Exploiting natural variation in crown root traits via genome-wide association studies in maize

Houmiao Wang,Yingying Fan,Chenwu Xu,Pengcheng Li,Xiaoyi Yang,Yang Xu,Zefeng Yang,Xiao Tang

doi:10.1186/s12870-021-03127-x

Houmiao Wang, Yingying Fan + Show 6 more

Open Access

https://doi.org/10.1186/s12870-021-03127-x

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Abstract

BackgroundRoot 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.MethodsIn this study, the CRA, CRD, and CRN of 316 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 two single-locus methods (GLM and MLM) and three multi-locus methods (FarmCPU, FASTmrMLM, and FASTmrEMMA) with 140,421 SNP.ResultsA total of 38 QTL including 126 SNPs were detected for CRA, CRD, and CRN. Additionally, 113 candidate genes within 50 kb of the significant SNPs were identified. Combining the gene annotation information and the expression profiles, 3 genes including GRMZM2G141205 (IAA), GRMZM2G138511 (HSP) and GRMZM2G175910 (cytokinin-O-glucosyltransferase) were selected as potentially candidate genes related to 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 in different environments. Four haplotypes were detected based on these significant variants, and Hap1 has more CRN.ConclusionsThese 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.

Highlights

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
The objectives of this study were (i) to study phenotypic variation of crown root traits within a maize association panel, (ii) to identify significant SNPs associated with CRA, CRD and CRN, and (iii) to detected potential candidate genes and natural variations for crown root development
Earlier research proved that CRN, CRA, and CRD are critical factors that define the maize RSA [11, 16, 42]

Summary

Introduction

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. The genetic mechanisms regulating crown root traits in the field remain unclear. Current yield increases for major crops will likely not be able to satisfy the future demand. Improving plant architecture, both above and below ground, is one of the most effective ways to increase crop productivity. Research regarding plant roots has been limited by the complexity of phenotyping the underground plant parts and because there is relatively little relevant genetic information available to breeders. A recent study confirmed that modifying the root architecture can increase resource use efficiency and yields [4], which has prompted plant scientists to focus more of their attention on plant roots. Clarifying the genetic mechanism regulating root development is critical for enhancing crop performance and increasing food security

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