Issue 4
December 2014

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Diane Mather
T +61 8 8313 7156

Ken Chalmers
T +61 8313 6812

A 2-marker toolkit for boron tolerance in wheat

A team led by Tim Sutton at the Australian Centre for Plant Functional Genomics recently isolated several Bot5 boron transporter genes from wheat, and demonstrated that allelic variation at these genes explains variation in boron tolerance among varieties and lines of wheat. See Pallotta et al. (2014, Nature 514, 88) for the research article and GRDC Ground Cover for a news article.

Among the various alleles of these genes, there are four that confer boron tolerance:
  • Bot--B5b, which confers boron tolerance in Halberd bread wheat
  • Bot-B5c (from Lingzji Baimong Baidami), which confers boron tolerance in Kalka, Tjilkuri and WID802 durum wheat
  • Bot(Tp4A)-B5c, which confers boron tolerance in the wheat landrace G61450
  • Bot-D5b, which confers boron tolerance in the synthetic hexaploid SW48
Of these, Bot-B5b and Bot-B5c are the most relevant to Australian wheat breeding. Depending on the target region, breeders may want to select for or against these alleles in bread wheat (Bot-B5b) or durum wheat (Bot-B5c).

To provide simple tools for marker-assisted selection for or against boron tolerance, AWBMMP-GA developed two new KASPmarkers. One of these differentiates the 'Halberd' allele Bot-B5b from all other known Bot5 alleles. The other differentiates the 'Halberd' allele Bot5b, the 'Lingzhi' allele Bot-B5c  and the 'G61450 allele Bot(Tp4A)-B5c from all other known Bot5 alleles.

Members of the Australian cereal breeding and pre-breeding community can access primer sequences and assay protocols, by logging in to our project website.  CLICK HERE to login or to request a userid. Once you have logged in, click on MARKER RESOURCES.
[PROJECT: UA00143]

Australian wheat varieties genotyped on 820K and 35K Axiom® arrays

The BBSRC-funded Wheat Improvement Strategic Program (WISP), working with Affymetrix researchers, have designed and synthesised 820K and 35K Axiom SNP arrays for wheat. A panel of international wheat varieties has been genotyped on both arrays. Australian varieties (both durum and bread wheat) are well represented, with 191 of the 556 varieties in the panel having been provided by AWBMMP-GA. Genotyping data from the 35K 'Breeders Array' can be downloaded from the CerealsDB website. Warning!! The file is 66.9 MB and contains about 19 million genotyping data points. For the 820K array, probe sequences and other information are can be downloaded (121 MB) and genotypic data should be available soon (100s of millions of data points).
[PROJECT: UA00143]

Wheat660: a new array from CAAS

The Wheat660 array, which  was designed by the Chinese Academy of Agricultural Science and synthesised by Affymetrix, can detect more than 630,000 SNPs in wheat. For more information, see the Graingenes website for an announcement.

Getting more out of 90K SNP genotyping

The recently developed 90K wheat SNP chip (Wang et al. 2014 Plant Biotech J 12, 787) has been used extensively to genotype bread, durum and synthetic wheat accessions from around the world. Besides assaying more than 80,000 gene-associated loci with high accuracy and genotype call rate, the 90K SNP chip provides an accurate and efficient way to compare genotypic datasets generated in different laboratories and to anchor genotypic information to other wheat genomic resources.
Current status of the 90K wheat SNP genotyping assay
  • 72K SNP assays reveal polymorphism in worldwide wheat
  • 65K SNP loci are genetically mapped
  • Genotypes can be called for 55K of the mapped SNP loci in unrelated germplasm
  • 10-15K polymorphic SNPs are typically called in bi-parental mapping crosses
  • Genotype call rate per sample typically exceeds 95%
  • 90K SNPs are gene-associated and connected to various international wheat genotyping and sequencing resources, including the IWGSC flow-sorted wheat chromosome contigs
One of the most intriguing features of the 90K wheat SNP chip is its transferability to related species, which results from its ability to discover and genotype new polymorphism. For example, we have used the 90K SNP chip to construct genetic maps for T. monococcum and Ae. tauschii, as  well as to tag introgressed alien segments in wheat genetic backgrounds.

Within GRDC Project DAV00127, we are working to get more value out of the 90K SNP chip by developing a capability for imputation. This capability is based on exome sequences from >300 genetically diverse bread wheat accessions including cultivars, landraces and synthetic derivatives.

To illustrate the power of genotype imputation, we investigated its potential to improve genome-wide association studies (GWAS).  Using 678 Watkins’ bread wheat accessions that had been phenotyped by Dr U Bansal (PBI Cobbitty) in the field over multiple seasons for response to rust diseases Yr, Lr and Sr, we performed separate GWAS using 31,000 SNPs from the 90K assay, and 344,544 imputed SNPs. Analysis of marker-trait associations at sites around validated loci for rust resistance showed that the imputed SNPs performed similarly to SNPs directly genotyped using the 90K assay, however the imputed SNPs significantly increased marker-density (Figure 1). This example demonstrates the potential of imputation to improve GWAS, as well as to facilitate map-based cloning.

Figure 1. Genotype imputations at a stem rust disease resistance locus on chromosome 7A (grey box). SNP sites directly genotyped using the 90K SNP array are shown as red dots. Imputed SNPs are shown as black dots. 48  genotyped NPS and 1178 imputed SNPs were associated with the resistance locus.

90K SNP genotyping is available to GRDC-funded pre-breeding projects through GRDC Project DAV000127. Contact Kerrie Forrest ( for further information.

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