Widening the wheat gene pool

Our most dominant crop has a worrying lack genetic diversity. Here, we learn about a UK programme aiming to change this, whilst also improving the germplasm pool to yield better crops Used for human food and livestock feed, wheat is the dominant crop in temperate countries. In modern times, particularly since the 1950s, wheats have been repeatedly selected for higher yields and greater disease resistance. Scientists at the centre of wheat breeding have grown somewhat concerned recently that the improvements made since the 1950s may have reached a plateau of sorts and they are worried that there is not enough genetic diversity in the wheat grown today. To ensure continued robust wheat crops, the Biotechnology and Biological Sciences Research Council (BBSRC) approved funding for a six-year program called the Wheat Institute Strategic Programme (WISP). It brings together resources from five UK institutions: John Innes Centre, National Institute for Agricultural Botany, University of Nottingham, University of Bristol, and Rothamsted Research. The goal of the WISP program, which runs from 2011 through 2017, is to produce novel wheat germplasm with desirable traits and identify genetic markers for selecting these traits. Both genotyping and phenotyping are important parts of these efforts. There are three broad pillars to the WISP work. The first is to integrate wild landraces into the elite germplasm pool. It utilises a collection of diverse wheat lines gathered in the 1930s from all around the world and now held at the UK John Innes Centre. The second pillar and the focus of the UK National Institute for Agricultural Botany, is the resynthesis of synthetic hexaploid wheats. Wheat naturally occurred as a hexaploid about 10,000 years ago, the result of a hybridisation event between a tetraploid and a diploid species. We can recreate an event like this today by taking a current tetraploid line like durham wheat, which is widely used to make pasta, and crossing it with diploids to come up with new hexaploids. We can get around the “evolutionary bottleneck” if we make more hexaploids and bring in more diverse donors. The third pillar is ancestral gene introgression – bringing in chunks of genome for related species to wheat such as rye and Thinopyrum, which can have useful characteristics like drought tolerance or disease resistance. This work is being carried out at the University of Nottingham. Once the material has been developed from these three pillars, it will be genetically characterised at the University of Bristol and phenotyped at Rothamsted Research and the University of Nottingham. The genotyping and phenotyping results will help us to decide which produced lines have the right segments of DNA and the right traits, to go forward and be integrated into commercial wheat lines by the breeders. The University of Bristol collaborated with Affymetrix to develop a wheat array in 96-well plate format on their Axiom genotyping platform. The resulting Axiom Wheat Genotyping Array consists of 817,000 markers (from wheat and its related progenitor species – particularly rye and durham, which we didn’t have before) and its design is unique because it includes functional and positional annotation information for a variety of wheat species.  The SNPs on the Axiom Wheat Array include markers from hexaploid landraces and those from the synthetic and ancestral lines exhibiting different ploidy levels. 70% of the SNPS we put on the array were validated. We were able to complete the design and analysis in less than three months. The collaboration with Affymetrix, bringing in the expertise of their bioinformatics and product support teams, made the streamlined timeline possible. The results from the Axiom Wheat Array, which we presented at the 2014 Plant and Animal Genome Conference in San Diego, California in January, have helped WISP attain one of its main goals, which is to track the different segments of “wheat relative” line and incorporate them into hexaploid bread wheat through the breeding process. A subset of the successful SNPs found on the Axiom Wheat Array are now being transferred onto Axiom 384HT-format arrays to create multiple focused wheat array designs. Each of these Axiom wheat array designs will contain approximately 35,000 markers and each design is expected to serve a different purpose in wheat breeding. The 384HT format enables ultra high-throughput processing of 384 samples simultaneously and will be used to screen thousands of samples in a highly cost-effective manner. Affymetrix will make these new Axiom arrays publicly available before the spring wheat season. The first of these HT arrays is aimed at wheat breeders and will enable them to cost-effectively screen 35K validated hexaploid wheat markers against their breeding material. Subsequent 35K sub-arrays will be targeted at more specific needs, such as tracking introgressions from our landraces and progenitors into hexaploid wheat. On this format, we can process 384 wheat samples at a time, enabling us to make decisions on which lines to take forward. With Affymetrix’s advanced bioinformatics and innovative design strategies, Axiom genotyping array designs routinely support genome-wide genotyping and accurately call the genotypes of both diploid and polyploid species. “We are pleased to be able to support the goals of the University of Bristol and contribute efforts to help sustain wheat production in the face of challenges from a growing world population and climate change,” said Dr. Andy Last, Executive Vice President and Chief Operating Officer at Affymetrix. “The Axiom platform enables researchers to publish results sooner and breeders to accelerate their genomic programs.” Author Dr. Gary Barker, University of Bristol