Applied Statistical Solutions

Royal Leamington Spa, United Kingdom

Applied Statistical Solutions

Royal Leamington Spa, United Kingdom
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Chapman N.H.,University of Nottingham | Bonnet J.,Syngenta | Grivet L.,Syngenta | Lynn J.,Applied Statistical Solutions | And 9 more authors.
Plant Physiology | Year: 2012

Fruit firmness in tomato (Solanum lycopersicum) is determined by a number of factors including cell wall structure, turgor, and cuticle properties. Firmness is a complex polygenic trait involving the coregulation of many genes and has proved especially challenging to unravel. In this study, a quantitative trait locus (QTL) for fruit firmness was mapped to tomato chromosome 2 using the Zamir Solanum pennellii inter specific introgression lines (ILs) and fine-mapped in a population consisting of 7,500 F2 and F3 lines from IL 2-3 and IL 2-4. This firmness QTL contained five distinct subpeaks, Firs.p.QTL2.1 to Firs.p.QTL2.5, and an effect on a distal region of IL 2-4 that was nonoverlapping with IL 2-3. All these effects were located within an 8.6-Mb region. Using genetic markers, each subpeak within this combinatorial locus was mapped to a physical location within the genome, and an ethylene response factor (ERF) underlying Firs.p.QTL2.2 and a region containing three pectin methylesterase (PME) genes underlying Firs.p.QTL2.5 were nominated as QTL candidate genes. Statistical models used to explain the observed variability between lines indicated that these candidates and the nonoverlapping portion of IL 2-4 were sufficient to account for the majority of the fruit firmness effects. Quantitative reverse transcription-polymerase chain reaction was used to quantify the expression of each candidate gene. ERF showed increased expression associated with soft fruit texture in the mapping population. In contrast, PME expression was tightly linked with firm fruit texture. Analysis of a range of recombinant lines revealed evidence for an epistatic interaction that was associated with this combinatorial locus. © 2012 American Society of Plant Biologists. All Rights Reserved.

Atkinson L.D.,Monsanto Corporation | McHale L.K.,Ohio State University | Truco M.J.,University of California at Davis | Hilton H.W.,SGS UK Ltd | And 5 more authors.
Theoretical and Applied Genetics | Year: 2013

Minimally processed salad packs often suffer from discolouration on cut leaf edges within a few days after harvest. This limits shelf life of the product and results in high wastage. Recombinant inbred lines (RILs) derived from a cross between lettuce cvs. Saladin and Iceberg were shown to be suitable for genetic analysis of postharvest discolouration traits in lettuce. An intra-specific linkage map based on this population was generated to enable genetic analysis. A total of 424 markers were assigned to 18 linkage groups covering all nine chromosomes. The linkage map has a total length of 1,040 cM with an average marker distance of 2.4 cM within the linkage groups and was anchored to the ultra-dense, transcript-based consensus map. Significant genetic variation in the postharvest traits 'pinking', 'browning' and 'overall discolouration' was detected among the RILs. Seven significant quantitative trait loci (QTL) were identified for postharvest discolouration traits providing markers linked to the QTL that can be used for marker-assisted selection. Phenotypic stability was confirmed for extreme lines possessing the corresponding QTL parental alleles and which had shown transgressive segregation. This study indicates that a desired phenotype with reduced levels of postharvest discolouration can be achieved by breeding using natural variation. © 2013 Springer-Verlag Berlin Heidelberg.

Burns I.G.,University of Warwick | Zhang K.,University of Warwick | Turner M.K.,University of Warwick | Lynn J.,Applied Statistical Solutions | And 3 more authors.
Journal of the Science of Food and Agriculture | Year: 2011

BACKGROUND: The causes of the natural variation in nitrate accumulation and associated traits are studied using a diverse population of 48 mature lettuce accessions grown hydroponically in winter and summer seasons. Information on the effects of genotype, environment and their interactions will inform future selection strategies for the production of low-nitrate varieties more suited to meeting EU requirements for harvested produce. RESULTS: The effects of genotype (G), environment (E) and G × E interactions were all significant, with nitrate concentrations lower but covering a wider range in summer. Concentrations of nitrate-N were positively correlated with those of water and total-N and negatively with assimilated-C in the shoot in both seasons, with all relationships partitioned according to morphotype and/or seasonal type. Corresponding relationships between nitrate-N and assimilated-N or with shoot fresh or dry weight were generally weak or inconsistent. Nitrate concentrations at an early growth stage were strongly related to those at maturity in winter, but not in summer when light levels were less variable. CONCLUSION: The effects of genotype and environment on nitrate accumulation in lettuce are strongly influenced by morphotype, with most G × E interactions between accessions within the same morphotype predominantly of the non-crossover type. All low-nitrate-accumulating genotypes have increased concentrations of organic solutes (concentration regulation) and reduced water (volume regulation) to help stabilise osmotic potential within the shoots. Variability in nitrate accumulation arises more from differences in uptake than in efficiency of its chemical reduction. Genotypic differences in nitrate accumulation can be masked by changes in head morphology during maturation, provided that they are not confounded by substantial changes in intercepted light. Recent selection strategies do not appear to have produced lower-nitrate-accumulating cultivars. © 2011 Society of Chemical Industry.

Burns I.G.,University of Warwick | Durnford J.,University of Warwick | Lynn J.,Applied Statistical Solutions | McClement S.,University of Warwick | And 2 more authors.
Plant and Soil | Year: 2012

Background and aims: Characterisation of genetic variation in nitrate accumulation by lettuce will inform strategies for selecting low-nitrate varieties more capable of meeting EU legislation on harvested produce. This study uses a population of recombinant inbred lines (RILs) of lettuce to determine how genotypic differences influence N uptake, N assimilation and iso-osmotic regulation, and to identify key related traits prior to future genetic analysis. Methods: Measurements were made on plants grown to maturity in soil fertilised with ammonium nitrate, and in a complete nutrient solution containing only nitrate-N. A simple osmotic balance model was developed to estimate variations in shoot osmotic concentration between RILs. Results: There were significant genotypic variations in nitrate accumulation when plants were grown either with nitrate alone or in combination with ammonium. Ammonium-N significantly reduced nitrate in the shoot but had no effect on its relative variability, or on the ranking of genotypes. Shoot nitrate-N was correlated positively with total-N and tissue water, and negatively with assimilated-C in both experiments. Corresponding relationships with assimilated-N and shoot weight were weaker. Estimated concentrations of total osmotica in shoot sap were statistically identical in all RILs, despite variations in nitrate concentration across the population. Conclusions: Approximately 73% of the genotypic variability in nitrate accumulation within the population of RILs arose from differences in nitrate uptake and only 27% from differences in nitrate assimilated, irrespective of whether or not part of the N was recovered as ammonium, or whether the plants were grown in soil or solution culture. Genotypic variability in nitrate accumulation was associated with changes in concentrations of other endogenous solutes (especially carboxylates and soluble carbohydrates) and of tissue water, which minimised differences in osmotic potential of shoot sap between RILs. This offers the opportunity of using the regulation of these solutes as additional traits to manipulate nitrate accumulation. © 2011 Springer Science+Business Media B.V.

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