The Top 10 oomycete pathogens in molecular plant pathology

Oomycetes form a deep lineage of eukaryotic organisms that includes a large number of plant pathogens which threaten natural and managed ecosystems. We undertook a survey to query the community for their ranking of plant-pathogenic oomycete species based on scientific and economic importance. In total, we received 263 votes from 62 scientists in 15 countries for a total of 33 species. The Top 10 species and their ranking are: (1) Phytophthora infestans; (2, tied) Hyaloperonospora arabidopsidis; (2, tied) Phytophthora ramorum; (4) Phytophthora sojae; (5) Phytophthora capsici; (6) Plasmopara viticola; (7) Phytophthora cinnamomi; (8, tied) Phytophthora parasitica; (8, tied) Pythium ultimum; and (10) Albugo candida. This article provides an introduction to these 10 taxa and a snapshot of current research. We hope that the list will serve as a benchmark for future trends in oomycete research.

Conserved RXLR Effector Genes of Phytophthora infestans Expressed at the Early Stage of Potato Infection Are Suppressive to Host Defense

Late blight has been the most devastating potato disease worldwide. The causal agent, Phytophthora infestans, is notorious for its capability to rapidly overcome host resistance. Changes in the expression pattern and the encoded protein sequences of effector genes in the pathogen are responsible for the loss of host resistance. Among numerous effector genes, the class of RXLR effector genes is well-known in mediating host genotype-specific resistance. We therefore performed deep sequencing of five genetically diverse P. infestans strains using in planta materials infected with zoospores (12 h post inoculation) and focused on the identification of RXLR effector genes that are conserved in coding sequences, are highly expressed in early stages of plant infection, and have defense suppression activities. In all, 245 RXLR effector genes were expressed in five transcriptomes, with 108 being co-expressed in all five strains, 47 of them comparatively highly expressed. Taking sequence polymorphism into consideration, 18 candidate core RXLR effectors that were conserved in sequence and with higher in planta expression levels were selected for further study. Agrobacterium tumefaciens-mediated transient expression of the selected effector genes in Nicotiana benthamiana and potato demonstrated their potential virulence function, as shown by suppression of PAMP-triggered immunity (PTI) or/and effector-triggered immunity (ETI). The identified collection of core RXLR effectors will be useful in the search for potential durable late blight resistance genes. Analysis of 10 known Avr RXLR genes revealed that the resistance genes R2, Rpi-blb2, Rpi-vnt1, Rpi-Smira1, and Rpi-Smira2 may be effective in potato cultivars. Analysis of 8 SFI (Suppressor of early Flg22-induced Immune response) RXLR effector genes showed that SFI2, SFI3, and SFI4 were highly expressed in all examined strains, suggesting their potentially important function in early stages of pathogen infection.

Potato late blight field resistance from QTL dPI09c is conferred by the NB-LRR gene R8

Following the often short-lived protection that major nucleotide binding, leucine-rich-repeat (NB-LRR) resistance genes offer against the potato pathogen Phytophthora infestans, field resistance was thought to provide a more durable alternative to prevent late blight disease. We previously identified the QTL dPI09c on potato chromosome 9 as a more durable field resistance source against late blight. Here, the resistance QTL was fine-mapped to a 186 kb region. The interval corresponds to a larger, 389 kb, genomic region in the potato reference genome of Solanum tuberosum Group Phureja doubled monoploid clone DM1-3 (DM) and from which functional NB-LRRs R8, R9a, Rpi-moc1, and Rpi_vnt1 have arisen independently in wild species. dRenSeq analysis of parental clones alongside resistant and susceptible bulks of the segregating population B3C1HP showed full sequence representation of R8. This was independently validated using long-range PCR and screening of a bespoke bacterial artificial chromosome library. The latter enabled a comparative analysis of the sequence variation in this locus in diverse Solanaceae. We reveal for the first time that broad spectrum and durable field resistance against P. infestans is conferred by the NB-LRR gene R8, which is thought to provide narrow spectrum race-specific resistance.

Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen

BACKGROUND

Outbreaks caused by asexual lineages of fungal and oomycete pathogens are a continuing threat to crops, wild animals and natural ecosystems (Fisher MC, Henk DA, Briggs CJ, Brownstein JS, Madoff LC, McCraw SL, Gurr SJ, Nature 484:186-194, 2012; Kupferschmidt K, Science 337:636-638, 2012). However, the mechanisms underlying genome evolution and phenotypic plasticity in asexual eukaryotic microbes remain poorly understood (Seidl MF, Thomma BP, BioEssays 36:335-345, 2014). Ever since the 19th century Irish famine, the oomycete Phytophthora infestans has caused recurrent outbreaks on potato and tomato crops that have been primarily caused by the successive rise and migration of pandemic asexual lineages (Goodwin SB, Cohen BA, Fry WE, Proc Natl Acad Sci USA 91:11591-11595, 1994; Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, Kamoun S, PLoS Pathog 10:e1004028, 2014; Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, et al. eLife 2:e00731, 2013; Cooke DEL, Cano LM, Raffaele S, Bain RA, Cooke LR, Etherington GJ, Deahl KL, Farrer RA, Gilroy EM, Goss EM, et al. PLoS Pathog 8:e1002940, 2012). However, the dynamics of genome evolution within these clonal lineages have not been determined. The objective of this study was to use a comparative genomics and transcriptomics approach to determine the molecular mechanisms that underpin phenotypic variation within a clonal lineage of P. infestans.

RESULTS

Here, we reveal patterns of genomic and gene expression variation within a P. infestans asexual lineage by comparing strains belonging to the South American EC-1 clone that has dominated Andean populations since the 1990s (Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, Kamoun S, PLoS Pathog 10e1004028, 2014; Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, et al. eLife 2:e00731, 2013; Delgado RA, Monteros-Altamirano AR, Li Y, Visser RGF, van der Lee TAJ, Vosman B, Plant Pathol 62:1081-1088, 2013; Forbes GA, Escobar XC, Ayala CC, Revelo J, Ordonez ME, Fry BA, Doucett K, Fry WE, Phytopathology 87:375-380, 1997; Oyarzun PJ, Pozo A, Ordonez ME, Doucett K, Forbes GA, Phytopathology 88:265-271, 1998). We detected numerous examples of structural variation, nucleotide polymorphisms and loss of heterozygosity within the EC-1 clone. Remarkably, 17 genes are not expressed in one of the two EC-1 isolates despite apparent absence of sequence polymorphisms. Among these, silencing of an effector gene was associated with evasion of disease resistance conferred by a potato immune receptor.

CONCLUSIONS

Our findings highlight the molecular changes underpinning the exceptional genetic and phenotypic plasticity associated with host adaptation in a pandemic clonal lineage of a eukaryotic plant pathogen. We observed that the asexual P. infestans lineage EC-1 can exhibit phenotypic plasticity in the absence of apparent genetic mutations resulting in virulence on a potato carrying the Rpi-vnt1.1 gene. Such variant alleles may be epialleles that arose through epigenetic changes in the underlying genes.

Diversity, Pathogenicity, and Current Occurrence of Bacterial Wilt Bacterium Ralstonia solanacearum in Peru

The current bacterial wilt infestation level in the potato fields in the Peruvian Andes was investigated by collecting stem samples from wilted plants and detecting Ralstonia solanacearum. In total 39 farmers' fields located in the central and northern Peru between the altitudes 2111 and 3742 m above sea level were sampled. R. solanacearum was detected in 19 fields, and in 153 out of the 358 samples analyzed. Phylogenetic analysis using the partial sequence of the endoglucanase gene on strains collected in Peru between 1966 and 2016 from potato, pepper, tomato, plantain or soil, divided the strains in phylotypes I, IIA, and IIB. The Phylotype IIB isolates formed seven sequevar groups including the previously identified sequevars 1, 2, 3, 4, and 25. In addition to this, three new sequevars of phylotype IIB were identified. Phylotype IIA isolates from Peru clustered together with reference strains previously assigned to sequevars 5, 39, 41, and 50, and additionally one new sequevar was identified. The Phylotype I strain was similar to the sequevar 18. Most of the Peruvian R. solanacearum isolates were IIB-1 strains. In the old collection sampled between 1966 and 2013, 72% were IIB-1 and in the new collection at 2016 no other strains were found. The pathogenicity of 25 isolates representing the IIA and IIB sequevar groups was tested on potato, tomato, eggplant and tobacco. All were highly aggressive on potato, but differed in pathogenicity on the other hosts, especially on tobacco. All IIA strains caused latent infection on tobacco and some strains also caused wilting, while IIB strains caused only few latent infections on this species. In conclusion, high molecular diversity was found among the R. solanacearum strains in Peru. Most of the variability was found in areas that are no longer used for potato cultivation and thus these strains do not pose a real threat for potato production in the country. Compared to the previous data from the 1990s, the incidence of bacterial wilt has decreased in Peru. The epidemics are likely caused by infected seed tubers carrying the clonal brown rot strain IIB-1.

Conditional QTL underlying resistance to late blight in a diploid potato population

A large number of quantitative trait loci (QTL) for resistance to late blight of potato have been reported with a "conventional" method in which each phenotypic trait reflects the cumulative genetic effects for the duration of the disease process. However, as genes controlling response to disease may have unique contributions with specific temporal features, it is important to consider the phenotype as dynamic. Here, using the net genetic effects evidenced at consecutive time points during disease development, we report the first conditional mapping of QTL underlying late blight resistance in potato under five environments in Peru. Six conditional QTL were mapped, one each on chromosome 2, 7 and 12 and three on chromosome 9. These QTL represent distinct contributions to the phenotypic variation at different stages of disease development. By comparison, when conventional mapping was conducted, only one QTL was detected on chromosome 9. This QTL was the same as one of the conditional QTL. The results imply that conditional QTL reflect genes that function at particular stages during the host-pathogen interaction. The dynamics revealed by conditional QTL mapping could contribute to the understanding of the molecular mechanism of late blight resistance and these QTL could be used to target genes for marker development or manipulation to improve resistance.

Tuber shape and eye depth variation in a diploid family of Andean potatoes

Background

Tuber appearance is highly variable in the Andean cultivated potato germplasm. The diploid backcross mapping population ‘DMDD’ derived from the recently sequenced genome ‘DM’ represents a sample of the allelic variation for tuber shape and eye depth present in the Andean landraces. Here we evaluate the utility of morphological descriptors for tuber shape for identification of genetic loci responsible for the shape and eye depth variation.

Results

Subjective morphological descriptors and objective tuber length and width measurements were used for assessment of variation in tuber shape and eye depth. Phenotypic data obtained from three trials and male–female based genetic maps were used for quantitative trait locus (QTL) identification. Seven morphological tuber shapes were identified within the population. A continuous distribution of phenotypes was found using the ratio of tuber length to tuber width and a QTL was identified in the paternal map on chromosome 10. Using toPt-437059, the marker at the peak of this QTL, the seven tuber shapes were classified into two groups: cylindrical and non-cylindrical. In the first group, shapes classified as ‘compressed’, ‘round’, ‘oblong’, and ‘long-oblong’ mainly carried a marker allele originating from the male parent. The tubers in this group had deeper eyes, for which a strong QTL was found at the same location on chromosome 10 of the paternal map. The non-cylindrical tubers classified as ‘obovoid’, ‘elliptic’, and ‘elongated’ were in the second group, mostly lacking the marker allele originating from the male parent. The main QTL for shape and eye depth were located in the same genomic region as the previously mapped dominant genes for round tuber shape and eye depth. A number of candidate genes underlying the significant QTL markers for tuber shape and eye depth were identified.

Conclusions

Utilization of a molecular marker at the shape and eye depth QTL enabled the reclassification of the variation in general tuber shape to two main groups. Quantitative measurement of the length and width at different parts of the tuber is recommended to accompany the morphological descriptor classification to correctly capture the shape variation.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-015-0213-0) contains supplementary material, which is available to authorized users.

Genetic diversity of arctic bramble (Rubus arcticusL. subsp.arcticus) as measured by amplified fragment length polymorphism

The levels of genotypic and genetic variation were estimated in six natural populations of arctic bramble (Rubus arcticus L. subsp. arcticus) in Finland. Using three primer combinations, a total of 117 amplified fragment length polymorphisms (AFLP) were found. The results were highly reproducible and allowed identification of 78 genets among the 122 plants of arctic bramble studied. Genotypic variation measured as Simpson index (D) was high in all populations, ranging from 0.72 to 0.94. Also, the level of genetic variation measured as Shannon index was relatively high in all populations, ranging from 0.19 to 0.32 (average 0.26). The high levels of genetic diversity indicate that sexual reproduction has played a significant role in these populations. The hierarchical analysis of molecular variance (AMOVA) partitioned 48% of the genetic variation among populations, suggesting a high level of population differentiation and a low level of interpopulation gene flow. Genetic diversity among ten currently grown cultivars of arctic bramble and hybrid arctic bramble (R. arcticus subsp. arcticus × R. arcticus subsp. stellatus) was large, and the subspecies were clearly distinguished from each other based on the AFLP marker data.Key words: AFLP, AMOVA, population, natural habitat, Rubus arcticus subsp. arcticus, Rubus arcticus subsp. stellatus.

Phenotypic stability and genome-wide association study of late blight resistance in potato genotypes adapted to the tropical highlands

Potato genotypes from a breeding population adapted to tropical highlands were analyzed for the stability of late blight resistance and also for marker-phenotype association. We harmonized the historical evaluation data, consisting of observations spanning 6 years from two field sites utilizing a resistance scale constructed by comparing the area under the disease progress curve (AUDPC) values of 172 genotypes with that of susceptible control 'Yungay'. In total, 70 potato genotypes had a coefficient of variability <0.5 and were considered stable across the environments tested. A principal component analysis demonstrated that the ensemble of experiments formed two distinct groups that reflect the stability of genotype resistance to late blight. Phytophthora infestans isolates present in the experimental fields belonged to the EC-1 clonal lineage and showed variation in virulence beyond the concept of the avirulence determined by the conventionally used R1-R11 differential set. A single-nucleotide polymorphism (SNP) marker on chromosome 9 was associated with late blight resistance and linked to instability. Genotypes with either AACC or AAAC combinations for this SNP were highly resistant only in some environments, while the genotypes with the AAAA combination had more moderate levels of resistance but were stable across environments.

Sequencing depth and genotype quality: accuracy and breeding operation considerations for genomic selection applications in autopolyploid crops

KEY MESSAGE

Polypoid crop breeders can balance resources between density and sequencing depth, dosage information and fewer highly informative SNPs recommended, non-additive models and QTL advantages on prediction dependent on trait architecture. The autopolyploid nature of potato and sweetpotato ensures a wide range of meiotic configurations and linkage phases leading to complex gene-action and pose problems in genotype data quality and genomic selection analyses. We used a 315-progeny biparental F1 population of hexaploid sweetpotato and a diversity panel of 380 tetraploid potato, genotyped using different platforms to answer the following questions: (i) do polyploid crop breeders need to invest more for additional sequencing depth? (ii) how many markers are required to make selection decisions? (iii) does considering non-additive genetic effects improve predictive ability (PA)? (iv) does considering dosage or quantitative trait loci (QTL) offer significant improvement to PA? Our results show that only a small number of highly informative single nucleotide polymorphisms (SNPs; ≤ 1000) are adequate for prediction in the type of populations we analyzed. We also show that considering dosage information and models considering only additive effects had the best PA for most traits, while the comparative advantage of considering non-additive genetic effects and including known QTL in the predictive model depended on trait architecture. We conclude that genomic selection can help accelerate the rate of genetic gains in potato and sweetpotato. However, application of genomic selection should be considered as part of optimizing the entire breeding program. Additionally, since the predictions in the current study are based on single populations, further studies on the effects of haplotype structure and inheritance on PA should be studied in actual multi-generation breeding populations.

Comparison of transcript profiles in late blight-challenged Solanum cajamarquense and B3C1 potato clones

Two Solanum genotypes, a wild relative of cultivated potato S. cajamarquense (Cjm) and an advanced tetraploid clone B3C1 (B3), were inoculated with two Phytophthora infestans isolates and leaves were sampled at 72 and 96 h after inoculation. Gene expression in the inoculated versus noninoculated samples was monitored using the Institute of Genomic Research (TIGR) 10K potato array and real-time reverse transcriptase-polymerase chain reaction (RT-PCR). The current experiment is study number 83 of the TIGR expression profiling service project, and all data are publicly available in the Solanaceae Gene Expression Database (SGED) at ftp://ftp.tigr.org/pub/data/s_tuberosum/SGED. Differentially regulated cDNA clones were selected separately for each isolate-time point interaction by significant analysis of microarray (SAM), and differentially regulated clones were classified into functional categories by MapMan. The results show that the genes activated in B3 and Cjm have largely the same biological functions and are commonly activated when plants respond to pathogen attack. The genes activated within biological function categories were considerably different between the genotypes studied, suggesting that the defence pathways activated in B3 and Cjm during the tested conditions may involve unique genes. However, as indicated by real-time RT-PCR, some of the genes thought to be genotype specific may be activated across genotypes at other time points during disease development.

Identification of Natural Resistance Mediated by Recognition of Phytophthora infestans Effector Gene Avr3aEM in Potato

Late blight is considered the most renowned devastating potato disease worldwide. Resistance gene (R)-based resistance to late blight is the most effective method to inhibit infection by the causal agent Phytophthora infestans. However, the limited availability of resistant potato varieties and the rapid loss of R resistance, caused by P. infestans virulence variability, make disease control rely on fungicide application. We employed an Agrobacterium tumefaciens-mediated transient gene expression assay and effector biology approach to understand late blight resistance of Chinese varieties that showed years of promising field performance. We are particularly interested in PiAvr3a^EM , the most common virulent allele of PiAvr3a^KI that triggers a R3a-mediated hypersensitive response (HR) and late blight resistance. Through our significantly improved A. tumefaciens-mediated transient gene expression assay in potato using cultured seedlings, we characterized two dominant potato varieties, Qingshu9 and Longshu7, in China by transient expression of P. infestans effector genes. Transient expression of 10 known avirulence genes showed that PiAvr4 and PiAvr8 (PiAvrsmira2) could induce HR in Qingshu9, and PiAvrvnt1.1 in Longshu7, respectively. Our study also indicated that PiAvr3a^EM is recognized by these two potato varieties, and is likely involved in their significant field performance of late blight resistance. The identification of natural resistance mediated by PiAvr3a^EM recognition in Qingshu9 and Longshu7 will facilitate breeding for improved potato resistance against P. infestans.

Linking the potato genome to the conserved ortholog set (COS) markers

BACKGROUND

Conserved ortholog set (COS) markers are an important functional genomics resource that has greatly improved orthology detection in Asterid species. A comprehensive list of these markers is available at Sol Genomics Network (http://solgenomics.net/) and many of these have been placed on the genetic maps of a number of solanaceous species.

RESULTS

We amplified over 300 COS markers from eight potato accessions involving two diploid landraces of Solanum tuberosum Andigenum group (formerly classified as S. goniocalyx, S. phureja), and a dihaploid clone derived from a modern tetraploid cultivar of S. tuberosum and the wild species S. berthaultii, S. chomatophilum, and S. paucissectum. By BLASTn (Basic Local Alignment Search Tool of the NCBI, National Center for Biotechnology Information) algorithm we mapped the DNA sequences of these markers into the potato genome sequence. Additionally, we mapped a subset of these markers genetically in potato and present a comparison between the physical and genetic locations of these markers in potato and in comparison with the genetic location in tomato. We found that most of the COS markers are single-copy in the reference genome of potato and that the genetic location in tomato and physical location in potato sequence are mostly in agreement. However, we did find some COS markers that are present in multiple copies and those that map in unexpected locations. Sequence comparisons between species show that some of these markers may be paralogs.

CONCLUSIONS

The sequence-based physical map becomes helpful in identification of markers for traits of interest thereby reducing the number of markers to be tested for applications like marker assisted selection, diversity, and phylogenetic studies.

Consumer Preference Testing of Boiled Sweetpotato Using Crowdsourced Citizen Science in Ghana and Uganda

Crowdsourced citizen science is an emerging approach in plant sciences. The triadic comparison of technologies (tricot) approach has been successfully utilized by demand-led breeding programmes to identify varieties for dissemination suited to specific geographic and climatic regions. An important feature of this approach is the independent way in which farmers individually evaluate the varieties on their own farms as “citizen scientists.” In this study, we adapted this approach to evaluate consumer preferences to boiled sweetpotato [Ipomoea batatas (L.) Lam] roots of 21 advanced breeding materials and varieties in Ghana and 6 released varieties in Uganda. We were specifically interested in evaluating if a more independent style of evaluation (home tasting) would produce results comparable to an approach that involves control over preparation (centralized tasting). We compiled data from 1,433 participants who individually contributed to a home tasting (de-centralized) and a centralized tasting trial in Ghana and Uganda, evaluating overall acceptability, and indicating the reasons for their preferences. Geographic factors showed important contribution to define consumers' preference to boiled sweetpotato genotypes. Home and centralized tasting approaches gave similar rankings for overall acceptability, which was strongly correlated to taste. In both Ghana and Uganda, it was possible to robustly identify superior sweetpotato genotypes from consumers' perspectives. Our results indicate that the tricot approach can be successfully applied to consumer preference studies.

Global multi-environment resistance QTL for foliar late blight resistance in tetraploid potato with tropical adaptation

The identification of environmentally stable and globally predictable resistance to potato late blight is challenged by the clonal and polyploid nature of the crop and the rapid evolution of the pathogen. A diversity panel of tetraploid potato germplasm bred for multiple resistance and quality traits was genotyped by genotyping by sequencing (GBS) and evaluated for late blight resistance in three countries where the International Potato Center (CIP) has established breeding work. Health-indexed, in vitro plants of 380 clones and varieties were distributed from CIP headquarters and tuber seed was produced centrally in Peru, China, and Ethiopia. Phenotypes were recorded following field exposure to local isolates of Phytophthora infestans. QTL explaining resistance in four experiments conducted across the three countries were identified in chromosome IX, and environment-specific QTL were found in chromosomes III, V, and X. Different genetic models were evaluated for prediction ability to identify best performing germplasm in each and all environments. The best prediction ability (0.868) was identified with the genomic best linear unbiased predictors (GBLUPs) when using the diploid marker data and QTL-linked markers as fixed effects. Genotypes with high levels of resistance in all environments were identified from the B3, LBHT, and B3-LTVR populations. The results show that many of the advanced clones bred in Peru for high levels of late blight resistance maintain their resistance in Ethiopia and China, suggesting that the centralized selection strategy has been largely successful.

Cytoplasmic Male Sterility Incidence in Potato Breeding Populations with Late Blight Resistance and Identification of Breeding Lines with a Potential Fertility Restorer Mechanism

Cytoplasmic male sterility (CMS) in potato is a common reproductive issue in late blight breeding programs since resistant sources usually have a wild cytoplasmic background (W or D). Nevertheless, in each breeding cycle male fertile lines have been observed within D- and T-type cytoplasms, indicating the presence of a fertility restorer (Rf) mechanism. Identifying sources of Rf and complete male sterility to implement a CMS-Rf system in potato is important since hybrid breeding is a feasible breeding strategy for potato. The objective of this study was to identify male fertile breeding lines and potential Rf candidate lines in the CIP late blight breeding pipeline. We characterized male fertility/sterility-related traits on 142 breeding lines of known cytoplasmic type. We found that pollen viability is not a reliable estimate of male sterility in diverse backgrounds. Breeding lines of the T-type cytoplasmic group had higher levels of male fertility than breeding lines of the D-type cytoplasmic group. With the help of pedigree records, reproductive traits evaluations and test crosses with female clones of diverse background, we identified four male parental lines segregating for Rf and three female parental lines that generated 100% male sterile progeny. These identified lines and generated test cross progenies will be valuable to develop validation populations for mitochondrial or nuclear markers for the CMS trait and for dihaploid generation of Rf+ lines that can be later employed in diploid hybrid breeding.

Expresión de efectores RXLR en el linaje clonal EC-1 de Phytophthora infestans en Perú

La papa (Solanum tuberosum L.) es en nuestros días uno de los cultivos alimenticios más importantes. Esta es propensa a la enfermedad de Tizón Tardío, causada por el oomiceto patógeno Phytophthora infestans, el cual secreta cientos de efectores que actúan como factores de virulencia. Poco se conoce sobre la diversidad de genes de virulencia de las cepas pertenecientes al linaje de reproducción clonal EC-1. En el presente estudio, mediante el secuenciamiento del transcriptoma de la interacción de la papa y P. infestans durante los primeros días después de la infección en las hojas de papa, se identificó la expresión diferencial de genes efectores tipo RXLR en dos cepas de P. infestans EC-1, siendo confirmados por qRT-PCR. Estas cepas, aisladas de papas cultivadas en el centro de los Andes peruanos, tienen diferentes patrones de virulencia. Los genes efectores, fueron silenciados en una cepa, para Avr-vnt1 en POX109 y para el homólogo Avh9.1 en POX067, pero expresados en la otra. Los resultados de transcriptoma fueron comparados con tres cepas adicionales del linaje EC-1. La información del repertorio de los efectores del patógeno y su expresión podrían ser informativos para el mejoramiento genético de la resistencia. El descubrimiento de efectores silenciados en las poblaciones del patógeno pueden guiar al uso de genes R específicos en los programas de mejoramiento genético. Por ejemplo, en el contexto de los Andes, donde el linaje clonal EC-1 predomina, el gen Rpi-vnt1 podría no ser recomendado.

Targeting market segment needs with public-good crop breeding investments: A case study with potato and sweetpotato focused on poverty alleviation, nutrition and gender

Crop breeding programs have often focused on the release of new varieties that target yield improvement to achieve food security and reduce poverty. While continued investments in this objective are justified, there is a need for breeding programs to be increasingly more demand-driven and responsive to the changing customer preferences and population dynamics. This paper analyses the responsiveness of global potato and sweetpotato breeding programs pursued by the International Potato Center (CIP) and its partners to three major development indicators: poverty, malnutrition and gender. The study followed a seed product market segmentation blueprint developed by the Excellence in Breeding platform (EiB) to identify, describe, and estimate the sizes of the market segments at subregional levels. We then estimated the potential poverty and nutrition impacts of investments in the respective market segments. Further, we employed the G+ tools involving multidisciplinary workshops to evaluate the gender-responsiveness of the breeding programs. Our analysis reveals that future investments in breeding programs will achieve greater impacts by developing varieties for market segments and pipelines that have more poor rural people, high stunting rates among children, anemia prevalence among women of reproductive age, and where there is high vitamin A deficiency. In addition, breeding strategies that reduce gender inequality and enhance appropriate change of gender roles (hence gender transformative) are also required.

Potato and sweetpotato breeding at the international potato center: approaches, outcomes and the way forward

Root and tuber crop breeding is at the front and center of CIP's science program, which seeks to develop and disseminate sustainable agri-food technologies, information and practices to serve objectives including poverty alleviation, income generation, food security and the sustainable use of natural resources. CIP was established in 1971 in Peru, which is part of potato's center of origin and diversity, with an initial mandate on potato and expanding to include sweetpotato in 1986. Potato and sweetpotato are among the top 10 most consumed food staples globally and provide some of the most affordable sources of energy and vital nutrients. Sweetpotato plays a key role in securing food for many households in Africa and South Asia, while potato is important worldwide. Both crops grow in a range of conditions with relatively few inputs and simple agronomic techniques. Potato is adapted to the cooler environments, while sweetpotato grows well in hot climates, and hence, the two crops complement each other. Germplasm enhancement (pre-breeding), the development of new varieties and building capacity for breeding and variety testing in changing climates with emphasis on adaptation, resistance, nutritional quality and resource-use efficiency are CIP's central activities with significant benefits to the poor. Investments in potato and sweetpotato breeding and allied disciplines at CIP have resulted in the release of many varieties some of which have had documented impact in the release countries. Partnership with diverse types of organizations has been key to the centers way of working toward improving livelihoods through crop production in the global South.

The phased Solanum okadae genome and Petota pangenome analysis of 23 other potato wild relatives and hybrids

Potato is an important crop in the genus Solanum section Petota. Potatoes are susceptible to multiple abiotic and biotic stresses and have undergone constant improvement through breeding programs worldwide. Introgression of wild relatives from section Petota with potato is used as a strategy to enhance the diversity of potato germplasm. The current dataset contributes a phased genome assembly for diploid S. okadae, and short read sequences and de novo assemblies for the genomes of 16 additional wild diploid species in section Petota that were noted for stress resistance and were of interest to potato breeders. Genome sequence data for three additional genomes representing polyploid hybrids with cultivated potato, and an additional genome from non-tuberizing S. etuberosum, which is outside of section Petota, were also included. High quality short reads assemblies were achieved with genome sizes ranging from 575 to 795 Mbp and annotations were performed utilizing transcriptome sequence data. Genomes were compared for presence/absence of genes and phylogenetic analyses were carried out using plastome and nuclear sequences.

Targeted genotyping-by-sequencing of potato and data analysis with R/polyBreedR

Mid-density targeted genotyping-by-sequencing (GBS) combines trait-specific markers with thousands of genomic markers at an attractive price for linkage mapping and genomic selection. A 2.5K targeted GBS assay for potato (Solanum tuberosum L.) was developed using the DArTag technology and later expanded to 4K targets. Genomic markers were selected from the potato Infinium single nucleotide polymorphism (SNP) array to maximize genome coverage and polymorphism rates. The DArTag and SNP array platforms produced equivalent dendrograms in a test set of 298 tetraploid samples, and 83% of the common markers showed good quantitative agreement, with RMSE (root mean squared error) <0.5. DArTag is suited for genomic selection candidates in the clonal evaluation trial, coupled with imputation to a higher density platform for the training population. Using the software polyBreedR, an R package for the manipulation and analysis of polyploid marker data, the RMSE for imputation by linkage analysis was 0.15 in a small half-diallel population (N = 85), which was significantly lower than the RMSE of 0.42 with the random forest method. Regarding high-value traits, the DArTag markers for resistance to potato virus Y, golden cyst nematode, and potato wart appeared to track their targets successfully, as did multi-allelic markers for maturity and tuber shape. In summary, the potato DArTag assay is a transformative and publicly available technology for potato breeding and genetics.

Tester selection for combining ability estimation of storage root yield and sweetpotato virus disease in sweetpotato breeding

General combining ability (GCA) is the major selection criterion for new sweetpotato (Ipomoea batatas) parents in a reciprocal recurrent selection (RRS) scheme. Here we aimed to estimate GCA and specific combining ability (SCA) by using 16 potential testers involved in an 8 × 8 partial diallel and propose a procedure to identify testers in sweetpotato breeding. Data on storage root yield in tons per hectare (rytha), and sweetpotato virus disease (vir2) from 64 families (1,913 clones) were collected in five trials at two locations in Uganda. The estimates of the female GCA accounted for the largest additive genetic variation for storage root yield compared to the male GCA for both traits. Mid-parent heterosis ranged from - 6.2 to 7% for rytha, and - 1.1 to 1.3% for vir2 in the progeny families. A stepwise procedure to identify testers top-ranked 'NASPOT 7' as a dual tester for both traits. Besides this parent, 'Ejumula' and 'NASPOT 10 O' for rytha, and 'NASPOT 1', 'NK259L', 'SPK004', and 'NASPOT 11' for vir2 are particularly suitable as respective single-trait testers. Testers are important in many plant breeding programs to enhance efficiency of RRS, and thus other crop species might benefit from the strategy and methods applied herein.