Phillip A. Wadl

Keymessage: Standardized microhaplotype databases for eight diverse crops enable multiallelic analyses, comparative genetics, and breeding decisions. Microhaplotypes are short genomic segments that contain multiple tightly linked variants, providing multi-allelic data that can enhance genetic resolution compared to traditional biallelic single nucleotide polymorphism (SNP) markers. Here, we present the creation and utilization of separate microhaplotype databases for eight crop species representing diverse genome sizes, ploidy levels, and breeding systems. We developed a standardized, species-agnostic pipeline for processing, filtering, and databasing microhaplotypes generated using the DArTag targeted genotyping platform. To enhance user accessibility, we developed a no-code, user-friendly application, HapApp, that uses an R Shiny front-end interface to allow breeders and researchers to add unique, standardized microhaplotype identities from raw DArTag reports and iteratively update the existing crop-specific database with the newly discovered microhaplotypes. Selected case studies with these databases highlight the operational advantages of microhaplotypes, especially for challenging, highly heterozygous, or polyploid species. They offer an informative alternative to traditional biallelic SNP analyses for resolving population structures and improving linkage map ordering. This integrated framework provides a reproducible and scalable foundation for managing and exploiting microhaplotype data in plant breeding and genetic research, enabling robust cross-project comparisons and facilitating trait discovery in both simple and complex crop genomes, while enabling comparative genomics and cross-species functional transfer that accelerates genetic gains across all crop species.

Fusarium wilt is caused by the soil borne fungus (Fusarium oxysporum f.sp. batatas) and affects sweetpotato by causing significant damage to crop yield and quality. The use of resistant cultivars is one of the most effective ways to reduce disease incidence. Screening for the disease is time-consuming and resource-draining. Trait-linked molecular markers represent an efficient, stable, and alternative screening approach. In this study, a genome-wide association study (GWAS) was conducted on a Louisiana sweetpotato breeding population to identify novel loci associated with Fusarium wilt resistance and to gain insights underlying resistance. Phenotypic data for disease traits were collected for 254 F ₁ diverse lines over two years. The sweetpotato accessions were genotyped using the 3K DArTag® marker panel. GWAS identified one marker that was significantly associated with Fusarium wilt resistance, providing putative target for future validation and potential use in marker-assisted selection (MAS). These findings offer valuable resources for MAS and lay the groundwork for developing Fusarium wilt-resistant sweetpotato cultivars.

Powdery mildew, caused by Podosphaera xanthii, poses a significant threat to watermelon (Citrullus lanatus) cultivation. Development of resistant cultivars is one of the best strategies to manage powdery mildew. To elucidate the genetic basis of resistance, bulked segregant analysis (BSA) was conducted on an F ₂ population derived from a cross between resistant (USVL608-PMR) and susceptible (USVL677-PMS) genotypes. A 570-kb region on chromosome 2 was identified using QTLseq, containing 99 single-nucleotide polymorphisms (SNP) and eight putative genes. A tightly linked kompetitive allele specific PCR (KASP) marker was developed and validated across three F ₂ populations (USVL608-PMR × USVL677-PMS, USVL608-PMR × ‘Sugar Baby,’ USVL608-PMR × ‘Dixie Lee’), showing a 3:1 segregation ratio and very strong linkage to resistance. Marker-disease resistance linkage was further validated in the F ₃ generation of all three populations. RNAseq analysis revealed the upregulation of lipoxygenase (LOX), jasmonic acid (JA), and reactive oxygen species (ROS) pathways after inoculation, suggesting their role in powdery mildew resistance in watermelon. The development of tightly linked KASP markers in three different backgrounds for powdery mildew resistance and a molecular understanding of disease resistance will be useful for breeding and selecting new disease-resistant watermelon cultivars.

Anaerobic soil disinfestation (ASD) is a promising alternative to synthetic chemical-driven pest management methods facilitated by incorporating carbon sources into the soil, tarping the soil with plastic mulch, and irrigating to soil saturation. To evaluate the impact of ASD on southern root-knot nematode [Meloidogyne incognita (Kofoid & White), SRKN] and yellow nutsedge (Cyperus esculentus L.) management in organically grown sweetpotato, greenhouse studies were conducted. The treatments were structured as a factorial of two carbon amendments [chicken manure + molasses (CM + M), and no additional carbon (control)] by 20 sweetpotato genotypes with 4 replications using a randomized complete block design. The results suggest that the microcosms receiving the carbon amendment spent the most time under anaerobic conditions (<200 mvh). Planting of sweetpotato genotypes in CM + M-treated microcosms resulted in 60–90% and 56–92% suppression of soil population and egg reproduction of SRKN as compared to no additional carbon. The application of CM + M reduced overall weed cover by 79% relative to the control. Sweetpotatoes in CM + M-treated microcosms had significantly higher dry above-ground biomass (6.8 g) as compared to the control (3.6 g). The results of this study demonstrated that ASD has the potential to manage nematodes and weeds in organic sweetpotato production systems.

Sweet potato (Ipomoea batatas) is an important food crop that plays a pivotal role in preserving worldwide food security. Due to its polyploid genome, high heterogeneity, and phenotypic plasticity, sweet potato genetic characterization and breeding is challenging. Genome-wide association studies (GWASs) can provide important resources for breeders to improve breeding efficiency and effectiveness. GWASpoly was used to identify 28 single nucleotide polymorphisms (SNPs), comprising 21 unique genetic loci, associated with sweet potato storage root traits including dry matter (4 loci), subjective flesh color (5 loci), flesh hue angle (3 loci), and subjective skin color and skin hue angle (9 loci), in 384 accessions from the USDA sweet potato germplasm collection. The I. batatas ‘Beauregard’ and I. trifida reference genomes were utilized to identify candidate genes located within 100 kb from the SNPs that may affect the storage traits of dry matter, flesh color, and skin color. These candidate genes include transcription factors (especially Myb, bHLH, and WRKY family members), metabolite transporters, and metabolic enzymes and associated proteins involved in starch, carotenoid, and anthocyanin synthesis. A greater understanding of the genetic loci underlying sweet potato storage root traits will enable marker-assisted breeding of new varieties with desired traits. This study not only reinforces previous research findings on genes associated with dry matter and β-carotene content but also introduces novel genetic loci linked to these traits as well as other root characteristics.

Weeds and nematodes are particularly problematic in organic sweetpotato production due to a lack of effective pesticides. Anaerobic soil disinfestation (ASD) has the potential to fit into current pest management practices as an alternative to pesticide application. Greenhouse studies were conducted at the Clemson Coastal Research and Education Center (CREC) in Charleston, SC, to investigate the impact of carbon source amendment and a no carbon source treatment, and soil type on cumulative anaerobicity, weed control, nematode population, and sweetpotato vigor. Microcosms were filled with one of three different soil types (Charleston—loamy/native; Blackville—high coarse sand content; and Clemson—high clay content) and were mixed with cottonseed meal (CSM) or no carbon amendment. The pots were then sealed with plastic totally impenetrable film (Tif) for 6 weeks, followed by the transplanting of sweetpotato (cv Bayou Belle) slips. The results suggested that the CSM-treated microcosms spent more time under anaerobic conditions than those treated with the no carbon amendment. The microcosms that experienced a longer duration of anaerobicity had a lower percent weed cover (49%), fewer nematode egg masses, and a lower gall index when compared to microcosms which experienced a shorter duration of anaerobicity. Significantly higher instances of leaf necrosis were observed in the sweetpotato slips sown in the CSM-treated microcosms. The addition of CSM as a carbon source to facilitate ASD resulted in similar above-ground biomasses of the sweetpotato plants compared to the treatments containing no carbon amendment. However, a significantly lower below-ground biomass of the sweetpotato plants was observed in the CSM-treated microcosms.

Small public breeding programs focused on specialty crops have many barriers to adopting technology, particularly creating and using genetic marker panels for genomic-based decisions in selection. Here, we report the creation of a DArTag panel of 3120 loci distributed across the sweetpotato (Ipomoea batatas [L.] Lam) genome for molecular-marker-assisted breeding and genomic prediction. The creation of this marker panel has the potential to bring cost-effective and rapid genotyping capabilities to sweetpotato breeding programs worldwide. The open access provided by this platform will allow the genetic datasets generated on the marker panel to be compared and joined across projects, institutions, and countries. This genotyping resource has the power to make routine genotyping a reality for any breeder of sweetpotato.

The reniform nematode (Rotylenchulus reniformis Linford and Oliveira) adversely impacts the quality and quantity of sweetpotato storage roots. Management of R. reniformis in sweetpotato remains a challenge because host plant resistance is not available, fumigants are detrimental to the environment and health, and crop rotation is not effective. We screened a core set of 24 sweetpotato plant introductions (PIs) against R. reniformis. Four PIs were resistant, and 10 were moderately resistant to R. reniformis, suggesting these PIs can serve as sources of resistance for sweetpotato resistance breeding programs. PI 595869, PI 153907, and PI 599386 suppressed 83 to 89% egg production relative to the susceptible control ‘Beauregard’, and these PIs were employed in subsequent experiments to determine if their efficacy against R. reniformis can be further increased by applying nonfumigant nematicides oxamyl, fluopyram, and fluensulfone. A 34 to 93% suppression of nematode reproduction was achieved by the application of nonfumigant nematicides, with oxamyl providing the best suppression followed by fluopyram and fluensulfone. Although sweetpotato cultivars resistant to R. reniformis are currently not available and there is a need for the development of safer yet highly effective nonfumigant nematicides, results from the current study suggest that complementing host plant resistance with nonfumigant nematicides can serve as an important tool for effective and sustainable nematode management.