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

Abstract

Background Oilseed rape (Brassica napus L.) is a crucial source of edible oil and livestock feeding, and is a promising biofuel crop. The increasing demand for oilseed rape requires strategies to increase yield while retaining quality. Breeding crops with an ideal root system architecture (RSA) for high phosphorus use efficiency (PUE) is an effective way to reduce the use of phosphate fertilizers. However, the genetic mechanisms that underpin PUE in rapeseed remain elusive. To address that, we performed a genome-wide association study (GWAS) in 327 rapeseed accessions to unravel the genetic variations in 13 root and biomass traits under low phosphorus (LP; 0.01mM P+). Results All measured traits exhibited significant variations with heritabilities ranging from 0.47 to 0.72, and most traits revealed substantial correlations. GWAS identified 39 significant and 31 suggestive trait-SNP associations that integrated into 11 valid quantitative trait loci (QTL) clusters and explained 4.24–24.43% of the phenotypic variance. Furthermore, RNA-sequencing among high and low PUE lines evaluated the expression levels of candidate genes in root at two-time points. In total, 692, 1076, 648, and 934 differentially expressed genes (DEGs) specific to HP1/LP1, HP1CK/LP1CK, HP2/LP2, and HP2CK/LP2CK, respectively, while 761 and 860 DEGs were found common for HP1/LP1/HP1CK/LP1CK and HP2/LP2/HP2CK/LP2CK, respectively. Twelve genes have been identified as associated with root growth and development under LP stress using an integrated approach of GWAS, weighted co-expression network, and differential expression analysis. In previous studies, six genes (BnaA04g23490D, BnaA09g08440D, BnaA09g04320D, BnaA09g04350D, BnaA09g04930D, BnaA09g09290D) that showed differential expression were identified as promising candidate genes for the target traits. Conclusion 11 QTL clusters and 12 candidate genes associated with root and development under LP stress were identified in this study. Our study's phenotypic and genetic information may be exploited for genetic improvement of root traits to increase PUE in rapeseed.