Genome-wide association study reveals genomic regions controlling root and shoot traits at late growth stages in wheat.

Long Li,Ruilian Jing,Zhi Peng,Xinguo Mao,Matthew Reynolds,Xiaoping Chang,Jingyi Wang

doi:10.1093/aob/mcz041

Long Li, Ruilian Jing + Show 5 more

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https://doi.org/10.1093/aob/mcz041

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Abstract

Background and AimsRoot system morphology is important for sustainable agriculture, but the genetic basis of root traits and their relationship to shoot traits remain to be elucidated. The aim of the present study was to dissect the genetic basis of root traits at late growth stages and its implications on shoot traits in wheat.MethodsAmong 323 wheat accessions, we investigated phenotypic differences in root traits at booting and mid-grain fill stages in PVC tubes, shoot traits including plant height (PH), canopy temperature (CT) and grain yield per plant (YPP) in a field experiment, and performed a genome-wide association study with a Wheat 660K SNP Array.Key ResultsDeep-rooted accessions had lower CT and higher YPP than those with shallow roots, but no significant relationship was identified between root dry weight and shoot traits. Ninety-three significantly associated loci (SALs) were detected by the mixed linear model, among which three were hub SALs (Co-6A, Co-6B and Co-6D) associated with root depth at both booting and mid-grain fill stages, as well as CT and YPP. Minirhizotron system scanning results suggested that the causal genes in the three SALs may regulate root elongation in the field. The heritable independence between root depth and PH was demonstrated by linkage disequilibrium analysis. The YPP was significantly higher in genotypes which combined favourable marker alleles (FMAs) for root depth and PH, suggesting that a deep root and shorter plant height are suitable traits for pyramiding target alleles by molecular marker-assisted breeding.ConclusionsThese results uncovered promising genomic regions for functional gene discovery of root traits in the late growth period, enhanced understanding of correlation between root and shoot traits, and will facilitate intensive study on root morphology and breeding through molecular design.

Highlights

Wheat (Triticum aestivum L.) is a worldwide staple food grain
The coefficient of variation of plant height (PH), yield per plant (YPP) and canopy temperature (CT) is 20.2, 25.5 and 2.2 %, respectively, indicating that CT was a relatively stable shoot trait across accessions, which could be distinguished by small differences
These results suggested that the specific marker alleles in the peak single nucleotide polymorphism (SNP) in Co-6A, Co-6B and Co-6D could predict root depth in the field, and the causal genes influenced root length, the association among root depth and shoot traits in wheat

Summary

Introduction

As a result of global climate change and scarcity of water and nutrients, abiotic stresses increasingly curtail wheat yield (Barnabas et al, 2008; Mondal et al, 2015b). 20 years), breeding wheat varieties with eurytopicity and efficient use of water and nutrients are urgently required (Tester and Langridge, 2010; Odegard and van der Voet, 2014). Roots are primary organs that absorb water and minerals, and perceive stress signals from the soil; their characteristics determine absorption capacity and response to stress Modifying the distribution of roots in the soil to optimize water and nutrient uptake was expected to be a major breakthrough for the second Green Revolution partly based on tolerance of low soil fertility (Ehdaie et al, 2012)

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