Biology subjects

Pichon, J.-P.

Publications and source records attributed to Pichon, J.-P..

2 recordsLinked to original sources

bioRxiv2022

SNP discovery by exome capture and resequencing in a pea genetic resource collection

Background & SummaryIn addition to being the model plant used by Mendel1 to establish genetic laws, pea (Pisum sativum L., 2n=14) is a major pulse crop cultivated in many temperate regions of the world. In order to face new challenges imposed particularly by global climate change and new regulations targeted at reducing chemical inputs, pea breeders have to take advantage of the genetic diversity present in the Pisum genepool to develop improved, resilient varieties. The aim of this study was to assess the genetic diversity of a pea germplasm collection and allow genome-wide association studies using this collection. To be able to perform genome-wide association approaches with high resolution, genotyping with a large set of genetic markers such as Single Nucleotide Polymorphism (SNP) markers well-spread over the genome is required. Rapid advances in second-generation sequencing technologies and the development of bioinformatic tools have revolutionized the access to and the characterization of available genetic diversity. High-density, high-throughput genotyping has been possible for a large number of species, including those with large and complex genomes2 such as pea (2n=14) which genome size is estimated to be 4.45 Gb3. In this study, which is part of the PeaMUST project4, we used a target capture technology based on pea transcriptome sequences to generate exome-enriched genomic libraries that were further subjected to Illumina sequencing in paired-end mode. This methodology was chosen because whole-genome resequencing is relatively expensive for species with large genomes and because capturing genetic variations in repeated non-coding regions is difficult to achieve or to interpret5. Whole-exome sequencing represented an interesting alternative that focused on coding regions only6,7. Mapping the obtained reads on the reference pea genome sequence enabled the discovery of an abundant set of SNPs. The development of this resource is a crucial cornerstone in research and breeding projects towards boosting the improvement of pea production and quality.

genomics↗

bioRxiv2018

High throughput genotyping of structural variations in a complex plant genome using an original Affymetrix(R) Axiom(R) array

BackgroundInsertions/deletions (InDels) and more specifically presence/absence variations (PAVs) are pervasive in several species and have strong functional and phenotypic effect by removing or drastically modifying genes. Genotyping of such variants on large panels remains poorly addressed, while necessary for approaches such as association mapping or genomic selection.\n\nResultsWe have developed, as a proof of concept, a new high-throughput and affordable approach to genotype InDels. We first identified 141,000 InDels by aligning reads from the B73 line against the genome of three temperate maize inbred lines (F2, PH207, and C103) and reciprocally. Next, we designed an Affymetrix(R) Axiom(R) array to target these InDels, with a combination of probes selected at breakpoint sites (13%) or within the InDel sequence, either at polymorphic (25%) or non-polymorphic sites (63%) sites. The final array design is composed of 662,772 probes and targets 105,927 InDels, including PAVs ranging from 35bp to 129kbp. After Affymetrix(R) quality control, we successfully genotyped 86,648 polymorphic InDels (82% of all InDels interrogated by the array) on 445 maize DNA samples with 422,369 probes. Genotyping InDels using this approach produced a highly reliable dataset, with low genotyping error (~3%), high call rate (~98%), and high reproducibility (>95%). This reliability can be further increased by combining genotyping of several probes calling the same InDels (<0.1% error rate and >99.9% of call rate for 5 probes). This \"proof of concept\" tool was used to estimate the kinship matrix between 362 maize lines with 57,824 polymorphic InDels. This InDels kinship matrix was highly correlated with kinship estimated using SNPs from Illumina 50K SNP arrays.\n\nConclusionsWe efficiently genotyped thousands of small to large InDels on a sizeable number of individuals using a new Affymetrix(R) Axiom(R) array. This powerful approach opens the way to studying the contribution of InDels to trait variation and heterosis in maize. The approach is easily extendable to other species and should contribute to decipher the biological impact of InDels at a larger scale.

genomics↗