Nucleotide diversity of the ZmPox3 maize peroxidase gene: Relationships between a MITE insertion in exon 2 and variation in forage maize digestibility

BACKGROUND: Polymorphisms were investigated within the ZmPox3 maize peroxidase gene, possibly involved in lignin biosynthesis because of its colocalization with a cluster of QTL related to lignin content and cell wall digestibility. The purpose of this study was to identify, on the basis of 37 maize lines chosen for their varying degrees of cell wall digestibility and representative of temperate regions germplasm, ZmPox3 haplotypes or individual polymorphisms possibly associated with digestibility. RESULTS: Numerous haplotypes with high diversity were identified. Frequency of nucleotide changes was high with on average one SNP every 57 bp. Nucleotide diversity was not equally distributed among site categories: the estimated π was on average eight times higher for silent sites than for non-synonymous sites. Numerous sites were in linkage disequilibrium that decayed with increasing physical distance. A zmPox3 mutant allele, carrying an insertion of a transposable element in the second exon, was found in lines derived from the early flint inbred line, F7. This element possesses many structural features of miniature inverted-repeat transposable elements (MITE). The mutant allele encodes a truncated protein lacking important functional sites. An ANOVA performed with a subset of 31 maize lines indicated that the transposable element was significantly associated with cell wall digestibility. This association was confirmed using an additional set of 25 flint lines related to F7. Moreover, RT-PCR experiments revealed a decreased amount of corresponding mRNA in plants with the MITE insertion. CONCLUSION: These results showed that ZmPox3 could possibly be involved in monolignol polymerisation, and that a deficiency in ZmPox3 peroxidase activity seemingly has a negative effect on cell wall digestibility. Also, genetic diversity analyses of ZmPox3 indicated that this peroxidase could be a relevant target for grass digestibility improvement using specific allele introgressions

Genetic and ecophysiological dissection of tolerance to drought and heat stress in bread wheat: from environmental characterization to QTL detection

National audienc

Clustering of Environmental Parameters Discriminates Drought and Heat Stress Bread Wheat Trials

International audienceWheat (Triticum aestivum L.) is the most widely cultivated crop worldwide and faces a wide range of stresses. To make effective crop improvement decisions, environmental characterization is of paramount importance. This study presents a new methodology for characterizing the environment that enables replacing the conventional arbitrary classification of the environment by a series of environmental covariates that capture and describe the stresses the plant encounters. Three CIMMYT bread wheat populations, combining complementary heat and drought adaptive traits, were grown over 3 yr in northwestern Mexico under limited irrigation, heat stress, and irrigated conditions. The network comprised 15 trials representing seven treatment x year combinations as experimental environments, referred to here as the "Environment". Environmental characterization was performed at the trial scale. Twelve stress thresholds related to eight environmental factors were combined to obtain 11 potential growth limiting factors. Thirty-three environmental covariates were obtained by calculating when these limiting factors occurred for each of three key-developmental-phases across all trials. Cluster analysis allowed grouping environmental covariates into six distinct clusters corresponding to six "environmental scenarios". One representative environmental covariate was extracted from each cluster and taken together explained more than 90% of the variance for yield in the Environment. Principal component analysis discriminated the seven experimental environments and identified its stress characteristics. We conclude that the method developed characterized the main stresses and their impact on average population performance, and the representative covariates efficiently replaced the Environment. As such, they will facilitate the dissection of genotype x environment interaction (GEI) for yield-related traits

Genetic Architecture of Flowering Time in Maize As Inferred From Quantitative Trait Loci Meta-analysis and Synteny Conservation With the Rice Genome

Genetic architecture of flowering time in maize was addressed by synthesizing a total of 313 quantitative trait loci (QTL) available for this trait. These were analyzed first with an overview statistic that highlighted regions of key importance and then with a meta-analysis method that yielded a synthetic genetic model with 62 consensus QTL. Six of these displayed a major effect. Meta-analysis led in this case to a twofold increase in the precision in QTL position estimation, when compared to the most precise initial QTL position within the corresponding region. The 62 consensus QTL were compared first to the positions of the few flowering-time candidate genes that have been mapped in maize. We then projected rice candidate genes onto the maize genome using a synteny conservation approach based on comparative mapping between the maize genetic map and japonica rice physical map. This yielded 19 associations between maize QTL and genes involved in flowering time in rice and in Arabidopsis. Results suggest that the combination of meta-analysis within a species of interest and synteny-based projections from a related model plant can be an efficient strategy for identifying new candidate genes for trait variation

Environmental characterization and QTL detection to dissect wheat tolerance to drought and high temperature

International audienc

Le maïs et le blé, céréales modèles pour la recherche en biologie intégrative et son application à la sélection

66 ref. chap. 23National audienc

MAIZEWALL. Database and developmental gene expression profiling of cell wall biosynthesis and assembly in maize

MAIZEWALL database : http://www.polebio.scsv-tlse.fr/MAIZEWALLInternational audienc

Identification of glu-B1-1 as a candidate gene for the quantity of high-molecular-weight glutenin in bread wheat (Triticum aestivum L.) by means of an association study

A previous study in wheat (Triticum aestivum L.) identified two candidate genes controlling a quantitative trait locus (QTL) for high-molecular-weight glutenin subunit (HMW-GS) GluBx. These candidates were Glu-B1-1, the structural gene coding for Glu1Bx,and the B homoeologous gene coding for SPA (spa-B), a seed storage protein activator. The goal of this study was to identify the best candidate gene for this QTL. Single nucleotide polymorphisms (SNPs) are an abundant source of DNA polymorphisms that have been successfully used to identify loci associated with particular phenotypes. As no linkage disequilibrium was detected between Glu-B1-1 and spa-B, we performed an association study to identify the individual gene responsible for the QTL. Six SNPs, three located in Glu-B1-1 and three in spa-B, were genotyped by mass spectrometry in a collection of 113 bread wheat lines. These lines were also evaluated for protein content as well as the total quantity of HMW-GSs and of each HMW-GS in seed samples from two harvest years. Significant associations were detected only between Glu-B1-1 polymorphism and most of the traits evaluated. Spa-B was unambiguously discarded as a candidate. To our knowledge, this is the first report on an association study that was successfully used to discriminate between two candidate genes