Linkage Disequilibrium Mapping of Yield and Yield Stability in Modern Spring Barley Cultivars

Abstract

Associations between markers and complex quantitative traits were investigated in a collection of 146 modern two-row spring barley cultivars, representing the current commercial germ plasm in Europe. Using 236 AFLP markers, associations between markers were found for markers as far apart as 10 cM. Subsequently, for the 146 cultivars the complex traits mean yield, adaptability (Finlay-Wilkinson slope), and stability (deviations from regression) were estimated from the analysis of variety trial data. Regression of those traits on individual marker data disclosed marker-trait associations for mean yield and yield stability. Support for identified associations was obtained from association profiles, i.e., from plots of P-values against chromosome positions. In addition, many of the associated markers were located in regions where earlier QTL were found for yield and yield components. To study the oligogenic genetic base of the traits in more detail, multiple linear regression of the traits on markers was carried out, using stepwise selection. By this procedure, 18-20 markers that accounted for 40-58% of the variation were selected. Our results indicate that association mapping approaches can be a viable alternative to classical QTL approaches based on crosses between inbred lines, especially for complex traits with costly measurements.T HE genetic dissection of complex traits still prepleiotropic effects on a number of performance traits in barley, but Cattivelli et al. (2002) concluded that sents a challenge. The oligo/polygenic character little is known about the regulatory mechanisms controlof complex traits, combined with interactions between ling stress responses, mainly because all stress responses loci, makes the task a priori difficult and intricate. In involve many genes. addition, environmental factors trigger and modify geneThe polygenic basis of complex traits has conseactions and thereby further complicate the analysis.quences for the application of quantitative trait locus Yield is the classical example of a complex trait. Yield (QTL) mapping methodology, as many markers that fluctuations in relation to environmental factors are are associated with the trait need to be identified. Typioften described in terms of adaptability and stability.cally, for QTL mapping, a cross between two inbred The latter can be considered to constitute complex traits lines is made and the cosegregation of alleles of mapped on their own. Parameters quantifying adaptability and marker loci and phenotypic traits allows the identificastability require observations across a range of environtion of linked markers. For complex traits with GE interments for their estimation. The parameters are typically action, this approach implies large-scale testing of spedefined in terms of linear and quadratic functions of cial mapping populations across a range of environments. the genotype by environment (GE) interaction (Lin et

Linkage Disequilibrium Mapping of Morphological, Resistance, and Other Agronomically Relevant Traits in Modern Spring Barley Cultivars

“…A total of 148 modern European two-row spring barley cultivars were used, representing commercial germplasm used all over north-west Europe in the past 15 years (see Kraakman et al 2004 for more details). The list of cultivars and the breeding companies that bred them are presented as supplementary data.…”

“…In sugar beet, LD extended up to 3 cM (Kraft et al 2000), while in some Arabidopsis populations LD exceeded even 50 cM (Nordborg et al 2002). Kraakman et al (2004) showed that in a set of 148 modern spring barley cultivars markers at distances up to 10 cM tend to be in LD (see their Figure 2). …”

“…two inbred lines, and the association between mapped marker loci and phenotypic traits allows the identification of QTLs on the genome. Recently, instead of bi-parental crosses, collections of cultivars, lines, or landraces are used to identify marker -trait associations in rice (Virk et al 1996), oat (Beer et al 1997), and barley (Igartua et al 1999;Kraakman et al 2004). This methodology has become popular in human genetics under names as association mapping or linkage disequilibrium (LD) mapping, and led to a number of successes (see for a review Cardon and Bell 2001).…”

Assessment and Utilization of the Genetic Diversity in Rice (Orysa sativa L.)

“…Through detecting abundant genetic markers loci locating in genome or those nearby candidate genes, the loci which link tightly with QTLs and show correlated to QTLs can be found. The application of association mapping to plant breeding appears to be a promising approach to overcome the limitations of conventional linkage mapping (Kraakman et al, 2004).…”

Fine mapping of the awn gene on chromosome 4 in rice by association and linkage analyses

“…Moreover, association mapping can detect the majority of loci controlling the same complex traits and multiple alleles of the same locus. Association mapping was first used to detect alleles in human disease and has now been widely applied to gene mapping in plants [14][15][16][17][18][19][20][21].…”