Genome-Wide Association Study of Root System Architecture in Maize

Abstract

Roots are important plant organs for the absorption of water and nutrients. To date, there have been few genome-wide association studies of maize root system architecture (RSA) in the field. The genetic basis of maize RSA is poorly understood, and the maize RSA-related genes that have been cloned are very limited. Here, 421 maize inbred lines of an association panel were planted to measure the root systems at the maturity stage, and a genome-wide association study was performed. There was a strong correlation among eight RSA traits, and the RSA traits were highly correlated with the aboveground plant architecture traits (e.g., plant height and ear leaf length, r = 0.13–0.25, p < 0.05). The RSA traits of the stiff stalk subgroup (SS) showed lower values than those of the non-stiff stalk subgroup (NSS) and tropical/subtropical subgroup (TST). Using the RSA traits, the genome-wide association study identified 63 SNPs and 189 candidate genes. Among them, nine candidate genes co-localized between RSA and aboveground architecture traits. A further co-expression analysis identified 88 candidate genes having high confidence levels. Furthermore, we identified four highly reliable RSA candidate genes, GRMZM2G099797, GRMZM2G354338, GRMZM2G085042, and GRMZM5G812926. This research provides theoretical support for the genetic improvement of maize root systems, and it identified candidate genes that may act as genetic resources for breeding.

Deciphering the Genetic Basis of Root and Biomass Traits in Rapeseed (Brassica napus L.) through the Integration of GWAS and RNA-Seq under Nitrogen Stress

“…Nitrogen stress is a major limiting factor for crop production worldwide, and plant RSA is of great significance in nutrient stress tolerance [ 39 ]. In recent years, the use of RSA is predicted to result in a “second green revolution” in agriculture [ 13 , 40 ]. Different phenotyping methodologies for early crops’ RSA screening were used, expecting that genotypes with diverse root architecture at the seedling stage would respond similarly at the adult stage when water and/or nutrients became limited for grain yield [ 12 ].…”

Genome-Wide Association Study of Complex Traits in Maize Detects Genomic Regions and Genes for Increasing Grain Yield and Grain Quality

“…These results provide an important strategy to develop high-quality varieties in maize breeding program. A total of 63 loci and 189 candidate genes associated with root system architecture in maize were identified by Wu et al [22] using GWAS analysis. This GWAS analysis performed by using 1.25 million SNPs and 421 maize inbred lines.…”

“…Right now, GWAS have been widely used to detect the genomic regions correlated with the complex traits in human, animals, and plants. In plants, GWAS have been detected many genes associated to the complex traits, such as in Arabidopsis, rice, maize, sorghum, wheat, barley, and many other plants [2,[9][10][11][12][13][14][15][16][17][18][19][20][21][22]. Phenotypic data and genome-wide genotypes are required in GWAS.…”

GWAS and Transcriptome Analysis Reveal Key Genes Affecting Root Growth under Low Nitrogen Supply in Maize

“…Because LD often involves a relatively broad region surrounding each significant locus, candidate genes often remain unknown. Several previous studies suggested that integrating GWAS results and gene expression data is a powerful way to detect candidate genes [ 33 , 54 , 55 , 56 ]. In the current study, the integration of GWAS and DEG data led to the identification of 48 candidate genes.…”