Identification and verification of QTLs for agronomic traits using wild barley introgression lines

Abstract

A set of 39 wild barley introgression lines (hereafter abbreviated with S42ILs) was subjected to a QTL study to verify genetic effects for agronomic traits, previously detected in the BC2DH population S42 (von Korff et al. 2006 in Theor Appl Genet 112:1221-1231) and, in addition, to identify new QTLs and favorable wild barley alleles. Each line within the S42IL set contains a single marker-defined chromosomal introgression from wild barley (Hordeum vulgare ssp. spontaneum), whereas the remaining part of the genome is exclusively derived from elite spring barley (H. vulgare ssp. vulgare). Agronomic field data of the S42ILs were collected for seven traits from three different environments during the 2007 growing season. For detection of putative QTLs, a two-factorial mixed model ANOVA and, subsequently, a Dunnett test with the recurrent parent as a control were conducted. The presence of a QTL effect on a wild barley introgression was accepted, if the trait value of a particular S42IL was significantly (P<0.05) different from the control, either across all environments and/or in a particular environment. A total of 47 QTLs were localized in the S42IL set, among which 39 QTLs were significant across all tested environments. For 19 QTLs (40.4%), the wild barley introgression was associated with a favorable effect on trait performance. Von Korff et al. (2006 in Theor Appl Genet 112:1221-1231) mapped altogether 44 QTLs for six agronomic traits to genomic regions, which are represented by wild barley introgressions of the S42IL set. Here, 18 QTLs (40.9%) revealed a favorable wild barley effect on the trait performance. By means of the S42ILs, 20 out of the 44 QTLs (45.5%) and ten out of the 18 favorable effects (55.6%) were verified. Most QTL effects were confirmed for the traits days until heading and plant height. For the six corresponding traits, a total of 17 new QTLs were identified, where at six QTLs (35.3%) the exotic introgression caused an improved trait performance. In addition, eight QTLs for the newly studied trait grains per ear were detected. Here, no QTL from wild barley exhibited a favorable effect. The introgression line S42IL-107, which carries an introgression on chromosome 2H, 17-42 cM is an example for S42ILs carrying several QTL effects simultaneously. This line exhibited improved performance across all tested environments for the traits days until heading, plant height and thousand grain weight. The line can be directly used to transfer valuable Hsp alleles into modern elite cultivars, and, thus, for breeding of improved varieties.

High-Throughput Phenotyping to Detect Drought Tolerance QTL in Wild Barley Introgression Lines

“…A third QTL (QHei.S42IL-7H) with an increasing effect of the Hsp allele was detected on chromosome 7H. Here an effect that was already found in the studies of von Korff et al [10], Schmalenbach et al [15] and March et al (in prep.) could be verified.…”

“…March et al (in prep.) and Schmalenbach et al [15] found the same effect in their studies. Von Korff et al [10] found a similar effect in the region where the Hsp introgression of S42IL-109 was mapped.…”

“…The second largest effect, after QHei.S42IL 3Hb, was associated with QHei.S42IL-4H in S42IL-121. This QTL corresponds to QHei.S42IL-4H.a in Schmalenbach et al [15]. In both studies the Hsp allele increased plant height by 18%.…”

Genome-Wide Association Mapping in the Global Diversity Set Reveals New QTL Controlling Root System and Related Shoot Variation in Barley

“…Early and delayed heading are usually correlated with lesser and more Sdw, respectively (Wang et al, 2010; Arifuzzaman et al, 2014). A dominant early heading allele Ppd-H1 has been reported in wild barley accession ISR42-8 and its effect has been confirmed in introgression lines S42IL-107 harboring ISR42-8 Ppd-H1 allele in Scarlett (spring type) background (Schmalenbach et al, 2009; Arifuzzaman et al, 2014). However, here we identified two unique haplotypes HOR2692 (Iranian wild accession) and NGB4673 (Landrace from Afghanistan) having heterozygous alleles at QTL QSdw.2H.b.…”

Exploiting Barley Genetic Resources for Genome Wide Association Scans (GWAS)

“…Many studies have demonstrated the value of alleles originating from un-adapted and unimproved germplasm showing that centuries of selective breeding have not necessarily resulted in the accumulation of all the optimal alleles. For example, several barley cultivars have been released in Europe that contain fungal resistance genes introgressed recently from H. spontaneum (von Korff et al 2005;Schmalenbach et al 2009). A major challenge for the future is to streamline this process using high throughput genomics approaches.…”