Application of marker‐assisted selection and genome‐wide association scanning to the development of winter food barley germplasm resources

Abstract

Barley (Hordeum vulgare) is an important component of heart-healthy whole grain diets because it contains b-glucan. All current US barley varieties with high b-glucan are spring habit and have waxy starch. Winter varieties have agronomic advantages but require low-temperature tolerance (LTT). Vernalization sensitivity (VS) is associated with higher levels of LTT. To rapidly develop fall-sown varieties with LTT and higher grain b-glucan, we therefore used marker-assisted selection (MAS) at the WX and VRN-H2 loci. The MAS-derived lines, together with unrelated non-waxy germplasm developed via phenotypic selection (PS), were used for a genome-wide association scan (GWAS). The panel was phenotyped for grain b-glucan, LTT and VS. It was genotyped with 3072 single-nucleotide polymorphisms (SNPs) and allele-specific primers. Marker-assisted selection fixed target alleles at both loci but only one of the target phenotypes (higher b-glucan percentage) was achieved. Variation for VS and LTT is attributable to (i) incomplete information about VRN-H1 at the outset of the project and (ii) unexpected allelic variation at VRN-H3 with a large effect on VS and LTT.

Developing Winter Food Barley for the Pacific Northwest of the US

“…Anker-Nilssen et al (2008) reported that barley grown in hotter and drier climates tends to have higher b-glucan than barley grown in wetter climates. Chutimanitsakun et al (2013) also found that b-glucan content was significantly higher with increased daytime temperatures, even under irrigated conditions. There are qualitative and quantitative genetic components to grain b-glucan.…”

“…No hull-less check was used because there were no adapted winter food barleys before this trial. The 14 food barley selections were developed using either MAS or PS as described by Chutimanitsakun et al (2013). Briefly, the MAS project was designed to develop high b-glucan and winter growth habit germplasm via selection for specific alleles at the WX and VRN-H2 loci.…”

“…Kernel hardness was measured using 300 kernels per sample on a SKCS 4100 (Perten Instruments, Springfield, yield advantage over spring growth habit types. Therefore, we have focused our food barley breeding efforts on the former, using both marker-assisted selection (MAS) and phenotypic selection (PS) (Chutimanitsakun et al, 2013). Advanced lines were tested in the Oregon Food Barley (OFOOD) trial over a 2-yr period under dryland (average annual rainfall between 400 and 600 mm yr -1 without supplemental irrigation), irrigated (average annual rainfall of less than 400 mm yr -1 with supplemental irrigation applied), high rainfall (average annual rainfall greater than 800 mm yr -1 ), organic (using management practices in compliance with organic regulations), and conventional (using management methods not suitable for organic production) conditions (Western Regional Climate Center, 2015).…”

Quantitative Trait Loci Associated with the Tocochromanol (Vitamin E) Pathway in Barley

“…Whole grain barley, however, brings valuable components to human diets in addition to tocochromanols, including β-glucan [ 46 , 47 ]. Therefore, the focus for breeding food barley should more realistically be on the total nutritional composition, and not exclusively on tocochromanol content.…”

A genome wide association scan for (1,3;1,4)-β-glucan content in the grain of contemporary 2-row Spring and Winter barleys

“…No hulless varieties were included in our grain (1,3;1,4)-β-glucan content analysis. Finally, Chutimanitsakun et al [ 49 ], reported a QTL for grain (1,3;1,4)-β-glucan content associated with granule-bound starch synthase I ( GBSS1 ) at the Waxy ( WX ) locus on the short arm of chromosome 7H (12.5 cM). While the precise mechanism for this remains unknown, perturbations in starch metabolism have been shown previously to affect grain (1,3;1,4)-β-glucan content [ 50 ] and this observation may represent another natural example of the regulatory link between starch and (1,3;1,4)-β-glucan metabolism [ 19 ].…”