Genetic Dissection of Seedling Root System Architectural Traits in a Diverse Panel of Hexaploid Wheat through Multi-Locus Genome-Wide Association Mapping for Improving Drought Tolerance.

Thippeswamy Danakumara,Anjan Kumar Pradhan,Amit Kumar Singh,Subodh Kumar Sinha,Shivani Sharma,Mahesh C Yadav,Shailendra Kumar Jha,Jyoti Kumari,Ruchi Bansal,Sundeep Kumar,Girish Kumar Jha,P.V Vara Prasad

doi:10.3390/ijms22137188

Abstract

Cultivars with efficient root systems play a major role in enhancing resource use efficiency, particularly water absorption, and thus in drought tolerance. In this study, a diverse wheat association panel of 136 wheat accessions including mini core subset was genotyped using Axiom 35k Breeders’ Array to identify genomic regions associated with seedling stage root architecture and shoot traits using multi-locus genome-wide association studies (ML-GWAS). The association panel revealed a wide variation of 1.5- to 50-fold and were grouped into six clusters based on 15 traits. Six different ML-GWAS models revealed 456 significant quantitative trait nucleotides (QTNs) for various traits with phenotypic variance in the range of 0.12–38.60%. Of these, 87 QTNs were repeatedly detected by two or more models and were considered reliable genomic regions for the respective traits. Among these QTNs, eleven were associated with average diameter and nine each for second order lateral root number (SOLRN), root volume (RV) and root length density (RLD). A total of eleven genomic regions were pleiotropic and each controlled two or three traits. Some important candidate genes such as Formin homology 1, Ubiquitin-like domain superfamily and ATP-dependent 6-phosphofructokinase were identified from the associated genomic regions. The genomic regions/genes identified in this study could potentially be targeted for improving root traits and drought tolerance in wheat.

Highlights

The objectives of this research were: (1) to study genetic variation of seedling root system architecture in a diverse set of wheat genotypes including a subset of wheat mini core collection; and (2) to identify genomic regions/candidate regions linked with these traits using association mapping
This study revealed wide variability for root system architecture (RSA) and shoot traits at the seedling stage in the studied association panel
Putative candidate genes were identified from the associated genomic region that could be validated using a functional genomics approach

Summary

Introduction

Wheat (Triticum aestivum L.) is one of the most important cultivated food grain crops with an area and production of 218.54 million hectares and 771.71 million tons, respectively [1]. Wheat ranks second after rice (Oryza sativa L.) as a major staple food crop in India with an acreage of 30.55 million hectares, and total production and productivity of 107.18 million tons and 3508 kg/ha, respectively [2]. Drought is one of the major challenges that limits crop growth and yield in different areas of the world [5,6]. Drought stress can cause significant yield reduction in wheat and its impact varies with intensity, timing and duration of stress relative to crop growth stages

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