Performing Department
Sponsored Research Services
Non Technical Summary
Polyploid specialty crops contribute significantly to food, fiber and ornamental production throughout the world. Among these polyploid crops are the most produced tuber/root (potato, sweet potato), beverage (coffee), fruit (strawberry, blackberry, blueberry, plum, tart cherry, persimmon), vegetable (leek) and ornamental (rose, chrysanthemum, lily, lantana) crops within the USA and in the world. The annual value of these crops in the US is over $9 billion and many times greater on a global scale. With rapid advances in genomics technology and associated reductions in cost, there has been a proliferation of genomic resources available for plants. However, few analytical tools are available for polyploid crops. The highly heterozygous nature and the more complex genetics of polyploids as compared to diploid plants creates many analytical challenges. Although some genetic/genomic/analytical tools have been developed for polyploid crops, there is a critical need to consolidate the work over multiple crops and create breeder-friendly formats. The scarcity of tools specifically designed for complex polyploid crops has limited our ability to capitalize on the genomic revolution for applied breeding purposes and, consequently, has reduced breeding progress for these challenging crops compared to their diploid counterparts. The genetic performance of cultivars is the key to success for any specialty crop production system. The genomic/genetic/analytical tools developed in this project should reduce redundancies among species-specific efforts and accelerate genetic gain and lead to improved cultivars. This planning process will coordinate the research to resolve the common genomic/genetic/analytical issues faced by all polyploid crops across multiple plant families (Asteraceae, Actinidiaceae, Convolvulaceae, Ericaceae, Rosaceae, Rubiaceae, Solanaceae) representing many economically important food and ornamental crops throughout the world. This project will have wide-ranging impacts by increasing the rate of genetic gain of polyploid crops, resulting in cultivars with higher and more consistent yield and quality, and tolerance to a wider range of biotic and abiotic stresses. These improved cultivars will benefit multiple stakeholders involved in polyploid crop breeding, production, research, and consumption as well as support industry stakeholders involved in DNA sequencing, genotyping, and phenotyping. These advances will lead to improved profitability via better yields and quality, as well as reduced environmental impacts resulting from improved tolerance to biotic and abiotic stresses.
Animal Health Component
0%
Research Effort Categories
Basic
10%
Applied
80%
Developmental
10%
Goals / Objectives
This planning grant proposes to have polyploid crop breeders work directly with genomic/genetic/analytical scientists to assess the current situation and determine the specifications for breeder-friendly tools and software packages to facilitate molecular breeding of polyploid crop species. The interactions, collaborations, and sharing of knowledge and analytical tools facilitated by this planning grant will enable the development of a suite of breeder-tested genomic/genetic/analytical tools capable of properly analyzing the range of heterozygosity/ploidy conditions found among polyploid specialty crops. Thus the long range goals are to: 1. Develop a suite of genomic/genetic/analytical tools and training materials that integrate genomic information into applied polyploid plant breeding programs; 2. Accelerate the genetic gain and phenotypic outcomes in polyploid plant breeding; 3. Improve the yield, stress tolerance, quality, and profitability of polyploid crops.The specific objectives of this project are to:1) Establish an interdisciplinary team of polyploid specialty crop scientists, including breeders and experts in the development of genomic/genetic/analytical tools;2) Identify the current status and gaps in the genomic/genetic/analytical tools for polyploid crops;3) Survey public and private breeders of polyploid crops to determine their current status and needs vis-a-vis utilization of genomic information in their programs;4) Develop a SCRI CAP to integrate genomic methods with applied polyploid plant breeding via a suite of integrated genomic/genetic/analytical tools and training materials for polyploid crops.
Project Methods
Phase 1. Assessment of breeder needs and the state of available genomic toolsa. Identify and survey breeders of polyploid specialty crops. Polyploid crops range over multiple families and no comprehensive list of breeders exists. Thus we need to create this list and then survey the breeders to characterize the genomic status and breeding needs of each crop and the limitations they face in using DNA-informed breeding approaches. A key goal is to engage with the breeding community early so we properly design the tools and training for applied breeding programs to ensure their downstream adoption.b. Assess the status of sequencing technologies appropriate for de novo assembly of polyploids and the detection of subgenome-specific genomic variants for haplotyping and dosage estimation.c. Assess the computational tools available for polyploid species. A list of current genomic tools and gaps will be developed. Possible tools could include those for genome assembly, GBS, haplotyping, allelic dosage determination, subgenome specific marker analysis, linkage map construction, genomic selection, GWAS, QTL analysis, parentage analysis, and other tools needed for DNA-informed breeding..Phase 2. Organize a meeting with the following objectives: 1. to present the results of the first phase assessments for discussion, 2. to assemble these assessments of the major gaps/needs into a white paper to serve as the basis of a manuscript for publication and an SCRI CAP grant proposal, and 3. to create collaborative teams based on crop/ploidy status and analytical tasks to lead the development of the various sections of the white paper and grant proposal.Phase 3. Develop a strategic planning document to serve as an information resource about the breeding of and genomic tools available for polyploid specialty crops. The white paper documenting the status and needs of the analytical tools for polyploid crop breeding programs will be developed and submitted for publication to a peer-reviewed journal. This will serve as the basis of the development of a SCRI CAP grant proposal.