A comprehensive study of the genomic differentiation between temperate Dent and Flint maize.
Tuesday, 2016/07/19 | 08:06:59
|
Unterseer S, Pophaly SD, Peis R, Westermeier P, Mayer M, Seidel MA, Haberer G, Mayer KF, Ordas B, Pausch H, Tellier A, Bauer E, Schön CC.
Genome Biol. 2016 Jul 8;17(1):137. doi: 10.1186/s13059-016-1009-x. AbstractBACKGROUND: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. 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. RESULTS:We 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. CONCLUSIONS:In 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.
See: http://www.ncbi.nlm.nih.gov/pubmed/27387028
Figure 1: Population structure of the investigated 136 Dent and Flint elite lines and detection of pool-specific selection signatures. a Images of maize cobs with Dent-type (left) and Flint-type kernels (right) as an example for phenotypic differences between the two germplasm pools. b Population structure and assignment of 136 temperate maize elite lines to Dent (red; N = 70) and Flint (blue; N = 66) pools. Bar plots indicate the relative ancestral composition of the lines. c Sweep statistics based on the panel of 136 temperate inbred lines shown exemplarily for a region on chromosome 8 that includes the Vgt1 locus (dashed gray lines) and Rap2 (solid gray line). Within-group statistics (π, TD, and CLR) are shown in red for Dent and in blue for Flint. Horizontal dashed lines indicate the cutoff per statistic (10 % quantile for π and TD, 90 % quantile for CLR and F ST). For the region encompassed by the two loci Vgt1 and Rap2, the four major haplotypes observed in the panel are shown. Light gray boxes indicate the B73 reference allele and dark gray boxes the alternative allele of each SNP. Numbers on the right side of the haplotype plot refer to the number of observations per haplotype within the Dent and the Flint panels |
Back Print View: 660 |
[ Other News ]___________________________________________________
|