1 of chromosome doubled triploid hybrids (6x, AAAABB) to 4х S. tuberosum dependent on belonging to A or B subgenome; to study their inheritance in BC2 and BC3 in the framework of four introgression schemes and marker assisted selection of the gene Rpi-sto1. The markers of late blight (LB) resistance genes Rpi-sto1, R3b, R2, potato virus Y (PVY) resistance genes Rysto, Ryadg were located on the subgenome B and the marker of PVY resistance gene Rychc – on the subgenome A. We observed an appearance of unexpected sporadic hybrids free of markers in BC1 that may be explained by rare cases of homeological recombination of A and B subgenome chromosomes. The segregation of the markers in BC2 (close to 1 : 1) matched in general to that expected in the case of random transfer of the corresponding chromosomes of the subgenome B. Some promising for breeding hybrids have been selected in BC3 having the marker of the gene Rpi-sto1.

Status and way-forward in breeding potato (Solanum tuberosum) for resistance to late blight

Improving host resistance to late blight (Phytophthora infestans) has been a major concern of potato breeders since the Irish famine of 1840s. Since then, a number of late blight resistant potato (Solanum tuberosum L.) cultivars have been developed using both conventional and molecular techniques. However, resistance to late blight did not last long and broke down due to the emergence of more virulent races of Phytophthora infestans. This perspective paper presents the status of sources of resistance to late blight, defence mechanism of host against the pathogen and late blight resistance genes mapped, cloned, and transferred to cultivated potato. Considerable progress has been made in all aspects of breeding potato for resistance to late blight. However, a critical appraisal of the status of potato breeding for resistance to late blight suggests the continued need to identify new sources of resistance, transfer of resistance genes from diverse sources and stacking them in maximum number into individual plants. Other breeding strategies to combat this dreaded disease are also discussed.

Diversity of Late Blight Resistance Genes in the VIR Potato Collection

Late blight (LB) caused by the oomycete Phytophthora infestans (Mont.) de Bary is the greatest threat to potato production worldwide. Current potato breeding for LB resistance heavily depends on the introduction of new genes for resistance to P. infestans (Rpi genes). Such genes have been discovered in highly diverse wild, primitive, and cultivated species of tuber-bearing potatoes (Solanum L. section Petota Dumort.) and introgressed into the elite potato cultivars by hybridization and transgenic complementation. Unfortunately, even the most resistant potato varieties have been overcome by LB due to the arrival of new pathogen strains and their rapid evolution. Therefore, novel sources for germplasm enhancement comprising the broad-spectrum Rpi genes are in high demand with breeders who aim to provide durable LB resistance. The Genbank of the N.I. Vavilov Institute of Plant Genetic Resources (VIR) in St. Petersburg harbors one of the world's largest collections of potato and potato relatives. In this study, LB resistance was evaluated in a core selection representing 20 species of seven Petota series according to the Hawkes (1990) classification: Bulbocastana (Rydb.) Hawkes, Demissa Buk., Longipedicellata Buk., Maglia Bitt., Pinnatisecta (Rydb.) Hawkes, Tuberosa (Rydb.) Hawkes (wild and cultivated species), and Yungasensa Corr. LB resistance was assessed in 96 accessions representing 18 species in the laboratory test with detached leaves using a highly virulent and aggressive isolate of P. infestans. The Petota species notably differed in their LB resistance: S. bulbocastanum Dun., S. demissum Lindl., S. cardiophyllum Lindl., and S. berthaultii Hawkes stood out at a high frequency of resistant accessions (7-9 points on a 9-point scale). Well-established specific SCAR markers of ten Rpi genes-Rpi-R1, Rpi-R2/Rpi-blb3, Rpi-R3a, Rpi-R3b, Rpi-R8, Rpi-blb1/Rpi-sto1, Rpi-blb2, and Rpi-vnt1-were used to mine 117 accessions representing 20 species from seven Petota series. In particular, our evidence confirmed the diverse Rpi gene location in two American continents. The structural homologs of the Rpi-R2, Rpi-R3a, Rpi-R3b, and Rpi-R8 genes were found in the North American species other than S. demissum, the species that was the original source of these genes for early potato breeding, and in some cases, in the South American Tuberosa species. The Rpi-blb1/Rpi-sto1 orthologs from S. bulbocastanum and S. stoloniferum Schlechtd et Bché were restricted to genome B in the Mesoamerican series Bulbocastana, Pinnatisecta, and Longipedicellata. The structural homologs of the Rpi-vnt1 gene that were initially identified in the South American species S. venturii Hawkes and Hjert. were reported, for the first time, in the North American series of Petota species.

Resistance Evaluation for Native Potato Accessions against Late Blight Disease and Potato Cyst Nematodes by Molecular Markers and Phenotypic Screening in India.

The potato originated in southern Peru and north-western Bolivia (South America). However, native accessions have also been cultivated in India for many years. Late blight, caused by the fungus Phytophthora infestans, is the most devastating potato disease, while potato cyst nematode (Globodera spp.) (PCN) is another economically significant quarantine-requiring pest in India. In this study, we have generated a new Indian native collection of 94 potato accessions collected from different parts India. These accessions were screened against late blight and potato cyst nematode resistance by using gene-based molecular markers and phenotypic screening methods. Marker assisted selection using R1 gene-specific marker CosA210 revealed a late blight resistance gene in 11 accessions. PCN resistance bands were found in 3 accessions with marker TG689141, 5 accessions with marker 57R452, and 1 accession having Gro1-4-1602 marker for G. rostochiensis (Ro1,4), while 64 accessions amplified marker HC276 indicating G. pallida (Pa2,3) resistance gene (GpaVvrn QTL). On the other hand, phenotypic screening against late blight resistance under natural epiphytic conditions (hot-spot) revealed three accessions with high resistance, while others were resistant (1 accession), moderately resistant (5 accessions), susceptible (29 accessions), and highly susceptible (56 accessions). For G. rostochiensis (golden cyst nematode) and G. pallida (white cyst nematode) resistance, accessions were grouped into highly resistant (3, 3), resistant (0, 2), moderately resistant (6, 29), susceptible (32, 30), and highly susceptible (53, 30), respectively, for the two PCN species. Collectively, we identified promising accessions with high resistance to late blight (JG-1, Kanpuria Safed, and Rangpuria), and also highly resistant to both Globodera species (Garlentic, Jeevan Jyoti, and JG-1). Our findings suggested that these accessions would be useful for late blight and PCN resistance breeding, as well as future molecular studies in potatoes.

Homologs of Late Blight Resistance Genes in Representatives of Tuber-Bearing Species of the Genus Solanum L.

Homologs of Late Blight Resistance Genes in Representatives of Tuber-Bearing Species of the Genus Solanum L.

A potato late blight resistance gene protects against multiple Phytophthora species by recognizing a broadly conserved RXLR-WY effector

Species of the genus Phytophthora, the plant killer, cause disease and reduce yields in many crop plants. Although many Resistance to Phytophthora infestans (Rpi) genes effective against potato late blight have been cloned, few have been cloned against other Phytophthora species. Most Rpi genes encode nucleotide-binding domain, leucine-rich repeat-containing (NLR) immune receptor proteinsthat recognize RXLR (Arg-X-Leu-Arg) effectors. However, whether NLR proteins can recognize RXLR effectors from multiple Phytophthora species has rarely been investigated. Here, we identified a new RXLR-WY effector AVRamr3 from P. infestans that is recognized by Rpi-amr3 from a wild Solanaceae species Solanum americanum. Rpi-amr3 associates with AVRamr3 in planta. AVRamr3 is broadly conserved in many different Phytophthora species, and the recognition of AVRamr3 homologs by Rpi-amr3 activates resistance against multiple Phytophthora pathogens, including the tobacco black shank disease and cacao black pod disease pathogens P. parasitica and P. palmivora. Rpi-amr3 is thus the first characterized resistance gene that acts against P. parasitica or P. palmivora. These findings suggest a novel path to redeploy known R genes against different important plant pathogens.

Markers of genes for resistance to late blight, potato virus <i>Y</i> and potato cyst nematode identified in advanced interspecific potato hybrids

Background. The harmful organisms affecting potato cause great economic damage in all areas where the crop is grown. One of the most economically important pathogens is the potato late blight (agent Phytophthora infestans Mont. (de Bary)). Also, Potato Virus Y (PVY) and potato cyst nematode (PCN) of the Ro1 pathotype, the only one that occurs in the Russian Federation, cause significant yield losses. Materials and methods. Phytopathological and molecular screening was carried out on original interspecific potato hybrids obtained in 11 crossing combinations, seven of which were studied for the first time. Hybrids resulted from crosses that involved Mexican and South American potato species as sources of late blight and PVY resistance. Field observations of late blight resistance were conducted during three seasons under high infection pressure. A part of plant material was screened in laboratory tests. PCR tests employed 9 DNA markers of genes associated with resistance to Ph. infestans, PVY and PCN of Ro1 pathotype used in our previous study. Results. In field evaluation, hybrid clones mostly expressed high, and a part of them moderate late blight resistance. Of the 6 markers of the used Rpi genes, at least two were detected in most clones, while some had 3 or 4 markers. Some clones were found to have markers of PCN resistance genes and of several genes for resistance to PVY. The cytoplasm type was determined for all plant material. Conclutions. Within a small but pedigree-diverse set of interspeсific hybrids, the markers of resistance genes to all three pests were found. A part of clones obtained by using the sources of PVY and late blight resistance which we had identified, were found to contain two or more resistance genes to these pathogens. According to the results of molecular tests, the clones were found to carry several markers of late blight and PVY resistance genes. Original interspecific potato hybrids with determined late blight resistance levels, cytoplasm type and availability of markers of genes for resistance to three pests can be used in further hybridization.

Two Tomato (Solanum lycopersicum) Thaumatin-Like Protein Genes Confer Enhanced Resistance to Late Blight (Phytophthora infestans)

Late blight (caused by Phytophthora infestans) poses a serious threat to tomato production, but the number of late blight resistance genes isolated from tomato is limited, making resistance gene mining a high research priority. In this study, highly resistant CLN2037E and susceptible No.5 tomato inbred lines were used to identify late blight resistance genes. Using transcriptome sequencing, we discovered 36 differentially expressed genes (DEGs), including 21 nucleotide binding site-leucine-rich repeat (NBS-LRR) and 15 pathogenesis-related (PR) disease resistance genes. Cluster analysis and real-time quantitative PCR (RT-qPCR) showed that these 36 genes possessed similar expression patterns in different inbred lines after inoculation with P. infestans. Moreover, two PR genes with unique responses were chosen to verify their functions when exposed to P. infestans: Solyc08g080660 and Solyc08g080670, both of which were thaumatin-like protein (TLP) genes and were clustered in the tomato genome. Functions of these two genes were identified by gene overexpression and gene editing technology. Overexpression and knockout of single Solyc08g080660 and Solyc08g080670 corresponded to an increase and decrease in resistance to late blight, respectively, and Solyc08g080660 led to a greater change in disease resistance compared with Solyc08g080670. Co-transformation of dual genes resulted in a much greater effect than any single gene. This study provides novel candidate resistance genes for tomato breeding against late blight and insights into the interaction mechanisms between tomato and P. infestans.

Comparative transcriptome analysis of R3a and Avr3a-mediated defense responses in transgenic tomato.

Late blight caused by Phytophthora infestans is one of the most devastating diseases in potatoes and tomatoes. At present, several late blight resistance genes have been mapped and cloned. To better understand the transcriptome changes during the incompatible interaction process between R3a and Avr3a, in this study, after spraying DEX, the leaves of MM-R3a-Avr3a and MM-Avr3a transgenic plants at different time points were used for comparative transcriptome analysis. A total of 7,324 repeated DEGs were detected in MM-R3a-Avr3a plants at 2-h and 6-h, and 729 genes were differentially expressed at 6-h compared with 2-h. Only 1,319 repeated DEGs were found in MM-Avr3a at 2-h and 6-h, of which 330 genes have the same expression pattern. Based on GO, KEGG and WCGNA analysis of DEGs, the phenylpropanoid biosynthesis, plant-pathogen interaction, and plant hormone signal transduction pathways were significantly up-regulated. Parts of the down-regulated DEGs were enriched in carbon metabolism and the photosynthesis process. Among these DEGs, most of the transcription factors, such as WRKY, MYB, and NAC, related to disease resistance or endogenous hormones SA and ET pathways, as well as PR, CML, SGT1 gene were also significantly induced. Our results provide transcriptome-wide insights into R3a and Avr3a-mediated incompatibility interaction.

Insertion of Badnaviral DNA in the Late Blight Resistance Gene (R1a) of Brinjal Eggplant (Solanum melongena)

Endogenous viral elements (EVEs) are widespread in plant genomes. They result from the random integration of viral sequences into host plant genomes by horizontal DNA transfer and have the potential to alter host gene expression. We performed a large-scale search for co-transcripts including caulimovirid and plant sequences in 1,678 plant and 230 algal species and characterized 50 co-transcripts in 45 distinct plant species belonging to lycophytes, ferns, gymnosperms and angiosperms. We found that insertion of badnavirus EVEs along with Ty-1 copia mobile elements occurred into a late blight resistance gene (R1) of brinjal eggplant (Solanum melongena) and wild relatives in genus Solanum and disrupted R1 orthologs. EVEs of two previously unreported badnaviruses were identified in the genome of S. melongena, whereas EVEs from an additional novel badnavirus were identified in the genome of S. aethiopicum, the cultivated scarlet eggplant. Insertion of these viruses in the ancestral lineages of the direct wild relatives of the eggplant would have occurred during the last 3 Myr, further supporting the distinctiveness of the group of the eggplant within the giant genus Solanum.

Characterization of a Late Blight Resistance Gene Homologous to R2 in Potato Variety Payette Russet

Breeding for late blight resistance has traditionally relied on phenotypic selection, but as the number of characterized resistance (R) genes has grown, so have the possibilities for genotypic selection. One challenge for breeding russet varieties is the lack of information about the genetic basis of resistance in this germplasm group. Based on observations of strong resistance by ‘Payette Russet’ to genotype US-23 of the late blight pathogen Phytophthora infestans in inoculated experiments, we deduced the variety must contain at least one major R gene. To identify the gene(s), 79 F1 progeny were screened using a detached leaf assay and classified resistant vs. susceptible. Linkage mapping using markers from the potato SNP array revealed a single resistant haplotype on the short arm of chromosome group 4, which coincides with the R2/Rpi-abpt/Rpi-blb3 locus. PCR amplification and sequencing of the gene in Payette revealed it is homologous to R2, and transient expression experiments in Nicotiana benthamiana confirmed its recognition of the Avr2 effector. Sequencing of a small diversity panel revealed a SNP unique to resistant haplotypes at the R2 locus, which was converted to a KASP marker that showed perfect prediction accuracy in the F1 population and diversity panel. Although many genotypes of P. infestans are virulent against R2, even when defeated this gene may be valuable as one component of a multi-genic approach to quantitative resistance.

Genome sequence analysis provides insights on genomic variation and late blight resistance genes in potato somatic hybrid (parents and progeny).

Wild Solanum species are the important resources for potato improvement. With the availability of potato genome and sequencing progress, knowledge about genomic resources is essential for novel genes discovery. Hence, the aim of this study was to decipher draft genome sequences of unique potato genotypes i.e. somatic hybrid P8 (J1), wild species S. pinnatisectum (J2), progeny MSH/14-112 (P8 × cv. Kufri Jyoti) (J3), and S. tuberosum dihaploid C-13 (J4). Draft genome sequencing using Illumina platform and reference-based assemblies with the potato genome yielded genome assembly size of 725.01Mb (J1), 724.95Mb (J2), 725.01Mb (J3), and 809.59Mb (J4). Further, 39,260 (J1), 25,711 (J2), 39,730 (J3) and 30,241 (J4) genes were identified and 17,411 genes were found common in the genotypes particularly late blight resistance genes (R3a, RGA2, RGA3, R1B-16, Rpi-blb2, Rpi and Rpi-vnt1). Gene ontology (GO) analysis showed that molecular function was predominant and signal transduction was major KEGG pathways. Further, gene enrichment analysis revealed dominance of metabolic process (GO: 0008152) in all the samples. Phylogeny analysis showed relatedness with potato and other plant species. Heterozygous single nucleotide polymorphism (SNP) was more than homozygous, and SNP in genic region was more than inter-genic region. Copy number variation (CNV) analysis indicated greater number of deletions than duplications. Sequence diversity and conserved motifs analysis revealed variation for late blight resistance genes. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed differential expression of late blight resistance genes. Our study provides insights on genome sequence, structural variation and late blight resistance genes in potato somatic hybrid (parents and progeny) for future research.

Genome-wide association analysis for late blight resistance of potato resources

<p indent=0mm>The mining of broad-spectrum resistance genes is the basis of the breeding of potato varieties with high late blight resistance. In this study, 288 samples of late disease resistance selected by the International Potato Center (CIP) for years were planted and were investigated for two consecutive years, which could provide some theoretical and material basis for breeding of late blight resistant varieties and help to study on disease resistance mechanism. The late blight resistance of each sample was evaluated using AUDPC and sAUDPC values. The population simplified genome sequencing was performed by SLAF-seq and carried out by genome-wide association analysis in order to discover the genetic loci and candidate genes related to late blight resistance. There were wide genetic differences in resistance to late blight among 288 samples. Through genome-wide association analysis, based on five analytical models, a total of 82 loci significantly correlated with late blight resistance were identified. Combined with genomic annotation, there were 54 candidate genes known or likely to be associated with late blight resistance in the association interval. Among them, 23 genes were resistant genes, including late blight resistance gene <italic>R1</italic> homolog, <italic>Sw-5</italic> homolog (<italic>R8</italic>) and <italic>Rpi-vnt1</italic>, as well as gene encoding pleiotropic resistance protein. Five genes encoded MAPK protein and WRKY transcription factor; one gene was involved in the JA pathway; three genes were associated with salicylic acid pathway; six genes were related to the course of the disease; three genes were involved in the synthesis of phenylpropionic acid. Other genes related to resistance to late blight included HMGR gene (2) and cytochrome P450 (21).

Marker-assisted pyramiding of potato late blight resistance genes Rpi-rzc1 and Rpi-phu1 on di- and tetraploid levels

Late blight is a disease with the biggest economic impact on potato cultivation worldwide. Pyramiding of the resistance genes originating from potato wild relatives is a breeding strategy that has a potential to produce potato cultivars durably resistant to late blight. Growing such cultivars would allow limiting the intensive chemical control of the disease. The goal of this work was to transfer the late blight resistance gene Rpi-rzc1 from Solanum ruiz-ceballosii to the tetraploid level of cultivated potato and to pyramid it with the Rpi-phu1 gene. We obtained two diploid and, through 4x-2x cross, a tetraploid potato population segregating for the Rpi-rzc1 presence, as well as one diploid and one tetraploid population where both genes were introgressed. In total, 754 progeny clones were tested for resistance to late blight in detached leaflet assays. Pathogen isolates avirulent on plants with both genes and virulent on plants with the Rpi-phu1 were used. The selection was assisted by two PCR markers flanking the Rpi-rzc1 gene and a newly designed, highly specific intragenic marker indicating the Rpi-phu1 gene presence. We obtained 26 diploid and 49 tetraploid potato clones with pyramid of both genes that should enhance the durability and spectrum of their late blight resistance and that can be exploited in potato breeding. The specificity of the marker for the Rpi-phu1 gene and the precision of the Rpi-rzc1 mapping were improved in this work.

Detection of Novel QTLs for Late Blight Resistance Derived from the Wild Potato Species Solanum microdontum and Solanum pampasense.

Wild potato species continue to be a rich source of genes for resistance to late blight in potato breeding. Whilst many dominant resistance genes from such sources have been characterised and used in breeding, quantitative resistance also offers potential for breeding when the loci underlying the resistance can be identified and tagged using molecular markers. In this study, F1 populations were created from crosses between blight susceptible parents and lines exhibiting strong partial resistance to late blight derived from the South American wild species Solanum microdontum and Solanum pampasense. Both populations exhibited continuous variation for resistance to late blight over multiple field-testing seasons. High density genetic maps were created using single nucleotide polymorphism (SNP) markers, enabling mapping of quantitative trait loci (QTLs) for late blight resistance that were consistently expressed over multiple years in both populations. In the population created with the S. microdontum source, QTLs for resistance consistently expressed over three years and explaining a large portion (21–47%) of the phenotypic variation were found on chromosomes 5 and 6, and a further resistance QTL on chromosome 10, apparently related to foliar development, was discovered in 2016 only. In the population created with the S. pampasense source, QTLs for resistance were found in over two years on chromosomes 11 and 12. For all loci detected consistently across years, the QTLs span known R gene clusters and so they likely represent novel late blight resistance genes. Simple genetic models following the effect of the presence or absence of SNPs associated with consistently effective loci in both populations demonstrated that marker assisted selection (MAS) strategies to introgress and pyramid these loci have potential in resistance breeding strategies.