Haplotype Analysis of the Pre-harvest Sprouting Resistance Locus Phs-A1 Reveals a Causal Role of TaMKK3-A in Global Germplasm

Pre-harvest sprouting (PHS) is an important cause of quality loss in many cereal crops and is particularly prevalent and damaging in wheat. Resistance to PHS is therefore a valuable target trait in many breeding programs. The <i>Phs-A1</i> locus on wheat chromosome arm 4AL has been consistently shown to account for a significant proportion of natural variation to PHS in diverse mapping populations. However, the deployment of sprouting resistance is confounded by the fact that different candidate genes, including the tandem duplicated <i>Plasma Membrane 19</i> (<i>PM19</i>) genes and the <i>mitogen-activated protein kinase kinase 3</i> (<i>TaMKK3-A)</i> gene, have been proposed to underlie <i>Phs-A1</i>. To further define the <i>Phs-A1</i> locus, we constructed a physical map across this interval in hexaploid and tetraploid wheat. We established close proximity of the proposed candidate genes which are located within a 1.2 Mb interval. Genetic characterization of diverse germplasm used in previous genetic mapping studies suggests that <i>TaMKK3-A</i>, and not <i>PM19</i>, is the major gene underlying the <i>Phs-A1</i> effect in European, North American, Australian and Asian germplasm. We identified the non-dormant <i>TaMKK3-A</i> allele at low frequencies within the A-genome diploid progenitor <i>Triticum urartu</i> genepool, and show an increase in the allele frequency in modern varieties. In United Kingdom varieties, the frequency of the dormant <i>TaMKK3-A</i> allele was significantly higher in bread-making quality varieties compared to feed and biscuit-making cultivars. Analysis of exome capture data from 58 diverse hexaploid wheat accessions identified fourteen haplotypes across the extended <i>Phs-A1</i> locus and four haplotypes for <i>TaMKK3-A</i>. Analysis of these haplotypes in a collection of United Kingdom and Australian cultivars revealed distinct major dormant and non-dormant <i>Phs-A1</i> haplotypes in each country, which were either rare or absent in the opposing germplasm set. The diagnostic markers and haplotype information reported in the study will help inform the choice of germplasm and breeding strategies for the deployment of <i>Phs-A1</i> resistance into breeding germplasm.