Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array

By Shichen Wang, Debbie Wong, K. Forrest, Alexandra M. Allen, S. Chao, Bevan Emma Huang, M. Maccaferri, S. Salvi, S. Milner, L. Cattivelli and 30 more. Plant Biotechnology Journal, 2014

1,649 citations recorded by the source corpus.

High-density single nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships between individuals in populations and studying marker–trait associations in mapping experiments. We developed a genotyping array including about 90 000 gene-associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations. The array includes a significant fraction of common genome-wide distributed SNPs that are represented in populations of diverse geographical origin. We used density-based spatial clustering algorithms to enable high-throughput genotype calling in complex data sets obtained for polyploid wheat. We show that these model-free clustering algorithms provide accurate genotype calling in the presence of multiple clusters including clusters with low signal intensity resulting from significant sequence divergence at the target SNP site or gene deletions. Assays that detect low-intensity clusters can provide insight into the distribution of presence–absence variation (PAV) in wheat populations. A total of 46 977 SNPs from the wheat 90K array were genetically mapped using a combination of eight mapping populations. The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat.

Subfields: Genetics, Plant Science

View Paper: https://www.semanticscholar.org/paper/6e964047676dbe8ac297d17df450489a73039e49

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

1. L. Guarino
2. M. Saadalla
3. P. Stephen Baenziger
4. I. El-Basyoni
5. H. Bockelman
6. Sabah Morsy
7. H. Dempewolf

In Plant Science

1. Y. Moënne‐Loccoz
2. L. Guarino
3. M. Saadalla
4. John Foulkes
5. Jacques Le Gouis
6. P. Stephen Baenziger
7. B. Hirel
8. F. Cormier

Citations in the corpus

• Past and Future Use of Wild Relatives in Crop Breeding (2017, background): “Several crops now have dense single-nucleotide polymorphism (SNP) chip platforms (biallelic SNP arrays) (Comadran et al., 2012; Wang et al., 2014), and the cost of DNA sequencing has continued to drop significantly with time.”
• Breeding for increased nitrogen‐use efficiency: a review for wheat (T. aestivum L.) (2016, background): “As the volume of genotyping information is increasing with the recent development of several wheat SNP arrays (90K, Wang et al. 2014; 420K, 670K, and 820K), genomic prediction methods may overpass these limitations and facilitate breeding.”
• Cell Membrane Stability and Association Mapping for Drought and Heat Tolerance in a Worldwide Wheat Collection (2017, methodology): “The wheat panel was genotyped with the 9K SNP wheat iSelect assay [53].”