Exploiting Natural Variation in Crown Root Traits via Genome-Wide Association Studies in Maize

Abstract

Background: Root system architecture (RSA), which is determined by the crown root angle (CRA), crown root diameter (CRD), and crown root number (CRN), is an important factor affecting the ability of plants to obtain nutrients and water from the soil. However, the genetic mechanisms regulating crown root traits in the field remain unclear. Methods: In this study, the CRA, CRD, and CRN of 348 diverse maize inbred lines were analysed in three field trials. Substantial phenotypic variations were observed for the three crown root traits in all environments. A genome-wide association study was conducted using three multi-locus methods (FarmCPU, FASTmrMLM, and FASTmrEMMA).Results: A total of 91, 116, and 117 marker–trait associations were identified for CRA, CRD, and CRN, respectively. Additionally, 683 candidate genes within 50 kb of the significant SNPs were identified. A combined analysis of gene annotations and expression profiles revealed 20 promising genes related to auxin synthesis and signal transduction, cytokinin oxidase/dehydrogenase, and transcription factors. These candidate genes may be associated with crown root development. Moreover, GRMZM2G141205, encoding an AUX/IAA transcriptional regulator, was resequenced in all tested lines. Five variants were identified as significantly associated with CRN based on the data for 16SY and 17SY as well as the average values for the three environments. Four haplotypes were detected based on these significant variants, and Hap1 was the optimal haplotype for CRN. Conclusions: These findings may be useful for clarifying the genetic basis of maize root system architecture. Furthermore, the identified candidate genes and variants may be relevant for breeding new maize varieties with root traits suitable for diverse environmental conditions.

Enhancing cereal productivity by genetic modification of root architecture

“…Altogether, they contribute to the typical fibrous RS of the monocots. [ 9 ] Up to now, root development has been intensively studied in rice, [ 22 ] but also in different cereals, including maize, [ 28–30 ] wheat, [ 31 ] barley, [ 32,33 ] brachypodium, [ 34 ] or pearl millet. [ 35 ]…”

Integrating advancements in root phenotyping and genome‐wide association studies to open the root genetics gateway

“…To find functional markers for salt tolerance in the high‐affinity potassium transporter 1 ( ZmHKT1 ) gene, six root traits were phenotyped, and marker‐trait association found 16 SNPs significantly associated with six seedling traits in the untranslated region (UTR), and 8 SNPs in the promoter region was significantly associated with average root diameter (Li, Pan, et al, 2019). Similarly, crown root phenotyping of maize inbred lines under three different field conditions identified an IAA‐transcription factor (GRMZM2G141205), a heat shock protein (HSP), and a cytokinin‐ O ‐glucosyltransferase gene (Wang et al, 2021). Moreover, GWAS and transcriptome analysis identified the molecular mechanism of drought‐induced maize seminal root growth and found seminal root length to be more favorable for developing drought resistance cultivars (Guo et al, 2020).…”