Search

Characterizing the genomic diversity of species is critical to understand the molecular origin of phenotypic variations. Whole genome sequence assemblies at the chromosome scale with low amount of missing data are critical resources for answering such questions. Our aim is to explore combination of technologies to answer those questions, and to find the best one. Using a specific Maize line, we have tested different sequencing applications to build a "high quality genome" and identify a large collection of genome variants. Here we demonstrate that the use of HIFI reads combined with Hi-C and Linked-reads generate a chromosome-scale genome assembly with a better contiguity than the reference genome B73. Moreover we show, that PacBio CLR reads allow a wide detection of structural variants of the genomes.

Understanding the mechanisms of adaptation to the environment in cultivated plants is a promising way to meet the challenge of maintaining food security in the context of global warming. In the case of maize, high-throughput sequencing has revealed that structural variations represent a large part of the genome and could have huge phenotypic effects. Among these, Presence Absence Variants (PAVs, which include insertion/deletion of large DNA sequences) may be involved in adaptation of maize to its environment, but their contribution to the genetic determinism of traits and genotype by environment interactions remains largely unknown. To address this issue, we performed a genome-wide association study between two types of polymorphisms, SNPs and InDels, and molecular traits obtained from proteomics and metabolomics analyses to detect quantitative trait loci (QTLs). The genetic panel used for this study was composed of 254 dent inbred lines genotyped with 978,134 SNPs and 72,041 InDels. The latter encompassed from 37 to 129,700 pb, including thousands of PAVs that are not present in the B73 reference genome. Proteins and metabolites were quantified by mass spectrometry in leaf samples from F1 hybrids obtained by crossing the inbred lines with one flint tester line. Hybrid plants were grown under two watering conditions (well-watered and water deficit) in greenhouse. In total, we detected 61,225 QTLs associated with proteome or metabolome variations. Among these, 4,766 QTLs were exclusively detected by InDels. To take into account the difference of marker density between InDels and SNPs, we used a re-sampling approach which showed that there was no difference between InDels and SNPs regarding the number and effect of the QTLs detected . Additionally, the QTLs detected by the two types of polymorphism were equally distributed in the two watering conditions. These preliminary results show that InDels are worse considering to detect new genetic regions of interest. They also suggest that InDels and SNPs equally contribute to molecular trait variation and response to drought stress.

International audience; Aquaporins are channel proteins facilitating the movement of water and other small solutes across biological membranes. They are involved in multiple cellular and physiological processes and play indisputable roles in the adaptation to the environment. While the dynamics of aquaporin genes expression profiles over daytime, organs, development stages and in response to environmental cues, has been extensively reported, descriptions of some precise molecular components of this regulation are scarce.Measurements of gene expression of five plasma membrane aquaporins (PIPgenes) in maize leaves (elongation and mature zones) across a 252-hybrid panel (DROPS panel) by RT-qPCR revealed the existing diversity and pointed at different profiles of variability thatimply different effects of selection over time on different aquaporin isoforms. GWAS and covariate GWAS allowed mapping numerous eQTLs, both local and distant. The implementation of a double fluorescent promoter activity reporter assay, transformed by biolistic into entire maize plants, allowed the evaluation of bothcisandtrans-acting regulatory candidates. Among them, a MITE-containing indel within aPIPgene promoter region, and a distant NAC transcription factor, were successfully identified as actors of thePIPgene regulation. Further steps should be directed to reveal the physiological relevance of such regulations.

International audience; Understanding the mechanisms of adaptation to the environment in cultivated plants is a promising way to meet the challenge of maintaining food security in the context of global warming. In the case of maize, high-throughput sequencing has revealed that structural variations represent a large part of the genome and could have huge phenotypic effects. Among these, Presence Absence Variants (PAVs) may be involved in adaptation of maize to its environment, but their contribution to the genetic determinism of traits and genotype by environment interactions remains largely unknown. To address this issue, we performed a genome-wide association study between two types of polymorphisms, SNPs and Insetions/Deletions (InDels), and molecular traits obtained from proteomics and metabolomics analyses. The genetic panel used for this study was composed of 254 dent inbred lines genotyped with 978,134 SNPs and 72,041 InDels. The latter encompassed from 37 to 129,700 pb, including thousands of PAVs that are not present in the B73 reference genome. Proteins and metabolites were quantified by mass spectrometry in leaf samples from F1 hybrids obtained by crossing the inbred lines with one flint tester line. Hybrid plants were grown under two watering conditions (well-watered and water deficit) in greenhouse. In total, we detected 61,225 QTLs associated with proteome or metabolome variations. Among these, 4,766 QTLs were exclusively detected by InDels. To take into account the difference of marker density between InDels and SNPs, we used a re-sampling approach which showed that there is no difference for effect size distribution of QTLs between InDels and SNPs and for the number of QTLs detected by InDels or SNPs. Additionally, the QTLs detected by the two types of polymorphism were equally distributed in the two watering conditions. Our results suggest that InDels and SNPs equally contributed to molecular trait variation and response to drought stress.

From the 17th century until the arrival of hybrids in 1960s, maize landraces were cultivated in the South-West of France, a traditional region for maize cultivation. A set of landraces were collected in this region between the 1950s and 1980s and were then conservedex situin a germplam collection. Previous studies using molecular markers on approx. twenty landraces fo this region showed that they belonged to a Pyrenees-Galicia Flint genetic group and originated from hybridization between Caribbean and Northern Flint germplasms introduced in Europe. In this study, we assessed the structure and genetic diversity of 194 SWF maize landraces to elucidate their origin, using a 50K SNP array and a bulk DNA approach. We identified two weakly differentiated genetic groups, one in the Western part and the other in the Eastern part. We highlighted the existence of a longitudinal gradient along the SWF area that was probably maintained through the interplay between genetic drifts and restricted gene flows, rather than through differential climatic adaptation. The contact zone between the two groups observed near the Garonne valley may be the result of these evolutionnary forces. We found only few significant cases of hybridization between Caribbean and Northern Flint germplasms in the region. We also found gene flows from various maize genetic groups to SWF landraces. Thus, we assumed that SWF landraces had a multiple origin with a slightly higher influence of Tropical germplasm in the West and preponderance of Northern Flint germplasm in the East.

Background and objectives Characterizing the genomic diversity of maize is critical to understand the molecular origin of structural variation, and is a prerequisite to underpin the functional variation underlying phenotypic variation. Whole genome sequence assemblies at the chromosome scale with low amount of missing data are critical resources for answering such questions. Whole genome sequence assemblies are now available for several maize inbred lines, but this is still missing for a number of key founders used in European maize breeding programs. This concerns the dent genetic pool and the European specific flint genetic group. Therefore, we have established a list of 13 priority lines for de novo sequencing as part of the SeqOccIn project.