Development of diagnostic SNP markers for quality assurance and control in sweetpotato [Ipomoea batatas (L.) Lam.] breeding programs

Comprehensive review of sweetpotato flavor compounds: Opportunities for developing consumer-preferred varieties

Flavor contributes significantly to consumer preferences of cooked sweetpotato. Sugars largely drive the sweet taste, while the volatile organic compounds (VOCs), mainly classified as alcohols, aldehydes, ketones, and terpenes, provide characteristic aromas and influence the overall perception of flavor. In this paper, we review sweetpotato VOCs identified in the literature from 1980 to 2024 and discuss the efforts to understand how these compounds influence sensory perception and consumer preferences. Over 400 VOCs have been identified in cooked sweetpotato with 76 known to be aroma-active. Most of these aroma-active compounds are generated from Maillard reactions, Strecker, lipid and carotenoid degradation, or thermal release of terpenes from glycosidic bonds during cooking. Suggested mechanisms of formation of these aroma-active compounds are described. However, specific VOCs that are responsible for different aromas and flavors in cooked sweetpotatoes are yet to be fully characterized. There are significant opportunities to further identify the key predictors of aroma and flavor attributes in sweetpotato, which can be used to enhance the quality of existing varieties and develop new ones using a wide range of genetic tools. This review summarizes 44 years of research aimed at identifying key aroma compounds in cooked sweetpotato and provides a roadmap for future studies to guide breeders in developing high-quality, consumer-preferred varieties.

Genotyping Genebank Collections: Strategic Approaches and Considerations for Optimal Collection Management

The maintenance of plant germplasm and its genetic diversity is critical to preserving and making it available for food security, so this invaluable diversity is not permanently lost due to population growth and development, climate change, or changing needs from the growers and/or the marketplace. There are numerous genebanks worldwide that serve to preserve valuable plant germplasm for humankind's future and to serve as a resource for research, breeding, and training. The United States Department of Agriculture (USDA) National Plant Germplasm System (NPGS) and the Consultative Group for International Agricultural Research (CGIAR) both have a network of plant germplasm collections scattered across varying geographical locations preserving genetic resources for the future. Besides the USDA and CGIAR, there are germplasm collections established in many countries across the world that also aim to preserve crop and plant collections. Due to the advancement of technology, genotyping and sequencing whole genomes of plant germplasm collections is now feasible. Data from genotyping can help define genetic diversity within a collection, identify genetic gaps, reveal genetic redundancies and verify uniqueness, enable the comparison of collections of the same crop across genebanks (rationalization), and determine errors or mix-ups in genetic identity that may have occurred in a germplasm collection. Large-scale projects, such as genotyping germplasm collections, require strategic planning and the development of best practices. This article details strategies and best practices to consider when genotyping whole collections, considerations for the identity verification of germplasm and determining genetic replicates, quality management systems (QMS)/QC genotyping, and some use cases.

Genetic diversity and population structure studies of West African sweetpotato [Ipomoea batatas (L.) Lam] collection using DArTseq

BACKGROUND

Sweetpotato is a vegetatively propagated crop cultivated worldwide, predominantly in developing countries, valued for its adaptability, short growth cycle, and high productivity per unit land area. In most sub-Saharan African (SSA) countries, it is widely grown by smallholder farmers. Niger, Nigeria, and Benin have a huge diversity of sweetpotato accessions whose potential has not fully been explored to date. Diversity Arrays Technology (DArTseq), a Genotyping by Sequencing (GBS) method, has been developed and enables genotyping with high-density single nucleotide polymorphisms (SNPs) in different crop species. The aim of this study was to assess the genetic diversity and population structure of the West African sweetpotato collection using Diversity Arrays Technology through Genotyping by Sequencing (GBS).

RESULTS

29,523 Diversity Arrays Technology (DArTseq) single nucleotide polymorphism markers were used to genotype 271 sweetpotato accessions. Genetic diversity analysis revealed an average polymorphic information content (PIC) value of 0.39, a minor allele frequency of 0.26, and an observed heterozygosity of 10%. The highest value of polymorphic information content (PIC) (0.41) was observed in chromosomes 4, while the highest proportion of heterozygous (He) (0.18) was observed in chromosomes 11. Molecular diversity revealed high values of polymorphic sites (Ps), theta (θ), and nucleotide diversity (π) with 0.973, 0.158, and 0.086, respectively, which indicated high genetic variation. The pairs of genetic distances revealed a range from 0.08 to 0.47 with an overall average of 0.34. Population structure analysis divided the 271 accessions into four populations (population 1 was characterised by a mixture of accessions from all countries; population 2, mostly comprised of Nigerian breeding lines; population 3 contained exclusively landraces from Benin; and population 4 was composed by only landraces from West African countries) at K = 4, and analysis of molecular variance (AMOVA) based on PhiPT values showed that most of the variation was explained when accessions were categorized based on population structure at K = 4 (25.25%) and based on cluster analysis (19.43%). Genetic distance showed that group 4 (which constituted by landraces of Niger and Benin) was genetically distant (0.428) from groups 2 (formed by 75% of breeding lines of Nigeria), while group 1 was the closest (0.182) to group 2.

CONCLUSIONS

This study employed 7,591 DArTseq-based SNP markers, revealing extensive polymorphism and variation within and between populations. Variability among countries of origin (11.42%) exceeded that based on biological status (9.13%) and storage root flesh colour (7.90%), emphasizing the impact of migration on genetic diversity. Population structure analysis using principal component analysis (PCA), Neighbor-Joining (NJ) tree, and STRUCTURE at K = 4 grouped 271 accessions into distinct clusters, irrespective of their geographic origins, indicating widespread genetic exchange. Group 4, dominated by landraces (95%), showed significant genetic differentiation (Nei's Gst = 0.428) from Group 2, mainly comprising breeding lines, suggesting their potential as heterotic groups for breeding initiatives like HEBS or ABS.

HybridQC: A SNP-Based Quality Control Application for Rapid Hybridity Verification in Diploid Plants

Background/Objectives: Hybridity authentication is an important component of quality assurance and control (QA/QC) in breeding programs. Here, we introduce HybridQC v1.0, a QA/QC software program specially designed for parental purity and hybridity determination. HybridQC rapidly detects molecular marker polymorphism between parents of a cross and utilizes only the informative markers for hybridity authentication. Methods: HybridQC is written in Python and designed with a graphical user interface (GUI) compatible with Windows operating systems. We demonstrated the QA/QC analysis workflow and functionality of HybridQC using Kompetitive allele-specific PCR (KASP) SNP genotype data for cowpea (Vigna unguiculata). Its performance was validated in other crop data, including sorghum (Sorghum bicolor) and maize (Zea mays). Results: The application efficiently analyzed low-density SNP data from multiple cowpea bi-parental crosses embedded in a single Microsoft Excel file. HybridQC is optimized for the auto-generation of key summary statistics and visualization patterns for marker polymorphism, parental heterozygosity, non-parental alleles, missing data, and F1 hybridity. An added graphical interface correctly depicted marker efficiency and the proportions of true F1 versus self-fertilized progenies in the data sets used. The output of HybridQC was consistent with the results of manual hybridity discernment in sorghum and maize data sets. Conclusions: This application uses QA/QC SNP markers to rapidly verify true F1 progeny. It eliminates the extensive time often required to manually curate and process QA/QC data. This tool will enhance the optimization efforts in breeding programs, contributing to increased genetic gain.

Validation of SNP Markers for Diversity Analysis, Quality Control, and Trait Selection in a Biofortified Cassava Population

A validated marker system is crucial to running an effective genomics-assisted breeding program. We used 36 Kompetitive Allele-Specific PCR (KASP) markers to genotype 376 clones from the biofortified cassava pipeline, and fingerprinted 93 of these clones with DArTseq markers to characterize breeding materials and evaluate their relationships. The discriminating ability of the 36-quality control (QC) KASP and 6602 DArTseq markers was assessed using 92 clones genotyped in both assays. In addition, trait-specific markers were used to determine the presence or absence of target genomic regions. Hierarchical clustering identified two major groups, and the clusters were consistent with the breeding program origins. There was moderate genetic differentiation and a low degree of variation between the identified groups. The general structure of the population was similar using both assays. Nevertheless, KASP markers had poor resolution when it came to differentiating the genotypes by seed sources and overestimated the prevalence of duplicates. The trait-linked markers did not achieve optimal performance as all markers displayed variable levels of false positive and/or false negative. These findings represent the initial step in the application of genomics-assisted breeding for the biofortified cassava pipeline, and will guide the use of genomic selection in the future.

Promiscuous potato: elucidating genetic identity and the complex genetic relationships of a cultivated potato germplasm collection

A total of 3,860 accessions from the global in trust clonal potato germplasm collection w3ere genotyped with the Illumina Infinium SolCAP V2 12K potato SNP array to evaluate genetic diversity and population structure within the potato germplasm collection. Diploid, triploid, tetraploid, and pentaploid accessions were included representing the cultivated potato taxa. Heterozygosity ranged from 9.7% to 66.6% increasing with ploidy level with an average heterozygosity of 33.5%. Identity, relatedness, and ancestry were evaluated using hierarchal clustering and model-based Bayesian admixture analyses. Errors in genetic identity were revealed in a side-by-side comparison of in vitro clonal material with the original mother plants revealing mistakes putatively occurring during decades of processing and handling. A phylogeny was constructed to evaluate inter- and intraspecific relationships which together with a STRUCTURE analysis supported both commonly used treatments of potato taxonomy. Accessions generally clustered based on taxonomic and ploidy classifications with some exceptions but did not consistently cluster by geographic origin. STRUCTURE analysis identified putative hybrids and suggested six genetic clusters in the cultivated potato collection with extensive gene flow occurring among the potato populations, implying most populations readily shared alleles and that introgression is common in potato. Solanum tuberosum subsp. andigena (ADG) and S. curtilobum (CUR) displayed significant admixture. ADG likely has extensive admixture due to its broad geographic distribution. Solanum phureja (PHU), Solanum chaucha (CHA)/Solanum stenotomum subsp. stenotomum (STN), and Solanum tuberosum subsp. tuberosum (TBR) populations had less admixture from an accession/population perspective relative to the species evaluated. A core and mini core subset from the genebank material was also constructed. SNP genotyping was also carried out on 745 accessions from the Seed Savers potato collection which confirmed no genetic duplication between the two potato collections, suggesting that the collections hold very different genetic resources of potato. The Infinium SNP Potato Array is a powerful tool that can provide diversity assessments, fingerprint genebank accessions for quality management programs, use in research and breeding, and provide insights into the complex genetic structure and hybrid origin of the diversity present in potato genetic resource collections.

Identification of diagnostic KASP-SNP markers for routine breeding activities in yam (Dioscorea spp.)

Maintaining genetic purity and true-to-type clone identification are important action steps in breeding programs. This study aimed to develop a universal set of kompetitive allele-specific polymerase chain reaction (KASP)-based single nucleotide polymorphism (SNP) markers for routine breeding activities. Ultra-low-density SNP markers were created using an initial set of 173,675 SNPs that were obtained from whole-genome resequencing of 333 diverse white Guinea yam (Dioscorea rotundata Poir) genotypes. From whole-genome resequencing data, 99 putative SNP markers were found and successfully converted to high-throughput KASP genotyping assays. The markers set was validated on 374 genotypes representing six yam species. Out of the 99 markers, 50 were highly polymorphic across the species and could distinguish different yam species and pedigree origins. The selected SNP markers classified the validation population based on the different yam species and identified potential duplicates within yam species. Through penalized analysis, the male parent of progenies involved in polycrosses was successfully predicted and validated. Our research was a trailblazer in validating KASP-based SNP assays for species identification, parental fingerprinting, and quality control (QC) and quality assurance (QA) in yam breeding programs.

Validation of sorghum quality control (QC) markers across African breeding lines

Sorghum [Sorghum bicolor (L.) Moench] is a cereal crop of critical importance in the semi-arid tropics, particularly in Africa where it is second only to maize (Zea mays L.) by area of cultivation. The International Crops Research Institute for the Semi-Arid Tropics sorghum breeding program for Eastern and Southern Africa is the largest in the region and develops improved varieties for target agro-ecologies. Varietal purity and correct confirmation of new crosses are essential for the integrity and efficiency of a breeding program. We used 49 quality control (QC) kompetitive allele-specific PCR single nucleotide polymorphism (SNP) markers to genotype 716 breeding lines. Note that 46 SNPs were polymorphic with the top 10 most informative revealing polymorphism information content (PIC), minor allele frequency (MAF), and observed heterozygosity (Ho) of 0.37, 0.43, and 0.02, respectively, and explaining 45% of genetic variance within the first two principal components (PC). Thirty-nine markers were highly informative across 16 Burkina Faso breeding lines, out of which the top 10 revealed average PIC, MAF, and Ho of 0.36, 0.39, and 0.05, respectively. Discriminant analysis of principal components done using top 30 markers separated the breeding lines into five major clusters, three of which were distinct. Six of the top 10 most informative markers successfully confirmed hybridization of crosses between genotypes IESV240, KARIMTAMA1, F6YQ212, and FRAMIDA. A set of 10, 20, and 30 most informative markers are recommended for routine QC applications. Future effort should focus on the deployment of these markers in breeding programs for enhanced genetic gain.

Development of a diagnostic single nucleotide polymorphism (SNP) panel for identifying geographic origins of Cochliomyia hominivorax, the New World screwworm

The New World screwworm, Cochliomyia hominivorax, causes myiasis in livestock, humans, and other warm-blooded animals in much of South America and the Caribbean. It has been eradicated from North and Central America using the sterile insect technique and a biological barrier is currently maintained at the Panama - Colombian border. However, C. hominivorax is still a threat to eradicated areas as outbreaks can and do occur. In order to identify the origin of a fly involved in an outbreak scenario, diagnostic tools would be beneficial. Recently, the geographic population structure of this species was identified using single nucleotide polymorphisms (SNPs). Here we characterize the three major regional clusters: South America, the Inner Caribbean, and the Outer Caribbean. The objective of this study was to develop a SNP (single nucleotide polymorphism) panel to distinguish between these three clusters. A panel was developed using two unique SNPs per region for a total of six SNPs. This diagnostic SNP assay will allow for rapid source determination of flies from future incursions in order to intercept introductory pathways and aid in the control of New World screwworm.

Exploring and exploiting genetics and genomics for sweetpotato improvement: Status and perspectives

Sweetpotato (Ipomoea batatas (L.) Lam.) is one of the most important root crops cultivated worldwide. Because of its adaptability, high yield potential, and nutritional value, sweetpotato has become an important food crop, particularly in developing countries. To ensure adequate crop yields to meet increasing demand, it is essential to enhance the tolerance of sweetpotato to environmental stresses and other yield-limiting factors. The highly heterozygous hexaploid genome of I. batatas complicates genetic studies and limits improvement of sweetpotato through traditional breeding. However, application of next-generation sequencing and high-throughput genotyping and phenotyping technologies to sweetpotato genetics and genomics research has provided new tools and resources for crop improvement. In this review, we discuss the genomics resources that are available for sweetpotato, including the current reference genome, databases, and available bioinformatics tools. We systematically review the current state of knowledge on the polyploid genetics of sweetpotato, including studies of its origin and germplasm diversity and the associated mapping of important agricultural traits. We then outline the conventional and molecular breeding approaches that have been applied to sweetpotato. Finally, we discuss future goals for genetic studies of sweetpotato and crop improvement via breeding in combination with state-of-the-art multi-omics approaches such as genomic selection and gene editing. These approaches will advance and accelerate genetic improvement of this important root crop and facilitate its sustainable global production.

Analysis of genetic diversity and population structure among cultivated potato clones from Korea and global breeding programs

Characterizing the genetic diversity and population structure of breeding materials is essential for breeding to improve crop plants. The potato is an important non-cereal food crop worldwide, but breeding potatoes remains challenging owing to their auto-tetraploidy and highly heterozygous genome. We evaluated the genetic structure of a 110-line Korean potato germplasm using the SolCAP 8303 single nucleotide polymorphism (SNP) Infinium array and compared it with potato clones from other countries to understand the genetic landscape of cultivated potatoes. Following the tetraploid model, we conducted population structure analysis, revealing three subpopulations represented by two Korean potato groups and one separate foreign potato group within 110 lines. When analyzing 393 global potato clones, country/region-specific genetic patterns were revealed. The Korean potato clones exhibited higher heterozygosity than those from Japan, the United States, and other potato landraces. We also employed integrated extended haplotype homozygosity (iHS) and cross-population extended haplotype homozygosity (XP-EHH) to identify selection signatures spanning candidate genes associated with biotic and abiotic stress tolerance. Based on the informativeness of SNPs for dosage genotyping calls, 10 highly informative SNPs discriminating all 393 potatoes were identified. Our results could help understanding a potato breeding history that reflects regional adaptations and distinct market demands.

Functional Markers for Precision Plant Breeding

Advances in molecular biology including genomics, high-throughput sequencing, and genome editing enable increasingly faster and more precise cultivar development. Identifying genes and functional markers (FMs) that are highly associated with plant phenotypic variation is a grand challenge. Functional genomics approaches such as transcriptomics, targeting induced local lesions in genomes (TILLING), homologous recombinant (HR), association mapping, and allele mining are all strategies to identify FMs for breeding goals, such as agronomic traits and biotic and abiotic stress resistance. The advantage of FMs over other markers used in plant breeding is the close genomic association of an FM with a phenotype. Thereby, FMs may facilitate the direct selection of genes associated with phenotypic traits, which serves to increase selection efficiencies to develop varieties. Herein, we review the latest methods in FM development and how FMs are being used in precision breeding for agronomic and quality traits as well as in breeding for biotic and abiotic stress resistance using marker assisted selection (MAS) methods. In summary, this article describes the use of FMs in breeding for development of elite crop cultivars to enhance global food security goals.