Wheat (Triticum aestivum) is a complex and valuable crop to genotype in agrigenomics. As one of the “big three” grains alongside rice and barley, supplying approximately 20% of global nutrition calories,1 wheat is also the least well mapped for genetic diversity and useful trait variations. However, Professor Jizeng Jia, from the Institute of Crop Sciences at the Chinese Academy of Agricultural Sciences in Beijing, China, sees this changing with development of the Applied Biosystems Axiom Wheat 660K Genotyping Array. (More information about the custom Axiom 660K Genotyping Array is available from Professor Jia. Thermo Fisher Scientific also offers commercially available Axiom Wheat Genotyping Arrays). His team’s 2017 publication uses the genotyping array to map the homoeologous relationship between wheat and a wild relative using genetic linkage maps that could prove valuable to plant scientists for increasing crop diversity.2
Wheat research lags behind rice research because of a lack of genomic sequence and fine mapping information, according to Professor Jia, who has more than 40 years’ experience in this particular field.
Wheat is an ancient crop, and modern strains come from historical cross-breeding among grass species. As a result, the wheat genome is highly complex. Not only does it contain approximately five times the number of base pairs (17 Gb) as the human genome, but 80% of the wheat genome comprises highly repetitive sequences, making it extremely difficult to identify regions within the genome. Furthermore, although wheat has only seven chromosomes, each exists in triplicate. This hexaploidy, though confusing, is considered a benefit, as it yields diversity. However, it also means that the wheat genome is highly dynamic and therefore difficult to study.
Diversity for crop improvement
Improving crop strains is an ongoing area of interest in agriculture, not only for improving yields but also in terms of introducing biotic stress tolerance, disease resistance and climate adaptation—all valuable for long-term agricultural strategy. Diversity in wheat comes from intentional breeding with wild relatives of commercial wheat strains.
However, in order to successfully improve crop strains, wheat researchers need detailed maps of beneficial traits as they relate to the wheat genome. Since these high-resolution genetic maps did not exist, Professor Jia and his team set out to develop an integrated genomics platform for wheat. They sequenced the D genome of approximately 100 wheat varieties and discovered 51 million single nucleotide polymorphisms (SNPs ). In comparison, the human genome contains around 10 million SNPs. By examining SNP clustering and generating a HapMap—the map showing haplotype locations valuable for genome-wide association studies into beneficial traits—wheat researchers could accelerate crop improvement.
Wheat genotyping custom solutions
The Thermo Fisher Scientific bioinformatics team worked alongside Professor Jia and his team to create a high-density custom array for wheat research on the Axiom Genotyping Solution platform. Highly knowledgeable and experienced in collaborating with industrial and academic agricultural experts, the team developed the Axiom Wheat 660K Genotyping Array—a powerful tool for evaluating genetic diversity and investigating the genetic basis of trait variations in polyploid wheat.
Jia identifies dissatisfaction with existing tools, the Illumina 9K and 90K arrays, as the reason for creating the genotyping solution. “There were three main problems with the Illumina SNP arrays,” he states, listing difficulty with genotyping due to multi-copy locations of most SNP markers, less polymorphism in common wheat, and insufficient numbers of markers to use.
“A custom array for the D genome markers was needed. To solve these challenges, we developed the Axiom Wheat 660K Genotyping Array with Thermo Fisher Scientific,” Jia explains.
Array in action
The success of the partnership is borne out in results shown in Professor Jia’s paper,2 which creates extensive linkage maps between wheat and Agropyron Gaertn. (P genome), a wild relative of wheat. The team genotyped two parents and 119 progenies of the wild relative with the 660K array, describing the workflow as an efficient high-throughput screening method. From these data, the researchers then examined homoeologous relationships between wild and common wheat, showing close associations on genetic linkage maps.
In summary, Jia and his coauthors note that these results could “significantly accelerate the introgression of genetic variation from Agropyron into wheat for exploitation in wheat improvement programmes.”
Being able to explicitly map wheat SNPs as third-generation molecular markers is important to wheat research. Jia explains that SNPs will last longer than previous markers, RFLP (restriction fragment length polymorphism, 1990– 994) and SSR (simple sequence repeat, 1995–2015) and “will be widely applied in wheat genomics, genetics, and breeding in the future.”
Where previously wheat researchers did not have access to an ideal SNP array, Professor Jia considers that the high-density Axiom Wheat 660K Genotyping Array can at last “push the studies of wheat genomics, genetic diversity detection and HapMap development, and gene cloning and development.”
1. Brenchley, R., et al. (2012) “Analysis of the bread wheat genome using whole-genome shotgun sequencing,” Nature, 491 (pp. 705–710). doi:10.1038/nature11650.
2. Zhou, S., et al. (2017) “Construction of Agropyron Gaertn. genetic linkage maps using a wheat 660K SNP array reveals a homoeologous relationship with the wheat genome,” Plant Biotechnology Journal, 16(3) (pp. 818–827). doi: 10.1111/pbi.12831.