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Characterization of major resistance (R) genes to late blight (LB) –caused by the oomycete Phytophthora infestans– is very important for potato breeding. The objective of this study was to identify novel genes for resistance to LB from cultivated diploid Solanum goniocalyx. Using comparative analysis with a bio-conductor package for differential expression analysis of transcriptomes of two S. goniocalyx accessions with contrasting levels of resistance to LB were analyzed digital gene expression data (edgeR). As a result, various differentially expressed genes (P ≤ 0.0001, Log2FC ≥ 2, FDR < 0.001) were noted. The combination of transcriptomic analysis provided a reasonable number of candidate genes that are overexpressed and under expressed, thereby giving to S. goniocalyx high resistance to LB. The functional analysis of R genes and their corresponding proteins related to disease resistance, NBS-LRR domain proteins and specific disease resistance proteins. Comparative analysis of specific tissue transcriptomes in resistant and susceptible genotypes can be used for identifying rapidly candidate R genes, thus adding novel genes from S. goniocalyx for host plant resistance to P. infestans in potato.

The contamination of water resources by effluents from various industries often contains heavy metals, which cause irreversible damage to the environment and health. The objective was to evaluate different biosorbents from the weed Rumex acetosella to remove metal cations in wastewater. Drying, grinding and sieving of the stems was carried out to obtain the biomass, retaining the fractions of 250 to 500 µm and 500 to 750 µm, which served to obtain the biosorbents in natura (unmodified), acidic, alkaline, and mixed. Proximal analysis, PZC, TOC, removal capacity, influence of pH, functional groups, thermal analysis, structural characteristics, adsorption isotherms, and kinetic study were evaluated. The 250 µm mixed treatment was the one that presented the highest removal percentages, mainly due to the OH, NH, -C-H, COOH, and C-O functional groups achieving the removal of up to 96.14% of lead, 36.30% of zinc, 34.10% of cadmium and 32.50% of arsenic. For contact times of 120 min and an optimum pH of 5.0, a loss of cellulose mass of 59% at 328 °C and a change in the surface of the material were also observed, which allowed for obtaining a topography with greater chelating capacity, and the Langmuir and pseudo-second order models were better fitted to the adsorption data. The new biosorbents could be used in wastewater treatment economically and efficiently.

Sweet cucumber (Solanum muricatum) sect. Basarthrum, is a neglected horticultural crop native of the Andean region. It is naturally distributed very close to potatoes (Solanum sect. Petota) and tomatoes (Solanum sect. Lycopersicon), two groups of high economic importance. To date, molecular tools for this crop are still undetermined. We here obtained the first complete chloroplast (cp) genome of sweet cucumber and compared with seven Solanaceae species. Pair-end clean reads were obtained by PE 150 library and the Illumina HiSeq 2500 platform. The complete cp genome of S. muricatum had a 155,681 bp with typical quadripartite structure, containing a large single copy (LSC) region (86,182 bp) and a small single-copy (SSC) region (18,360 bp), separated by two inverted repeat (IR) regions (25,568 bp). The annotation of chloroplast genome predicted 88 protein-coding genes (CDS), 8 ribosomal RNA (rRNA) genes, 37 transfer RNA (tRNA) genes, and one pseudogene. A total of 48 perfect microsatellites were identified, divided in mononucleotide repeats (32), followed by tetranucleotide (6) and dinucleotides (5). SSRs with trinucleotides repeats (3), pentanucleotide (1) and hexanucleotide (1) repeats motifs in these genomes were identified in lower quantity. Most of these repeats were distributed in the noncoding regions. Whole chloroplast genome comparison with the other seven Solanaceae species revealed that the small and large single copy regions showed more divergence than inverted regions. Finally, phylogenetic analysis resolved that S. muricatum is a sister species to members of sections Petota + Lycopersicum + Etuberosum. This study reports for the first time the genome organization, gene content, and structural features of the cp genome of S. muricatum. Also, this study may provide the basis for evaluating genetic diversity within Solanum, and will be useful to examine the evolutionary processes in sweet cucumber landraces.

Globodera pallida is a white potato cyst nematode present in the Andes, which causes huge losses to Peruvian farmers. An RNA-seq analysis allowed the identification of candidate genes that could mediate resistance against this pathogen. Two varieties, “María Huanca” (Solanum andigena) clone resistant (CIP 279142.12) and “Chimbina Colorada” (Solanum chaucha) (CIP 701013) clone susceptible to G. pallida, were used to identify differentially expressed genes. Total RNA from roots was extracted 72 hours post inoculation with second stage juveniles. Sequencing was done using the Illumina Hiseq 2500 platform. Reads were screened for quality issues and then mapped to the reference potato genome (clone DM1-3516 R44 v4.03). Here, we report 27717 and 27750 genes expressed in the resistant and susceptible variety respectively. The comparative analysis of expression identified 100 candidate genes. 91 genes were associated with resistance to G. pallida with Fold Change ≥ 2 (p

The Andean native potato is an important food security crop and constitutes a gene pool for potato-breeding. To establish the current state of the native potatoes diversity in the influence zone of the Camisea Gas Project, North Ayacucho, Peru, landraces (n = 144) were collected. Three sampling populations (Anco, Chungui and Ticllas) were resolved using 10 simple sequence repeats (SSRs) markers that amplified 67 polymorphic alleles. Principal component, correspondence and cluster analysis revealed a minimum set of six SSRs to achieve DNA fingerprinting and cost-effective genetic diversity analysis. Analysis of molecular variance (AMOVA), average fixation index (FST = 0.279), and genetic distance index (SB) indicated that the genetic diversity of the native potatoes is high at the intra- and inter-population levels, and each of the three sampling populations constituted closed populations. The three populations were genetically distinct and contained unique genotypes and exclusive alleles. Misidentified native potatoes (10.41%) were found.

The genome of potato, a major global food crop, was recently sequenced. The work presented here details the integration of the potato reference genome (DM) with a new sequence-tagged site marker-based linkage map and other physical and genetic maps of potato and the closely related species tomato. Primary anchoring of the DM genome assembly was accomplished by the use of a diploid segregating population, which was genotyped with several types of molecular genetic markers to construct a new similar to 936 cM linkage map comprising 2469 marker loci. In silico anchoring approaches used genetic and physical maps from the diploid potato genotype RH89-039-16 (RH) and tomato. This combined approach has allowed 951 superscaffolds to be ordered into pseudomolecules corresponding to the 12 potato chromosomes. These pseudomolecules represent 674 Mb (similar to 93%) of the 723 Mb genome assembly and 37,482 (similar to 96%) of the 39,031 predicted genes. The superscaffold order and orientation within the pseudomolecules are closely collinear with independently constructed high density linkage maps. Comparisons between marker distribution and physical location reveal regions of greater and lesser recombination, as well as regions exhibiting significant segregation distortion. The work presented here has led to a greatly improved ordering of the potato reference genome superscaffolds into chromosomal pseudomolecules. Potato Genome Sequencing grant, UK; Scottish Government Rural and Environmental Science and Analytical Services Division (RESAS); Department for Environment, Food and Rural Affairs (DEFRA)Department for Environment, Food & Rural Affairs (DEFRA); Agriculture and Horticulture Development Board (AHDB)-Potato Council; Biotechnology and Biological Sciences Research Council (BBSRC)Biotechnology and Biological Sciences Research Council (BBSRC) [BB/F012640]; New Zealand Institute for Crop & Food Research Ltd Strategic Science Initiative; New Zealand Institute for Plant & Food Research Ltd Capability Fund, New Zealand; NMEA (Netherlands Ministry of Economic Affairs); CBSG (Centre for BioSystems Genomics); STW (Netherlands Technology Foundation), The Netherlands [07796]; Teagasc Core Funding; DAFF-Research Stimulus Fund, Ireland; International Potato Center (CIP-CGIAR)/CRP RTB, Peru; CONICYTComision Nacional de Investigacion Cientifica y Tecnologica (CONICYT) [Fondap 1509007, PBCT-PSD-03]; CONICYT (Basal CMM); CIRIC INRIA; INIA-Ministry of Agriculture of Chile, Chile; FEMCIDI OEA [PE/09/02 MINCyT-CONCyTEC]; Instituto Nacional de Tecnologia Agropecuaria (INTA-Core Funds); Ministerio de Ciencia y Tecnologia (MINCyT), Argentina; Proyecto FEMCIDI-OEA [SEDI/AE-305 /09]; Proyecto Bilateral Argentina, Per; FINCyT [099-FINCyT-EQUIP-2009) / (076-FINCyT-PIN-2008)]; Prestamo BID [1663/OC-PE]; Instituto Nacional de Innovacion Agraria, Ministry of Agriculture of Peru; Peruvian Ministry of Agriculture, Technical Secretariat of coordination; CGIAR; Consejo Nacional de Ciencia, Tecnologia e Innovacion Tecnologica, Peru (CONCYTEC); Special Multilateral Fund of the Inter-American Council for Integral Development (FEMCIDI-Peru); Biotechnology and Biological Sciences Research CouncilBiotechnology and Biological Sciences Research Council (BBSRC) [BB/F012640/1] We thank Andrzej Kilian (Diversity Arrays Technology, Australia) for DArT genotyping of the DMDD mapping population. We acknowledge Peter E. Hedley and Clare Booth (The James Hutton Institute, UK) for help with SNP genotyping. We thank S. B. Divito (Instituto Nacional de Tecnologia Agropecuaria, Balcarce, Argentina) for technical assistance. We are also grateful to Luke Ramsay and Peter E. Hedley (The James Hutton Institute, UK) for comments on the manuscript. AFLP and WGP are (registered) trademarks owned by KeyGene N.V. We acknowledge the funding made available by the Potato Genome Sequencing grant, UK [Scottish Government Rural and Environmental Science and Analytical Services Division (RESAS), Department for Environment, Food and Rural Affairs (DEFRA), Agriculture and Horticulture Development Board (AHDB)-Potato Council, Biotechnology and Biological Sciences Research Council (BBSRC, Grant BB/F012640)]; New Zealand Institute for Crop & Food Research Ltd Strategic Science Initiative and the New Zealand Institute for Plant & Food Research Ltd Capability Fund, New Zealand; NMEA (Netherlands Ministry of Economic Affairs), CBSG (Centre for BioSystems Genomics), STW (Netherlands Technology Foundation grant 07796), The Netherlands; Teagasc Core Funding, DAFF-Research Stimulus Fund, Ireland; International Potato Center (CIP-CGIAR)/CRP RTB, Peru; CONICYT (Fondap 1509007, Basal CMM, PBCT-PSD-03), CIRIC INRIA, INIA-Ministry of Agriculture of Chile, Chile; FEMCIDI OEA, PE/09/02 MINCyT-CONCyTEC, 2010-2011, Instituto Nacional de Tecnologia Agropecuaria (INTA-Core Funds) and Ministerio de Ciencia y Tecnologia (MINCyT), Argentina; Proyecto FEMCIDI-OEA SEDI/AE-305 /09 (2008-2012), Proyecto Bilateral Argentina, Per; FINCyT (099-FINCyT-EQUIP-2009) / (076-FINCyT-PIN-2008), Prestamo BID no. 1663/OC-PE, Instituto Nacional de Innovacion Agraria, Ministry of Agriculture of Peru, Peruvian Ministry of Agriculture, Technical Secretariat of coordination with the CGIAR, Consejo Nacional de Ciencia, Tecnologia e Innovacion Tecnologica, Peru (CONCYTEC), Special Multilateral Fund of the Inter-American Council for Integral Development (FEMCIDI-Peru).