Genome-wide Association Analysis Of Phosphorus Efficiency In Brassica Napus

Oilseed rape(Brassica napus, OSR) is an important oilseed crop in China. More than 80% of the plant area is occupied by Brassica napus which is sensitive to low phosphorus(P) stress. In this study, a natural population containing 189 OSR varieties was employed to conduct hydroponic experiments to investigate shoot and root dry weight, root and shoot ratio and P efficiency coefficient at seedling stage, and to conduct field trials to evaluate the seed yield and yield-related traits at maturing stage under normal P(NP) and low P(LP) conditions, respectively. Genome wide association mapping(GWAS) was conducted to detect the significant genetic loci associated with P efficiency in the association panal of OSR. Comparative analysis between P efficiency associated loci and and quantitative trait loci(QTLs) for P efficiency detected in previous research was carried out, and several major-effect QTLs/SNPs were identified. The candidate genes underlying these genetic loci for P efficiency at seedling stage were predicted. The main results are as follow.1) Phenotypic variation of P efficiency traits of OSR at seedling stage and maturing stage. All the P efficiency related traits investigated at low and normal P treatments showed continuous phenotypic variation in three hydroponic experiments and two-year field trials, indicating all of these traits were quantitative traits and controlled by multiple genes. The coefficient of variation of these traits under different environment was different, ranging from 9.6% to 63.4%. Significant positive correlations were existed for the same trait at the same P treatment between each two trials, which suggested that these P efficient traits were stable in OSR. Hydroponic experiment and field trial could be reliable to evaluate the phenotypic variation of P efficiency related traits.2) GWAS of P-efficiency-related traits of OSR at the seedling stage and mature stage. A total of 625 significant SNP/Indel loci associated with related P efficiency traits were detected by GWAS, including 59 repeatedly detected loci. Of the 51 loci, six were detected at LP treatment, 28 were detected at NP, and 25 were detected for PEC. Four repeatedly detected loci associated with root dry weight(RDW) were detected on chromosome A5, C1 and C6, explaining 8.18-14.09% of phenotypic variation. The repeatedly detected loci was only detected on A7 associated with shoot dry weight(SDW) and total dry weight(TDW), respectively, and the explained phenotypic variation ranged from 1.30% to 4.04%. Sixteen repeatedly detected loci associated with R/S were detected on chromosome A3, A6, A7, C3 and C6, explaining 1.04-9.30% of total phenotypic variation. Twenty-five repeatedly detected loci associated with PEC at seedling stage were detected on chromosome A1, A2, A3, A4, A7, A10, C2 and C3, explaining 3.86-12.80% of phenotypic variation. Twelve repeatedly detected loci associated with plant height(PH) were detected on chromosome A1, A2, A3, A7, A8 and C4, explaining 7.87-24.95% of phenotypic variation. Two repeatedly detected loci associated with FBH were both detected on chromosome A7, explaining 14.63-17.62% of phenotypic variation. One repeatedly detected loci associated with PY was detected on chromosome A9, explaining 3.13% of phenotypic variation.3) Comparative analysis of genome-wide associated P –efficient loci with QTL for P efficiency. Totally, 16 repeatedly detected loci were co-located with 17 QTLs identified in our previous studies. Three loci(indel163230, snp977044 and indel162821) on A6 were co-located with two QTLs controlling SDW and TDW under NP treatment; two loci(indel195116 and snp1180298) on A7 were overlapped with two QTLs for SDW and TDW at LP treatment. Nine loci controlling PEC at seedling stage(snp430986, indel73918, indel93902, snp545597, snp546860, snp1180139, indel195094, snp1165851 and snp2197310) were co-located with nine QTLs on linkage group A03, A04, A07 and C03 for SDW and TDW under both NP and LP levels and other traits, respectively. In addition, two loci(indel235036 and snp1426632) on A8 for PH at NP treatment were co-located with or close to four QTLs for branch number and PH at LP level.4) Candidate genes underlying the genetic loci for P efficiency of Brassica napus. Based on the comparative analysis above, 12 repeatedly detected loci for P efficiency, which were snp728722, snp1962681, snp1618972, snp152244, snp490582, snp1180139, indel211392, snp430986, indel93902, indel163230, snp1165851 and snp2197310, were used to predict the candidate genes. These loci were related to many traits including dry weight and seed yield under LP levels. Finally, a total of 20 candidate genes were identified to be related with P efficiency in Brassica napus. These genes involved in hydrolysis of organic P, and P absorption and transport and regulation under low P environment.