Data integration and network reconstruction with ∼omics data using Random Forest regression in potato

Acharjee, Animesh; Kloosterman, Bjorn; Vos, Ric C. H. de; Werij, Jeroen S.; Bachem, Christian W.B.; Visser, Richard G. F.; Maliepaard, Chris

doi:10.1016/j.aca.2011.03.050

Cited by 61 publications

(53 citation statements)

References 37 publications

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“…tuber shape, tuber size, eye depth, flesh color, among others). The development and characteristics of the population and the parental lines are described in detail (Celis-Gamboa, 2002;Werij et al, 2011). For starch-and cold sweetening-related traits, the values for the parental lines lie very close to each other centered on these normally distributed traits (data not shown), demonstrating the large amount of transgression present in this population.…”

Section: Plant Materialsmentioning

confidence: 92%

“…A similar approach was used to predict flesh color and enzymatic discoloration from transcriptomics and liquid chromatography-MS data sets (Acharjee et al, 2011). This study resulted in the successful identification of associated genes and metabolites, of which some were known to be involved in the regulation of the traits under study.…”

Section: Putative Predictors Of Starch Phosphorylationmentioning

confidence: 99%

“…A multilevel integrative approach to study organisms as a system of genetic, proteomic, and metabolic events may enable us to achieve a higher level of understanding of the interactions occurring in a biological system of interest. In potato, although this field is still in its infancy, some examples have already shown the advantages of such approaches to identify, and hypothesize about, the components in biologically relevant pathways (Acharjee et al, 2011). Furthermore, the genome sequence of potato (Potato Genome Sequencing Consortium, 2011) has now revealed genes specific to this highly heterozygous crop, bringing a platform that will ultimately facilitate the elucidation of the genetic basis of complex traits of high importance in breeding for tuber quality.…”

Section: Putative Predictors Of Starch Phosphorylationmentioning

confidence: 99%

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Untargeted Metabolic Quantitative Trait Loci Analyses Reveal a Relationship between Primary Metabolism and Potato Tuber Quality

et al. 2012

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Recent advances in -omics technologies such as transcriptomics, metabolomics, and proteomics along with genotypic profiling have permitted dissection of the genetics of complex traits represented by molecular phenotypes in nonmodel species. To identify the genetic factors underlying variation in primary metabolism in potato (Solanum tuberosum), we have profiled primary metabolite content in a diploid potato mapping population, derived from crosses between S. tuberosum and wild relatives, using gas chromatography-time of flight-mass spectrometry. In total, 139 polar metabolites were detected, of which we identified metabolite quantitative trait loci for approximately 72% of the detected compounds. In order to obtain an insight into the relationships between metabolic traits and classical phenotypic traits, we also analyzed statistical associations between them. The combined analysis of genetic information through quantitative trait locus coincidence and the application of statistical learning methods provide information on putative indicators associated with the alterations in metabolic networks that affect complex phenotypic traits.The variation observed in phenotypic trait values in plants is often of quantitative nature, and it remains challenging to unravel the genetic basis of these traits. Quantitative trait locus (QTL) mapping is currently the most commonly used approach to dissect the genetic factors underlying complex traits. The goal of QTL mapping is to identify genomic regions associated with a specific complex phenotype by statistical analysis of the associations between genetic markers and phenotypic variation (Doerge, 2002). Recently, advances in highthroughput analysis and analytical detection methods have facilitated more integrated approaches to measure global phenotypic variation at the molecular level. Metabolite profiling is a rapidly evolving technology that has significantly increased the possibilities of performing high-throughput analysis of hundreds to thousands of compounds in a range of plants, including complex crop species. Metabolite composition is of great importance in crop plants, as a number of important traits such as biotic and abiotic stress resistance, postharvest processing, and nutritional value are largely dependent on the metabolic content (Fernie and Schauer, 2009).In potato (Solanum tuberosum) breeding, metabolomic studies have progressively increased in importance, as many potato tuber traits such as content and quality of starch, chipping quality, flesh color, taste, and glycoalkaloid content have been shown to be linked to a wide range of metabolites (Coffin et al., 1987;Dobson et al., 2008). As a result, tuber quality can be assessed by assaying a range of metabolites. Gas chromatography-time of flight-mass spectrometry (GC-TOF-MS) has been shown to be useful for the rapid and highly sensitive detection of a large fraction of plant metabolites covering the central pathways of primary metabolism (Roessner et al., 2000;Lisec et al., 2006). In potato, untargeted metab...

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Section: Plant Materialsmentioning

confidence: 92%

Section: Putative Predictors Of Starch Phosphorylationmentioning

confidence: 99%

Section: Putative Predictors Of Starch Phosphorylationmentioning

confidence: 99%

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Untargeted Metabolic Quantitative Trait Loci Analyses Reveal a Relationship between Primary Metabolism and Potato Tuber Quality

et al. 2012

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“…Транскриптомное и ме таболомное (LCMS) профилирование клубней родитель ских диплоидных селекционных клонов C (USW533.7) и Е (77.2102.37), а также гибридной С × Е расщепляющейся популяции позволило прояснить механизмы формирова ния важных качественных признаков, таких как окраска кожуры и мякоти клубней, а также ферментативное обесцвечивание клубней после очистки (Acharjee et al, 2011). Применение RF для установления связи метабо лома и окраски мякоти клубней выявило несколько зна чимых метаболитов.…”

Section: метаболомика и фенотип картофеляunclassified

“…Спектр метаболитов, статистически связанный с ферментативным обесцвечиванием клубней после очистки, отличался от предыдущего, однако 6 метаболитов были общими для обоих признаков, в том числе виолоксантин. Интеграция метаболомных и транскриптомных данных позволила существенно увеличить выявляемую долю дисперсии признаков клубней, объясняемую при RFанализе, по сравнению с рассчитанными отдельно -либо в транскрип томном, либо в метаболомном анализах: 82 % дисперсии для окраски клубней и 51 % для признака обесцвечивания клубней после очистки (Acharjee et al, 2011).…”

Section: метаболомика и фенотип картофеляunclassified

The perspectives of metabolomics studies of potato plants

et al. 2017

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According to FAO (Food and Agricultural Organization of the United Nation), potato is the fourth crop in terms of food production after rice, wheat and maize, and the first among the tubers and roots. The importance of potato is difficult to overestimate; it is a valuable source of carbohydrates, antioxidants and vitamins. A huge number of investigations are focused on the study of metabolic processes occurring in the potato plant in order to elucidate the mechanisms responsible for productivity and accumulation of compounds that determine taste and nutritional quality, keeping quality of tubers, plant resistance, etc. The sum of metabolites, which is produced as a result of metabolic network activity, is defined as metabolome. Complex studies of metabolic diversity with the use of modern state-of-the-art chromatography approaches and highly precise detection of individual compounds revealed specificity of metabolic spectra from subcellular to organism levels and its amazing plasticity under the influence of a variety of internal and external stimuli. Metabolomic approaches are already in use for phenotyping available species, lines and varieties as well as for evaluation of potato plant resistance to environmental challenges and for detection of changes in tubers during storage. Metabolome profiling is widely employed to study differences between genetically modified forms of potatoes from untransformed relatives. A limited number of systemic studies on potatoes combines metabolome investigation with genome, transcriptome and proteome analysis and suggests an important role of the genome in the determination of metabolic rates. It is obvious that the search for biochemical markers depends on standartization of cultivation techniques, sample preparation and subsequent analysis similar to what has been developed for progress in genomic and transcriptomic studies. In the future, potato metabolome studies might complete classical and molecular approaches to develop new lines and varieties.Key words: potato; metabolomics; system biology; breeding.По данным FAO, картофель представляет собой четвертую по объемам производства продовольственную культуру после риса, пшеницы, кукурузы и первую среди клубнеплодных и корнеплод-ных культур. Он служит ценным источником углеводов, антиокси-дантов и витаминов. Огромное число работ сфокусировано на изучении метаболических процессов, происходящих в растениях картофеля, с тем чтобы расшифровать механизмы, отвечающие за продуктивность и накопление соединений, определяющих вкусовые и питательные качества, продолжительность периода покоя клубней, устойчивость растений и др. Результатом функци-онирования метаболических сетей является совокупность мета-болитов, которую принято называть метаболомом. Комплексные исследования метаболического разнообразия с применением самых современных методов хроматографического анализа и детекции индивидуальных соединений выявили специфичность метаболомных спектров от субклеточного до организменного уровня, удивительную пластичность этих спектров при де...

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Integrating “Omics” Data and Expression QTL to Understand Maize Heterosis

Rustenholz

Schnable

2013

Polyploid and Hybrid Genomics

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Data integration and network reconstruction with ∼omics data using Random Forest regression in potato

Cited by 61 publications

References 37 publications

Untargeted Metabolic Quantitative Trait Loci Analyses Reveal a Relationship between Primary Metabolism and Potato Tuber Quality

Untargeted Metabolic Quantitative Trait Loci Analyses Reveal a Relationship between Primary Metabolism and Potato Tuber Quality

The perspectives of metabolomics studies of potato plants

Integrating “Omics” Data and Expression QTL to Understand Maize Heterosis

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