Team members Jim McCreight (USDA, ARS), Shaker Kousik (USDA, ARS), Michael Mazourek (Cornell Univ), Pat Wechter (USDA, ARS), Bill Wintermantel (USDA, ARS) reported on their lab’s progress and plans.
Progress Reports and Work Plans
Perform GBS analysis of PI collections, establish core populations, provide community resource for genome wide association studies (GWAS) & GBS of cucurbit species, establish molecular-informed core populations
- Genotyped the available NPGS melon accessions and heirloom (n= 2,084) by GBS methods. Population structure, pattern of LD, and redundant accessions were analyzed using the genotype data
- Selected 384-member molecular-informed core population, i.e., functional panel or diversity panel, from the 2,084 based on molecular data analysis and historic importance.
- Validated the utility of the diversity panel for identification of loci that determine quantitative and qualitative traits based on GWAS of 100-seed weight, fruit characteristics, and flower sex expression.
- The panel was planted March 6 in a field in Imperial Valley for phenotyping, in particular with respect to those traits that define melon horticultural groups.
- A manuscript is in preparation that will report results of population structure analyses using a suite of tools, LD decay, Core collection selections, and GWAS using historical and project-generated data.
- Analyses of GBS and endorna virus data of 42 melo ssp. agrestis var. texanus accessions collected in the U.S. and Mexico confirmed their unique identity among the 19 melon horticultural groups in the recently revised melon classification scheme.
Powdery Mildew (Podosphaera xanthii) resistance in MR1xAY RIL & Genomic assisted breeding for disease resistance & QTL map resistances: Screen for resistance, develop populations, phenotype, sequence, QTL map
Charleston, South Carolina Race 1
- GBS has been completed on 180 RIL lines derived from MR1 x AY.
- Two independent powdery mildew race 1 greenhouse assays were completed on the RILs.
- QTL analysis was performed and markers mapped to the genome.
- We have identified two major QTL and two minor QTL linked to powdery mildew race 1 resistance.
- There appears to be epistatic interactions between two of the QTL.
California Field Tests
Two replicated field tests of cucurbit powdery mildew race differentials subjected to natural infection.
- Imperial Valley. University of California, Desert Research and Extension Center, Holtville; watered March 9, 2017, disease reactions evaluated mid-June; melon race 1 present in the field
- Central Valley. University of California, Westside (Westside Research and Extension Center, Five Points; Planted 27 June, evaluated early to mid-September; infection insufficient for evaluation.
Fusarium Wilt resistance in MR1xAY RIL
- GBS has been completed on 180 RIL lines derived from MR1 x AY.
- Two independent Fusarium oxysporum f. sp. melonis (FOM) race 2 assays for resistance of the RILs were completed.
- Two independent Fusarium oxysporum f. sp. melonis (FOM) race 1 assays for resistance of the RILs were completed.
- QTL analysis was performed for each race, and a genetic map generated from the MR1 x AY cross.
- We have identified one major QTL and three minor QTL linked to Fom race 1 resistance.
- We have identified one major QTL associated with Fom race 2 resistance in melon.
- We have generated the most saturated SNP-based map to date of melon with 5663-binned markers.
- RILs were grown and fruit was processed and tested for carotenoids in collaboration with Dr. Li Li, ARS, Ithaca, NY.
- We have identified a major QTL for total carotenoids in the MR1 x AY RIL population.
- Planted in December 2017, 184 F2 PI 313970 x Top Mark for production of the F2:F3 generation in a greenhouse. The entire population was sequenced using GBS and is in the process of genetic analysis. Due to delays in female flower production, the material was planted in the field in Imperial Valley in early-March and will be sampled for DNA analysis using GBS and self-pollination in the field.
- Planted in January 2018, 184 F2 PI 313970 x TGR 1551 (PI 482420) for production of the F2:F3 generation in a greenhouse. DNA samples have been collected for GBS analysis.
- Advanced CMV-resistant lines (western U.S. shipping type cantaloupe, and honeydew) developed by M. Kyle-Jahn and H.M. Munger were increased for assessment of CMV resistance in controlled-inoculation greenhouse tests and adaptation and fruit quality in field tests at three locations in Arizona and California. Virus resistance assays were initiated in March 2018. Due to limited seed supply, the material will be planted only at the UC Westside Research and Extension Center, Five Points, CA; planting date in late June 2018.
Additional Related Virus Information and Activity Cucurbit yellow stunting disorder virus (CYSDV) impacts production of melon and other cucurbit crops in the southwestern and southeastern US, and Texas. Research has led to the advancement of germplasm for resistance to CYSDV, with reduced symptom development. Previous studies by our laboratory demonstrated reduced CYSDV titer early in symptom development correlates with decreased symptom development in plants. This allowed laboratory-based screening of selections in 2016, prior to field studies conducted in 2017. Further greenhouse evaluations of CYSDV have been delayed due to limits on whitefly populations and greenhouse renovations. Renovations have now been completed and we anticipate completion of greenhouse germplasm evaluations during the summer of 2018. Evaluations will involve whitefly inoculation of CYSDV followed by treatment of plants with imidocloprid to prevent whitefly buildup per APHIS regulations.
Cucurbit plants evaluated for virus infection in California during in 2017 demonstrated typical moderate levels of CYSDV incidence in spring melons. Fall production is not viable in most desert production regions due to this virus, but information from growers indicated lower than average levels of CYSDV incidence in spring/summer melons. CMV and Watermelon mosaic virus (WMV) were also present in Imperial County melon. Whitefly incidence in the San Joaquin Valley emerged late in the fall season, but no whitefly-transmitted viruses have been identified to date in cucurbit crops. San Joaquin Valley virus incidence was predominantly WMV, CMV, and limited Cucurbit aphid-borne yellows virus (CABYV). Through cooperation with extension and growers we will again monitor prevalent viruses affecting cucurbit production in the San Joaquin and Imperial Valleys of California during the 2018 growing season to determine level of potential virus threats as well as whether WMV continues to emerge as a growing production concern. This virus has the potential to produce fruit scarring and blemishes that can impact marketability.
Cucumber mosaic virus (CMV).
CMV has emerged as an increasing problem for melon production in western states, particularly in California and Arizona. Melon seed was received from the Cornell University breeding program in January after increase during the previous year in the Mazourek Lab. The 25 breeding lines are for evaluation of resistance to CMV, and adaptation and fruit quality. Seed was divided between the breeding and virology programs with 15 seeds of each line reserved for field evaluations and the remainder for replicated greenhouse experiments. A CMV isolate collected previously from infected melon plants in California has been maintained frozen at ARS, Salinas. All 25 lines are currently being evaluated against this isolate, with initial results anticipated by early April 2018. Seeds were sown and transplanted in a greenhouse, and will be inoculated by mechanical (rub) inoculation of cotyledons in March. Evaluation of plants will include visual symptoms and ELISA using commercial CMV antiserum. All tests are expected to be completed by late-May, allowing time for further increase of resistant germplasm this year.
RNA interference (RNAi) methods for control of whiteflies on tomato, melon, and cassava.
Whiteflies and whitefly-transmitted viruses result in significantly decreased agricultural productivity throughout the world through reduced yields and plant longevity, yet little resistance exists to whitefly and only limited natural resistance is available to many virus diseases. The Wintermantel Lab in collaboration with the Fei Lab (BTI) sequenced the transcriptome (RNA used for gene expression) of the whitefly in response to transmission of Cucurbit yellow stunting disorder virus (genus Crinivirus, family Closteroviridae) and identified over 250 differentially expressed genes in response to virus infection of the melon source plant on which the whitefly fed. This information is being used to understand how these viruses interact with the whitefly vector and for development of RNA interference (RNAi), a method for specific elimination of the whitefly vector (and not other insects) in vegetable crops and cassava through another project involving team members Wintermantel, Ling, and Fei. A related collaborative project involving W.M. Wintermantel and K-.S. Ling at USDA-ARS in Salinas, CA and Charleston, SC, respectively, in collaboration with Zhangjun Fei at the Boyce Thompson Institute in Ithaca, NY have been evaluating RNAi approaches for control of whitefly in other crops. The Wintermantel Lab has been conducting preliminary testing to evaluate performance of RNAi constructs effective on these other crops for efficacy in control of whitefly on melon. Research is in progress.
ARS-Salinas maintains isolates of CMV and CYSDV for research on evaluation and advancement of resistance in melon and other cucurbits. A new isolate of WMV is also being maintained, as this virus appears to be reemerging in California as a production threat.
Marker development and verification
- No planned research for this period
- No planned research for this period. Will do 3’RNA seq in the next year pending confirmation of phenotypes.
Introgress resistance into advanced breeding lines
- See 1.2.: CYSDV
- We have begun making crosses of the best performing RILs with multiple resistances into Top Mark.
- Backcrossed resistant field selections from Fall 2016 in a greenhouse.
- Evaluated F2 and S1 from several backcross families of orange flesh and honeydew melon from crosses with 8 different resistance sources for reaction to natural infection in Imperial Valley in Fall 2017.
- CYSDV-resistant, single plant selections from F2 and S1 of backcross populations taken as vegetative cuttings for backcrossing and selfing in a greenhouse at Salinas and subsequent round of selection in fall 2019.
- Seeds of advanced CMV-resistant lines were increased for testing in Arizona and California.