Genetic architecture of complex agronomic traits examined in two testcross populations of rye (Secale cereale L.)

Thomas Miedaner,Grit Haseneyer,Marlen Hübner,Eva Bauer,Brigitta Schmiedchen,Peer Wilde,Jochen C Reif,Viktor Korzun

doi:10.1186/1471-2164-13-706

Thomas Miedaner, Grit Haseneyer + Show 6 more

Open Access

https://doi.org/10.1186/1471-2164-13-706

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Abstract

BackgroundRye is an important European crop used for food, feed, and bioenergy. Several quality and yield-related traits are of agronomic relevance for rye breeding programs. Profound knowledge of the genetic architecture of these traits is needed to successfully implement marker-assisted selection programs. Nevertheless, little is known on quantitative loci underlying important agronomic traits in rye.ResultsWe used 440 F3:4 inbred lines from two biparental populations (Pop-A, Pop-B) fingerprinted with about 800 to 900 SNP, SSR and/or DArT markers and outcrossed them to a tester for phenotyping. The resulting hybrids and their parents were evaluated for grain yield, single-ear weight, test weight, plant height, thousand-kernel weight, falling number, protein, starch, soluble and total pentosan contents in up to ten environments in Central Europe. The quality of the phenotypic data was high reflected by moderate to high heritability estimates. QTL analyses revealed a total of 31 QTL for Pop-A and 52 for Pop-B. QTL x environment interactions were significant (P < 0.01) in most cases but variance of QTL main effect was more prominent.ConclusionsQTL mapping was successfully applied based on two segregating rye populations. QTL underlying grain yield and several quality traits had small effects. In contrast, thousand-kernel weight, test weight, falling number and starch content were affected by several major QTL with a high frequency of occurrence in cross validation. These QTL explaining a large proportion of the genotypic variance can be exploited in marker-assisted selection programs and are candidates for further genetic dissection.

Highlights

Rye is an important European crop used for food, feed, and bioenergy
Progeny means resembled parental means well. Both populations differed in their medians for all traits, but the genotypic variances indicated by the 50% quantile were rather similar (Figure 1)
We provide in this study the first comprehensive quantitative trait loci (QTL) analysis in rye based on a high-density genetic map including about 900 markers per population

Summary

Introduction

Rye is an important European crop used for food, feed, and bioenergy. Several quality and yield-related traits are of agronomic relevance for rye breeding programs. Rye (Secale cereale L.) is an important European crop grown on 4 million hectares. Rye grain is used for bread making, as feed for livestock, for ethanol production, and as substrate in biogas plants. The economically most important trait in hybrid rye breeding is grain yield. Relevant quality traits differ depending on the end use of rye. For example, high pentosan and starch content play a major role coupled with a low protein content. For ethanol production, breeding for high starch content is of central importance. Several pairs of the above mentioned quality traits are negatively correlated such as protein and starch content, which hampers simultaneous breeding for the different end uses of rye

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