Abstract
BackgroundDent and Flint represent two major germplasm pools exploited in maize breeding. Several traits differentiate the two pools, like cold tolerance, early vigor, and flowering time. A comparative investigation of their genomic architecture relevant for quantitative trait expression has not been reported so far. Understanding the genomic differences between germplasm pools may contribute to a better understanding of the complementarity in heterotic patterns exploited in hybrid breeding and of mechanisms involved in adaptation to different environments.ResultsWe perform whole-genome screens for signatures of selection specific to temperate Dent and Flint maize by comparing high-density genotyping data of 70 American and European Dent and 66 European Flint inbred lines. We find 2.2 % and 1.4 % of the genes are under selective pressure, respectively, and identify candidate genes associated with agronomic traits known to differ between the two pools. Taking flowering time as an example for the differentiation between Dent and Flint, we investigate candidate genes involved in the flowering network by phenotypic analyses in a Dent–Flint introgression library and find that the Flint haplotypes of the candidates promote earlier flowering. Within the flowering network, the majority of Flint candidates are associated with endogenous pathways in contrast to Dent candidate genes, which are mainly involved in response to environmental factors like light and photoperiod. The diversity patterns of the candidates in a unique panel of more than 900 individuals from 38 European landraces indicate a major contribution of landraces from France, Germany, and Spain to the candidate gene diversity of the Flint elite lines.ConclusionsIn this study, we report the investigation of pool-specific differences between temperate Dent and Flint on a genome-wide scale. The identified candidate genes represent a promising source for the functional investigation of pool-specific haplotypes in different genetic backgrounds and for the evaluation of their potential for future crop improvement like the adaptation to specific environments.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1009-x) contains supplementary material, which is available to authorized users.
Highlights
Dent and Flint represent two major germplasm pools exploited in maize breeding
The array comprises more than 600 k single nucleotide polymorphism (SNP) markers, which were identified based on mid- to high-coverage whole-genome sequence data of 30 representative temperate Dent and
More SNPs were polymorphic in the Flint compared to the Dent panel (95.4 % versus 93.1 %), but the majority of SNPs segregated in both germplasm pools (88.6 %)
Summary
Dent and Flint represent two major germplasm pools exploited in maize breeding. Several traits differentiate the two pools, like cold tolerance, early vigor, and flowering time. Northern Flints reached the highest latitudes like the northern regions of the U.S and Canada, which required selection for early maturity and cold tolerance [3]. These Northern Flints, together with Caribbean germplasm, were major progenitors of European maize and enabled the rapid adaptation to European climates [4]. In cooler regions of Europe, breeding programs exploit heterotic effects between Dent lines tracing back to U.S Corn Belt Dents and Flint lines, with Flint contributing early vigor and good cold tolerance and Dent contributing high productivity to the hybrids. Alternative approaches are needed to investigate the divergence of Dent and Flint on a genomic level and to further elucidate how selection shaped the pool-specific genomic diversity
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