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

• Published in: Plant breeding Vol. 132; no. 6; pp. 563 - 570
• Main Authors: Chutimanitsakun, Yada, Cuesta-Marcos, Alfonso, Chao, Shiaoman, Corey, Ann, Filichkin, Tanya, Fisk, Scott, Kolding, Mathias, Meints, Brigid, Ong, Yee-Ling, Rey, Juan Ignacio, Ross, Andrew S., Hayes, Patrick M.
• Format: Journal Article
• Language: English
• Published: Berlin Blackwell Publishing Ltd 01.12.2013; Wiley Subscription Services, Inc
• Subjects: betaglucan; Diets; food barley; Genomes; Genomics; Germplasm; Hordeum vulgare; low temperature tolerance; marker assisted selection; vernalization; winter barley
• ISSN: 0179-9541; 1439-0523
• DOI: 10.1111/pbr.12086

Barley (Hordeum vulgare) is an important component of heart‐healthy whole grain diets because it contains β‐glucan. All current US barley varieties with high β‐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 β‐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 β‐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 β‐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.