SNP diversity within and among Brassica rapa accessions reveals no geographic differentiation

Genetic diversity was studied in a collection of 61 accessions of Brassica rapa, which were mostly oil-type turnip rapes but also included two oil-type subsp. dichotoma and five subsp. trilocularis accessions, as well as three leaf-type subspecies (subsp. japonica, pekinensis, and chinensis) and five turnip cultivars (subsp. rapa). Two-hundred and nine SNP markers, which had been discovered by amplicon resequencing, were used to genotype 893 plants from the B. rapa collection using Illumina BeadXpress. There was great variation in the diversity indices between accessions. With STRUCTURE analysis, the plant collection could be divided into three groups that seemed to correspond to morphotype and flowering habit but not to geography. According to AMOVA analysis, 65% of the variation was due to variation within accessions, 25% among accessions, and 10% among groups. A smaller subset of the plant collection, 12 accessions, was also studied with 5727 GBS-SNPs. Diversity indices obtained with GBS-SNPs correlated well with those obtained with Illumina BeadXpress SNPs. The developed SNP markers have already been used and will be used in future plant breeding programs as well as in mapping and diversity studies. Keywords: Brassica rapa, SNP, genetic diversity, GBS, STRUCTURE. La diversite genetique a ete etudiee au sein d'une collection de 61 accessions du Brassica rapa, laquelle comprenait principalement des navettes oleagineuses, deux accessions oleagineuses de la subsp. dichotoma et cinq accessions appartenant a la subsp. trilocularis, ainsi que trois sous-especes a feuilles (subsp. japonica pekinensis et chinensis) et cinq cultivars de navet (subsp. rapa). Deux cents neuf marqueurs SNP, decouverts par sequen^age d'amplicons, ont ete employes pour genotyper 893 plantes de cette collection de B. rapa a l'aide d'un appareil Illumina BeadXpress. Une grande variation a ete observee pour les indices de diversite entre accessions. Au moyen d'une analyse STRUCTURE, la collection a ete divisee en trois groupes correspondant au type morphologique et au mode de floraison, mais non ti l'origine geographique. Suite a une analyse AMOVA, il a ete observe que 65% de la variation existait au sein des accessions, 25% entre les accessions et 10% entre les groupes. Un plus petit sous-ensemble de la collection compose de 12 accessions a egalement ete caracterise au moyen de 5727 marqueurs GBS-SNP. Les indices de diversite obtenus a l'aide des GBS-SNP concordaient bien avec ceux obtenus au moyen des SNP Illumina BeadXpress. Les marqueurs SNP ainsi mis au point ont deja ete employes et le seront encore dans de futurs travaux en selection de meme que dans le cadre d'etudes de cartographie et de diversite genetiques. [Traduit par la Redaction] Mots-cles : Brassica rapa, SNP, diversite genetique, GBS, STRUCTURE.
Introduction Brassica rapa L. (2n = 20, AA, haploid genome size 485 Mb) is an obligate out-crossing crucifer grown worldwide. The species is morphologically very variable and contains a large [...]