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GENOMICS, MOLECULAR GENETICS & BIOTECHNOLOGY

PCR-Based Markers Diagnostic for Spring and Winter Seasonal Growth Habit in Barley

The John Bingham Lab., National Institute of Agricultural Botany, Huntington Road, Cambridge CB3 0LE, UK

^* Corresponding author (james.cockram{at}niab.com).

Toward the ultimate goal of replacing field-based evaluation of seasonal growth habit, we describe the design and validation of a multiplex polymerase chain reaction assay diagnostic for allelic status at the barley (Hordeum vulgare ssp. vulgare L.) vernalization locus, VRN-H1. By assaying for the presence of all known insertion–deletion polymorphisms thought to be responsible for the difference between spring and winter alleles, this assay directly tests for the presence of functional polymorphism at VRN-H1. Four of the nine previously recognized VRN-H1 haplotypes (including both winter alleles) give unique profiles using this assay. The remaining five spring haplotypes share a single profile, indicative of function-altering deletions spanning, or adjacent to, the putative "vernalization critical" region of intron 1. When used in conjunction with a previously published PCR-based assay diagnostic for alleles at VRN-H2, it was possible to predict growth habit in all the 100 contemporary UK spring and winter lines analyzed in this study. This assay is likely to find application in instances when seasonal growth habit needs to be determined without the time and cost of phenotypic assessment and during marker-assisted selection using conventional and multicross population analysis.

Abbreviations: InDel, insertion–deletion • LD, linkage disequilibrium • LTR, long terminal repeat • MITE, miniature inverted-repeat transposable element • PCR, polymerase chain reaction • SGH, seasonal growth habit • TE, transposable element • UPOV, International Union for the Protection of New Varieties of Plants