A reference genetic map of C. clementina hort. ex Tan.; citrus evolution inferences from comparative mapping

Background: Most modern citrus cultivars have an interspecific origin. As a foundational step towards deciphering the interspecific genome structures, a reference whole genome sequence was produced by the International Citrus Genome Consortium from a haploid derived from Clementine mandarin. The availability of a saturated genetic map of Clementine was identified as an essential prerequisite to assist the whole genome sequence assembly. Clementine is believed to be a 'Mediterranean' mandarin x sweet orange hybrid, and sweet orange likely arose from interspecific hybridizations between mandarin and pummelo gene pools. The primary goals of the present study were to establish a Clementine reference map using codominant markers, and to perform comparative mapping of pummelo, sweet orange, and Clementine. Results: Five parental genetic maps were established from three segregating populations, which were genotyped with Single Nucleotide Polymorphism (SNP), Simple Sequence Repeats (SSR) and Insertion-Deletion (Indel) markers. An initial medium density reference map (961 markers for 1084.1 cM) of the Clementine was established by combining male and female Clementine segregation data. This Clementine map was compared with two pummelo maps and a sweet orange map. The linear order of markers was highly conserved in the different species. However, significant differences in map size were observed, which suggests a variation in the recombination rates. Skewed segregations were much higher in the male than female Clementine mapping data. The mapping data confirmed that Clementine arose from hybridization between 'Mediterranean' mandarin and sweet orange. The results identified nine recombination break points for the sweet orange gamete that contributed to the Clementine genome. Conclusions: A reference genetic map of citrus, used to facilitate the chromosome assembly of the first citrus reference genome sequence, was established. The high conservation of marker order observed at the interspecific level should allow reasonable inferences of most citrus genome sequences by mapping next-generation sequencing (NGS) data in the reference genome sequence. The genome of the haploid Clementine used to establish the citrus reference genome sequence appears to have been inherited primarily from the 'Mediterranean' mandarin. The high frequency of skewed allelic segregations in the male Clementine data underline the probable extent of deviation from Mendelian segregation for characters controlled by heterozygous loci in male parents

Analyse et exploitation de séquences Sanger

École thématiqu

Early and long term body composition evolution post kidney transplantation influenced by the pre transplant nutritional characteristics: results of the CORPOS study

Many previous studies of renal transplant recipients have demonstrated that weight gain post kidney transplantation (KT) is frequent and may predispose to co morbidity. The aim of this prospective study was to evaluate changes in body composition (BC) during the first two years post KT and to determine predictors of these changes, with a special focus on pre KT parameters. When listed for a KT, 41 patients (14 women - 27 men) were included between 2007 and 2008 in a longitudinal study of evaluation of BC. Fat Free Mass (FFM) and Fat Mass (FM) were estimated by Dual-energy X- ray absorptiometry. At the same time, Extra Cellular Water (ECW) was measured by bio impedance spectroscopy. Cellular Active Mass (CAM) was defined as FFM – ECW. Energy and protein intake (EI –PI), physical activity (PA), biochemical and nutritional parameters were also recorded. Patients were evaluated every 6 months before KT, and 15 days, 1, 3, 6, 12 and 24 months after KT. During the first 2 years post KT, FM increase 0.09 kg/month (p=0.007), FFM by 0.06kg/month (p=0.0556) and MCA by 0.04kg/month (p=0.04). Univariate analysis showed that during the first 30 days post KT, FFM is strongly influenced by male gender, higher BMI, higher PIbefore KT, higher PA before KT and lower CRP post KT. During the first 2 years, FFM evolution is associated with male gender, higher EI and PI post KT. Early post KT evolution of FM is related to high BMI and high cumulative dose of corticosteroids. Long term evolution is associated with EI and use of corticosteroids. Pre KT EI and PI, as well as male gender and BMI influenced significantly the early evolution of MCA. In adjusted analyses, BMI and gender remained independently associated with FM, FFM and CAM. Furthermore, higher FFM level was associated with higher EI. We confirm that successful KT is associated with BC modifications; which can be detected very early post KT. These very early changes are strongly associated with energy, protein intake and physical activity level pre KT. Management of post KT weight gain should be anticipated with a special care on nutritional intake and physical activity in patients waiting kidney transplantation

BSA-NGS combined strategy for faster identification of micro-tom tomato genes affecting PVX resistance

National audienc

Stratégie combinée de NGS et de Bulk Segregant Analysis pour accélérer le clonage positionnel et identifier des gènes impliqués dans la résistance au <em>Potato virus X</em> chez la tomate

National audienc

BSA-Seq : an efficient method to decipher a complex trait on Poplar, a highly heterozygous diploid genome

The efficiency of the Bulk Segregant Analysis (BSA) had clearly been demonstrated to detect genomic regions and genes involved in diverse traits. It allows large experiments reducing the cost and time and preserving the power of full individual's population analysis. These past few years the combination of BSA and New Generation Sequence (NGS) data (BSA-Seq) gave a new accuracy and depth to the discovery on many traits of interest, mainly on crop and model species. In our study, we applied the BSA-Seq in a heterozygous and diploid genome context. We worked on the progenies derived from an interspecific cross Populus deltoides x Populus trichocarpa in which segregates the resistance to Melampsora larici populina (Mlp) leaf rust. We detected DNA variations with freebayes/0.9.21 and the soft masked genome of Populus trichocarpa Nisqually v3.0 as reference. Comparing DNA variations in between parents and bulks we obtained 27 regions or Quantitative Trait Loci based on NGS analysis (QTL-Seq) which could explain the resistance to Mlp. We first evaluated the strategy retrieving a previously cloned Mlp resistance gene governing the uredinia size in Populus trichocarpa clone 101-74 (RUS). Then we identified genomic markers which should better characterize this locus. So we demonstrated that, in our context, BSA-Seq allows us to improve the fine mapping of a major gene. We think it can be a promising method on a high heterozygous diploid genome as Poplar, to decipher complex trait. Next step is to proceed with it to fine map the other QTL-Seq

High throughput SNPs discovery in grapevine, poplar and tomato

International audienc

BSA-Seq : An efficient tool to characterize loci involved in the Poplar leaf rust resistance.

The efficiency of the Bulk Segregant Analysis (BSA) had clearly been demonstrated to detect genomic regions and genes involved in diverse traits. It allows large experiments reducing the cost and time and preserving the power of full individual's population analysis. These past few years the combination of BSA and New Generation Sequence (NGS) data (BSA-Seq) gave a new accuracy and depth to the discovery on many traits of interest, mainly on crop and model species. In our study, we applied the BSA-Seq to narrow down Populus genomic regions involved in the resistance to Melampsora larici populina (Mlp) leaf rust. We worked on the 1417 progenies derived from an interspecific cross Populus deltoides clone 73028-62 (Pd) x Populus trichocarpa clone 101-74 (Pt) in which segregates qualitative and quantitative Mlp resistances. Four bulks were constituted based on (1) the phenotypes for uredinias size (bulk1: large, bulk2 and bulk3: intermediate, bulk4: small) and (2) the Pt genotypes at the RUS locus governing the uredinia size (bulk1 and bulk3 : [RUS], bulk2 and bulk4 : [rUS]). We used independently the soft masked genomes of Populus trichocarpa Nisqually v3.0 (Ptv3) and Populus deltoides v2.0 (Pdv2) as references to map parents and bulks Illumina reads with the BWAmem/0.7.15 suite and to detect DNA variations with Freebayes/0.9.21. For each common variant position between parents and bulks, we tracked the specific alleles of Pt and/or Pd in the bulks. Respectively from Ptv3 and Pdv2, we identified 13 and 11 regions. We first evaluated the strategy retrieving the previously finally mapped RUS gene, designed new genomic markers from Ptv3 to better characterize this locus and performed the in silico validation. Then we proceed with it to fine map the other regions. Most of them co-locate with QTL and could explain the resistance to Mlp. So we demonstrated that, in our context, even if the reference genome is different to the studied genomes, BSA-Seq allowed us to detect quickly and costly, regions which may be involved in a complex trait and improve the fine mapping of a major gene. We think it can be a promising method on a high heterozygous diploid genome as Poplar, to decipher complex trait. Next step is to identify candidate genes within the regions and better describe the mechanisms of resistance