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

Oluwaseyi Shorinola,Miroslav Valárik,Jessica Hyles,Matthew J Hayden,Barbara Balcárková,Cristobal Uauy,Katarina Holušova,Jose M Barrero,Josquin F G Tibbits,Atsushi Torada,Assaf Distelfeld

doi:10.3389/fpls.2017.01555

Abstract

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 Phs-A1 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 Plasma Membrane 19 (PM19) genes and the mitogen-activated protein kinase kinase 3 (TaMKK3-A) gene, have been proposed to underlie Phs-A1. To further define the Phs-A1 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 TaMKK3-A, and not PM19, is the major gene underlying the Phs-A1 effect in European, North American, Australian and Asian germplasm. We identified the non-dormant TaMKK3-A allele at low frequencies within the A-genome diploid progenitor Triticum urartu genepool, and show an increase in the allele frequency in modern varieties. In United Kingdom varieties, the frequency of the dormant TaMKK3-A 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 Phs-A1 locus and four haplotypes for TaMKK3-A. Analysis of these haplotypes in a collection of United Kingdom and Australian cultivars revealed distinct major dormant and non-dormant Phs-A1 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 Phs-A1 resistance into breeding germplasm.

Highlights

Pre-harvest sprouting (PHS) refers to the too-early germination of physiologically matured grains while still on the ear, but before harvest
We examined the allelic diversity across the extended Phs-A1 interval with the aim of elucidating the haplotype structure across this region
We observed near perfect sequence and gene content conservation in the interval between hexaploid and tetraploid physical maps

Summary

INTRODUCTION

Pre-harvest sprouting (PHS) refers to the too-early germination of physiologically matured grains while still on the ear, but before harvest. Despite the multi-genic control of PHS resistance, a few major loci have been consistently shown to account for a significant proportion of natural variation to sprouting in diverse mapping populations This include the homoeologous R (Red color) genes on the long arms of chromosome group 3 controlling seed coat color, Qphs.pseru-3AS (same as QPhs.ocs-3A.1) on chromosome 3AS and a locus on chromosome arm 4AL, designated as Phs-A1 (Flintham, 2000; Himi and Noda, 2005; Mori et al, 2005; Liu et al, 2008; reviewed by Mares and Mrva, 2014). Tetraploid and hexaploid accessions to further trace the origin of the sprouting susceptible TaMKK3-A allele and used exome capture data from the wheat HapMap panel (Jordan et al, 2015) to examine the haplotype variation across the Phs-A1 locus

MATERIALS AND METHODS

RESULTS

Findings

DISCUSSION