Natural Variation and Domestication Selection of ZmCKX5 with Root Morphological Traits at the Seedling Stage in Maize.

Chenwu Xu,Pengcheng Li,Hui Sun,Houmiao Wang,Zefeng Yang,Haofeng Xia,Tingting Wu

doi:10.3390/plants10010001

Abstract

Root system architecture plays a crucial role in water and nutrient acquisition in maize. Cytokinins, which can be irreversibly degraded by the cytokinin oxidase/dehydrogenase (CKX), are important hormones that regulate root development in plants. In this study, ZmCKX5 was resequenced in 285 inbred lines, 68 landraces, and 32 teosintes to identify the significant variants associated with root traits in maize. Sequence polymorphisms and nucleotide diversity revealed that ZmCKX5 might be selected during domestication and improvement processes. Marker–trait association analysis in inbred lines identified 12 variants of ZmCKX5 that were significantly associated with six root traits, including seed root number (SRN), lateral root length (LRL), total root area (RA), root length in 0 to 0.5 mm diameter class (RL005), total root volume (RV), and total root length (TRL). SNP-1195 explained the most (6.01%) phenotypic variation of SRN, and the frequency of this allele G increased from 6.25% and 1.47% in teosintes and landraces, respectively, to 17.39% in inbred lines. Another significant variant, SNP-1406, with a pleiotropic effect, is strongly associated with five root traits, with the frequency of T allele increased from 25.00% and 23.73% in teosintes and landraces, respectively, to 35.00% in inbred lines. These results indicate that ZmCKX5 may be involved in the development of the maize root system and that the significant variants can be used to develop functional markers to accelerate the improvement in the maize root system.

Highlights

The root system architecture (RSA) is associated with plants’ ability to absorb water and nutrients from the soil and resist various abiotic stresses in many crops
Our results showed that ZmCKX5 were significantly associated with five root traits at the seedling stage (Table S1)
The genomic sequence of ZmCKX5 from B73 (RefGen_v3) was used as a reference, and the multiple sequence alignment was performed on all ZmCKX5 sequences obtained from plant individuals

Summary

Introduction

The root system architecture (RSA) is associated with plants’ ability to absorb water and nutrients from the soil and resist various abiotic stresses in many crops. Varieties with a larger root system are excellent candidates to obtain desired traits, such as faster growth, higher yield, and better abiotic stress tolerance [1]. In the past decades, breeding new varieties is the driving force to achieve higher yields in maize [2]. Direct selection for optimal RSA is not routine in these maize breeding programs. The potential of root traits for maize improvement remains largely unexploited [3]. Identified gene and natural variation of root growth could help to breed new maize varieties with root traits suitable for diverse environmental conditions

Methods

Results

Conclusion