Genome-wide association study between structural variation, agronomic traits variation and heterosis in maize – CNV-MAIZE

Structural variation (SV) – that encompasses sequence deletions, duplications, insertions, inversions and translocations – has long been considered as rare and meaningless for phenotypic evolution. From recent studies, it is now clear that SV is common to many species including maize, and involves a much greater proportion of the genome than previously thought. Understanding the nature and content of SV in maize will allow to elucidate the structure, evolution and variability of the maize genome. Because maize is a major crop, discovery of particular SVs such as Copy Number Variants (CNVs) or Presence Absence Variants (PAVs) is important regarding their potential contribution to phenotypes, especially as they may account for part of the genetic variation of complex traits and heterosis. The maize germplasm contains contrasted lines that are likely to show large SV. Therefore, to investigate the potential implications of SV in important agronomic traits and heterosis, it is essential to characterize SV for several representative lines.
In the CNV-Maize project, we propose to address these issues using an original approach that combines next generation sequencing and array-based Comparative Genomic Hybridization (aCGH) to reveal maize SVs at the whole genome level. This project will be conducted by 3 French laboratories which are leaders in maize genetics and genomics and statistics. Their partnership gathers complementary skills in molecular biology, bioinformatics and statistics. This project will also take advantage of strong interactions with a U.S. laboratory pioneer in this domain which has been deeply involved in maize genome sequencing, as well as support of a biotechnology company that develops arrays, and of the french National Center for Sequencing (CNS).
In the first part of our project will be to capture SVs among a core collection of genetically distant European and American maize lines, using aCGH array. The maize genome has been sequenced by an American consortium using the B73 U.S. line, and a CGH array for this sequence is available. To capture as many SVs as possible from our core collection, we will complement this array with sequences that are specific of the French F2 line, which is widely used in French breeding programs. Hybridization of the DNAs of our core collection on this pangenomic CGH array will allow to characterize the extent, organization and nature of SV in maize, and will generate a comprehensive dataset of maize SVs.
In the second part of the project, the most relevant SVs will be selected to develop an innovative CGH array dedicated to the genotyping of a large association panel. To decipher whether the use of SVs as genotyping markers will provide information complementary to that of conventional markers such as SNPs for genetic association studies, we will characterize the nature and prevalence of each relevant SV, as well as its link with other polymorphisms. SV data will then be used to investigate the genotype-phenotype association for agronomic traits using an SV-adapted Linkage Disequilibrium mapping approach, with a particular interest in understanding how SVs can be predictive to the heterotic response observed when crossing lines from different genetic groups. We will also develop methodologies to include this new type of information within breeding programs. Finally, high-throughput molecular markers will be derived from the most associated SVs, leading to the construction of a «CNV markers toolkit » that will be useful for the whole maize community, including breeders and researchers. These CNV markers will likely be particularly powerful for further prospects on recombination, heterosis and chromosome plasticity, which are key processes to be elucidated for genetics and breeding programs. Inclusion of markers that are specific to European lines will lead to major improvement for European breeding and is likely to pave the way for future maize research in Europe.