Papers by Grégoire Aubert
Plant Physiology
Rhizobium–legume nitrogen-fixing symbiosis involves the formation of a specific organ, the root n... more Rhizobium–legume nitrogen-fixing symbiosis involves the formation of a specific organ, the root nodule, which provides bacteria with the proper cellular environment for atmospheric nitrogen fixation. Coordinated differentiation of plant and bacterial cells is an essential step of nodule development, for which few transcriptional regulators have been characterized. Medicago truncatula ETHYLENE RESPONSE FACTOR REQUIRED FOR NODULE DIFFERENTIATION (MtEFD) encodes an APETALA2/ETHYLENE RESPONSIVE FACTOR (ERF) transcription factor, the mutation of which leads to both hypernodulation and severe defects in nodule development. MtEFD positively controls a negative regulator of cytokinin signaling, the RESPONSE REGULATOR 4 (MtRR4) gene. Here we showed that that the Mtefd-1 mutation affects both plant and bacterial endoreduplication in nodules, as well as the expression of hundreds of genes in young and mature nodules, upstream of known regulators of symbiotic differentiation. MtRR4 expressed wi...
The timing of developmental phase transitions is crucial for plant reproductive success, and two ... more The timing of developmental phase transitions is crucial for plant reproductive success, and two microRNAs (miRNA), miR156 and miR172, are implicated in the control of these changes, together with their respective SQUAMOSA promoter binding-like (SPL) and APETALA2 (AP2)-like targets. While their patterns of regulation have been studied in a growing range of species, to date they have not been examined in pea (Pisum sativum), an important legume crop and model species. We analysed the recently-released pea genome and defined nine miR156, 21 SPL, four miR172, and five AP2-like genes. Phylogenetic analysis of the SPL genes in pea, Medicago and Arabidopsis confirmed the eight previously defined clades, and identified a ninth potentially legume-specific SPL clade in pea and Medicago. Among the PsSPL, 14 contain a miR156 binding site and all five AP2-like transcription factors in pea include a miR172 binding site. Phylogenetic relationships, expression levels and temporal expression change...
Nature Genetics, 2019
ea (Pisum sativum L., 2n = 14) is the second most important grain legume in the world after commo... more ea (Pisum sativum L., 2n = 14) is the second most important grain legume in the world after common bean and is an important green vegetable with 14.3 t of dry pea and 19.9 t of green pea produced in 2016 (). Pea belongs to the Leguminosae (or Fabaceae), which includes cool season grain legumes from the Galegoid clade, such as pea, lentil (Lens culinaris Medik.), chickpea (Cicer arietinum L.), faba bean (Vicia faba L.) and tropical grain legumes from the Milletoid clade, such as common bean (Phaseolus vulgaris L.), cowpea (Vigna unguiculata (L.) Walp.) and mungbean (Vigna radiata (L.) R. Wilczek). It provides significant ecosystem services: it is a valuable source of dietary proteins, mineral nutrients, complex starch and fibers with demonstrated health benefits 1-4 and its symbiosis with N-fixing soil bacteria reduces the need for applied N fertilizers so mitigating greenhouse gas emissions . Pea was domesticated ~10,000 years ago by Neolithic farmers of the Fertile Crescent, along with cereals and other grain legumes 8 . The large reservoir of genetic diversity in Pisum has facilitated its spread throughout Asia, Europe, Africa, the Americas and Oceania where it has adapted to diverse environments and culinary practices (). Due to its large genome size (1 C ~ 4.45 gigabases, Gb 9 ), pea genomics has lagged behind that of legumes with smaller genomes, such as Medicago truncatula Gaertn. 10 , Lotus japonicus L. 11 or soybean (Glycine max (L.) Merr) 12 . Yet, pea has been studied as a genetic model since the eighteenth century; the analysis of the inheritance of different pea morphotypes led Gregor Mendel to uncover the laws of genetics 13 . Several pea developmental mutations have since been characterized 14 and chromosomal regions controlling agronomic traits identified 15 , but tools exploiting pea diversity for plant breeding, identifying favorable alleles underlying phenotypic variations and accelerating
Frontiers in Plant Science, 2019
Frontiers in Plant Science, 2018
Genome-Wide-Association Mapping in Pea associated with plant architecture overlapped with GWA int... more Genome-Wide-Association Mapping in Pea associated with plant architecture overlapped with GWA intervals previously identified for resistance to A. euteiches. This study provides innovative results about genetic interdependency of root disease resistance and RSA inheritance. It identifies pea lines, QTL, closely-linked markers and candidate genes for marker-assisted-selection of RSA loci to reduce Aphanomyces root rot severity in future pea varieties.
Plant Physiology, 2017
Three pea (Pisum sativum) loci controlling photoperiod sensitivity, HIGH RESPONSE (HR), DIE NEUTR... more Three pea (Pisum sativum) loci controlling photoperiod sensitivity, HIGH RESPONSE (HR), DIE NEUTRALIS (DNE), and STERILE NODES (SN), have recently been shown to correspond to orthologs of Arabidopsis (Arabidopsis thaliana) circadian clock genes EARLY FLOWERING3 (ELF3), ELF4, and LUX ARRHYTHMO, respectively. A fourth pea locus, PHOTOPERIOD (PPD), also contributes to the photoperiod response in a similar manner to SN and DNE, and recessive ppd mutants on a springflowering hr mutant background show early, photoperiod-insensitive flowering. However, the molecular identity of PPD has so far remained elusive. Here, we show that the PPD locus also has a role in maintenance of diurnal and circadian gene expression rhythms and identify PPD as an ELF3 co-ortholog, termed ELF3b. Genetic interactions between pea ELF3 genes suggest that loss of PPD function does not affect flowering time in the presence of functional HR, whereas PPD can compensate only partially for the lack of HR. These results provide an illustration of how gene duplication and divergence can generate potential for the emergence of more subtle variations in phenotype that may be adaptively significant.
BMC Genomics, 2015
Background: Pea (Pisum sativum L.), a major pulse crop grown for its protein-rich seeds, is an im... more Background: Pea (Pisum sativum L.), a major pulse crop grown for its protein-rich seeds, is an important component of agroecological cropping systems in diverse regions of the world. New breeding challenges imposed by global climate change and new regulations urge pea breeders to undertake more efficient methods of selection and better take advantage of the large genetic diversity present in the Pisum sativum genepool. Diversity studies conducted so far in pea used Simple Sequence Repeat (SSR) and Retrotransposon Based Insertion Polymorphism (RBIP) markers. Recently, SNP marker panels have been developed that will be useful for genetic diversity assessment and marker-assisted selection. Results: A collection of diverse pea accessions, including landraces and cultivars of garden, field or fodder peas as well as wild peas was characterised at the molecular level using newly developed SNP markers, as well as SSR markers and RBIP markers. The three types of markers were used to describe the structure of the collection and revealed different pictures of the genetic diversity among the collection. SSR showed the fastest rate of evolution and RBIP the slowest rate of evolution, pointing to their contrasted mode of evolution. SNP markers were then used to predict phenotypes -the date of flowering (BegFlo), the number of seeds per plant (Nseed) and thousand seed weight (TSW)-that were recorded for the collection. Different statistical methods were tested including the LASSO (Least Absolute Shrinkage ans Selection Operator), PLS (Partial Least Squares), SPLS (Sparse Partial Least Squares), Bayes A, Bayes B and GBLUP (Genomic Best Linear Unbiased Prediction) methods and the structure of the collection was taken into account in the prediction. Despite a limited number of 331 markers used for prediction, TSW was reliably predicted. The development of marker assisted selection has not reached its full potential in pea until now. This paper shows that the high-throughput SNP arrays that are being developed will most probably allow for a more efficient selection in this species.
Agronomy, 2012
Pea (Pisum sativum L.) was the original model organism used in Mendel's discovery (1866) of the l... more Pea (Pisum sativum L.) was the original model organism used in Mendel's discovery (1866) of the laws of inheritance, making it the foundation of modern plant genetics. However, subsequent progress in pea genomics has lagged behind many other plant species. Although the size and repetitive nature of the pea genome has so far restricted its sequencing, comprehensive genomic and post genomic resources already exist. These include BAC libraries, several types of molecular marker sets, both transcriptome and proteome datasets and mutant populations for reverse genetics. The availability of the full genome sequences of three legume species has offered significant opportunities for genome wide comparison revealing synteny and co-linearity to pea. A combination of a candidate gene and colinearity approach has successfully led to the identification of genes underlying agronomically important traits including virus resistances and plant architecture. Some of this knowledge has already been applied to marker assisted selection (MAS) programs, increasing precision and shortening the breeding cycle. Yet, complete translation of marker discovery to pea breeding is still to be achieved. Molecular analysis of pea collections has shown that although substantial variation is present within the cultivated genepool, wild material offers the possibility to incorporate novel traits that may have been inadvertently eliminated. Association mapping analysis of diverse pea germplasm promises to identify genetic variation related to desirable agronomic traits, which are historically difficult to breed for in a traditional manner. The availability of high throughput 'omics' methodologies offers great promise for the development of novel, highly accurate selective breeding tools for improved pea genotypes that are sustainable under current and future climates and farming systems.
The Plant Journal, 2011
The number of root nodules developing on legume roots after rhizobial infection is controlled by ... more The number of root nodules developing on legume roots after rhizobial infection is controlled by the plant shoot through autoregulation and mutational inactivation of this mechanism leads to hypernodulation. We have characterised the Pisum sativum (pea) Sym28 locus involved in autoregulation and shown that it encodes a protein similar to the Arabidopsis CLAVATA2 (CLV2) protein. Inactivation of the PsClv2 gene in four independent sym28 mutant alleles, carrying premature stop codons, results in hypernodulation of the root and changes to the shoot architecture. In the reproductive phase sym28 shoots develops additional flowers, the stem fasciates, and the normal phyllotaxis is perturbed. Mutational substitution of an amino acid in one leucine rich repeat of the corresponding Lotus japonicus LjCLV2 protein results in increased nodulation. Similarly, down-regulation of the Lotus Clv2 gene by RNAi mediated reduction of the transcript level also resulted in increased nodulation. Gene expression analysis of LjClv2 and Lotus hypernodulation aberrant root formation Har1 (previously shown to regulate nodule numbers) indicated they have overlapping organ expression patterns. However, we were unable to demonstrate a direct protein-protein interaction between LjCLV2 and LjHAR1 proteins in contrast to the situation between equivalent proteins in Arabidopsis. LjHAR1 was localised to the plasma membrane using a YFP fusion whereas LjCLV2-YFP localised to the endoplasmic reticulum when transiently expressed in Nicotiana benthamiana leaves. This finding is the most likely explanation for the lack of interaction between these two proteins.
PROTEOMICS, 2011
Legume seeds are a major source of dietary proteins for humans and animals. Deciphering the genet... more Legume seeds are a major source of dietary proteins for humans and animals. Deciphering the genetic control of their accumulation is thus of primary significance towards their improvement. At first, we analysed the genetic variability of the pea seed proteome of three genotypes over 3 years of cultivation. This revealed that seed protein composition variability was under predominant genetic control, with as much as 60% of the spots varying quantitatively among the three genotypes. Then, by combining proteomic and quantitative trait loci (QTL) mapping approaches, we uncovered the genetic architecture of seed proteome variability. Protein quantity loci (PQL) were searched for 525 spots detected on 2-D gels obtained for 157 recombinant inbred lines. Most protein quantity loci mapped in clusters, suggesting that the accumulation of the major storage protein families was under the control of a limited number of loci. While convicilin accumulation was mainly under the control of cis-regulatory regions, vicilins and legumins were controlled by both cis-and trans-regulatory regions. Some loci controlled both seed protein composition and protein content and a locus on LGIIa appears to be a major regulator of protein composition and of protein in vitro digestibility.
Plant Physiology, 2010
Sulfate is required for the synthesis of sulfur-containing amino acids and numerous other compoun... more Sulfate is required for the synthesis of sulfur-containing amino acids and numerous other compounds essential for the plant life cycle. The delivery of sulfate to seeds and its translocation between seed tissues is likely to require specific transporters. In Arabidopsis (Arabidopsis thaliana), the group 3 plasmalemma-predicted sulfate transporters (SULTR3) comprise five genes, all expressed in developing seeds, especially in the tissues surrounding the embryo. Here, we show that sulfur supply to seeds is unaffected by T-DNA insertions in the SULTR3 genes. However, remarkably, an increased accumulation of sulfate was found in mature seeds of four mutants out of five. In these mutant seeds, the ratio of sulfur in sulfate form versus total sulfur was significantly increased, accompanied by a reduction in free cysteine content, which varied depending on the gene inactivated. These results demonstrate a reduced capacity of the mutant seeds to metabolize sulfate and suggest that these tra...
Journal of Experimental Botany, 2014
To complement N 2 fixation through symbiosis, legumes can efficiently acquire soil mineral N thro... more To complement N 2 fixation through symbiosis, legumes can efficiently acquire soil mineral N through adapted root architecture. However, root architecture adaptation to mineral N availability has been little studied in legumes. Therefore, this study investigated the effect of nitrate availability on root architecture in Medicago truncatula and assessed the N-uptake potential of a new highly branched root mutant, TR185. The effects of varying nitrate supply on both root architecture and N uptake were characterized in the mutant and in the wild type. Surprisingly, the root architecture of the mutant was not modified by variation in nitrate supply. Moreover, despite its highly branched root architecture, TR185 had a permanently N-starved phenotype. A transcriptome analysis was performed to identify genes differentially expressed between the two genotypes. This analysis revealed differential responses related to the nitrate acquisition pathway and confirmed that N starvation occurred in TR185. Changes in amino acid content and expression of genes involved in the phenylpropanoid pathway were associated with differences in root architecture between the mutant and the wild type.
Genome, 2002
A genetic linkage map of Brassica juncea based on AFLP and RAPD markers was constructed using 131... more A genetic linkage map of Brassica juncea based on AFLP and RAPD markers was constructed using 131 F1-derived doubled-haploid (DH) plants from a cross between two mustard lines. The map included 273 markers (264 AFLP, 9 RAPD) arranged on 18 linkage groups, and covered a total genetic distance of 1641 cM; 18.3% of the AFLP markers showed a segregation distortion (P < 0.01). The markers with biased segregation were clustered on seven linkage groups. QTLs for oil contents, palmitic acid (16:0), stearic acid (18:0), oleic acid (18:1), linoleic acid (18:2), linolenic acid (18:3), eicosenoic acid (20:1), and erucic acid (22:1), were mapped on the AFLP linkage map. Correlation studies among fatty acids in the DH population and the localization of QTLs involved in their control indicated that a major gene located on linkage group (LG) 2 controlled the elongation step of erucic acid.Key words: Brassica juncea, doubled haploid, AFLP genetic linkage map, fatty acids, QTL.
BMC Genomics
Background Frost is a limiting abiotic stress for the winter pea crop (Pisum sativum L.) and iden... more Background Frost is a limiting abiotic stress for the winter pea crop (Pisum sativum L.) and identifying the genetic determinants of frost tolerance is a major issue to breed varieties for cold northern areas. Quantitative trait loci (QTLs) have previously been detected from bi-parental mapping populations, giving an overview of the genome regions governing this trait. The recent development of high-throughput genotyping tools for pea brings the opportunity to undertake genetic association studies in order to capture a higher allelic diversity within large collections of genetic resources as well as to refine the localization of the causal polymorphisms thanks to the high marker density. In this study, a genome-wide association study (GWAS) was performed using a set of 365 pea accessions. Phenotyping was carried out by scoring frost damages in the field and in controlled conditions. The association mapping collection was also genotyped using an Illumina Infinium® BeadChip, which all...
β-Amyrin Synthase1 Controls the Accumulation of the Major Saponins Present in Pea (Pisum sativum)
Plant and Cell Physiology
The use of pulses as ingredients for the production of food products rich in plant proteins is in... more The use of pulses as ingredients for the production of food products rich in plant proteins is increasing. However, protein fractions prepared from pea or other pulses contain significant amounts of saponins, glycosylated triterpenes which can impart an undesirable bitter taste when used as an ingredient in foodstuffs. In this paper, we describe the identification and characterization of a gene involved in saponin biosynthesis during pea seed development, by screening mutants obtained from two Pisum sativum TILLING (Targeting Induced Local Lesions in Genomes) populations in two different genetic backgrounds. The mutations studied are located in a gene designated PsBAS1 (β-amyrin synthase1) which is highly expressed in maturing pea seeds and which encodes a protein previously shown to correspond to an active β-amyrin synthase. The first allele is a nonsense mutation, while the second mutation is located in a splice site and gives rise to a mis-spliced transcript encoding a truncated,...
PLOS Genetics
Strigolactones (SLs) are well known for their role in repressing shoot branching. In pea, increas... more Strigolactones (SLs) are well known for their role in repressing shoot branching. In pea, increased transcript levels of SL biosynthesis genes are observed in stems of highly branched SL deficient (ramosus1 (rms1) and rms5) and SL response (rms3 and rms4) mutants indicative of negative feedback control. In contrast, the highly branched rms2 mutant has reduced transcript levels of SL biosynthesis genes. Grafting studies and hormone quantification led to a model where RMS2 mediates a shoot-to-root feedback signal that regulates both SL biosynthesis gene transcript levels and xylem sap levels of cytokinin exported from roots. Here we cloned RMS2 using synteny with Medicago truncatula and demonstrated that it encodes a putative auxin receptor of the AFB4/5 clade. Phenotypes similar to rms2 were found in Arabidopsis afb4/5 mutants, including increased shoot branching, low expression of SL biosynthesis genes and high auxin levels in stems. Moreover, afb4/5 and rms2 display a specific resistance to the herbicide picloram. Yeast-two-hybrid experiments supported the hypothesis that the RMS2 protein functions as an auxin receptor. SL root feeding using hydroponics repressed auxin levels in stems and down-regulated transcript levels of auxin biosynthesis genes within one hour. This auxin down-regulation was also observed in plants treated with the polar auxin transport inhibitor NPA. Together these data suggest a homeostatic feedback loop in which auxin up-regulates SL synthesis in an RMS2-dependent manner and SL down-regulates auxin synthesis in an RMS3 and RMS4dependent manner.
G3&#58; Genes|Genomes|Genetics
Pea (Pisum sativum, L.) is a major pulse crop used both for animal and human alimentation. Owing ... more Pea (Pisum sativum, L.) is a major pulse crop used both for animal and human alimentation. Owing to its association with nitrogen-fixing bacteria, it is also a valuable component for low-input cropping systems. To evaluate the genetic diversity and the scale of linkage disequilibrium (LD) decay in pea, we genotyped a collection of 917 accessions, gathering elite cultivars, landraces, and wild relatives using an array of 13,000 single nucleotide polymorphisms (SNP). Genetic diversity is broadly distributed across three groups corresponding to wild/landraces peas, winter types, and spring types. At a finer subdivision level, genetic groups relate to local breeding programs and type usage. LD decreases steeply as genetic distance increases. When considering subsets of the data, LD values can be higher, even if the steep decay remains. We looked for genomic regions exhibiting high level of differentiation between wild/landraces, winter, and spring pea, respectively. Two regions on linkage groups 5 and 6 containing 33 SNPs exhibit stronger differentiation between winter and spring peas than would be expected under neutrality. Interestingly, QTL for resistance to cold acclimation and frost resistance have been identified previously in the same regions. KEYWORDS genetic diversity linkage disequilibrium F ST Pisum sativum In crops, patterns of genetic diversity and the extent of linkage disequilibrium (LD) often result from a complex evolutionary history, including domestication bottlenecks, selection of favorable alleles, secondary admixture, or introgression of genetic material from wild relatives into cultivars. Studying these processes in crop species has proved of tremendous interest to evolutionary geneticists and breeders alike (Vigouroux et al. 2002; Ross-Ibarra et al. 2007). The domestication process of pea (Pisum sativum, L.), although as ancient as 10,000 yr (Zohary and Hopf 2000) is still a matter of debate. A few studies, however, have investigated genetic diversity at the species level, and results tend to indicate a surprisingly high level of genetic diversity in the cultivated gene pool given its highly inbreeding reproductive system (Baranger et al. 2004; Jing et al. 2010; Burstin et al. 2015). This could result from a weak bottleneck at domestication, important diversification after diffusion in Asia, Africa, and Europe, and/or gene flow between wild and cultivated material, none of these being mutually exclusive. Concerns related to rapid human-induced climatic changes and increasing food demand owing to population growth have rekindled an interest in better characterization of the extant genetic and phenotypic diversity in cultivated plants. There is a wide spectrum of phenotypic diversity in pea, relating to varied agricultural practices and characteristics of the cultivated material (sowing date, usage, etc.). The genomic regions underlying many of these key adaptations are of particular interest, yet only a few have been roughly identified, mainly using QTL mapping approaches. The advent of high-throughput genotyping technologies in pea enables one to look for the footprints of selection using a
Crop Science
D omesticated pea (Pisum sativum L.) is a major food legume in temperate cropping systems across ... more D omesticated pea (Pisum sativum L.) is a major food legume in temperate cropping systems across Europe, Asia, and North America and a traditional protein crop in the East African highlands (Zohary et al., 2012). Pea is also grown for fodder and as a source of green seeds for processing, as well as a vegetable crop (e.g., snap pea) (Davies, 1993; Warkentin et al., 2015). Thanks to its symbiosis with nitrogen-fixing bacteria and to its role as a break crop for pathogens and pests in cereal-dominated cropping systems, pea is important in temperate agroecological systems. Genetic bottlenecks associated with domestication and breeding have eroded genetic diversity in many crops (Tanksley and McCouch, 1997), thus making them vulnerable to stresses. Hence, a major objective of plant science is to identify useful alleles in crop wild relatives and reintroduce them into modern germplasm (Gur and Zamir, 2004). Moreover, comparative study of wild species and their domesticated counterparts offers an opportunity to understand the physiological and genomic consequences of domestication and thereby the genetic basis of crop adaptations
BMC Research Notes, 2016
Background: The continuing increase in size and quality of the "short reads" raw data is a signif... more Background: The continuing increase in size and quality of the "short reads" raw data is a significant help for the quality of the assembly obtained through various bioinformatics tools. However, building a reference genome sequence for most plant species remains a significant challenge due to the large number of repeated sequences which are problematic for a whole-genome quality de novo assembly. Furthermore, for most SNP identification approaches in plant genetics and breeding, only the "Gene-space" regions including the promoter, exon and intron sequences are considered. Results: We developed the iPea protocol to produce a de novo Gene-space assembly by reconstructing, in an iterative way, the non-coding sequence flanking the Unigene cDNA sequence through addition of next-generation DNA-seq data. The approach was elaborated with the large diploid genome of pea (Pisum sativum L.), rich in repetitive sequences. The final Gene-space assembly included 35,400 contigs (97 Mb), covering 88 % of the 40,227 contigs (53.1 Mb) of the PsCam_low-copy Unigen set. Its accuracy was validated by the results of the built GenoPea 13.2 K SNP Array. Conclusion: The iPEA protocol allows the reconstruction of a Gene-space based from RNA-Seq and DNA-seq data with limited computing resources.
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Papers by Grégoire Aubert