Identification of Genes Differentially Expressed in Response to Cold in Pisum sativum Using RNA Sequencing Analyses

International audienceLow temperature stress affects growth and development in pea (Pisum sativum L.) and decreases yield. In this study, RNA sequencing time series analyses performed on lines, Champagne frost-tolerant and Térèse frost-sensitive, during a low temperature treatment versus a control condition, led us to identify 4981 differentially expressed genes. Thanks to our experimental design and statistical analyses, we were able to classify these genes into three sets. The first one was composed of 2487 genes that could be related to the constitutive differences between the two lines and were not regulated during cold treatment. The second gathered 1403 genes that could be related to the chilling response. The third set contained 1091 genes, including genes that could be related to freezing tolerance. The identification of differentially expressed genes related to cold, oxidative stress, and dehydration responses, including some transcription factors and kinases, confirmed the soundness of our analyses. In addition, we identified about one hundred genes, whose expression has not yet been linked to cold stress. Overall, our findings showed that both lines have different characteristics for their cold response (chilling response and/or freezing tolerance), as more than 90% of differentially expressed genes were specific to each of them

Development of a freezing test in controlled conditions for Pisum sativum

BAPGEAPSIFreezing is a major environmental limitation to crop productivity for a number of species including legumes. In the context of global climate change, winter crops will experiment milder autumn temperatures that could be detrimental to the achievement of cold acclimation, which is the ability for plants to increase their level of frost tolerance (FT) in response to low but non-freezing temperatures. For the pea crop, a modelling approach has shown that climate warming will increase the occurrence of freezing damage events, even if these latter will be less severe (Castel et al., 2014). Thus, breeding for frost tolerant winter peas requires not only to improve their FT threshold, but also to raise their cold acclimation rate. In order to evaluate the genetic variability of both traits, we are adjusting a protocol in controlled conditions, which provides an indirect evaluation of FT by the measurement of tissues’electrolyte leakage (EL). Pea stem samples have been collected after variable durations of cold acclimation at 4°C day/2°C night in a climatic chamber. They have been then progressively cooled at 2°C h-1 in a programmable temperature-test chamber to reach test temperatures ranging from +4°C to -36°C. After 14 days of cold acclimation, EL evaluation enabled the same ranking of genotypes according to their FT threshold as obtained in the Chaux-des-Prés field platform. Improvements of the protocol are however still needed to use it as a routine ranking test

The use of MapPop1.0 for choosing a QTL mapping sample from an advanced backcross population.

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Combining gene expression and genetic analyses to identify candidate genes involved in cold responses in pea

International audienceCold stress affects plant growth and development. In order to better understand the responses to cold (chilling or freezing tolerance), we used two contrasted pea lines. Following a chilling period, the Champagne line becomes tolerant to frost whereas the Terese line remains sensitive. Four suppression subtractive hybridisation libraries were obtained using mRNAs isolated from pea genotypes Champagne and Terese. Using quantitative polymerase chain reaction (qPCR) performed on 159 genes, 43 and 54 genes were identified as differentially expressed at the initial time point and during the time course study, respectively. Molecular markers were developed from the differentially expressed genes and were genotyped on a population of 164 RILs derived from a cross between Champagne and Terese. We identified 5 candidate genes colocalizing with 3 different frost damage quantitative trait loci (QTL) intervals and a protein quantity locus (PQL) rich region previously reported. This investigation revealed the role of constitutive differences between both genotypes in the cold responses, in particular with genes related to glycine degradation pathway that could confer to Champagne a better frost tolerance. We showed that freezing tolerance involves a decrease of expression of genes related to photosynthesis and the expression of a gene involved in the production of cysteine and methionine that could act as cryoprotectant molecules. Although it remains to be confirmed, this study could also reveal the involvement of the jasmonate pathway in the cold responses, since we observed that two genes related to this pathway were mapped in a frost damage QTL interval and in a PQL rich region interval, respectively

A conserved molecular basis for photoperiod adaptation in two temperate legumes

Legumes were among the first plant species to be domesticated, and accompanied cereals in expansion of agriculture from the Fertile Crescent into diverse environments across the Mediterranean basin, Europe, Central Asia, and the Indian subcontinent. Although several recent studies have outlined the molecular basis for domestication and eco-geographic adaptation in the two main cereals from this region, wheat and barley, similar questions remain largely unexplored in their legume counterparts. Here we identify two major loci controlling differences in photoperiod response between wild and domesticated pea, and show that one of these, HIGH RESPONSE TO PHOTOPERIOD (HR), is an ortholog of EARLY FLOWERING 3 (ELF3), a gene involved in circadian clock function. We found that a significant proportion of flowering time variation in global pea germplasm is controlled by HR, with a single, widespread functional variant conferring altered circadian rhythms and the reduced photoperiod response associated with the spring habit. We also present evidence that ELF3 has a similar role in lentil, another major legume crop, with a distinct functional variant contributing to reduced photoperiod response in cultivars widely deployed in short-season environments. Our results identify the factor likely to have permitted the successful prehistoric expansion of legume cultivation to Northern Europe, and define a conserved genetic basis for major adaptive changes in flowering phenology and growth habit in an important crop group