Association of barley photoperiod and vernalization genes with QTLs for flowering time and agronomic traits in a BC2DH population and a set of wild barley introgression lines

Abstract

The control of flowering time has important impacts on crop yield. The variation in response to day length (photoperiod) and low temperature (vernalization) has been selected in barley to provide adaptation to different environments and farming practices. As a further step towards unraveling the genetic mechanisms underlying flowering time control in barley, we investigated the allelic variation of ten known or putative photoperiod and vernalization pathway genes between two genotypes, the spring barley elite cultivar 'Scarlett' (Hordeum vulgare ssp. vulgare) and the wild barley accession 'ISR42-8' (Hordeum vulgare ssp. spontaneum). The genes studied are Ppd-H1, VRN-H1, VRN-H2, VRN-H3, HvCO1, HvCO2, HvGI, HvFT2, HvFT3 and HvFT4. 'Scarlett' and 'ISR42-8' are the parents of the BC(2)DH advanced backcross population S42 and a set of wild barley introgression lines (S42ILs). The latter are derived from S42 after backcrossing and marker-assisted selection. The genotypes and phenotypes in S42 and S42ILs were utilized to determine the genetic map location of the candidate genes and to test if these genes may exert quantitative trait locus (QTL) effects on flowering time, yield and yield-related traits in the two populations studied. By sequencing the characteristic regions of the genes and genotyping with diagnostic markers, the contrasting allelic constitutions of four known flowering regulation genes were identified as ppd-H1, Vrn-H1, vrn-H2 and vrn-H3 in 'Scarlett' and as Ppd-H1, vrn-H1, Vrn-H2 and a novel allele of VRN-H3 in 'ISR42-8'. All candidate genes could be placed on a barley simple sequence repeat (SSR) map. Seven candidate genes (Ppd-H1, VRN-H2, VRN-H3, HvGI, HvFT2, HvFT3 and HvFT4) were associated with flowering time QTLs in population S42. Four exotic alleles (Ppd-H1, Vrn-H2, vrn-H3 and HvCO1) possibly exhibited significant effects on flowering time in S42ILs. In both populations, the QTL showing the strongest effect corresponded to Ppd-H1. Here, the exotic allele was associated with a reduction of number of days until flowering by 8.0 and 12.7%, respectively. Our data suggest that Ppd-H1, Vrn-H2 and Vrn-H3 may also exert pleiotropic effects on yield and yield-related traits.

Fig. 1

Location of candidate genes and QTLs for flowering time regulation in the SSR map S42. The candidate genes are highlighted in bold. Their genetic position in cM is based on von Korff et al. (2004). QTLs are indicated by solid arrows right to the chromosome. The horizontal dashes in the arrows indicate the marker with the highest F value. The upward and downward orientation of the arrow head indicates an increasing and decreasing effect of the Hsp allele, respectively. The width of the arrows indicates the strength of the Hsp effect. QTL effects from non-candidate genes are taken from von Korff et al. (2006)

Fig. 2

Least squares means of number of days until heading (HEA) of ILs containing candidate genes compared to the recurrent parent ‘Scarlett’. The name of the candidate gene is placed in brackets behind the name of the IL which contains the respective exotic allele. ILs which significantly (P < 0.05) deviate from ‘Scarlett’ are indicated with an asterisks (*) and their least squares mean is given on top of the respective column (for details: see Table 8)