Genome wide association mapping and candidate gene mining for root architectural traits in rapeseed/canola (Brassica napus L.) at late growth stage

Abstract

Rapeseed/canola (Brassica napus L.) root system varied widely among the winter and spring growth habits in late growth stages. In this study, we have phenotyped seven different root architectural traits with a diversity panel consisting of 224 B. napus accessions grown in greenhouse during 2015 and 2016. A genome-wide association study with 37,500 single nucleotide polymorphism markers was conducted to detect marker trait association. A total of 52 significant marker loci were identified at 0.01 percentile tail P value cutoff for different root traits, ten loci for root length (RL), eleven loci for root angle (RA), nine loci each for number of primary root branches (PRB) and root dry weight, seven loci for root vigor score (RVS), and six loci for root diameters at two points (R1Dia and R2Dia). Majority of those significant marker loci were distributed on five chromosomes, A01, A02, A04, C03 and C06. Twenty-two candidate genes related to root traits and root development were detected within 50 kbp upstream and downstream of different significant markers. Three of these candidate genes, P-glycoprotein 6 (PGP6), Tetraspanin 7 (TET7) and ARABIDILLO-2 were detected within the marker loci chrC03_12098594 (RL), chrA01_8813067 (PRB), and chrA04_rand_54410 (R1Dia). Multiple marker loci associated with different root traits were detected within a close physical distances on chromosome A01, A02, A04 and C03 referring possible co-localization of the loci for different root traits. Twelve significant markers were validated the marker-trait association for PRB, RVS, RL and RA in 20 germplasm accessions.