Morphological and metabolic profiling of a tropical‐adapted potato association panel subjected to water recovery treatment reveals new insights into plant vigor

Toubiana, David; Cabrera, Rodrigo; Salas, Elisa; Maccera, Chiara; Santos, Glauber Eduardo de Oliveira; Cevallos, D.; Lindqvist‐Kreuze, Hannele; López, Juan M.; Maruenda, Helena

doi:10.1111/tpj.14892

Cited by 12 publications

(21 citation statements)

References 74 publications

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“…[ Here we introduced an approach that allows researchers to select a correlation coefficient threshold suitable to their studied system. In our recent study on a potato association panel we constructed a CN on tuber metabolites and plant morphological traits, where we applied a correlation coefficient threshold of 0.4 [12]. At this setting we identified a critical connection between fumaric acid and plant vigor, which enabled us to identify essential genes aiding the plant to cope with abiotic stresses.…”

Section: Discussionmentioning

confidence: 99%

“…3 and 4). At these threshold settings the crucial connection between fumaric acid and plant vigor was still present in the REC-CN but not in the NI-CN as suggested in [12]. To validate the proposed method, it was also applied to heart metabolite datasets of fed and fasted mice [10].…”

Section: Discussionmentioning

confidence: 99%

“…Datasets for metabolites and morphological traits were adopted from [ 12 ]. Preprocessing and quantification of metabolites and morphological traits were performed as described therein.…”

Section: Methodsmentioning

confidence: 99%

“…We have recently profiled the tuber of a potato association panel that was grown under normal irrigation (NI) and recovery (REC) treatments for 42 metabolites and also measured a set of 45 morphological traits of the plant. [ 12 ]. For each treatment, one CN was constructed, where the correlation coefficient threshold for both CNs was set to Pearson’s | r |≥ 0.4.…”

Section: Introductionmentioning

confidence: 99%

“…All data and material associated with the current study can be found in the supplementary data of [ 12 ].…”

mentioning

confidence: 99%

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Guidelines for correlation coefficient threshold settings in metabolite correlation networks exemplified on a potato association panel

Toubiana

Maruenda

2021

BMC Bioinformatics

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Background Correlation network analysis has become an integral tool to study metabolite datasets. Networks are constructed by omitting correlations between metabolites based on two thresholds—namely the r and the associated p-values. While p-value threshold settings follow the rules of multiple hypotheses testing correction, guidelines for r-value threshold settings have not been defined. Results Here, we introduce a method that allows determining the r-value threshold based on an iterative approach, where different networks are constructed and their network topology is monitored. Once the network topology changes significantly, the threshold is set to the corresponding correlation coefficient value. The approach was exemplified on: (i) a metabolite and morphological trait dataset from a potato association panel, which was grown under normal irrigation and water recovery conditions; and validated (ii) on a metabolite dataset of hearts of fed and fasted mice. For the potato normal irrigation correlation network a threshold of Pearson’s |r|≥ 0.23 was suggested, while for the water recovery correlation network a threshold of Pearson’s |r|≥ 0.41 was estimated. For both mice networks the threshold was calculated with Pearson’s |r|≥ 0.84. Conclusions Our analysis corrected the previously stated Pearson’s correlation coefficient threshold from 0.4 to 0.41 in the water recovery network and from 0.4 to 0.23 for the normal irrigation network. Furthermore, the proposed method suggested a correlation threshold of 0.84 for both mice networks rather than a threshold of 0.7 as applied earlier. We demonstrate that the proposed approach is a valuable tool for constructing biological meaningful networks.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

“…Datasets for metabolites and morphological traits were adopted from [ 12 ]. Preprocessing and quantification of metabolites and morphological traits were performed as described therein.…”

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…All data and material associated with the current study can be found in the supplementary data of [ 12 ].…”

mentioning

confidence: 99%

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Guidelines for correlation coefficient threshold settings in metabolite correlation networks exemplified on a potato association panel

Toubiana

Maruenda

2021

BMC Bioinformatics

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Potato Population Genomics

Meng

Tuttle

Shannon

2022

Population Genomics

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Potato and sweetpotato breeding at the International Potato Center: approaches, outcomes and the way forward

Lindqvist-Kreuze,

Bonierbale,

Grüneberg

et al. 2023

Theor Appl Genet

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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.

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Morphological and metabolic profiling of a tropical‐adapted potato association panel subjected to water recovery treatment reveals new insights into plant vigor

Cited by 12 publications

References 74 publications

Guidelines for correlation coefficient threshold settings in metabolite correlation networks exemplified on a potato association panel

Guidelines for correlation coefficient threshold settings in metabolite correlation networks exemplified on a potato association panel

Potato Population Genomics

Potato and sweetpotato breeding at the International Potato Center: approaches, outcomes and the way forward

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