Association mapping and haplotype analysis of the pre - 1 harvest sprouting resistance locus Phs - A 1 reveals a causal

42 Pre-harvest sprouting (PHS) is an important cause of quality loss in many cereal crops 43 and is particularly prevalent and damaging in wheat. Resistance to PHS is therefore a 44 valuable target trait in many breeding programmes. The Phs-A1 locus on wheat 45 chromosome arm 4AL has been consistently shown to account for a significant 46 proportion of natural variation to PHS in diverse mapping populations. However the 47 deployment of sprouting resistance is confounded by the fact that different candidate 48 genes, including the tandem duplicated Plasma Membrane 19 (PM19) genes and the 49 mitogen-activated protein kinase kinase 3 (TaMKK3-A) gene, have been proposed to 50 underlie Phs-A1. To further define the Phs-A1 locus, we constructed a physical map 51 across this interval in hexaploid and tetraploid wheat. We established close proximity 52 of the proposed candidate genes which are located within a 1.2 Mb interval. An 53 association analysis of diverse germplasm used in previous genetic mapping studies 54 suggests that TaMKK3-A, and not PM19, is the major gene underlying the Phs-A1 55 effect in European, North American, Australian and Asian germplasm. We identified 56 the non-dormant TaMKK3-A allele at low frequencies within the A-genome diploid 57 progenitor Triticum urartu genepool, and show an increase in the allele frequency in 58 modern varieties. In UK varieties, the frequency of the dormant TaMKK3-A allele was 59 significantly higher in bread-making quality varieties compared to feed and biscuit60 making cultivars. Analysis of exome capture data from 58 diverse hexaploid wheat 61 accessions identified fourteen haplotypes across the extended Phs-A1 locus and four 62 haplotypes for TaMKK3-A. Analysis of these haplotypes in a collection of UK and 63 Australian cultivars revealed distinct major dormant and non-dormant Phs-A1 64 haplotypes in each country, which were either rare or absent in the opposing 65 germplasm set. The diagnostic markers and haplotype information reported in the 66 study will help inform the choice of germplasm and breeding strategies for the 67 deployment of Phs-A1 resistance into breeding germplasm. 68