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Admixtures between wild animals and plants and their domesticated relatives are widely documented. This can have positive or negative impacts on the evolution of admixed populations in natural environments, yet the phenomenon is still misunderstood in long-lived woody species, contrary to short-lived crops. Wild oliveOlea europaeaL. occurs in the same eco-geographical range as domesticated olive, i.e. the Mediterranean Basin (MB). Moreover, it is an allogamous and anemophilous species whose seeds are disseminated by birds, i.e. factors that drive gene flow between crops and their wild relatives. Here we investigated the genetic structure of western MB wild olive populations in natural environments assuming a homogenous gene pool with limited impact of cultivated alleles, as previously suggested. We used a target sequencing method based on annotated genes from the Farga reference genome to analyze 27 western MB olive tree populations sampled in natural environments in France, Spain and Morocco. We also target sequenced cultivated olive tree accessions from the Worldwide Olive Germplasm Bank of Marrakech and Porquerolles and from an eastern MB wild olive tree population. We combined PCA, sNMF, pairwise Fst and TreeMix and clearly identified genuine wild olive trees throughout their natural distribution range along a north-south gradient including, for the first time, in southern France. However, contrary to our assumption, we highlighted more admixed than genuine wild olive trees. Our results raise questions regarding the admixed population evolution pattern in this environment, which might be facilitated by crop-to-wild gene flow.

Yams are important tubers widely consumed in developing countries in various forms, mainly boiled, pounded and fried. Tuber quality is a key criterion for acceptance by the various actors in the value chain. However, the genetics of yam tuber quality has not yet been comprehensively investigated. Given this lack of knowledge, we used population genomics and candidate gene association approaches to unravel the genetic basis of the three main quality attributes of boiled yam, namely texture, starch content and colour indices. We re-sequenced the whole genome of 127 yam genotypes with different quality attributes, and performed an enrichment of the already available functional genome annotation using comparative genomics. Population genomics analysis highlighted three main genetic groups and 1,053 genes under selection. We focused this work on three known quality trait-related pathways: pectin, starch content and flavonoid biosynthesis, and inventoried in the genome all the structural genes related to those pathways by comparative genomics. We improved the functional annotation of the three pathways with 48% more genes. A total of 18 candidate genes containing genetic variants significantly associated with the target traits were detected, including eight genes that were also found under selection. The texture-related candidate genes were distributed between the pectin and starch pathways. Overall, the use of comparative genomics has allowed the generation of an unprecedented genomic resource. The improved functional annotation of the yam genome is a promising predictive tool for identifying other core genes associated with any trait of interest to meet the growing need and diversified demands for yams.

The genetic architecture of resistance for witches' broom disease of cacao (WBD) was reexamined in an F2 population (Sca-6 × ICS-1), addressing symptom-specificity and possible genetic basis for the differences in disease scores from terminal and cushion brooms. A high-density genetic linkage map was constructed with 494 individuals and 2968 SNPs, obtaining 10 linkage groups comprising 1595 centiMorgans. The trees were evaluated under field conditions with high WBD pressure from 2015 to 2019, with low spatial autocorrelation tested by Moran's I. Five WBD symptoms and one tree growth trait were mapped, resulting in 23 minor-effects QTLs, primarily arranged in clusters and distributed in all linkage groups except 4 and 6, indicating that WBD has a polygenic inheritance. Terminal and cushion brooms shared a genomic region in linkage group 9, suggesting pleiotropy. In these conditions, the ICS-1 grandparent contributed with more QTLs than Sca-6 to WBD resistance, indicating that the resistance pattern has changed and confirming the susceptible parent's importance. Few QTLs were identified in the same or proximal loci comparing the 5-year, annual, or biennial periods. Several candidate genes such as glutathione peroxidases, threonine-serine receptors, and endochitinases were potentially associated with WBD resistance. These findings strongly suggest that WBD resistance is more complex than previously postulated, and future directions are presented and suggested to investigate further and improve the insights into WBD resistance.

Anthracnose disease caused by a fungus Colletotrichum gloeosporioides is the primary cause of yield loss in water yam (Dioscorea alata), the widely cultivated species of yam. Resistance to yam anthracnose disease (YAD) is a prime target in breeding initiatives to develop durable-resistant cultivars for sustainable management of the disease in water yam cultivation. This study aimed at tagging quantitative trait loci (QTL) for anthracnose disease resistance in a bi-parental mapping population of D. alata. Parent genotypes and their recombinant progenies were genotyped using the Genotyping by Sequencing (GBS) platform and phenotyped in two crop cycles for two years. A high-density genetic linkage map was built with 3184 polymorphic Single Nucleotide Polymorphism (NSP) markers well distributed across the genome, covering 1460.94 cM total length. On average, 163 SNP markers were mapped per chromosome with 0.58 genetic distances between SNPs. Four QTL regions related to yam anthracnose disease resistance were identified on three chromosomes. The proportion of phenotypic variance explained by these QTLs ranged from 29.54 to 39.40%. The QTL regions identified showed genes that code for known plant defense responses such as GDSL-like Lipase/Acylhydrolase, Protein kinase domain, and F-box protein. The results from the present study provide valuable insight into the genetic architecture of anthracnose resistance in water yam. The candidate markers identified herewith form a relevant resource to apply marker-assisted selection as an alternative to a conventional labor-intensive screening for anthracnose resistance in water yam.

Climate change has an impact. Droughts will become more common in the future and as a result is the drop of rubber production. Drought tolerant rubber genotypes, may reduce drought risk, could be discovered by selection of germplasm and crossing progenies. As perennial plant, conventional rubber selection of rubber needs long time. Molecular detection such as QTL (precise and fast detection) for screening to get drought tolerant rubber genotypes is very important to be conducted. A variable widely used to screen stress tolerance genotypes is Performance Index (PI). Measurement of PI in normal, moderate, and severe drought stress enables the calculation of the Drought Factor Index (DFI). DFI as an integrative parameter for drought tolerance trait provides simple and robust method to quantify the tolerance ability of plants to withstand drought condition. This research is the first application of DFI to select drought-tolerant rubber genotypes and to identify QTLs related to DFI. This research aimed to select candidate drought-tolerant genotypes from the biparental population PB 260 × SP 217 as well as to identify QTLs related to DFI variable. One hundred and thirty-two genotypes and four control commercial clones, namely PB 260, SP 217, GT1, and RRIM 600 have been successfully screened using DFI variable. Normal, moderate, and severe drought stresses were calibrated for each plant by monitoring the fraction of transpirable soil water (FTSW). Due to the skewed distribution of DFI data that was generated in the phenotyping step, the Kruskal-Wallis non-parametric test was used to test the significance of each QTLs using MapQTL version 6 software. From this research, it can be concluded that DFI can be used as a parameter for selection of drought tolerant rubber clones. Based on DFI calculation, the top ten high DFI genotypes/clones were genotype number 34, 206, 056, 007, 205, 225, 066, 235, 109, and clone RRIM 600. Furthermore, the most significant detection of QTL for DFI variables was found in locus g5TA2155, located at 0.553 cM in LG5. It indicated that this locus contained genes controlling DFI trait.

Two Dioscorea alata populations were generated by hand pollination between contrasted diploid genitors. Population A (74F × Kabusa) was composed of 121 progenies while population B (74F × 14M) involved 193 progenies. These two populations were assessed over two consecutive years regarding important tuber quality traits. Analysis of variance showed that the genotype had the greatest influence on the phenotypic scores. Also for some traits, effect of the year_replicate was strong. The heritabilities of most traits were high. Based on these data and a reference high-density genetic map of greater yam, a total of 34 quantitative trait loci (QTLs) were detected on 8 of the 20 yam chromosomes. They corresponded to five of each of the following traits: tuber size, shape regularity, tubercular roots, skin texture, tuber flesh oxidation, six for oxidation ratio and three for flesh colour. The fraction of total phenotypic variance attributable to a single QTL ranged from 11.1 to 43.5%. We detected significant correlations between traits and QTL colocalizations that were consistent with these correlations. A majority of QTLs (62%) were found on linkage group LG16, indicating that this chromosome could play a major role in genetic control of the investigated traits. In addition, an inversion involving this chromosome was detected in the Kabusa male. Nine QTLs were validated on a diversity panel, including three for tuber size, three for shape regularity, two for skin texture and one for tubercular roots. The approximate physical localization of validated QTLs allowed the identification of various candidates genes. The validated QTLs should be useful for breeding programs using marker-assisted selection to improve yam tuber quality.

International audience; Genotyping-by-sequencing (GBS) provides the marker density required for genomic predictions (GP). However, GBS gives a high proportion of missing SNP data which, for species without a chromosome-level genome assembly, must be imputed without knowing the SNP physical positions. Here, we compared GP accuracy with seven map-independent and two map-dependent imputation approaches, and when using all SNPs against the subset of genetically mapped SNPs. We used two rubber tree (Hevea brasiliensis) datasets with three traits. The results showed that the best imputation approaches were LinkImputeR, Beagle and FImpute. Using the genetically mapped SNPs increased GP accuracy by 4.3%. Using LinkImputeR on all the markers allowed avoiding genetic mapping, with a slight decrease in GP accuracy. LinkImputeR gave the highest level of correctly imputed genotypes and its performances were further improved by its ability to define a subset of SNPs imputed optimally. These results will contribute to the efficient implementation of genomic selection with GBS. For Hevea, GBS is promising for rubber yield improvement, with GP accuracies reaching 0.52.

Rootstocks are crucial for the sustainability of the citrus industry worldwide. Diploid intergeneric Citrus x Poncirus hybrids have contributed considerably to citrus rootstock improvement and their tetraploid (doubled-diploid) forms are important resources for the creation of a new generation of tetraploid rootstocks. To optimize the efficiency of tetraploid rootstock breeding strategies, more knowledge is required on inheritance in the allotetraploid genitors. A set of 159 new SNP markers that fully distinguish Poncirus trifoliata (L.) Raf. from Citrus species was developed from polymorphisms mined in GBS data and used to establish a genetic map of tetraploid citrumelo (C. x paradisi Macfad. x P. trifoliata) and to analyze the meiotic behavior of tetraploid citrumelo and citrandarin (C. reticulata Blanco x P. trifoliata). The tetraploid citrumelo genetic map was highly syntenic and collinear with the clementine reference genome. The apparent intergeneric recombination rate was strongly limited by high preferential chromosome pairing, resulting in intermediate inheritance with disomic tendency. Such inheritance, also observed in tetraploid citrandarin, results in the transmission by the diploid gametes of a high rate of intergeneric heterozygosity. It is therefore expected that a large part of the genetic value selected in the original diploid intergeneric rootstock is transmitted to the tetraploid sexual progenies.

Among legumes (Fabaceae) capable of nitrogen-fixing nodulation, several Aeschynomene spp. use a unique symbiotic process that is independent of Nod factors and infection threads. They are also distinctive in developing root and stem nodules with photosynthetic bradyrhizobia. Despite the significance of these symbiotic features, their understanding remains limited. To overcome such limitations, we conducted genetic studies of nodulation in Aeschynomene evenia, supported by the development of a genome sequence for A. evenia and transcriptomic resources for 10 additional Aeschynomene spp. Comparative analysis of symbiotic genes substantiated singular mechanisms in the early and late nodulation steps. A forward genetic screen also showed that AeCRK, coding a novel receptor-like kinase, and the symbiotic signaling genes AePOLLUX, AeCCamK, AeCYCLOPS, AeNSP2 and AeNIN, are required to trigger both root and stem nodulation. This work demonstrates the utility of the A. evenia model and provides a cornerstone to unravel new mechanisms underlying the rhizobium-legume symbiosis.

Background: Yam anthracnose disease (YAD) caused by Colletotrichum gloeosporioides is the primary cause of yield loss in water yam (Dioscorea alata), the widely cultivated species of yam. Development of resistant cultivars have been a prime target for sustainable management of anthracnose in water yam. Molecular breeding tools are required to expedite the development of improved yam varieties. QTL analysis using high density genetic maps serve as a powerful tool to discover key locations of quantitave traits. This study aimed at tagging quantitative trait loci (QTL) for anthracnose disease resistance in a bi-parental mapping population of D. alata.Results: In this study, two contrasting parents for yam anthracnose disease reaction and their 204 full- sib offspring were used to develop a high-density genetic linkage map with 3,257 SNP markers by the GBS technique. The total length of the consensus map was 1460.94 cM with an average of 163 markers per chromosome. Four QTLs were detected for anthracnose disease resistance in 4 locations on 3 chromosomes. The proportion of phenotypic variance explained by these QTLs ranged from 10 to 13%. Plant defense response genes including GDSL-like Lipase/Acylhydrolase, Protein kinase domain and F-box protein were also detected within the QTL regions. Conclusion: The results from the present study provide valuable insight into the genetic architecture of anthracnose resistance in water yam. The candidate markers and putative genes identified herewith form a relevant resource to apply marker-assisted selection as alternative to a conventional labor-intensive screening for anthracnose resistance in water yam.

International audience; Theobroma grandiflorum (Willd. ex Spreng.) Schum. is a tree originating in the Amazon forest. In Brazil, it is known as cupuassu and, like Theobroma cacao, belongs to the family of the Malvaceae. The pulp is used by the food industry and the seeds, which are rich in fatty acids, are used in cosmetics. As for cacao, cupuassu cultivation is affected by the witches' broom disease (WBD), caused by Moniliophthora perniciosa (M. perniciosa). Despite its economical value, cupuassu culture lacks genetic information, compromising its plant breeding program development. The aim of this research was to increase molecular knowledge about WBD resistance. The progeny of 168 individuals obtained by crossing two contrasting cupuassu clones (174 and 1074, resistant and susceptible to WBD, respectively) were evaluated. The first consensus genetic map consisting of 1438 markers was produced using genotyping by sequencing (GBS) and genome sequencing of the neighboring species T. cacao (Criollo B97) as reference. The analysis of synteny between T. cacao and T. grandiflorum showed that the average homology between the linkage groups of the two species was 97.2%. A resistance quantitative trait locus (QTL) was identified on chromosome 6 of resistant parent 174 at marker 6M1252980. The phenotypic data associated with that QTL corresponded to observations after natural and artificial infection with M. perniciosa. The biological process associated with this QTL may play a role in resistance and susceptibility to M. perniciosa.

International audience; Due to their central role in ecosystems functioning and their ability to rapidly respond to environmental changes, soil microorganisms could potentially be used for monitoring ecosystems recovery in the context of degraded land restoration. However, these belowground organisms have been, to date, largely neglected. Here, we investigated fungal and bacterial community diversity, composition, and structure from ultramafic soils in New Caledonia, an archipelago in the southwest Pacific recognized as a priority for conservation and restoration. The emerging approach of high-throughput amplicon sequencing of environmental DNA (eDNA)-metabarcoding of eDNAwas used to compare soil microbial communities from four different native vegetation types, representing different stages of a chronosequence and defined as reference ecosystems, to five distinct post-mining sites revegetated several years ago. Our results clearly revealed changes in soil microbial phyla and functional groups along the reference chronosequence and variable responses at the different revegetated sites, with two of the five sites showing a good trajectory of recovery. We thus propose three ratios as metrics for monitoring the restoration trajectory of soil microorganisms: the Ascomycota:Basidiomycota and Saprotrophic:Ectomycorrhizal ratios for fungi, and the Cyanobacteria:Chloroflexi ratios for bacteria. Our study, combined with recent works undertaken in other geographical areas, underpins the great promise that could represent soil microbial eDNA metabarcoding for monitoring restoration progress and success. With the emergence of these new cost-effective and scalable sequencing technologies, soil microbes could, in the near future, be included in guidelines for restoration operations in complement to more conventional approaches.

International audience; Olive (Olea europaea L.) is a major fruit crop in the Mediterranean Basin. Ex-situ olive management is essential to ensure optimal use of genetic resources in breeding programs. The Worldwide Olive Germplasm Bank of Córdoba (WOGBC), Spain, and Marrakech (WOGBM), Morocco, are currently the largest existing olive germplasm collections. Characterization, identification, comparison and authentication of all accessions in both collections could thus provide useful information for managing olive germplasm for its preservation, exchange within the scientific community and use in breeding programs. Here we applied 20 microsatellite markers (SSR) and 11 endocarp morphological traits to discriminate and authenticate 1091 olive accessions belonging to WOGBM and WOGBC (554 and 537, respectively). Of all the analyzed accessions, 672 distinct SSR profiles considered as unique genotypes were identified, but only 130 were present in both collections. Combining SSR markers and endocarp traits led to the identification of 535 cultivars (126 in common) and 120 authenticated cultivars. No significant differences were observed between collections regarding the allelic richness and diversity index. We concluded that the genetic diversity level was stable despite marked contrasts in varietal composition between collections, which could be explained by their different collection establishment conditions. This highlights the extent of cultivar variability within WOGBs. Moreover, we detected 192 mislabeling errors, 72 of which were found in WOGBM. A total of 228 genotypes as molecular variants of 74 cultivars, 79 synonyms and 39 homonyms as new cases were identified. Both collections were combined to define the nested core collections of 55, 121 and 150 sample sizes proposed for further studies. This study was a preliminary step towards managing and mining the genetic diversity in both collections while developing collaborations between olive research teams to conduct association mapping studies by exchanging and phenotyping accessions in contrasted environmental sites.

Background Among semi-aquatic species of the legume genus Aeschynomene, some have the property of being nodulated by photosynthetic Bradyrhizobium lacking the nodABC genes necessary for the synthesis of Nod factors. Knowledge of the specificities underlying this Nod-independent symbiosis has been gained from the model legume Aeschynomene evenia but our understanding remains limited due to the lack of comparative genetics with related taxa using a Nod factor-dependent process. To fill this gap, we combined different approaches to perform a thorough comparative analysis in the genus Aeschynomene. Results This study significantly broadened previous taxon sampling, including in allied genera, in order to construct a comprehensive phylogeny. In the phylogenetic tree, five main lineages were delineated, including a novel lineage, the Nod-independent clade and another one containing a polytomy that comprised several Aeschynomene groups and all the allied genera. This phylogeny was matched with data on chromosome number, genome size and low-copy nuclear gene sequences to reveal the diploid species and a polytomy containing mostly polyploid taxa. For these taxa, a single allopolyploid origin was inferred and the putative parental lineages were identified. Finally, nodulation tests with different Bradyrhizobium strains revealed new nodulation behaviours and the diploid species outside of the Nod-independent clade were compared for their experimental tractability and genetic diversity. Conclusions The extended knowledge of the genetics and biology of the different lineages sheds new light of the evolutionary history of the genus Aeschynomene and they provide a solid framework to exploit efficiently the diversity encountered in Aeschynomene legumes. Notably, our backbone tree contains all the species that are diploid and it clarifies the genetic relationships between the Nod-independent clade and the Nod-dependent lineages. This study enabled the identification of A. americana and A. patula as the most suitable species to undertake a comparative genetic study of the Nod-independent and Nod-dependent symbioses. Electronic supplementary material The online version of this article (10.1186/s12870-018-1567-z) contains supplementary material, which is available to authorized users.

Plant microbial communities may moderate the plant responses to different abiotic or biotic stresses like pathogens. On the other hand, plant genotypes may influence the composition and structure of the plant microbiota. In the Chinese Yuanyang terraces (YYT), a sustainable rice disease control has been achieved for centuries using mixtures of traditional genetically diverse rice varieties harboring a wide panel of resistance genes. However, this centuries-old agrosystem is currently challenged by the introduction of several “modern” rice varieties. The potential simplification of the rice varietal landscape is likely to drive a modification of the rice microbiota, which may have an impact on the plant-pathogen dynamics, and further on the frequency, extent and impact of disease emergence events. We here investigated the microbial communities (bacteria, fungi and viruses) associated with roots and aerial organs from eleven and eight YYT fields cultivated with traditional and “modern” rice varieties, respectively. Besides using a genotyping-by-sequencing approach (GBS) to decipher the rice genetic diversity, microbial communities were characterized by metagenomics approaches. The GBS approach confirms a shift of the rice genetic diversity and split the varieties into three lineages (traditional varieties, “modern” introduced varieties and one Japonica traditional variety). Metagenomics approaches show that microbial communities from aerial organs are lineage-dependent and that microbial communities from the roots are more homogeneous and not different among rice lineages. Interestingly, our study reveals a high prevalence (15%) of Southern rice black-streaked dwarf virus in Yuanyang terraces, and that this virus is significantly more prevalent in traditional local varieties.

Kava (Piper methysticum) is a major cash crop in the Pacific. The aim of this study was to assess genetic variation among 103 accessions of kava using SSRs and DArTs. Genetic structure was determined using clustering analyses (WPGMA) and principal coordinate analyses (PCA). Thirteen SSR primers and 75 DArT markers were found polymorphic, and the two types of markers generated similar clustering patterns. Genetic distances ranged from 0 to 0.65 with an average of 0.24 using SSRs and from 0 to 0.64 with an average of 0.24 using DArT. Eleven genotypes were identified with SSR while 28 genotypes were identified with DArT markers. By combining the two sets of markers, a total of only 30 distinct genotypes were observed. In the Vanuatu archipelago, noble cultivars originating from different islands clustered together within a very narrow genetic base despite their diversity of morphotypes. SSR and DArT fingerprints allowed the identification of kava cultivars unsuitable for consumption, so called two-days, and clearly differentiated the wild types classified as P. methysticum var. wichmannii from the cultivars as var. methysticum. Molecular data reveals that all noble cultivars evolved by the predominance of clonal selection. Although they are represented by clearly distinct morphotypes, these cultivars are genetically vulnerable and their potential to adapt to forthcoming changes is limited. These newly developed markers provide high resolution and will be useful for kava diversity analyses and quality assessment.

Evaluer la sélection génomique au sein de croisements bi-parentaux d’espèces pérennes fruitières génotypés par séquençage : point d’étape du projet FruitSelGen. Séminaire SelGen 2017 : "La sélection génomique, bilan et perspectives"

Reticulate evolution, including hybrid speciation, introgression and lateral gene transfer is frequentin plant species. When coupled with vegetative propagation, it results in mosaic genomes of large genomic fragments, from different species or sub species. These complex inter(sub)-‐specific genomic structures can support a major part of the phenotypic diversity organization. Cultivated Citrus are a good example of such genepool issued from reticulate evolution with limited number of further interspecific recombination. It is generally agreed that four ancestral taxa (Citrus maxima: pummelos, Citrus reticulata: mandarins, Citrus medica: citrons and Citrus micrantha: papedas) are the ancestors of all the cultivated citrus species. These four species, have undergone allopatric evolution. This has led to a strong genetic differentiation which is also found for many phenotypic characters. The so-­‐called secondary species (sweet and sour oranges, grapefruits, lemons and limes) are the result of a reticulate evolution between these four ancestral taxa. Facultative apomixis (nucellar polyembrionny) then limited the number of interspecific meiosis cycle. The aplication of NGS on reduced genome representation with methods such as GBS (Genotyping By Sequencing) coupled with the availability of a clementine reference sequence open the way for pangenomic studies of large populations. The objective of this work was to validate a GBS approach on citrus in order to identify a pangenomic panel of diagnostic markers (DSNPs) of each ancestral taxa and to decipher the phylogenomic structures of 56 citrus varieties representative of the ancestral taxa and secondary species. The DSNP panel was also used to analyse the phylogenomic structures of diploid and triploid recombining populations of the Cirad-­‐Inra breeding programs. GBS library were prepared with ApekI and a selective PCR to improve the depth of the analysis. 56 accessions were pooled and sequenced in one line of Illumina HISEQ-­‐2000 (single reads). Diversity structure analysis showed that the varieties are distributed among the four ancestral taxa in perfect consistency with the previous studies carried out with SSRs, Indels and SNPs markers. The GBS approach is thus validated. 14926 DSNPs were identified. These diagnostic markers allowed to infer efficiently the majority of the phylogenomic karyotypes of the 56 Citrus accessions and revealed the interspecific recombination point in the diploid hybrids of breeding populations. For polyploid germplasm and hybrids, needing the evaluation of allelic doses, we were not able to infer these doses from the relative reads number at individual locus level. The potential of analysis at genome fragment level, covering numerous DSNPs, is under study. This work demonstrate the potential of GBS for deciphering the phylogenomic structure of the modern citrus varieties and recent hybrids of breeding populations. It bring new insights on the origins of citrus fruit and open the way for genetic associations studies and QTLs analysis based on phylogenomics and further to genomic selection.

International audience; Aeschynomene evenia has emerged as a new model legume for the deciphering of the molecular mechanisms of an alternative symbiotic process that is independent of the Nod factors. Whereas most of the research on nitrogen-fixing symbiosis, legume genetics and genomics has so far fo-cused on Galegoid and Phaseolid legumes, A. evenia falls in the more basal and understudied Dalbergioid clade along with peanut (Arachis hypogaea). To provide insights into the symbiotic genes content and the structure of the A. evenia genome, we established a gene-based genetic map for this species. Firstly, an RNAseq analysis was performed on the two parental lines selected to generate a F 2 mapping population. The transcriptomic data were used to develop molecular markers and they allowed the identification of most symbiotic genes. The resulting map comprised 364 markers arranged in 10 linkage groups (2n ¼ 20). A comparative analysis with the sequenced genomes of Arachis duranensis and A. ipaensis, the diploid ancestors of peanut, indicated blocks of conserved macrosynteny. Altogether, these results provided important clues regarding the evolution of symbiotic genes in a Nod factor-independent context. They provide a Downloaded from https://academic.oup.com/dnaresearch/article-abstract/23/4/365/2469965 by BIU Montpellier user on 12 March 2020 basis for a genome sequencing project and pave the way for forward genetic analysis of symbio-sis in A. evenia.

This study aims to understand the genetic diversity of traditional Oceanian starchy bananas in order to propose an efficient conservation strategy for these endangered varieties. SSR and DArT molecular markers are used to characterize a large sample of Pacific accessions, from New Guinea to Tahiti and Hawaii. All Pacific starchy bananas are shown of New Guinea origin, by interspecific hybridization between Musa acuminata (AA genome), more precisely its local subspecies M. acuminata ssp. banksii, and M. balbisiana (BB genome) generating triploid AAB Pacific starchy bananas. These AAB genotypes do not form a subgroup sensu stricto and genetic markers differentiate two subgroups across the three morphotypes usually identified: Iholena versus Popoulu and Maoli. The Popoulu/Maoli accessions, even if morphologically diverse throughout the Pacific, cluster in the same genetic subgroup. However, the subgroup is not strictly monophyletic and several close, but different genotypes are linked to the dominant genotype. One of the related genotypes is specific to New Caledonia (NC), with morphotypes close to Maoli, but with some primitive characters. It is concluded that the diffusion of Pacific starchy AAB bananas results from a series of introductions of triploids originating in New Guinea area from several sexual recombination events implying different genotypes of M. acuminata ssp. banksii. This scheme of multiple waves from the New Guinea zone is consistent with the archaeological data for peopling of the Pacific. The present geographic distribution suggests that a greater diversity must have existed in the past. Its erosion finds parallels with the erosion of cultural traditions, inexorably declining in most of the Polynesian or Melanesian Islands. Symmetrically, diversity hot spots appear linked to the local persistence of traditions: Maoli in New Caledonian Kanak traditions or Iholena in a few Polynesian islands. These results will contribute to optimizing the conservation strategy for the ex-situ Pacific Banana Collection supported collectively by the Pacific countries.

Chickpea is an important food legume crop for the semi-arid regions, however, its productivity is adversely affected by various biotic and abiotic stresses. Identification of candidate genes associated with abiotic stress response will help breeding efforts aiming to enhance its productivity. With this objective, 10 abiotic stress responsive candidate genes were selected on the basis of prior knowledge of this complex trait. These 10 genes were subjected to allele specific sequencing across a chickpea reference set comprising 300 genotypes including 211 genotypes of chickpea mini core collection. A total of 1.3 Mbp sequence data were generated. Multiple sequence alignment (MSA) revealed 79 SNPs and 41 indels in nine genes while the CAP2 gene was found to be conserved across all the genotypes. Among 10 candidate genes, the maximum number of SNPs (34) was observed in abscisic acid stress and ripening (ASR) gene including 22 transitions, 11 transversions and one tri-allelic SNP. Nucleotide diversity varied from 0.0004 to 0.0029 while polymorphism information content (PIC) values ranged from 0.01 (AKIN gene) to 0.43 (CAP2 promoter). Haplotype analysis revealed that alleles were represented by more than two haplotype blocks, except alleles of the CAP2 and sucrose synthase (SuSy) gene, where only one haplotype was identified. These genes can be used for association analysis and if validated, may be useful for enhancing abiotic stress, including drought tolerance, through molecular breeding.

International audience; Climate change stresses the importance of exploring the genetic adaptation of plants to an increase of both temperature and water deficit. To this end, dense swards of Mediterranean and temperate cultivars of Dactylis and Festuca were seed harvested after 2 years under artificial climate scenarios (range of summer drought) in two environments (Mediterranean and temperate). To assess possible genetic changes, all populations of the next generation were assessed and compared with their parent population having not been subjected to these climate scenarios. The experiment was a spaced plant design in the temperate location. The results showed that a drought escape strategy through earlier heading time and reduced total plant yield was enhanced by scenarios of greater summer drought. However, the direction and the intensity of the response of the main measured traits suggested that the physiological plant adaptation to water stress differs between species. In Dactylis, the phenology appeared to be a very responsive trait in the late heading temperate cultivar and induced a plant size reduction, while no genetic variability seems to be still available for selection within the early flowering Mediterranean cultivar. By contrast, the balance between both traits was not found so crucial in Festuca which suggests a possible greater role of the rooting system in drought resistance for this species.

Asr (ABA, stress, ripening) genes represent a small gene family potentially involved in drought tolerance in several plant species. To analyze their interest for rice breeding for water-limited environments, this gene family was characterized further. Genomic organization of the gene family reveals six members located on four different chromosomes and with the same exon-intron structure. The maintenance of six members of the Asr gene family, which are the result of combination between tandem duplication and whole genome duplication, and their differential regulation under water stress, involves probably some sub-functionalization. The polymorphism of four members was studied in a worldwide collection of 204 accessions of Oryza sativa L. and 14 accessions of wild relatives (O. rufipogon and O. nivara). The nucleotide diversity of the Asr genes was globally low, but contrasted for the different genes, leading to different shapes of haplotype networks. Statistical tests for neutrality were used and compared to their distribution in a set of 111 reference genes spread across the genome, derived from another published study. Asr3 diversity exhibited a pattern concordant with a balancing selection at the species level and with a directional selection in the tropical japonica sub-group. This study provides a thorough description of the organization of the Asr family, and the nucleotide and haplotype diversity of four Asr in Oryza sativa species. Asr3 stood out as the best potential candidate. The polymorphism detected here represents a first step towards an association study between genetic polymorphisms of this gene family and variation in drought tolerance traits.

The ADOC project (GCP 2006-02) aimed to characterize allelic diversity at orthologous loci of candidate genes for drought tolerance in seven GCP crops (rice, barley, sorghum, bean, chickpea, cassava and potato), working on reference collections of around 300 accessions for each crop. Six gene families (ERECTA, DREB, SS, SPS, ASR and VIN) were selected as the initial subset of target genes. Except the DREB gene family, for which a specific focus has been given to DREB2A, and the SPS gene family in cereals, for which only the Os01g69030 orthology group was studied, they represent a set of relatively small gene families acting at different levels of the drought stress response (transcriptional regulation, carbohydrate metabolism...) for which a comparative analysis of gene families was undertaken. Obtaining complete gene families was easier in whole sequenced genomes like rice and sorghum. Polyploidy and heterozygosity induced difficulties in analyzing data for cassava and potato; However sequences for a few genes were obtained and analyzed for SNP diversity across all species. Population structure influenced partially haplotype patterns. A large range of haplotype diversity was found and the degrees of this differed between species. Different patterns and range of sequence diversity were found within gene families and between species for orthologous genes. For a few genes, computation of a sequence-based neutrality test suggested selection events acting at the species and/or subgroup level. (Texte intégral)

Au sein d'une unité de recherche Inra – Cirad de Montpellier, un système de management de la qualité a été initié en 2009 sur des plateaux techniques. Cette démarche d'amélioration continue vise à garantir la fiabilité des prestations de recherche proposées. En outre, elle permet d'établir une relation de confiance avec les parties intéressées. L'un des objectifs est l'obtention d'une certification ISO 9001. Dans ce cadre là, la mise en oeuvre de l'approche métrologique, pilotée par Cathy Carasco-Lacombe, au sein des plateaux est fondamentale. Cette démarche a permis de faire un bilan de l'existant et dans un second temps de sensibiliser le personnel aux exigences métrologiques implicites (définition des mesurandes, des principes de mesure, des erreurs maximales tolérées, raccordements aux étalons nationaux des équipements, traçabilité, estimation des incertitudes de mesure). Aujourd'hui, cette activité garantie la maîtrise des équipements scientifiques sur lesquels repose la production de données en analyse biologique. Cette démarche est accompagnée financièrement et techniquement par la Délégation qualité du Cirad.

Background The development of genome-wide association studies (GWAS) in crops has made it possible to mine interesting alleles hidden in gene bank resources. However, only a small fraction of the rice genetic diversity of any given country has been exploited in the studies with worldwide sampling conducted to date. This study presents the development of a panel of rice varieties from Vietnam for GWAS purposes. Results The panel, initially composed of 270 accessions, was characterized for simple agronomic traits (maturity class, grain shape and endosperm type) commonly used to classify rice varieties. We first genotyped the panel using Diversity Array Technology (DArT) markers. We analyzed the panel structure, identified two subpanels corresponding to the indica and japonica sub-species and selected 182 non-redundant accessions. However, the number of usable DArT markers (241 for an initial library of 6444 clones) was too small for GWAS purposes. Therefore, we characterized the panel of 182 accessions with 25,971 markers using genotyping by sequencing. The same indica and japonica subpanels were identified. The indica subpanel was further divided into six populations (I1 to I6) using a model-based approach. The japonica subpanel, which was more highly differentiated, was divided into 4 populations (J1 to J4), including a temperate type (J2). Passport data and phenotypic traits were used to characterize these populations. Some populations were exclusively composed of glutinous types (I3 and J2). Some of the upland rice varieties appeared to belong to indica populations, which is uncommon in this region of the world. Linkage disequilibrium decayed faster in the indica subpanel (r2 below 0.2 at 101 kb) than in the japonica subpanel (r2 below 0.2 at 425 kb), likely because of the strongest differentiation of the japonica subpanel. A matrix adapted for GWAS was built by eliminating the markers with a minor allele frequency below 5% and imputing the missing data. This matrix contained 21,814 markers. A GWAS was conducted on time to flowering to prove the utility of this panel. Conclusions This publicly available panel constitutes an important resource giving access to original allelic diversity. It will be used for GWAS on root and panicle traits. Electronic supplementary material The online version of this article (doi:10.1186/s12870-014-0371-7) contains supplementary material, which is available to authorized users.

Master; Le séquençage ciblé par capture est une application récente des NGS qui permet de séquencer des zones précises de génomes dans un grand nombre d’individus. Bien que l’analyse bioinformatique de ces données reste très similaires à celles réalisées classiquement en NGS, les procédés mis en oeuvre lors de la procédure de capture induisent des spécificités qu’il est essentiel de prendre en compte. De fait, il devient nécessaire d’adapter les outils bioinformatiques à l’analyse de données de séquençage par capture et d’en traiter les sorties afin d’établir un diagnostic sur l’efficacité de la capture. Suite à une demande croissante des projets utilisant la capture au sein de l’UMR AGAP, j’ai définit une procédure d’analyse générique implémentée dans un outil d’intégration permettant une utilisation facile en routine par des utilisateurs non bio-informaticien. De plus, le pipeline intègre un diagnostic graphique du nombre de séquences considérées à chaque étape de l’analyse (nettoyage, alignement et appel de variants) ainsi que de la profondeur de séquençage selon différentes spécificités de la capture ciblée (« sur cible », « hors cible », position sur la cible, taille de la cible). Ce pipeline est implémenté et prêt à l’utilisation sur le cluster de calcul du CIRAD, accompagné d’une documentation permettant la diffusion de cet outil.