A new genomics tool for cross-linking the genomes of crops to model species CALS Impact Statement uri icon


  • Abstract

    We used comparative genomics methods to develop high-throughput anchor markers that would amplify corresponding genes containing simple sequence repetitions in different species for the purpose of linking those genomes for transferring trait information.


    The use of southern hybridization using radio-labeled anchor probes, while laborious, has long been a reliable method for evaluation of genome relationships among species for comparative mapping. Unfortunately, PCR-based markers often do not amplify DNA of species other than the one for which they were designed and thus, cannot be used to cross-link genomes of different species. This is because primers for PCR markers may amplify non-orthologous loci or inadequately sampled sequence variation because of the specificity of the primers. To be useful for comparative mapping, a molecular marker must identify orthologous loci in two or more species and a map location must be determined for each. For PCR-based markers, these criteria are in direct conflict because DNA sequence variation is essential for polymorphism, whereas conservation of DNA sequence is essential for designing primers that function within and across species.


    Recently ESTs containing simple sequence repeats (SSRs) have been recognized as a valuable source of molecular markers (EST-SSRs). Our lab and others have found that primers designed for EST-SSRs can be used to identify orthologous loci across species. DNA sequences containing conserved regions of a gene that flank a hypervariable region are most useful for designing PCR-based markers that can amplify orthologous gene fragments across species. We used sequence similarity analysis to identify gene clusters composed of sequences from different species and then tested them on the genomic DNAs of four grass species; barley, maize, rice and wheat. A high percentage of the primers amplified DNA from two or more species. Like RFLP anchor probes, EST-SSRs can also be useful for identifying orthologous loci in the different genomes of polyploids, which is very useful for map construction. We have used these EST-SSR markers to supplement the comparative wheat/rice map. We have designed over 13,000 EST-SSR primer sets for wheat (5425), barley (3036) and rice (4726) and published in them in GrainGenes (http://wheat.pw.usda.gov/ggpages/ITMI/EST-SSR) for anyone to evaluate these materials. Researchers are requested to send any results from using those primers sets back to GrainGenes so that others can benefit from a community effort.


    Wheat, a hexaploid with a genome size 40 times larger than rice, 30 percent gene duplication, and 80 percent repeated DNA can clearly benefit from comparative genomics through the transfer of information from rice. The use of DNA sequence-based comparative genomics for evolutionary studies and for transferring information from model species to crop species has revolutionized molecular genetics and crop improvement strategies. Genetic parity can be realized for crops that are challenged by limited research funding and genomic complexity. This is accomplished through the efficient transfer of genetic information from model systems. Our anchor primer sets provide a new, high-throughput tool for genomics researchers to use for transferring genetic information from those model systems. Crop improvement programs can use comparative genetics to transfer information about genes from model species to their species of interest, to help identify the genes controlling agronomic traits of interest, and to assess within-species allelic diversity so that the best alleles can be identified and assembled in superior varieties. The use of these markers allows researcher to construct a direct link to the rice genome sequence. The ability to cross-reference these genomes has lead to new knowledge, hypotheses, and predictions about these species. The benefits of comparative genomics research permeate the entire life science research community.

    Funding Sources

    • Federal Formula Funds - Research (e.g., Hatch, McIntire-Stennis, Animal Health)
    • Other USDA (e.g., Water Quality, Special Grants, NRI)


    • Our primary collaborators in the development of this technology are Malay Saha at the Noble Foundation, Ardmore, OK and Rajeev Varshney at IPK-Gatersleben, Germany.

    Key Personnel

    • Mark Sorrells, Plant Breeding and Genetics
    • David Benscher, Plant Breeding and Genetics
    • Ju-Kyung Yu,Plant Breeding and Genetics
    • Chathuraka Jayasuriya, Plant Breeding and Genetics