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

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.

The accuracy of prediction of genomic selection in elite hybrid rye populations surpasses the accuracy of marker-assisted selection and is equally augmented by multiple field evaluation locations and test years

“…Data for grain yield (dt ha -1 ), plant height (cm), starch content (%) and total pentosan content (%) of hybrids were obtained as described by Miedaner et al [5]. Starch content (%) and total pentosan content (%) were determined by near-infrared reflectance spectroscopy (NIRS) recorded with a Bruker MPA FT- NIRS instrument (Bruker Optics Ettligen) in reflectance mode over the range from 850 to 2500 nm.…”

Bridging the gap between marker-assisted and genomic selection of heading time and plant height in hybrid wheat

“…After excluding SNP markers with (1) a rate of missing values above 5%, (2) a rate of heterozygosity above 5% or (3) a minor allele frequency of o0.05 (Miedaner et al, 2012), in total 1280 SNP markers were retained (Supplementary Table S1). In addition, in genes Ppd-D1 (Beales et al, 2007), Rht-B1 and Rht-D1 (Ellis et al, 2002), one SNP each was analyzed as a functional marker using LGC Genomics KASP assays (LGC Genomics, Berlin, Germany).…”

DArT Markers Effectively Target Gene Space in the Rye Genome

“…The first high-throughput genotyping technology was established for rye in 2009 with the development of a 1520-clone DArT genotyping panel (Bolibok-Bragoszewska et al, 2009). Since then, it was successfully applied for high density genetic map construction, both in rye and triticale (Bolibok-Bragoszewska et al, 2009; Milczarski et al, 2011; Tyrka et al, 2011, 2015), genome-wide germplasm characterization (Bolibok-Bragoszewska et al, 2014), QTL/gene mapping (Stojałowski et al, 2011; Miedaner et al, 2012; Myśków et al, 2012; Milczarski et al, 2016), and genomic selection (Wang et al, 2014, 2015; Schulthess et al, 2015). Following transcriptome sequencing a Rye5K SNP genotyping panel was developed and used for construction of high density transcript map (Haseneyer et al, 2011; Martis et al, 2013).…”