Genome-wide association study and genetic diversity analysis on nitrogen use efficiency in a Central European winter wheat (Triticum aestivum L.) collection.

István Monostori,Gábor Galiba,Tamás Árendás,Fruzsina Szira,Krisztián Gierczik,Alessandro Tondelli,Attila Vágújfalvi,Luigi Cattivelli,Aimin Zhang

doi:10.1371/journal.pone.0189265

Abstract

To satisfy future demands, the increase of wheat (Triticum aestivum L.) yield is inevitable. Simultaneously, maintaining high crop productivity and efficient use of nutrients, especially nitrogen use efficiency (NUE), are essential for sustainable agriculture. NUE and its components are inherently complex and highly influenced by environmental factors, nitrogen management practices and genotypic variation. Therefore, a better understanding of their genetic basis and regulation is fundamental. To investigate NUE-related traits and their genetic and environmental regulation, field trials were evaluated in a Central European wheat collection of 93 cultivars at two nitrogen input levels across three seasons. This elite germplasm collection was genotyped on DArTseq® genotypic platform to identify loci affecting N-related complex agronomic traits. To conduct robust genome-wide association mapping, the genetic diversity, population structure and linkage disequilibrium were examined. Population structure was investigated by various methods and two subpopulations were identified. Their separation is based on the breeding history of the cultivars, while analysis of linkage disequilibrium suggested that selective pressures had acted on genomic regions bearing loci with remarkable agronomic importance. Besides NUE, genetic basis for variation in agronomic traits indirectly affecting NUE and its components, moreover genetic loci underlying response to nitrogen fertilisation were also determined. Altogether, 183 marker-trait associations (MTA) were identified spreading over almost the entire genome. We found that most of the MTAs were environmental-dependent. The present study identified several associated markers in those genomic regions where previous reports had found genes or quantitative trait loci influencing the same traits, while most of the MTAs revealed new genomic regions. Our data provides an overview of the allele composition of bread wheat varieties anchored to DArTseq® markers, which will facilitate the understanding of the genetic basis of NUE and agronomically important traits.

Highlights

Wheat is grown on greater land area than any other commercial crops; its production has exceeded 700 million tons in the recent years, wheat became the most important food grain source for humans [1]
Genotyping the Hungarian wheat collection with DArTseq1 platform resulted in a final dataset comprising 4,201 quality-filtered, polymorphic DArTseq1 markers of which 3,290 were placed on the genetic map
Is presented a genome-wide association studies (GWAS) analysing nitrogen use efficiency (NUE) with its components and related agronomically relevant traits in a panel of commercially relevant Central European winter wheat cultivars genotyped on DArTseq1 platform

Summary

Introduction

Wheat is grown on greater land area than any other commercial crops; its production has exceeded 700 million tons in the recent years, wheat became the most important food grain source for humans [1]. We face the challenge to increase the average wheat yield from the current 3.4 t/ha to 5.42 t/ha. The environmental damages associated with the utilisation of N-based fertilisers are becoming significant not just at local and regional and global scales [5,6]. The effect of the negative environmental and economic impacts could be reduced through better agronomic practices and the utilisation of N-efficient cultivars with improved N use efficiency (NUE) [7]. With the improvement of NUE, as an adverse effect, the grain protein content (GPC) may decrease. The inverse relationship between grain yield (GY) and GPC makes it difficult to improve these two traits simultaneously.

Methods

Results

Discussion

Conclusion