Genomic prediction of starch content and chipping quality in tetraploid potato using genotyping-by-sequencing

peer-reviewedGenomic prediction models for starch content and chipping quality show promising results, suggesting that genomic selection is a feasible breeding strategy in tetraploid potato. Genomic selection uses genome-wide molecular markers to predict performance of individuals and allows selections in the absence of direct phenotyping. It is regarded as a useful tool to accelerate genetic gain in breeding programs, and is becoming increasingly viable for crops as genotyping costs continue to fall. In this study, we have generated genomic prediction models for starch content and chipping quality in tetraploid potato to facilitate varietal development. Chipping quality was evaluated as the colour of a potato chip after frying following cold induced sweetening. We used genotyping-by-sequencing to genotype 762 offspring, derived from a population generated from biparental crosses of 18 tetraploid parents. Additionally, 74 breeding clones were genotyped, representing a test panel for model validation. We generated genomic prediction models from 171,859 single-nucleotide polymorphisms to calculate genomic estimated breeding values. Cross-validated prediction correlations of 0.56 and 0.73 were obtained within the training population for starch content and chipping quality, respectively, while correlations were lower when predicting performance in the test panel, at 0.30-0.31 and 0.42-0.43, respectively. Predictions in the test panel were slightly improved when including representatives from the test panel in the training population but worsened when preceded by marker selection. Our results suggest that genomic prediction is feasible, however, the extremely high allelic diversity of tetraploid potato necessitates large training populations to efficiently capture the genetic diversity of elite potato germplasm and enable accurate prediction across the entire spectrum of elite potatoes. Nonetheless, our results demonstrate that GS is a promising breeding strategy for tetraploid potato.The Danish Council of Strategic Researc

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

peer-reviewedWild 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.Department of Agriculture, Food and the Marine, Irelan

Revealing the importance of meristems and roots for the development of hypersensitive responses and full foliar resistance to Phytophthora infestans in the resistant potato cultivar Sarpo Mira

The defence responses of potato against Phytophthora infestans were studied using the highly resistant Sarpo Mira cultivar. The effects of plant integrity, meristems, and roots on the hypersensitive response (HR), plant resistance, and the regulation of PR genes were analysed. Sarpo Mira shoots and roots grafted with the susceptible Bintje cultivar as well as non-grafted different parts of Sarpo Mira plants were inoculated with P. infestans. The progress of the infection and the number of HR lesions were monitored, and the regulation of PR genes was compared in detached and attached leaves. Additionally, the antimicrobial activity of plant extracts was assessed. The presented data show that roots are needed to achieve full pathogen resistance, that the removal of meristems in detached leaves inhibits the formation of HR lesions, that PR genes are differentially regulated in detached leaves compared with leaves of whole plants, and that antimicrobial compounds accumulate in leaves and roots of Sarpo Mira plants challenged with P. infestans. While meristems are necessary for the formation of HR lesions, the roots of Sarpo Mira plants participate in the production of defence-associated compounds that increase systemic resistance. Based on the literature and on the presented results, a model is proposed for mechanisms involved in Sarpo Mira resistance that may apply to other resistant potato cultivars.This work was funded by the Danish Agency for Science Technology and Innovation grant (no. 09-062975). Additional support was received from Coimbra Group and Wood-Whelan research fellowships (IUBMB).Peer reviewe

Gas-exchange, water use efficiency and yield responses of elite potato <i>(Solanum tuberosum</i> L.) cultivars to changes in atmospheric carbon dioxide concentration, temperature and relative humidity

AbstractIn spite of the agricultural importance of potato (Solanum tuberosum L.), most plant physiology studies have not accounted for the effect of the interaction between elevated carbon dioxide concentration ([CO2]) and other consequences of climate change on WUE. In 2010, a first controlled environment chamber experiment (E1) was performed with two treatments: one control at a [CO2] exposure level of 380ppm and the other at elevated [CO2] first to 700ppm and subsequently to 1000ppm. Plants grown at elevated [CO2] levels of 700 and 1000ppm showed a consistent significant increase in leaf level photosynthetic water use efficiency (pWUE) by stimulation in net photosynthesis rate (62% and 43% increase of An) with coincident decline in both stomatal conductance (21% and 43% decrease of gs) and leaf transpiration rate (19% and 40% decrease of E) resulting in pWUE increments of 89% and 147%. Furthermore, the ratio of leaf intercellular [CO2] to ambient air [CO2] (ci/ca) remained unchanged among treatments. In 2011, a second experiment was performed (E2), where two treatments comprised [CO2] levels of 380ppm (control) and elevated of 1000ppm. The plants were subjected to three temperature levels (14, 21 and 28°C). This procedure provided for investigation of WUE dependence of temperature at different [CO2]. At leaf-level, a consistent increase in pWUE of 28% across the three temperature levels was observed, caused by a significant stimulation in net photosynthesis rate (16%), and a significant decreased stomatal conductance (25%) with a simultaneous drop in transpiration rate although not significant. The ratio ci/ca was in contrast to the first experiment significantly higher in plants grown at elevated [CO2]. Despite this photosynthetic acclimation, concurrent stimulation of aboveground and belowground biomass accumulation was observed at elevated [CO2], resulting in higher harvest indices and irrigation WUE (45%), not significantly different from the increase of pWUE. Out of four cultivars investigated, the largest increase in irrigation WUE was found in the cultivar Ballerina, which also showed a six time increase in tuber yield, perhaps indicating less overall inhibition of photosynthesis by sugar accumulation. At all temperature levels, WUE was significantly larger at high [CO2]. This was the result of increased net photosynthesis rate (at low temperature), decreased transpiration rate and stomatal conductance (high temperature) or a combination of those two responses (moderate temperature). The results signify that beneficial effects of potato plant cultivation at elevated [CO2] comprise increased WUE at various temperature levels, but due to acclimation of photosynthesis the increase was smaller during prolonged than stepwise exposure. The experiment also showed that, in the conditions of climate change, associated higher T could decrease the response of photosynthesis to higher [CO2] and higher vapor pressure deficit will decrease the gain in WUE

Cytosolic glutamine synthetase is important for photosynthetic efficiency and water use efficiency in potato as revealed by high-throughput sequencing QTL analysis

KEY MESSAGE: WUE phenotyping and subsequent QTL analysis revealed cytosolic GS genes importance for limiting N loss due to photorespiration under well-watered and well-fertilized conditions. ABSTRACT: Potato (Solanum tuberosum L.) closes its stomata at relatively low soil water deficits frequently encountered in normal field conditions resulting in unnecessary annual yield losses and extensive use of artificial irrigation. Therefore, unraveling the genetics underpinning variation in water use efficiency (WUE) of potato is important, but has been limited by technical difficulties in assessing the trait on individual plants and thus is poorly understood. In this study, a mapping population of potatoes has been robustly phenotyped, and considerable variation in WUE under well-watered conditions was observed. Two extreme WUE bulks of clones were identified and pools of genomic DNA from them as well as the parents were sequenced and mapped to reference potato genome. Following a novel data analysis approach, two highly resolved QTLs were found on chromosome 1 and 9. Interestingly, three genes encoding isoforms of cytosolic glutamine synthase were located in the QTL at chromosome 1 suggesting a major contribution of this enzyme to photosynthetic efficiency and thus WUE in potato. Indeed, Glutamine synthetase enzyme activity of leaf extracts was measured and found to be correlated with contrasting WUE phenotypes. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00122-015-2573-2) contains supplementary material, which is available to authorized users