Integrating GWAS and Gene Expression Analysis Identifies Candidate Genes for Root Morphology Traits in Maize at the Seedling Stage.

Wei Wei,Ge Ge,Qian Qian,Xu Xu,Ni Ni,Fan Fan,Wang Wang,Yang Yang,Li Li

doi:10.3390/genes10100773

Abstract

Root system plays an essential role in water and nutrient acquisition in plants. Understanding the genetic basis of root development will be beneficial for breeding new cultivars with efficient root system to enhance resource use efficiency in maize. Here, the natural variation of 13 root and 3 shoot traits was evaluated in 297 maize inbred lines and genome-wide association mapping was conducted to identify SNPs associated with target traits. All measured traits exhibited 2.02- to 21.36-fold variations. A total of 34 quantitative trait loci (QTLs) were detected for 13 traits, and each individual QTL explained 5.7% to 15.9% of the phenotypic variance. Three pleiotropic QTLs involving five root traits were identified; SNP_2_104416607 was associated with lateral root length (LRL), root surface area (RA), root length between 0 and 0.5mm in diameter (RL005), and total root length (TRL); SNP_2_184016997 was associated with RV and RA, and SNP_4_168917747 was associated with LRL, RA and TRL. The expression levels of candidate genes in root QTLs were evaluated by RNA-seq among three long-root lines and three short-root lines. A total of five genes that showed differential expression between the long- and short-root lines were identified as promising candidate genes for the target traits. These QTLs and the potential candidate genes are important source data to understand root development and genetic improvement of root traits in maize.

Highlights

Over the 30 years, the global human population is expected to grow by 25% and reach10 billion, but the current pace of yield increase for major crops is insufficient to meet future demand [1].Water shortages, nutrient deficiency, and lodging caused by extreme weather can severely reduce crop productivity and threaten global food security [2]
To dissect the genetic basis of root traits at the maize seedling stage, 297 inbred maize lines were cultured in paper rolls for two weeks
Considerable phenotypic variation was detected among the lines, with coefficients of variation that ranged from 12.01% for primary root length (PRL) to 46.22% for RL1015

Summary

Introduction

Nutrient deficiency, and lodging caused by extreme weather can severely reduce crop productivity and threaten global food security [2]. Root systems provide mechanical support, uptake water and nutrients, and interact with rhizosphere microbes and are vital for plant growth and adaptation [3]. Root systems continue to expand in size to become structurally and functionally complex and sometimes may be bigger than above-ground parts [4]. Genes 2019, 10, 773 have developmental plasticity and are capable of altering root branching, root angle, and root growth rates to adapt to adverse soil conditions [5]. The root system architecture is instrumental for superior productivity, but it remains a largely untapped resource in plant breeding programs [6]

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