Quantitative trait loci mapping reveals important genomic regions controlling root architecture and shoot biomass under nitrogen, phosphorus, and potassium stress in rapeseed (Brassica napus L.)

Abstract

Plants rely on root systems for nutrient uptake from soils. Marker-assisted selection helps breeders to select desirable root traits for effective nutrient uptake. Here, 12 root and biomass traits were investigated at the seedling stage under low nitrogen (LN), low phosphorus (LP), and low potassium (LK) conditions, respectively, in a recombinant inbred line (RIL) population, which was generated from Brassica napus L. Zhongshuang11 and 4D122 with significant differences in root traits and nutrient efficiency. Significant differences for all the investigated traits were observed among RILs, with high heritabilities (0.43–0.74) and high correlations between the different treatments. Quantitative trait loci (QTL) mapping identified 57, 27, and 36 loci, explaining 4.1–10.9, 4.6–10.8, and 4.9–17.4% phenotypic variances under LN, LP, and LK, respectively. Through QTL-meta analysis, these loci were integrated into 18 significant QTL clusters. Four major QTL clusters involved 25 QTLs that could be repeatedly detected and explained more than 10% phenotypic variances, including two NPK-common and two specific QTL clusters (K and NK-specific), indicating their critical role in cooperative nutrients uptake of N, P, and K. Moreover, 264 genes within the four major QTL clusters having high expressions in roots and SNP/InDel variations between two parents were identified as potential candidate genes. Thirty-eight of them have been reported to be associated with root growth and development and/or nutrient stress tolerance. These key loci and candidate genes lay the foundation for deeper dissection of the NPK starvation response mechanisms in B. napus.

Integrating genome-wide association study with transcriptomic data to predict candidate genes influencing Brassica napus root and biomass-related traits under low phosphorus conditions

“…The associated population's extensive diversity was shown by a significant coefficient of variation (> 10%) for all investigated root and shoot biomass traits (Table 2 ). Seedlings cultivated under LP conditions had lower SFW and TFW but higher RSRF, SDW, and RSRD than seedlings grown under control (CK) conditions, as previously reported [ 11 , 49 ]. This may be attributed to the fact that plants tend to allocate a greater proportion of biomass to their roots.…”

“…The current study findings identified several loci which were in line with the previous reports on several dynamic traits in different crops [ 48 , 58 – 61 ]. Seven QTL clusters ( RT-A901-1, RT-A09-2, RT-A10-1, RT-C03-2, RT-C03-3, RT-C07-1, RT-C09-2 ) in the present study were co-localized with previously identified loci related to root and biomass traits under low nitrogen conditions using association mapping population [ 57 ], while two QTL clusters ( RT-A09-1, RT-C02-1 ) were found co-localized with the previously identified loci ( qc.A09-2, qcC02-2 ) related to root and biomass traits under low nitrogen, phosphorus, and potassium (NPK) and control conditions, respectively, using linkage mapping population in rapeseed [ 40 , 49 ]. These findings indicate that these genomic regions may harbor genes with pleiotropic effects related to different root and biomass traits under low-phosphorus conditions at the rapeseed seedling stage.…”

Genome-wide transcriptome analysis unravels genetic variants associated with root and biomass-related traits under low phosphorus conditions in Rapeseed (Brassica napus L.)

“…The associated population's extensive diversity was shown by a signi cant coe cient of variation (> 10%) for all investigated root and shoot biomass traits (Table 2). Seedlings cultivated under LP conditions had lower SFW and TFW but higher RSRF, SDW, and RSRD than seedlings grown under control (CK) conditions, as previously reported [11,45]. This may be attributed to the fact that plants tend to allocate a greater proportion of biomass to their roots.…”

Morpho-physiological, Genomic, and Transcriptional Diversities in Response to Potassium Deficiency in Rapeseed (Brassica napus L.) Genotypes

“…21 Significant differences in K use efficiency (KUE) or low K resistance were identified among different rapeseed genotypes, 22 which highlighted the complex response mechanisms. Studies on B. napus have investigated the impact of K deficiency on photosynthesis and leaf size, 23 root morphological traits as related to low K resistance, 24 variations in root growth performance of rapeseed, 18,25 and some other agronomic traits affecting low K resistance at the seedling stage. 20 Sufficient K was reported to improve inorganic phosphate-limited photosynthesis, 26 central carbon metabolism, 23 and diel leaf growth 12 and also influence the mesophyll structure 27 in B. napus.…”