Nucleotide Diversity and Association Analysis of ZmMADS60 with Root Length in the Maize Seedling Stage

Pengcheng Li,Houmiao Wang,Yang Xu,Zefeng Yang,Chenwu Xu,Jie Wei,Yunyun Wang,Zhenzhen Ge

doi:10.3390/agronomy10030342

Abstract

Root length is a determining factor of the root system architecture, which is essential for the uptake of water, nutrients and plant anchorage. In this study, ZmMADS60 was resequenced in 285 inbred lines, 68 landraces and 32 teosintes to detect the nucleotide diversity and natural variations associated with root length. Nucleotide diversity and neutral tests revealed that ZmMADS60 might be selected in domestication and improvement processes. ZmMADS60 in maize retained only 40.1% and 66.9% of the nucleotide diversity found in teosinte and landrace, respectively. Gene-based association analysis of inbred lines identified nine variants that were significantly associated with primary root length (PRL), lateral root length (LRL), root length between 0 mm and 0.5 mm in diameter (RL005) and total root length (TRL). One single-nucleotide polymorphism SNP1357 with pleiotropic effects was significantly associated with LRL, RL005 and TRL. The frequency of the increased allele T decreased from 68.8% in teosintes to 52.9% and 38.9% in the landrace and inbred lines, respectively. The frequency of the increased allele of another significant SNP723 associated with PRL also decreased during the maize domestication and improvement processes. The results of this study reveal that ZmMADS60 may be involved in the elongation of primary and lateral roots in the seedling stage and that significant variants can be used to develop functional markers to improve root length in maize.

Highlights

Root systems are crucial for plant survival; they provide anchorage for the plant and acquisition of essential mineral nutrients and water from soil, but they contribute to monitoring the changing environmental conditions [1]
The rootless concerning crown and seminal roots (RTCS) gene encodes a 25.5-kDa lateral organ boundaries (LOB) domain protein that is a central regulator of auxin signaling, and the maize mutant RTCS is defective in the initiation of seminal roots and the shoot-borne root system [6]
Map-based cloning demonstrated that rum1 encodes an Aux/IAA protein [7], and a transcriptional activator lateral root primordia 1 (LRP1) was further identified, the expression of which is repressed by the binding of rootless with undetectable meristem 1 (RUM1) to its promoter [8]

Summary

Introduction

Root systems are crucial for plant survival; they provide anchorage for the plant and acquisition of essential mineral nutrients and water from soil, but they contribute to monitoring the changing environmental conditions [1]. The root system architecture (RSA) can be modulated in several ways, such as primary root elongation, diameter, growth direction and adventitious and lateral root branching These traits reshape the root system architecture, allowing plants to efficiently absorb water and nutrients for plant. All root types form postembryonic lateral roots, which are major determinants of the plant root system architecture [2] These roots increase the total root length, biomass and surface area, potentially dramatically enhancing the contact area between the roots and soil for exploration of the soil environment for water and nutrients [5]. They are important for seedling vigor during plant early development. Map-based cloning demonstrated that rum encodes an Aux/IAA protein [7], and a transcriptional activator lateral root primordia 1 (LRP1) was further identified, the expression of which is repressed by the binding of rootless with undetectable meristem 1 (RUM1) to its promoter [8]

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