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Pedigree-based genome mapping for marker-assisted selection and recurrent parent recovery in wheat and barley

Bob Eisemann1, Phillip Banks1, David Butler1, Mandy Christopher1, Ian DeLacy2, David Jordan3, Emma Mace3, Paul McGowan1, Lynne McIntyre4, David Poulsen3, David Rodgers1 and John Sheppard1

1 DPI&F, Leslie Research Centre, Toowoomba, Qld 4350.
University of Queensland, St Lucia, Qld 4067.
DPI&F, Hermitage Research Station, Warwick, Qld 4370.
CSIRO Plant Industry, St Lucia, Qld 4067.


The pedigree-based genome mapping project will investigate and develop systems for implementing marker assisted selection to improve the efficiency of selection and increase the rate of genetic gain in breeding programs. This is a pilot project to test protocols for implementation of pedigree-based whole genome marker analysis in northern region winter cereal breeding programs. It aims to provide useful information about the use of simple sequence repeat (SSR) and other types of molecular markers for routine genomic analysis, the integration of genotypic, phenotypic and pedigree information for targeted wheat and barley lines, the genomic impacts of strong selection pressure in case study pedigrees, and directions for future pedigree-based marker development and analysis.

Media summary

Pedigree-based whole genome marker applications to increase the speed and efficiency of winter cereals breeding programs.

Key Words

Pedigree-based, whole genome mapping, marker-assisted selection, winter cereals, simple sequence repeats (SSRs), Diversity Array Technology (DArT)


Pedigree-based whole genome (PBWG) mapping offers significant potential to increase the genetic gain made in plant breeding programs through the development of systems for marker assisted selection. In in-breeding plants, the identification of genomic regions associated with traits of importance traditionally uses populations derived from single crosses of inbred lines. This strategy however is frequently sub-optimal for direct application in breeding programs for numerous reasons. The QTL (quantitative trait loci) - trait association strategies frequently use obscure or out-dated parents. This strategy competes directly with breeding programs for significant resources for phenotypic evaluation. It is also limited in coverage because it addresses only the genes segregating in the populations under study. Additionally this strategy provides no information about the frequency or value of the QTLs in the breeding populations and hence requires a further step of validating the usefulness of markers for direct application in the breeding program. Due to the wide-spread adoption of this QTL analysis approach with specific doubled haploid populations, marker application is being impeded through the lack of information about the polymorphism and marker-trait association in genetic material relevant to Australian northern region cereal improvement.

Pedigree-based whole genome marker application provides a vehicle for incorporating marker technologies into applied breeding programs by bridging the gap between development and implementation. The PBWG marker concept uses pedigree information to identify markers linked to traits based on identity by descent in breeding populations. The approach makes efficient use of pedigree, phenotypic and genotypic information collected in the normal breeding program, thereby exploiting this valuable resource. The PBWG approach integrates very closely with marker assisted recurrent parent recovery (MARPR), a technology already applied to many crops including barley, maize and rice, that can speed variety development in back-crossing strategies.

Effective use of a PBWG-MARPR marker approach requires relevant pedigree and phenotypic data, low-cost, high throughput genotyping and a data management and analysis system that combines pedigree information, genotypic and phenotypic data. Implementation of these components allows linkage to advanced molecular marker and related research, which directly addresses constraints and opportunities arising within the context of the breeding program. The current project is piloting the design and development of a system that integrates these components of PBWG and MARPR marker application for use in applied breeding programs.


This project aims to develop the protocols and systems necessary to implement the PBWG approach using the DPI&F and EGA northern region focussed wheat and barley breeding programs as case studies. Within each case study, the overall strategy is as follows; to identify appropriate interrelated sets of germplasm, to identify a suite of robust and polymorphic molecular markers, to fingerprint the germplasm and verify the pedigrees, to collate phenotypic, genotypic and pedigree information, to verify and repeat phenotypic information as necessary, to undertake linkage analysis, to validate the markers alternative branches of the pedigree and finally to validate the markers in un-related germplasm.

Wheat Case-Study

A core set of 126 wheat varieties and breeding lines from pedigrees relevant to the northern region with a focus on Condor and Cook related material has been catalogued (Figure 1). 118 SSR markers were selected for assessment in wheat spread at approximately 10cM intervals on chromosomes 2B, 2D, 3B, 3D, 4A, 4B, 4D and 7A. These chromosomes were chosen on the basis of location of genes and putative QTLs associated with height, milling yield, flour colour, black point resistance and rust resistances. In addition to the SSR markers, 63 DArT markers were applied to 93 genotypes by Triticarte P/L.

Figure 1. Pedigram of the released lines belonging to the wheat Condor-Cook family adapted to the Australian northern region

Barley Case-Study

A set of 66 barley genotypes was selected with lineage from Triumph and/or Koru), together with the other parents of the chosen advanced breeding lines (Figure 2). Both Triumph and Koru are European malting barleys which have contributed significantly to the development of malting and high yielding feed barleys with adaptation to the northern region of Australia. The result is a set of inter-related genotypes which are representative of a significant proportion of the Northern Barley Improvement Program (NBIP) gene pool. Fifty-five SSR markers linked to traits of importance to the barley industry have been applied to DNA fingerprinting the 66 barley genotypes. In addition to the SSR markers, 297 polymorphic DArT markers were applied to the same genotypes by Tritcarte P/L.

Figure 2. Diagrammatic representation of the genealogy of the selected barley genotypes.


Genotypic information has been obtained for 118 SSR markers from 126 wheat lines for pedigree-based genomic analysis. Additionally, information has been obtained for 63 DArT markers from 93 of the wheat lines. 297 polymorphic DArT markers have been identified and applied to the 66 barley lines, supplementing the genotypic data obtained from the 55 SSR markers. Pedigree data for the 126 wheat lines and 66 barley lines has been obtained, cleaned, validated and entered into PBMASS (Pedigree Based Marker Assisted Selection System). PBMASS is the software currently being developed for this project. Modules currently to beta testing stage include: import, export and storage of pedigree data, printable graphical display of pedigree data including functions to calculate COI and COP, import, export and storage of molecular marker data, printable display of graphical genotypes colour coded for parental origin (using identity-by-descent) for selected combinations of genotypes and chromosomes (Figure 3).

Figure 3. Examples of modules developed for PBMASS (Pedigree Based Marker Assisted Selection System) including graphical genotype with IBD.

Future Directions and Conclusions

Marker data will be analysed in conjunction with both existing and new phenotypic data. The wheat and barley applications will be assessed and compared to determine the effectiveness of PBWG marker analysis in producing relevant information for use in interpreting associations between traits and genomic regions under selection through the pedigrees targeted in each breeding program and for trait selection, parent characterisation and MARPR. The analysis of the PBGW mapping approach will allow for an enhanced understanding of the processes of selection within a breeding program, including identification of regions under selection and will act as a basis of validation of markers and QTLs for the more effective implementation of markers, through the confirmation of QTL location, the identification of markers which will work in other, distantly related populations and in the identification of QTLs which are effective in other populations. The expected outcomes from this project will encourage more sophisticated use of markers in targeted breeding populations as selection is applied to conserve and combine critical genomic regions for both environmental adaptation and grain and end-use quality. The use of a focussed set of genotypes means that the marker technology will be quickly available for use with a large proportion of the gene pools in the respective case study breeding programs, however the comparison of the two case studies will also allow for the identification of critical components of this approach for implementation in other crop plants.

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