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

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.

Fig 1. Principal coordinate analysis of 93 winter wheat genotypes based on Jaccard similarity index.

PCo 1 and PCo 2 are the first and second principal coordinates, respectively, and the numbers in parentheses refer to the proportion of variance explained by the principal coordinates.

Fig 2. Intra-chromosomal LD (r²) decay of marker pairs in the whole genome and in the three wheat genomes as a function of genetic distance (cM).

Horizontal line indicates the 95% percentile of the distribution of unlinked r², which gives the critical r²-value. Second-degree LOESS fitting curve illustrates the LD decay (grey line).

Fig 3. Genetic map showing the chromosomal locations of MTAs on chromosomes 1A, 2A, 3A and 4A.

Map distances (cM) are presented on the left side, while the corresponding marker ID and the type of trait are listed on the right side of the chromosome.

Fig 4. Genetic map showing the chromosomal locations of MTAs on chromosomes 5A, 6A and 7A.

Map distances (cM) are presented on the left side, while the corresponding marker ID and the type of trait are listed on the right side of the chromosome.

Fig 5. Genetic map showing the chromosomal locations of MTAs on chromosomes 1B, 2B and 3B.

Map distances (cM) are presented on the left side, while the corresponding marker ID and the type of trait are listed on the right side of the chromosome.

Fig 6. Genetic map showing the chromosomal locations of MTAs on chromosomes 4B, 5B, 6B and 7B.

Map distances (cM) are presented on the left side, while the corresponding marker ID and the type of trait are listed on the right side of the chromosome.

Fig 7. Genetic map showing the chromosomal locations of MTAs on chromosomes 2D, 5D, 6D and 7D.

Map distances (cM) are presented on the left side, while the corresponding marker ID and the type of trait are listed on the right side of the chromosome.