Genetic variation for lignin content and cell wall digestibility in early maize lines derived from ancient landraces

International audienceRemarkable genetic improvement in maize yield, lodging resistance, biotic and abiotic stress tolerance were obtained during the 1955 - 2000 period in Europe. However, a decline in the average cell wall digestibility of maize hybrids has been observed during the 1980 - 2000 period. This trend has now ceased with the breeding of specialized silage varieties. The cell wall degradability of the best current hybrids does not yet equal that of better old types of the 1960s era such as INRA258, mostly because the germplasm currently used in maize breeding corresponds to progenies of resources initially chosen for grain maize breeding. Nearly 110 new lines were thus derived by self-pollination in old or unused landraces and accessions in order to test the interest of this kind of genetic resources in maize breeding for cell wall degradability traits. Based on per se and topcross experiments, several lines representative of different and new germplasm displayed high or medium high cell wall digestibility. F7103 (Argentina-BBC143), F7104 (Argentina-BBC325), F7106 (Gelderland-VC150), F7114 (Zakarpatskaja-Zeltaja-Zubovidnaja), and F7121 (Comptons-Early) are likely among the more romising new resource lines for improvement of cell wall digestibility in elite dent or flint germplasm. These lines covered a large genetic diversity as F7103 and F7104 are mostly lowland tropical, F7106 and F7121 mostly northern flint, F7114 mostly Oh43/Minnesota13 related. Two other lines of medium-high cell wall digestibility, F7101 (St Engrace) and F7112 (Mecklenburger), were shown to be significantly related to lowland tropical germplasm. Several landraces or old varieties also gave lines of low cell wall digestibility such as F7124 (Curaco-de-Velez) or F7126 (Baanbreker), both related to the northern flint group. Average yield of top-crossed lines was nearly 7 t/ha lower than the average value of the three control hybrids and only one hybrid (F7104 x UH002) had yield and earliness equal to those of control hybrids. These low values were related to the fact that investigated lines were derived from old resources that did not get the last 60 years genetic improvements, and also to the only use of a flint male for top-crosses that did not optimize the genetic distance with all top-crossed lines. Allele sequencing and association genetics should give markers for targeted introgression of new alleles of interest originating from this specific set of lines in elite lines

FT genome A and D polymorphisms are associated with the variation of earliness components in hexaploid wheat

The transition from vegetative to floral meristems in higher plants is determined by the coincidence of internal and environmental signals. Contrary to the photoperiod pathway, convergent evolution of the cold-dependent pathway has implicated different genes between dicots and monocots. Whereas no association between natural variation in vernalization requirement and Flowering time locus T (FT) gene polymorphism has been described in Arabidopsis, recent studies in Triticeae suggest implication of orthologous copies of FT in the cold response. In our study, we show that nucleotide polymorphisms on A and D copies of the wheat FT gene were associated with variations for heading date in a collection of 239 lines representing diverse geographical origins and status (landraces, old or recent cultivars). Interestingly, polymorphisms in the non-coding intronic region were strongly associated to flowering variation observed on plants grown without vernalization. But differently from VRN1, no epistatic interaction between FT homeologous copies was revealed. In agreement with the results of association study, the A and D copies of FT were mapped in regions including major QTLs for earliness traits in hexaploid wheat. This work, by identifying additional homeoalleles involved in wheat vernalization pathway, will contribute to a better understanding of the control of flowering, hence providing tools for the breeding of varieties with enhanced adaptation to changing environments

Microsatellite markers for Pinus pinaster Ait.

Simple sequence repeats (SSRs) or microsatellites are valuable tools for genome mapping and population genetic studies for as they are codominant and highly polymorphic markers. Seventy-six SSR primer pairs from four Pinus species were tested to amplify microsatellites in Pinus pinaster. Twenty-six primer pairs were stemmed from a microsatellite library on P. pinaster and the other primer pairs were obtained in other species of the same genus (P. radiata, P. strobus and P. halepensis). Only three out of the 76 SSR primer pairs amplified at a single polymorphic locus in P. pinaster. The Mendelian inheritance of those three primer pairs was studied and their genetic map position was determined. The number of alleles and the level of heterozygosity were assessed in an analysis of a sample of 196 trees. The development of microsatellites in Pinus species has been reported to be a difficult task because of the size and complexity of their genome. The results of this study showed that cross-species amplification was quite unsuccessful.Marqueurs microsatellites chez Pinus pinaster Ait. Les microsatellites (SSRs) sont des outils de choix pour la cartographie génétique et les études de génétique des populations parce qu'ils sont des marqueurs codominants et très polymorphes. Soixante-seize paires d'amorces de quatre espèces de pin ont été utilisées afin d'amplifier des microsatellites chez Pinus pinaster. Vingt-neuf paires d'amorces étaient issues d'une banque enrichie en microsatellites sur P. pinaster et les autres paires d'amorces avaient été obtenues sur d'autres espèces du même genre (P. radiata, P. strobus et P. halepensis). Sur un total de 76 paires d'amorces, seulement trois ont amplifié un seul locus microsatellite polymorphe chez P. pinaster. Leur ségrégation mendélienne a été étudiée et chaque locus a été localisé sur une carte génétique. Le nombre d'allèles et l'hétérozygotie ont été ensuite évalués en analysant un échantillon de 196 arbres. Le développement de microsatellites chez les espèces du genre Pinus s'est révélée difficile en raison de la taille et de la complexité de leur génome. Les résultats de cette étude ont montré que l'amplification inter-espèces n'a rencontré que peu de succès

Maize genetic diversity and association mapping using transposable element insertion polymorphisms

Transposable elements are the major component of the maize genome and presumably highly polymorphic yet they have not been used in population genetics and association analyses. Using the Transposon Display method, we isolated and converted into PCR-based markers 33 Miniature Inverted Repeat Transposable Elements (MITE) polymorphic insertions. These polymorphisms were genotyped on a population-based sample of 26 American landraces for a total of 322 plants. Genetic diversity was high and partitioned within and among landraces. The genetic groups identified using Bayesian clustering were in agreement with published data based on SNPs and SSRs, indicating that MITE polymorphisms reflect maize genetic history. To explore the contribution of MITEs to phenotypic variation, we undertook an association mapping approach in a panel of 367 maize lines phenotyped for 26 traits. We found a highly significant association between the marker ZmV1-9, on chromosome 1, and male flowering time. The variance explained by this association is consistent with a flowering delay of +123 degree-days. This MITE insertion is located at only 289 nucleotides from the 3′ end of a Cytochrome P450-like gene, a region that was never identified in previous association mapping or QTL surveys. Interestingly, we found (i) a non-synonymous mutation located in the exon 2 of the gene in strong linkage disequilibrium with the MITE polymorphism, and (ii) a perfect sequence homology between the MITE sequence and a maize siRNA that could therefore potentially interfere with the expression of the Cytochrome P450-like gene. Those two observations among others offer exciting perspectives to validate functionally the role of this region on phenotypic variation

Identification and characterization of water-stress-responsive genes in hydroponically grown maritime pine (Pinus pinaster) seedlings

International audienc

Identification and characterization of water-stress-responsive genes in hydroponically grown maritime pine (Pinus pinaster) seedlings

International audienc

Disentangling group specific QTL allele effects from genetic background epistasis using admixed individuals in GWAS: An application to maize flowering.

When handling a structured population in association mapping, group-specific allele effects may be observed at quantitative trait loci (QTLs) for several reasons: (i) a different linkage disequilibrium (LD) between SNPs and QTLs across groups, (ii) group-specific genetic mutations in QTL regions, and/or (iii) epistatic interactions between QTLs and other loci that have differentiated allele frequencies between groups. We present here a new genome-wide association (GWAS) approach to identify QTLs exhibiting such group-specific allele effects. We developed genetic materials including admixed progeny from different genetic groups with known genome-wide ancestries (local admixture). A dedicated statistical methodology was developed to analyze pure and admixed individuals jointly, allowing one to disentangle the factors causing the heterogeneity of allele effects across groups. This approach was applied to maize by developing an inbred "Flint-Dent" panel including admixed individuals that was evaluated for flowering time. Several associations were detected revealing a wide range of configurations of allele effects, both at known flowering QTLs (Vgt1, Vgt2 and Vgt3) and new loci. We found several QTLs whose effect depended on the group ancestry of alleles while others interacted with the genetic background. Our GWAS approach provides useful information on the stability of QTL effects across genetic groups and can be applied to a wide range of species

Deciphering the genetic diversity of landraces with high-throughput SNP genotyping of DNA bulks: methodology and application to the maize 50k array Mariangela Arca

Genebanks harbor original landraces carrying many original favorable alleles for mitigating biotic and abiotic stresses. Their genetic diversity remains however poorly characterized due to their large within genetic diversity. We developed a high-throughput, cheap and labor saving DNA bulk approach based on SNP Illumina Infinium HD array to genotype landraces. Samples were gathered for each landrace by mixing equal weights from young leaves, from which DNA was extracted. We then estimated allelic frequencies in each DNA bulk based on fluorescent intensity ratio (FIR) between two alleles at each SNP using a two step-approach. We first tested either whether the DNA bulk was monomorphic or polymorphic according to the two FIR distributions of individuals homozygous for allele A or B, respectively. If the DNA bulk was polymorphic, we estimated its allelic frequency by using a predictive equation calibrated on FIR from DNA bulks with known allelic frequencies. Our approach: (i) gives accurate allelic frequency estimations that are highly reproducible across laboratories, (ii) protects against false detection of allele fixation within landraces. We estimated allelic frequencies of 23,412 SNPs in 156 landraces representing American and European maize diversity. Modified Roger’s genetic Distance between 156 landraces estimated from 23,412 SNPs and 17 SSRs using the same DNA bulks were highly correlated, suggesting that the ascertainment bias is low. Our approach is affordable, easy to implement and does not require specific bioinformatics support and laboratory equipment, and therefore should be highly relevant for large-scale characterization of genebanks for a wide range of species

Deciphering the Genetic Diversity of Landraces With High-Throughput SNP Genotyping of DNA Bulks: Methodology and Application to the Maize 50k Array

International audienceGenebanks harbor original landraces carrying many original favorable alleles for mitigating biotic and abiotic stresses. Their genetic diversity remains, however, poorly characterized due to their large within genetic diversity. We developed a high-throughput, cheap and labor saving DNA bulk approach based on single-nucleotide polymorphism (SNP) Illumina Infinium HD array to genotype landraces. Samples were gathered for each landrace by mixing equal weights from young leaves, from which DNA was extracted. We then estimated allelic frequencies in each DNA bulk based on fluorescent intensity ratio (FIR) between two alleles at each SNP using a two step-approach. We first tested either whether the DNA bulk was monomorphic or polymorphic according to the two FIR distributions of individuals homozygous for allele A or B, respectively. If the DNA bulk was polymorphic, we estimated its allelic frequency by using a predictive equation calibrated on FIR from DNA bulks with known allelic frequencies. Our approach: (i) gives accurate allelic frequency estimations that are highly reproducible across laboratories, (ii) protects against false detection of allele fixation within landraces. We estimated allelic frequencies of 23,412 SNPs in 156 landraces representing American and European maize diversity. Modified Roger’s genetic Distance between 156 landraces estimated from 23,412 SNPs and 17 simple sequence repeats using the same DNA bulks were highly correlated, suggesting that the ascertainment bias is low. Our approach is affordable, easy to implement and does not require specific bioinformatics support and laboratory equipment, and therefore should be highly relevant for large-scale characterization of genebanks for a wide range of species