Location: Vegetable Crops Research
2024 Annual Report
Objectives
Objective 1: Identify wild species relatives of cultivated potato with valuable disease resistance and tuber quality traits.
Goal 1a: Determine the resistance phenotypes of 200 clones to major pests and diseases, including soft rot, late blight, early blight, verticillium, scab, and Colorado potato beetle.
Goal 1b: Determine the phenotypes of 200 clones for vine maturity and tuber quality traits including, tuber shape, skin type, cold-induced sweetening resistance, and specific gravity.
Goal 1c: Image analysis and maintenance of phenotypic data.
Objective 2: Introgress discovered traits into cultivated potato by crossing with self-compatible diploid lines.
Goal 2a: Cross wild species clones to self-compatible diploid cultivated potatoes.
Goal 2b: Identify self-compatible individuals in progeny.
Goal 2c: Identify self-compatible interspecific hybrids that contain traits of interest.
Objective 3: Develop genetic resources and molecular markers associated with disease resistance traits that breeders can use when generating advanced breeding lines.
Goal 3a: Genotype wild species clones in the diversity panel using GBS.
Goal 3b: Use the dRenSeq hybrid capture approach to characterize the R genes present within the diversity panel.
Goal 3c: Marker development for traits associated with disease resistance to late blight and verticillium wilt.
Goal 3d: Data management of traits and markers information.
Approach
A total of 200 clones from 12 wild potato species will be screened for resistance to soft rot, late blight, early blight, verticillium, scab, and Colorado potato beetle and tuber quality traits including, tuber shape, skin type, cold-induced sweetening resistance, and specific gravity as part of Objective 1. Clone characteristics will be documented with photographs. Phenotype and genotype data will be added to the GRIN accession record and to Breedbase. To make traits more readily available for use in diploid breeding, clones will be crossed to diploid self-compatibility donors derived from cultivated potato in Objective 2. Self fertile F1 progeny containing the Sli gene will be identified and screened for parental traits of interest. F1 seeds will be made available to the breeding community. In Objective 3, each of the clones will also be genotyped using genotype-by-sequencing (GBS) and R-genes will be identified using sequence capture and long-read next generation sequencing. To assist breeders with selection for disease resistance traits, R gene sequence data and GBS markers will be used as a starting point for developing markers that segregate with the trait as part of Objective 3. Marker data and segregating markers will be contributed to Breedbase.
Progress Report
We have completed work in some areas, including disease resistance phenotyping, crossing to the collection to cultivated germplasm, and genotyping the clone collection. Work is continuing in other areas, including the curation of digital documentation of phenotypes and analysis of whole genome sequence for R genes. We have also published an analysis of diversity of the self-compatibility gene Sli in wild species (Ames et al., 2024).
Objective 1: Identify wild species relatives of cultivated potato with valuable disease resistance and tuber quality traits.
We have completed phenotyping for Alternaria solani (early blight) and Phytophthora infestans (late blight) using detached leaf assays and Pectobacterium caratovorum (soft rot) using greenhouse-grown tubers. Plants were evaluated in the field for resistance to Colorado potato beetle. Image acquisition of late blight and early blight disease phenotypes has been completed. In coordination with ARS colleagues and National Program staff we have developed a potato database for Breeding Insight. Image formatting and uploading will take place once the infrastructure is completed.
Objective 2: Introgress discovered traits into cultivated potato by crossing with self-compatible diploid lines.
More than 100 clones from this collection have been crossed with US-W4 and MSFF744-01 to generate true seed populations. The determination of self-compatibility of clones is ongoing, but we have completed an initial assessment of more than 100 clones from this collection. Of the self-compatible clones that have been identified, sequencing revealed that none of them have the self-compatible allele of Sli, suggesting an alternative mechanism for self-compatibility in these accessions.
Objective 3: Develop genetic resources and molecular markers associated with disease resistance traits that breeders can use when generating advanced breeding lines.
We have completed genotyping by sequencing of the entire collection of clones. Information is currently being analyzed. Resistance (R) gene sequencing is in process. We have determined that obtaining whole genome sequence of each clone and extracting R gene sequences bioinformatically is more cost-efficient than DNA enrichment sequencing and provides additional information that can be used for future objectives. However, the process to obtain whole genome sequence is more time consuming. We have already obtained WGS of several clones and have an efficient pipeline for R gene sequence extraction. Similarly, we are using WGS to extract S-RNase sequences, rather than rely on the less efficient amplicon sequencing. As with the images, we are waiting for the Breeding Insight infrastructure to be finalized before beginning to upload the sequences.
Accomplishments
1. Discovery and definition of genetic factors involved in self-compatibility in potato. Self-incompatibility is a reproductive strategy to prevent inbreeding and promote outcrossing in the Solanaceae family, which includes important food crops like potato, tomato, eggplant, and pepper. Studies to understand the molecular and evolutionary aspects of the self-incompatibility/self-compatibility system have been conducted in several Solanaceae family members including Petunia, Nicotiana, and Solanum. The desire to transform potato into a diploid (2x) inbred-hybrid crop has brought up the need to better understand the self-incompatibility system in wild species relatives of potatoes, most of which are diploid and self-incompatible. It is well known that S-RNAses are the pistil determinant of gametophytic self-incompatibility and multiple sequences of S-RNAse alleles have been identified in a few potato species. It is also known that the pollen component are the S-locus F-box (SLF) genes and that they are likely linked to S-RNases on chromosome 1 to determine a compatibility/incompatibility haplotype. However, SLF diversity, exact location with regard to S-RNases and their mechanism of interaction with S-RNases is unknown in potatoes. Using a combination of genome sequencing and transcriptome analysis of pollen and pistils of wild and cultivated diploid potatoes we determined the structure of the S-locus. Analysis by ARS researchers in Madison, Wisconsin, showed evidence that the SLF elements are exclusively expressed in pollen and that they are distributed in a span of 10-15 Mb flanking the S-RNase locus. This is the first evidence of haplotype characterization of female and male components in the S-locus and may shed light in understanding the interaction of these two pistil and pollen elements to determine self-compatibility. This finding will impact the development of potato germplasm that will be used for hybrid breeding, which has the potential to revolutionize how new potato varieties are developed.