Elsevier

Plant Science

Volume 268, March 2018, Pages 30-38
Plant Science

Genome-wide association studies of doubled haploid exotic introgression lines for root system architecture traits in maize (Zea mays L.)

https://doi.org/10.1016/j.plantsci.2017.12.004Get rights and content

Highlights

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    Considerable variation was observed for seedling root traits among exotic by elite-derived doubled haploid lines.

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    Significant trait associations involving the SNP S5_152926936 in Chromosome 5 were detected in three GWAS models.

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    Some SNPs were in linkage disequilibrium with known QTL for root development on Chromosomes 1, 2, 5, and 7.

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    Various SNPs on Chromosomes 2, 7, and 8 may be associated with root development in maize, based on in silico data.

Abstract

Root system architecture (RSA) is becoming recognized as important for water and nutrient acquisition in plants. This study focuses on finding single nucleotide polymorphisms (SNPs) associated with seedling RSA traits from 300 doubled haploid (DH) lines derived from crosses between Germplasm Enhancement of Maize (GEM) accessions and inbred lines PHB47 and PHZ51. These DH lines were genotyped using 62,077 SNP markers, while root and shoot phenotype data were collected from 14-day old seedlings. Genome-wide association studies (GWAS) were conducted using three models to offset false positives/negatives. Multiple SNPs associated with seedling root traits were detected, some of which were within or linked to gene models that showed expression in seedling roots. Significant trait associations involving the SNP S5_152926936 on Chromosome 5 were detected in all three models, particularly the trait network area. The SNP is within the gene model GRMZM2G021110, which is expressed in roots at seedling stage. SNPs that were significantly associated with seedling root traits, and closely linked to gene models that encode proteins associated with root development were also detected. This study shows that the GEM-DH panel may be a source of allelic diversity for genes controlling seedling root development.

Introduction

The root system plays a major role in the acquisition of water and nutrients essential for the plant’s survival and growth, hence the importance of root growth and development in N uptake. Selection for better root development may identify maize inbred lines with higher grain yield under low nitrogen (N) fertilization conditions [1,2]. Root growth, especially initiation and development of shoot-borne roots, as well as the amount of N taken up were found to be correlated with shoot growth and demand for nutrients [3]. Grain yield was closely associated with root system architecture traits in the early developmental stages of maize plants [4].

In maize, a hypothetical root ideotype, described as “steep, cheap, and deep,” was proposed by Lynch [5], with the objective of optimizing water and N acquisition. Several genes which affect root development in maize have also been identified: rtcs (rootless concerning crown and seminal roots), rth1 (roothairless 1), rth2 (roothairless 2), rth3 (roothairless 3), rth5 (roothairless 5) and rum1 (rootless with undetectable meristems 1). The gene rtcs controls crown root and seminal root formation [6] rth1, rth2, rth3, and rth5 control root hair elongation in maize [[7], [8], [9], [10]], and rum1 controls lateral root growth and seminal root growth [11]. In addition, rth3 has also been shown to affect grain yield in maize [9]. Quantitative trait locus (QTL) mapping for maize root system architecture traits using BC4F3 lines from the cross Ye478 x Wu312 detected 30 QTL [4]. Genome-wide association studies using the Ames panel [12] found 268 SNPs to be associated with seedling root traits, some of which were located within or linked to gene models or QTL associated with root development [13].

There is considerable genetic variation for root traits in maize [14]. In this study, doubled haploid (DH) lines from the Germplasm Enhancement of Maize (GEM) project [15] were used to identify single nucleotide polymorphisms (SNPs) associated with seedling root system architecture traits. In the allelic diversity component of the GEM project, crosses were made between landraces and elite inbred lines with expired plant variety protection (PVP), PHB47 and PHZ51 [16]. DH lines were derived from BC1 plants obtained after backcrossing initial crosses to the respective elite inbred lines, to enable photoperiod adaptation of these materials to Midwest U.S. conditions. Our hypothesis is that novel sources of genes associated with root development can be found in exotic maize germplasm. The objectives of this study were to (i) determine the extent of variation of root traits of 14-day old seedlings in the GEM-DH panel, (ii) find associations between SNP markers and seedling root system architecture traits, and (iii) identify candidate genes involved in root development.

Section snippets

Plant materials

Doubled haploid (DH) lines were derived from crosses between exotic maize landraces from the Germplasm Enhancement of Maize (GEM) project and expired PVP lines PHB47 and PHZ51 (Table S1). The GEM accessions used in this study were composed of 66 landraces from Central and South America. The DH lines were developed following the procedure described by Brenner et al. [16]. Briefly, GEM accessions were crossed with PHB47 and PHZ51 to produce F1 seed, and most of these were grown and backcrossed

Phenotypic analysis

Considerable variation was observed for most traits within the GEM-DH panel. Total root length and lateral root length had the largest standard deviations of 52.95 cm and 51.69 cm (Table 2), respectively. Most seedling traits followed a normal distribution, slightly skewed to the right. Some lines were consistently in the tails of trait distributions. DH line BGEM-0213-S ((PHB47/PISAN BOV344)/PHB47 #003-(2n)-001) had the highest values for root dry weight, total root length, surface area,

Phenotypic analysis

High-throughput and accurate phenotyping is one of the major constraints in genetic studies concerning roots [39]. Evaluation of root traits from seedlings grown in paper rolls, allows screening for a large number of lines quickly and more precisely, especially with the availability of root imaging software (e.g., ARIA [20], WinRhizo (Regent Instruments), or DIRT [40]). We found a moderate to strong positive (r between 0.42–0.63) and significant correlation (P < .0001) between root (length,

Authors’ contributions

DLS and TL conceived the study, designed the experiments, discussed the results, and finalized the manuscript. DLS, SL, and RI performed the experiments. DLS analyzed the data. MB provided the BGEM seeds. TL and MB edited the manuscript. All authors read and approved the final manuscript.

Acknowledgements

The authors would like to thank USDA’s National Institute of Food and Agriculture (Project Numbers: IOW04314, IOW01018), as well as the Plant Sciences Institute, RF Baker Center for Plant Breeding and K.J. Frey Chair in Agronomy at Iowa State University for funding this work. Darlene L. Sanchez was supported by the Research Training Fellowship of the Department of Agronomy, Iowa State University. The authors declare no conflicts of interest.

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