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

Abstract

Background Rapeseed (Brassica napus L.) is an essential source of edible oil and livestock feed, as well as a promising source of biofuel. 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 this, we conducted a genome-wide association study (GWAS) in 327 rapeseed accessions to elucidate the genetic variability of 13 root and biomass traits under low phosphorus (LP; 0.01 mM P +). Furthermore, RNA-sequencing was performed in root among high/low phosphorus efficient groups (HP1/LP1) and high/low phosphorus stress tolerance groups (HP2/LP2) at two-time points under control and P-stress conditions. Results Significant variations were observed in all measured traits, with heritabilities ranging from 0.47 to 0.72, and significant correlations were found between most of the traits. There were 39 significant trait–SNP associations and 31 suggestive associations, which integrated into 11 valid quantitative trait loci (QTL) clusters, explaining 4.24–24.43% of the phenotypic variance observed. In total, RNA-seq identified 692, 1076, 648, and 934 differentially expressed genes (DEGs) specific to HP1/LP1 and HP2/LP2 under P-stress and control conditions, respectively, while 761 and 860 DEGs common for HP1/LP1 and HP2/LP2 under both conditions. An integrated approach of GWAS, weighted co-expression network, and differential expression analysis identified 12 genes associated with root growth and development under LP stress. In this study, 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.

Genome-Wide Association Study (GWAS) for Identifying SNPs and Genes Related to Phosphate-Induced Phenotypic Traits in Tomato (Solanum lycopersicum L.)

“…The recent GWAS conducted in Brassica napus had successfully pinpointed 12 genes linked to root growth and development under low phosphorus (LP) stress. Out of the identified set of twelve genes, six (BnaA04g23490D, BnaA09g08440D, BnaA09g04320D, BnaA09g04350D, BnaA09g04930D, BnaA09g09290D) showcased distinct patterns of expression, signifying their potential as prime candidate genes linked to the desired traits [41]. Similar studies regarding the GWAS on plant biomass were conducted in soybeans, deciphering in total 10 loci encompassing 47 putative candidate genes.…”

Genome-wide association studies of root system architecture traits in a broad collection of Brassica genotypes

“…Furthermore, homologs of three ABC transporter proteins implicated in root suberin synthesis exhibited co-localization with peaks associated with leaf nitrate and phosphorus levels. In another RSA study, Ahmad et al (2023) identified 39 significant single nucleotide polymorphisms (SNPs) on Brassica chromosomes A04, A09, A10, C02, C03, C07, and C09 that were associated with RSA and biomass traits in 327 rapeseed accessions under low phosphorus conditions. Fletcher et al (2016) also reported 20 QTLs on chromosomes A03, A10 and C02, associated with flowering time and root mass in a B. napus doubled haploid population, demonstrating their association with adaptation to drought.…”

“…Furthermore, homologs of three ABC transporter proteins implicated in root suberin synthesis exhibited co-localization with peaks associated with leaf nitrate and phosphorus levels. In another RSA study, Ahmad et al. (2023) identified 39 significant single nucleotide polymorphisms (SNPs) on Brassica chromosomes A04, A09, A10, C02, C03, C07, and C09 that were associated with RSA and biomass traits in 327 rapeseed accessions under low phosphorus conditions.…”