Modelling the genetic architecture of flowering time control in barley through nested association mappingReport as inadecuate




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BMC Genomics

, 16:290

First Online: 12 April 2015Received: 12 October 2014Accepted: 09 March 2015DOI: 10.1186-s12864-015-1459-7

Cite this article as: Maurer, A., Draba, V., Jiang, Y. et al. BMC Genomics 2015 16: 290. doi:10.1186-s12864-015-1459-7

Abstract

BackgroundBarley, globally the fourth most important cereal, provides food and beverages for humans and feed for animal husbandry. Maximizing grain yield under varying climate conditions largely depends on the optimal timing of flowering. Therefore, regulation of flowering time is of extraordinary importance to meet future food and feed demands. We developed the first barley nested association mapping NAM population, HEB-25, by crossing 25 wild barleys with one elite barley cultivar, and used it to dissect the genetic architecture of flowering time.

ResultsUpon cultivation of 1,420 lines in multi-field trials and applying a genome-wide association study, eight major quantitative trait loci QTL were identified as main determinants to control flowering time in barley. These QTL accounted for 64% of the cross-validated proportion of explained genotypic variance pG. The strongest single QTL effect corresponded to the known photoperiod response gene Ppd-H1. After sequencing the causative part of Ppd-H1, we differentiated twelve haplotypes in HEB-25, whereof the strongest exotic haplotype accelerated flowering time by 11 days compared to the elite barley haplotype. Applying a whole genome prediction model including main effects and epistatic interactions allowed predicting flowering time with an unmatched accuracy of 77% of cross-validated pG.

ConclusionsThe elaborated causal models represent a fundamental step to explain flowering time in barley. In addition, our study confirms that the exotic biodiversity present in HEB-25 is a valuable toolbox to dissect the genetic architecture of important agronomic traits and to replenish the elite barley breeding pool with favorable, trait-improving exotic alleles.

KeywordsBarley Wild barley Nested association mapping NAM Flowering time Genome-wide association study GWAS Quantitative trait locus QTL Genomic prediction Epistasis Haplotypes AbbreviationsBC1Progeny of F1 after back-crossing with Barke

BC1S3Progeny of BC1 after three rounds of selfing

BC1S3:xProgeny of BC1S3 individual after x-3 rounds of bulk propagation

BLUEBest linear unbiased estimate

cMCentimorgan

F1First generation after initial crosses

GAGibberellic acid

GSGenetic similarity

GWASGenome-wide association study

HagHordeum agriocrithon

HEBHalle exotic barley

HIDHordeum identity

HspHordeum spontaneum

HvHordeum vulgare

LDLinkage disequilibrium

MNIMean imputation

NAMNested association mapping

PCPrincipal component

PCAPrincipal component analysis

pGProportion of explained genotypic variance

QTLQuantitative trait locus-loci

RR-BLUPRidge regression best linear unbiased prediction

SNPSingle nucleotide polymorphism

SSDSingle seed descent

Andreas Maurer and Vera Draba contributed equally to this work.

Electronic supplementary materialThe online version of this article doi:10.1186-s12864-015-1459-7 contains supplementary material, which is available to authorized users.

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