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Introduction and History of Tools for Polyploids

Welcome to the Tools for Polyploids project website!

       This effort emerged from the realization that polyploid specialty crops were not capitalizing on the rapid advances in genomics as were diploid crops due to the lack of computational tools needed to use the data in these complex genetic systems. This project coordinates efforts to resolve the common analytical issues faced by all polyploid crops across multiple plant families (Asteraceae, Actinidiaceae, Convolvulaceae, Ericaceae, Poaceae, Rosaceae, Rubiaceae, Solanaceae) representing many economically important food, fodder, and ornamental crops throughout the world. The list of polyploid specialty crops used for food includes roots and tubers (potato, sweet potato, yam), fruit (strawberry, blackberry, blueberry, European plum, tart cherry, kiwi, persimmon, banana), vegetables (leek, watermelon), and others (coffee, basil, hops). In addition to food crops, polyploid species are used as ornamentals (rose, chrysanthemum, lily, orchids, lantana) and for turfgrass (bentgrass, Kentucky bluegrass, tall fescue, ryegrass, Bermuda grass, zoysia grass).

        In the fall of 2016, a group of breeders, geneticists, and computational scientists working on polyploid specialty crops developed an SCRI Planning Grant proposal that was funded in September 2017. After assembling a mailing list of breeders and associated scientists working with polyploid crops (~250 individuals) a survey was developed to assess the crop characteristics, the current use of genomic tools, anticipated future use of genomic tools, and outreach preferences for this information. We received input from 115 polyploid breeding programs, including a range of tuber/root crops, fruit crops, turfgrass crops, and ornamental crops. Many polyploid specialty crops are highly heterozygous, have interspecific hybridization in their breeding history, are naturally outcrossing and sensitive to inbreeding depression, are frequently self-incompatible or sterile, are vegetatively propagated, have medium to large genomes, and have long variety development times. They ranged from allopolyploid to autopolyploid, with many intermediate or of unknown status. In terms of mating designs, a common theme was the need to analyze related F1 families (i.e., partial diallel).

       Survey respondents varied widely in their current use of genomic tools and molecular markers for breeding. The major impediments to using genomic tools were the availability of software suitable for polyploids (most developed for diploid crops), technical expertise, and training. Nevertheless, there was a medium to high confidence that these tools would be used routinely in their breeding programs within 5 to 10 years. The outreach preference was to establish a comprehensive website to serve as a community resource, develop a handbook and run a series of workshops about the use of genomic tools in polyploid breeding. The preference was to create open-source analytical tools maintained by a public entity. The January 2018 planning meeting in San Diego brought together polyploid plant breeders/companies, computational geneticists, molecular geneticists, and experts in genomics both from the private and public sectors to assess the status, identify the weaknesses and develop a plan to resolve the issues identified. See the Planning Grant tab to see the presentations.

       Subsequent discussions and objective development were done within the computational (Endelman, University of Wisconsin; Zeng, North Carolina State University; Maliepaard, Wageningen University) and breeding groups (Byrne and Vales, Texas A&M University; Endelman, University of Wisconsin; Vorsa, Rutgers University; Muñoz, University of Florida; Yencho, North Carolina State University; Worthington, University of Arkansas; Huff, Pennsylvania State University). This was done in consultation and input from a wide range of polyploid specialty crop breeders.

This project is funded by USDA NIFA Specialty Crop Research Initiative Award # 2020-51181-32156 to PD Dave Byrne (Texas A&M),  09/01/20 - 08/31/24

Dr. David Byrne - Project Coordinator
Rose Breeding and Genetics Program
Department of Horticultural Sciences
Texas A&M University