Abstracts (2023)

Here are the abstracts of the oral and poster presentations from the 2023 Tools for Polyploids Workshop. The recordings of each presentation will be available on this page after the workshop. Poster presentations can be downloaded by clicking on the title. 


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User Presentations

Construction of a strawberry breeding core collection to capture and exploit genetic variation

Tim Koorevaar, Johan Willemsen, Paul Arens, Chris Maliepaard, Richard Visser. Wageningen University and Research - Plant Breeding, the Netherlands. 

As genotyping by sequencing (GBS) methods are becoming cheaper their applications become broader. For genotyping, GBS has become an alternative to SNP arrays which have certain limitations that can be overcome by GBS, such as genome coverage and ascertainment bias. Ideally, all material in a plant breeding program would be screened by using high coverage and deep sequencing. However, this is not cost-effective and probably not needed because high-quality genotypes can also be obtained by more cost-effective GBS tools with lower depth and/or less coverage which are imputed by utilizing a high-quality haplotype reference panel. A reference panel (core collection) of genotypes that represents the full width of the breeding program is essential for accurate imputation. In this study, we show a stepwise approach to obtain a representative core collection in a commercial plant breeding program that can be used as a reference panel for the utilization of cost-effective GBS methods. First, the most important crossing parents of advanced selections and specific genotypes (with specific traits) are identified and selected because they represent future genetic variation. Then, the core collection is finalized by maximizing the representativeness of the core collection compared to the current whole breeding program. Constructing representative core collections is commonly done by using genetic distances but pedigree-genomic-based relationship coefficients allow for accurate relationship estimation without the need to genotype each genotype in the breeding program. These pedigree-genomic-based relationship coefficients can identify pedigree errors, correct for missing links, and estimate relationships among founder genotypes. Consequently, this pedigree-genomic-based relationship matrix was used to complement the core collection by maximizing the representativeness of the total core collection.


Genetic mapping and QTL analysis of the sex locus in tetraploid kiwiberry

Ran Wang, Chris Maliepaard, Peter Bourke, Jinbao Fang, Danny Esselink, Paul Arens, Roeland Voorrips, Richard G.F. Visser. Wageningen University and Research, the Netherlands.

The Actinidia genus is a perennial, dioecious, fruiting vine including 54 species. The main commercial crops are kiwifruit (Actinidia chinensis var. chinensis and Actinidia chinensis var. deliciosa) and kiwiberry (Actinidia arguta). The ‘kiwiberry’ is commonly referred to as the small, smooth-skinned, and hairless fruit. There are multiple ploidy levels in kiwiberry but the main cultivated cultivars are polyploid. Despite the availability of many genomic resources in kiwiberry, SNP genotyping is still a challenge given these different levels of polyploidy. Recent advances in SNP array technologies have offered a high-throughput genotyping platform of genome-wide DNA polymorphisms. In this study, we developed a high-density SNP genotyping array to facilitate genetic studies and breeding applications in kiwiberry. SNP discovery was performed by genome-wide DNA sequencing of 40 Actinidia genotypes. The identified SNPs were stringently filtered for sequence quality, predicted conversion performance, and distribution over the available diploid kiwifruit genome. A total of 134,729 unique SNPs were put on the array. The array was used to genotype a tetraploid kiwiberry F1 population using fitPoly. We constructed an integrated linkage map covering 3,060.9 cM across 29 linkage groups using polymapR. A high degree of collinearity was observed between the kiwiberry genetic map and the kiwifruit reference genome. Further, we performed QTL analysis for the sex locus using polyqtlR, and a single major QTL was identified on Linkage Group 3 (LG3) in kiwiberry. Finally, our investigation of chromosome pairing behaviour in the population showed that the kiwiberry is mostly tetrasomic inheritance with partial preferential pairing.


Discovery of major QTL conferring resistance to root-knot nematodes (Meloidogyne enterolobii, M. incognita) in the sweetpotato (Ipomoea batatas) mapping population ‘Tanzania’ x 'Beauregard' and development of KASP-based assays for marker-assisted breeding

Simon Fraher1, Tanner Schwarz1, Bonny Oloka1, Chris Heim1, Mercy Kitavi1, Gabriel de Siqueira Gesteira1, Marcelo Mollinari1, John Hamilton3, Guilherme da Silva Pereira2, Zhao-Bang Zeng1, Gina Brown-Guedira1, Adrienne Gorny1, C. Robin Buell3, G. Craig Yencho11North Carolina State University, Raleigh, NC. 2University of Vicosa, Vicosa, Minas Gerais, BR. 3University of Georgia, Athens, GA. 

Sweetpotato, Ipomoea batatas (L.) Lam. (2n=6x=90), is among the world’s most important food crops and it is North Carolina’s most important vegetable crop. The recent emergence of the plant parasitic nematode Meloidogyne enterolobii poses a significant economic threat to NC’s sweetpotato industry and breeding resistance into new varieties has become a high priority. Previous studies have shown that ‘Tanzania’, a released African sweetpotato landrace, demonstrated strong resistance toward the quarantined M. enterolobii as well as the economically significant but not quarantined M. incognita. We screened the biparental sweetpotato mapping population, ‘Tanzania’ x ‘Beauregard’, for resistance to M. enterolobii by inoculating 246 progeny each with 10,000 eggs under greenhouse conditions. ‘Tanzania’, the female parent, was highly resistant, while ‘Beauregard’ was highly susceptible. Bioassays exhibited strong skewing toward resistance for three measures of resistance: reproductive factor, eggs per gram of root tissue, and root gall severity rating. By all measures, a 1:1 segregation suggested a major gene conferred M. enterolobii resistance. Using a random-effect multiple interval mapping model, we identified a single major QTL, qIbMe-4.1, on linkage group 4 (57.5 cm) that explained 70% of the variation for resistance to M. enterolobii. A similar QTL was previously discovered in linkage group 7 for resistance to M. incognita, which we here describe as qIbMi-7.1. We aligned whole genome sequence data for ‘Tanzania’ and ‘Beauregard’ with the diploid I. trifida (NCNSP306) reference assembly to identify single dose SNP markers within these QTL. From a pool of 2,444 SNPs, we identified 35 as PCR-compatible and nearest to QTL peaks. DNA from 298 sweetpotato genotypes of known M. enterolobii and/or M. incognita resistance, including 122 TB progeny and 176 other diverse germplasm, was genotyped using competitive allele-specific PCR (KASP). Of the 35 putative markers genotyped, 20 amplified and were polymorphic. Bioassay and genotype data were compared using chi-square analyses to reveal four significant markers that predicted nematode resistance exceeding the NCSU sweetpotato breeding program’s requisite 80% accuracy. We report three markers for M. enterolobii resistance on linkage group 4: 7038814 with R2=0.22 (p=1.9e-05), 7038930 with R2=0.34 (p=2.6e-08), and 7039636 with R2=0.3434 (p=4.8e-08), and one marker for M. incognita resistance on linkage group 7: 1699509 with R2=0.34 (p=4.6e-08). Efficiency of these markers ranged from 89-93% concordance with bioassay data. Validation in additional germplasm may determine these markers to be suitable for what we believe to be the first implementation of marker-assisted breeding in sweetpotato.


Development and validation of KASP markers for marker-assisted selection in autohexaploid sweetpotato breeding

Carla Cristina da Silva1, Reuben Ssali2, Mariam Nakitto2, Mukani Moyo2, Judith Nantongo2, Edwin Serunkuma2, Joseph Kitalikyawe2, Hugo Campos2, Craig Yencho3, Guilherme da Silva Pereira11Federal University of Vicosa, Vicosa, Minas Gerais, BR. 2International Potato Center, Kampala, Uganda. 3North Carolina State University, Raleigh, NC.

Sweetpotato [Ipomoea batatas (L.) Lam.], the seventh most important food crop worldwide, is an autohexaploid (2n = 6x = 90) and highly heterozygous species. Due to its complex genome, the usage of genetic tools in breeding programs is relatively limited. Inference of allele dosage for biallelic single nucleotide polymorphisms (SNPs) helps to increase marker informativeness for genetic analysis purposes. Here we report the development and validation of competitive allele-specific PCR (KASP) markers for sweetpotato quality traits, namely dry matter (DMAT), glucose (GLUC) and β-amylase (BAMY) contents, and skin (SCOL) and flesh (FCOL) colors. The KASP markers were derived from SNPs within major quantitative trait loci (heritabilities ranging from 0.28 to 0.61) identified on chromosomes 3 (FCOL, DMAT, GLUC), 12 (FCOL, SCOL), and 13 (BAMY). Sixty KASPs were evaluated in a validation plate of 94 sweetpotato clones from a CIP-Uganda multi-parental breeding population, and allele dosage calling was performed with R package fitPoly v. 3.0. Simple linear regression models were fitted in R for 46 polymorphic, high-quality KASPs using both additive and dominant models for all traits except GLUC and BAMY (phenotypic data not available). BAMY markers were fitted against firmness measures (FIRM). Additive models performed best for DMAT (Chr03_3120259, P < 6.5e−06), FCOL (Chr03_3104492, P < 3.8e−07), and SCOL (Chr12_2427638, P < 1.1e−14), whereas a dominant model was selected for FIRM (Chr13_18657261, P < 2.6e−05). The R-squared values ranged from 0.21 (FIRM) to 0.54 (SCOL). BAMY is strongly and negatively correlated with FIRM (−0.40), which explains why variation for FIRM can be only partially explained by BAMY-associated marker. As sweetpotato phenotyping for some quality traits is costly and time-consuming, the KASP markers characterized here can be used to optimize the selection process in the early stages leading to increased genetic gains.


Effort towards yam breeding modernization using genomic tools

Paterne Agre, Patrick Adebola, Asrat Asfaw. International Institute of Tropical Agriculture, Ibadan, Nigeria. 

To modernize the yam breeding program, efforts have been made to adopt and apply novel breeding strategies, including genomic tools. Broadening the genetic base of breeding populations is being achieved using genebank accessions, landraces, and wild relatives. Sequencing a dynamic population of germplasms resources (genebank accessions, landraces, and wild relatives) through Diversity Arrays Technology (DArT) showed the presence of high genetic diversity that meet current and future breeding needs. This new source of desirable genes enabled the yam breeding program to develop highly impactful varieties combining high agronomic and tuber quality performances for variety replacement in Africa. The yam breeding through the traditional phenotype selection path is time-consuming; it takes over 10 years from the parent selection to make crosses and create variability to the selection and testing of superior variant and the delivery of it to the farmers. To shorten the breeding cycle, identifying genomic regions controlling key agronomic traits through trait association, quantitative linkage mapping, and genomic prediction were deployed. Outcomes from this genomic research have helped shorten the time in population development to three years. A toolkit with ultra-polymorphic and reliable SNP markers was developed for germplasm management, exchange, and variety tracking. The yam breeding has been providing adequate support to its partners for genomic resources management.
Keywords: Dioscorea spp, genomic resources, yam breeding, polyploids


Genome-wide association mapping of fruit quality-related traits in a diversity panel of blueberries

Lauren Redpath2, Rish Aryal1, Amanda Hulse-Kemp4, Jaimie Green3, April Nyberg3, Nahla Bassil3, Hamid Ashrafi11North Carolina State University, Raleigh, NC. 2Pairwise Inc., Durham, NC. 3USDA-ARS, National Clonal Germplasm Repository, Corvallis, OR. 4USDA-ARS, Genomics and Bioinformatics Research Unit, Raleigh NC.

Commercial blueberry is a perennial polyploid species that suffers from long generation times and a lack of advanced molecular breeding techniques. Southern breeding programs have prioritized interspecific hybridization and novel trait introgression. This study presents a comprehensive evaluation of eighteen fruit and agronomic traits paired with target capture genotyping utilizing 59,302 custom probes to identify trait-associated markers in a genome-wide association study (GWAS). Evaluated phenotypic traits included fruit size, weight, color, firmness, puncture-ability, soluble solids content, and titratable acidity, as well as agronomic traits of days to budbreak, full bloom, initial fruit maturity, and full fruit maturity. A total of 33,701 high-quality, high-confidence SNPs were identified, of which 9,855 SNPs aligned to twelve developed scaffolds, among which 21 significant SNPs were identified to have a trait association. Candidate genes were encoded by these SNPs with functions in anthocyanin acylation, firmness, fruit density, acidity, and flower development. The SNPs identified in this panel can be useful in the further identification of other unquantified novel characteristics. These data can be implemented in marker-assisted selection and development of advanced molecular breeding programs in blueberries.


Chromosome synteny by comparative genome analysis revisits polyploidy contribution to legumes evolution

Gabriel Henrique Santos Costa, Eduardo Velloso Oliveira, Gabriel Fernando Silva, Mateus Mondin. University of Sao Paulo, SP, Brazil.

Although the importance of the group with several crops, integration between genome organization, chromosome rearrangements, and polyploidy remains a key topic for the legume family. Efforts to analyze genome synteny and karyotype organization made important contributions, especially in closely related species. Meanwhile, the basic chromosome number proposed to the group suggests a series of WGD during species diversification. However, except for intrageneric cases, polyploidy is inconclusive in the legumes mainly due to the missed links across the evolutionary time. The availability of assembled genomes in legume species represents an opportunity to revisit the question concerning polyploidy. Four legume species were chosen to investigate polyploid events during evolution and diversification. Medicago truncatula [2n=2x=16] is used as a model and reference genome to compare the following polyploids. Glycine max [2n=x?=40] is a paleopolyploid with a missed origin. Arachis hypogaea is an allotetraploid [2n=4x=40, AABB], resulting from A. duranensis [2n=2x=20, AA] and A. ipaënsis [2n=2x=40, BB] crosses. Lupinus angustifolius [2n=x?=40] and Lupinus albus [2n=x?=50] are well-accepted as polyploids and phylogenetically more distant. Glycine max showed 20 unique chromosomes without significant levels of homeology. Almost the entire chromosome complement of M. truncatula is found inside the Glycine max. For example, M. truncatula chromosome 8 is split among G. max chromosomes 5, 7, 8, and 16. All the M. truncatula chromosomes appear represented in the maximum of four chromosomes of G. max, suggesting a tetraploid origin. Arachis hypogaea shows five homeologous chromosome pairs when compared to M. truncatula. Internal genome rearrangements occured after the chromosome doubling, once the complete haploid set is not homeologous to the ancestors. However, some chromosomes are still conserved and can be observed in all species, such as chromosomes 1 and 4. In the most distant phylogenetic group, L. albus shows three conserved homeologous chromosomes, while L. angustifolius has one pair only. These two species presented some chromosomes without synteny to M. truncatula, L. angustifolius with one chromosome, and L. albus with four chromosomes. Polyploidy played an important role in the origin of the species analyzed despite the complexity of the genome and chromosome structure compared to a model species. Ancestral whole genome duplications generated syntenic homeologous regions, and the comparative genome analysis across the species represents an essential tool for investigating the conservation of the genes across the evolutionary time in legumes.


Tools and Techniques for GWAS and Genomic Prediction in Blueberries with Breeding Insight

Lillian Hilsop1, Michael Hardigan1, Moira Sheehan2, Dongyan Zhao2, Claire Luby11USDA-ARS, Horticultural Crops Production and Genetic Improvement Research Unit, Corvallis, OR. 2Breeding Insight at Cornell University, Ithaca, NY.

Breeding Insight is a USDA initiative supporting underserved breeding programs with technologies and biotechnical expertise. The USDA-ARS Blueberry Breeding program in Corvallis, OR and Breeding Insight are teaming up to conduct genetic analysis of traits in a diverse population of blueberries adapted to the Pacific Northwest. This talk will outline the tools used in the analysis and the preliminary results. Five thousand genetically unique individuals from 85 bi-parental crosses were planted in Corvallis, OR in 2016 and 2017. In 2021, they were screened using the genetic marker platform developed by BI through Diversity Arrays Technology (DArT; Canberra, Australia). Marker data was cleaned and filtered using a UpDog, python, and R pipeline. From 2020-2022, phenotypes were collected using FieldBook software for plant physiology and fruit quality traits, such as berry size, acidity, firmness, obrix, and ripening time. Phenotypic data was stored in the BreedBase database. Genome-wide association and genomic prediction will be conducted using mapPoly, GWASPoly, and Stagewise. This presentation will share preliminary results, and the expected outcomes of the project. This work will benefit blueberry growers in the Pacific Northwest region where the blueberry industry is relatively new and growing rapidly by accelerating cultivar development and supporting public and private breeders with molecular breeding tools. 


The hidecan package: visual integration of GWAS and differential expression results

Olivia Angelin-Bonnet1, Matthieu Vignes2, Patrick Biggs2, Samantha Baldwin3, Susan Thomson31The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand. 2Massey University, Palmerston North, New Zealand. 3The New Zealand Institute for Plant and Food Research Limited, Lincoln, New Zealand. 

Genome-wide association studies (GWAS) are often conducted with the goal of ultimately detecting genes involved in the genetic control of a trait of interest. Thus, in order to complement the results of such a study, differential expression (DE) experiments can be used to identify genes whose expression varies between two conditions. Alternatively, if several traits are measured for the genotyped individuals, it can be interesting to assess whether there is any overlap between the genomic regions found associated with each of the traits. In both cases, there is currently a lack of clear visualisation to summarise and integrate the results of multiple GWAS and/or DE analyses. Manhattan plots are only suited for a single GWAS, and circos plots do not permit a good comparison of the results from several analyses. Here we present the hidecan R package, for visualising the results from multiple GWAS and/or differential expression (DE) experiments. Given markers or genes scores from one or more GWAS and DE analyses, the package displays the genomic position of the markers and genes whose score exceeds a threshold set by the user. The significance threshold can be set independently for GWAS and DE results. In addition, the user can provide a list of candidate genes (e.g. genes known to affect the trait investigated), which will be added to the visualisation. The resulting hidecan plot provides a clear visual summary of the different analyses, and can integrate prior knowledge about the trait(s) under study. It can be used to identify genomic regions associated with a trait of interest both through high-scoring markers and differentially expressed genes or highlight any overlap in the genetic control of several related traits. The hidecan package also offers a Shiny app through which the user can create a hidecan plot, which can then be exported as a PNG or PDF file.


Building Polyploid Statistical Genetics Workflows in R with the Targets and Future Packages

John McCallum, Roy Storey. New Zealand Institute for Plant and Food Research, Canterbury, New Zealand. 

Polyploid genetics workflows require multiple data preparation and modeling steps employing custom code and multiple software packages. Growing scale and computational demands require that this can be adapted to exploit available multicore and HPC resources. We will describe the usage of two R packages which provide key abstractions to manage the complexity of constructing and executing polyploid genetic workflows with HPC. The targets package (https://books.ropensci.org/targets) is a make-like tool that allows the construction of workflows as directed acyclic graphs (DAGs) which encourages a highly functional approach to using R and supports remote and parallel workflow execution via the future package ( https://www.futureverse.org). We will describe considerations for adopting such an approach and demonstrate an example of a polyploid GWAS workflow on HPC using GWASpoly (https://jendelman.github.io/GWASpoly/GWASpoly.html) 


Poster Presentations

Exploration of the Genetic Background of Potato Tuber Dormancy in Response to Cold Storage

Ao Jiao1, Sanjeev Gautam1, Jeewan Pandey1, Douglas Scheuring2, Jeffrey Koym1, M. Isabel Vales21Texas A&M University, College Station, TX. 2Texas A&M AgriLife Research and Extension Center, Lubbock, TX. 

Potato tuber dormancy is the incapacity of tubers to sprout even under favorable conditions. The dormancy period is measured from vine kill until tubers start sprouting. Since early dormancy break causes tuber spoilage and post-harvest quality reduction, long tuber dormancy is desired. Commercially, tuber sprouting is prevented by using sprout inhibitors or cold storage. As the use of sprout inhibitors continues to be restricted, emphasis is placed on cold storage and breeding for longer dormancy periods. The objective of this study was to compare the length of the tuber dormancy period of potato clones stored at room temperature with that observed under cold storage and to explore the genetic basis of the tuber dormancy period in response to cold storage. For three years, 217 potato clones from the Texas A&M Potato Breeding Program were grown in Springlake and Dalhart, Texas. The dormancy period was measured at room temperature and under cold storage. Cold storage significantly extended potato tuber dormancy, with most clones remaining dormant for up to 60% longer in cold storage. Genome-wide association studies were performed using GWASpoly with Infinium Illumina 22K V3 SNP Potato Array to identify genomic regions associated with tuber dormancy in response to cold storage. Three quantitative trait loci were identified, with two on chromosome 1 and one on chromosome 6, and they explained 9.7%, 10.9% and 10.7% of the variation, respectively. The findings of this study will contribute to a better understanding of potato tuber dormancy in response to cold storage and guide breeding.


Identification of Quantitative Trait Loci Controlling Shoot Length, Internode Length, and Number of Internodes in Tetraploid Roses

Haramrit Gill, Jeekin Lau, Luke Whiteley, David Byrne, Oscar Riera-Lizarazu. Texas A&M University, College Station, TX. 

Plant height is an important factor in rose bush architecture that affects its aesthetic value. Roses with longer stems, for example, are desirable in the cut flower industry; however, roses with shorter stems and overall compact bush are desirable for landscape and garden roses. Plant height in tetraploid roses is complex and is affected by both internode number and length, ultimately affecting the overall shoot length. To better understand the genetic basis of this trait in roses, we conducted a study to identify quantitative trait loci (QTL) associated with shoot length, internode length, and the number of internodes. For this, measurements of shoot and internode length, and the number of internodes were collected for two years in two tetraploid rose populations [‘Stormy Weather’ (SW) X ‘Brite Eyes’ (BE), and ‘My Girl’ (MG) X ‘Brite Eyes’ (BE)]. Our analysis suggests the presence of a QTL on chromosome 3 for internode length and QTL on chromosomes 3 and 5 for shoot length and the number of internodes. The location of the QTL on chromosome 3 encompasses two genes. These were GID1c, involved in regulating vegetative growth, and RoKSN, a floral repressor and a regulator of vegetative growth in roses. So, we conclude that these genes could be the potential candidate genes responsible for regulating the internode length and hence the overall shoot length of the rose plant.


Identification of QTLs related to fruit texture at harvest and postharvest in blueberry

Heeduk Oh2, Molla Mengist2, Marti Pottorff, Lara Giongo3, Penelope Perkins-Veazie1, Massimo Iorizzo21Plants for Human Health Institute, Kannapolis, NC. 2North Carolina State University, Raleigh, NC. 3Edmund Mach Research and Innovation Center, San Michele, NC. 

Blueberries (Vaccinium corymbosum L.) are produced and consumed worldwide for their enjoyable flavor and numerous human health benefits. However, blueberry fruits are highly perishable and soften rapidly, negatively affecting postharvest transport, storage, and consumer acceptance. In this study, fruit characteristics related to pre- and post-harvest texture and berry size were evaluated in a mapping population including 346 F1 genotypes (‘Reveille’ x ‘Arlen’) over two years (2021 and 2022) and used for quantitative trait loci (QTL) analysis. Fruits were stored between 24 hours (T0) and 6 weeks (T1) at 2 C and 14 mechanical texture parameters were collected with a TA.XTPlus Texture Analyzer. Extensive variation was observed for all the texture and size parameters, indicating segregation for these parameters in this population. Fruit weight and the texture parameter, ‘distance to maximum force’ (distance the skin stretches until puncture), were found to be those most closely associated with postharvest texture changes. In total, eight and seven QTLs were detected for pre-harvest and post-harvest parameters, respectively, with some QTLs detected at both time points. A QTL on chromosome 10 for ‘force linear distance’ (a texture parameter identifying the length of curve between the point of contact and 80% strain) was stable over two years for both T0 and T1. These results are establishing a framework for developing a marker-assisted selection strategy for improving pre- and post-harvest texture characteristics in blueberry breeding programs.


Genome-wide association studies of mineral content in potato tubers and identification of clones with high genomic-estimated breeding value

Jeewan Pandey1, Sanjeev Gautam1, Douglas Scheuring2, Jeffrey Koym1, M. Isabel Vales21Texas A&M University, College Station, TX. 1Texas A&M AgriLife Research and Extension Center, Lubbock, TX.

Malnutrition is a major public health problem in many parts of the world. This issue draws attention to all important sources of minerals for the human diet, including potatoes. Potato accounts for 18% of the recommended dietary allowances of potassium, 6% of copper, phosphorus, and magnesium; and 2% of calcium and zinc. Increased public interest in the nutritional value of foods has prompted the evaluation of mineral contents in potatoes and the investigation of the genetics underlying the traits. The objective of this study was to identify genomic regions associated with mineral content and obtain genomic-estimated breeding values to guide the selection of parents and the advancement of clones through the breeding pipeline in potatoes. A diversity panel with 214 potato clones was phenotyped in three field environments in Texas for 12 minerals and genotyped using the Infinium Illumina 22K V3 Potato SNP Array. A genome-wide association study for mineral content was performed using GWASpoly. Two QTLs on chromosome 7 associated with zinc content and three QTLs on chromosome 5 associated with potassium and manganese content were identified. The loci identified will contribute to a better understanding of the genetic basis of mineral content in potatoes and guide the enrichment of potato tuber with macro and micronutrients. Genomic-estimated breeding values were obtained using StageWise. Clones with high genomic-estimated breeding values should be used as parents to improve mineral content in potato tubers.


Elimination of Pungency in Allotetraploid Brassica juncea Through Gene Editing of the Multicopy Myrosinase Gene Family

Sathya Jali, Dale Karlson, Thomas Poorten, Shai Lawit, Raj Chauhan, Pradeep Marri, Gina Pham, Sharon Guffy, Justin Fear, Cherie Ochsenfeld, Tracey Chapman, Bruno Casamali, Jorge Venegas, Lolita Mathew, Aabid Shariff, Joseph Watts, HaeJin Kim, Mike Mann, Aaron Hummel, Ryan Rapp, Julius Mojica. Pairwise, Durham, NC.

We identified a novel opportunity to enhance the availability of nutritious, fresh leafy greens for human consumption. Here, we demonstrated the efficacy of disarming the ‘mustard bomb’ reaction in reducing pungency upon the mastication of fresh tissue—a major source of unpleasant flavor and/or odor in leafy Brassica. Using gene-specific mutagenesis via CRISPR-Cas12a, we created knockouts of 17 functional copies of the type-I myrosinase multigene family in tetraploid Brassica juncea. Our greenhouse and field trials demonstrate, via sensory and biochemical analyses, a stable reduction in pungency in edited plants across multiple environments. Collectively, these efforts provide a compelling path toward boosting the human consumption of nutrient-dense, fresh, leafy green vegetables. Pairwise is introducing this leafy green as a new, healthy leafy-green option for consumers under our Conscious Foods brand.


Turfgrass breeding dashboard for a multi-state collaborative project

Beatriz Tome Gouveia, Gabriel de Siqueira Gesteira. Susana Milla-Lewis. North Carolina State University, Raleigh, NC.

The turfgrass industry impacts the US economy, benefits the environment, and also provides aesthetic and health benefits to humans. Limited availability and reduced quality of water for irrigating turfgrass areas is the biggest challenge the turfgrass industry currently faces. Therefore, a collaborative project among North Carolina State University (NCSU), Oklahoma State University (OSU), University of Florida (UF), University of Georgia (UGA), University of California - Riverside, and Texas A&M University System (TAMUS) has been focused on addressing these problems by breeding four economically important warm-season turfgrass species in the southern US: bermudagrass [Cynodon spp. (C. dactylon [2n= 4x = 36] and triploid interspecific hybrids [2n = 3x = 27])], St. Augustinegrass [Stenotaphrum secundatum (2n = 2x = 18)], seashore paspalum [Paspalum vaginatum (2n = 2x = 20)] and zoysiagrass [Zoysia spp. (2n = 4x = 40)]. In the breeding pipeline, hundreds of breeding lines are evaluated for several traits in multi-environment for several years. To help turfgrass breeders easily identify superior breeding lines, we developed an R Shiny-based dashboard that enables users to explore results from several breeding trials interactively. In this application, users can select, filter, and visualize results from multi-environment trials in a robust yet user-friendly platform that integrates multiple sources of data. The app allows users to identify superior breeding lines for multiple traits through a principal components analysis and selection index, where they can create their own selection index based on user-defined weights for each trait. Users can also compare the performance of any set of breeding lines across environments and study the genotype-by-environment interaction through dimension reduction approaches. The app is under continuous development and can be extended to integrate other sources of data. The Turfgrass Dashboard has the potential to be adopted as a centralized framework for data sharing and exploration of turfgrass breeding trials.


Identification of Genomic Regions Associated with Bacterial Wilt Resistance in Southern Highbush Blueberries Using Genome-Wide Association Study

Lushan Ghimire, Norma Flor, Luis Felipe Ferrao, Juliana Benevenuto, Philip Harmon, Patricio Munoz. University of Florida, Gainesville, FL. 

Bacterial wilt in blueberries is caused by Ralstonia solanacearum. Annual Florida grower’s surveys for breeding trait priorities in southern highbush blueberries (SHB) has ranked bacterial wilt among the most important diseases in terms of recent outbreak. Given the current rate of expansion of the Florida blueberry industry, several wilt outbreaks are unavoidable, as blueberries are being planted in areas where endemic pathogen populations exists. Therefore, we aim to accelerate phenotyping of SHB genotypes for disease response and to identify genomic regions conferring resistance to bacterial wilt using genome-wide association study (GWAS). The ultimate goal is to apply marker-assisted selection for accelerating the development of resistant cultivars. For this, softwood stems (12 inches) were collected from each individual in a population of 326 advanced selections (genotypes) from the University of Florida blueberry breeding program. The stems were dip-inoculated with bacterial suspension at a concentration of 1*10^8 CFU/mL for 10 minutes. They were then placed over a tray containing water and incubated inside a plant growth room at 28°C, with a photoperiod of 12 hours of light and 12 hours of darkness for a duration of two weeks. Disease severity of each genotype was visually assessed through the extent of wilting symptoms. A second phenotyping round was conducted on fifteen of each of the most resistant, average, and susceptible genotypes previously screened and on additional 204 genotypes from a new set of advanced selections. In this case, stem cuttings were continuously incubated in the inoculum (1 x 10^6 CFU/mL). Days to wilting and disease severity of each genotype were assessed. All these individuals were genotyped using Capture-Seq for SNP detection. Breeding values (BV) for the disease severity were calculated for both rounds using mixed models and pedigree information. BV for the first and second rounds of phenotyping ranged from 18.94 to 90.09 and from 17.21 to 93.4 respectively. Narrow sense heritability for the wilt-resistance trait was 0.54 and 0.36 as per the first and second rounds of phenotyping respectively. Further analyses are underway to identify significant genomic regions associated with bacterial wilt resistance in SHB and to better understand the genetic architecture of this trait. Additionally, computer vision phenomics is being explored for its potential in phenotyping SHB affected by bacterial wilt. Results from this research (obtained from screening and high-throughput genotyping) can ultimately aid in strategic breeding decisions and speed up the process associated with the development of bacterial wilt-resistant blueberry cultivars through marker-assisted selection.


Integration of Genetic and Data-Driven Methods for Optimizing Genomic Prediction in Autotetraploid Blueberries

Paul Adunola, Felipe Ferrao, Patricio Munoz. University of Florida, Gainesville, FL. 

Genomic selection (GS) is a form of marker-assisted selection that estimates the effects of genome-wide markers to predict the genetic merit of non-phenotyped individuals. While its practical implementation required the allocation of resources, breeders must face the choice of budget allocation associated with genotyping and population designs. In this context, genomic prediction applied to blueberry (Vaccinum spp) has experienced extra obstacles, due to the autopolyploid form and perennial nature of the species, a fact that results in slower progress. Inspired by recent improvements in using genomic prediction at the University of Florida Blueberry Breeding Program, we proposed a combination of data-driven and genetic-based methodologies to allocate limited resources on genotyping. To this end, we used ten criteria to select the best probes for sequencing and compared predictive abilities computed using genomic BLUP (GBLUP) and single-step BLUP (ssBLUP). Our contribution to this study is two-fold: (i) first, we emphasize the importance of combining filtering parameters based on statistical genetics features to select the best set of molecular markers and tested genomic prediction studies; (ii) for practical implementation, we showed that number of markers size can be optimized, a fact that can leverage our predictive accuracies with reduced costs. In this study, we demonstrated the effectiveness of filtering criteria to select a panel of probes using data from fruit quality traits collected over the past two years at the University of Florida.


Investigating the genetic background of potato tuber defects caused by heat stress

Sanjeev Gautam1, Jeewan Pandey1, Douglas Scheuring1, Jeffrey Koym2, M. Isabel Vales11Texas A&M University, College Station, TX. 2Texas A&M AgriLife Research and Extension Center, Lubbock, TX.

Heat stress reduces marketable tuber yield and the quality of potatoes. The quality of potato produce is deteriorated by external (heat sprouts, chained tubers, knobs) and internal (vascular discoloration, internal heat necrosis) defects. Successful cultivation of potatoes under heat stress requires planting heat-tolerant varieties that can produce high yields of marketable tubers. Heat tolerance is a complex trait and understanding the genetic basis will aid in the improvement of potatoes. A genome-wide association study (GWAS) was performed to identify genomic regions associated with heat tolerance using 10,106 markers from Infinium Illumina 22 K V3 Potato Array in GWASpoly. A phenotypic panel of 217 diverse potato clones was evaluated for yield and quality attributes from Dalhart and Springlake, Texas which experience high-temperature conditions during crop period. The genotypes differed in their capacity of expressing the external as well as internal defects on tubers under heat stress. Genomic estimated breeding values for identifying superior clones were calculated using StageWise. QTLs were identified in chromosomes 3, 4, 6, and 7 for external (knobs, chain tubers, growth cracks) defects and explained around 2% variation. SNPs in chromosomes 1, 3, 4, 6, 7, 10, 11, and 12 were found to be associated with internal defects (hollow heart, blackspot, internal heat necrosis) and explained around 1.5 % variation in the trait. The identified genomic regions and genomic estimated breeding values will be important to improve heat tolerance in potatoes.


Development and characterization of a unique genetic resource for allele mining and peanut improvement in Africa.

Soukeye Conde1, Jean Francois Rami1, Daniel Fonceka1, Samba Ndao Sylla21Laboratoire Campus de Biotechonoligies Vegetales, Montpellier, France. 2CIRAD, Dakar, Senegal. 

Cultivated peanut (Arachis hypogaea L. ) has high morphological diversity but low variability at the DNA level. Diving into breeding lines, improved and local varieties diversity is important for mining alleles that can be used in breeding programs. To reach this objective, core collections have been reported as meaningful genetic resources for QTL mapping and gene discovery. We assembled a wide collection of peanut breeding lines, cultivars, and landraces from ten breeding programs in Africa. We genotyped this collection using a 40k Affymetrix SNP array and used the data for describing the genetic diversity and its structure using discriminant analysis of principal components. We also defined a core collection by combining breeders' knowledge and diversity data, that has been phenotype in 5 countries in West Africa. Overall, breeders in Africa hold large diversity with all botanical and commercial peanut types represented. However, this diversity is not evenly distributed, youngest breeding programs managing less variability than others. The analysis of population substructure showed a clustering based on geographical origin with groups composed mainly by Spanish variety from West Africa or Virginia from East and Southern Africa. The phenotyping of the core collection showed large variation for traits related to yield component and disease resistance. High genotype x location interactions have also been observed. We developed a very unique genetic resource for peanut breeding and alleles mining, that will allow breeders in Africa to efficiently tap into the useful diversity for varietal improvement.


Meta-analysis of rose rosette disease resistance quantitative trait loci and a search for candidate genes.

Tessa Hochhaus, Jeekin Lau, Cristiane Taniguti, David Byrne, Oscar Riera-Lizarazu. Texas A&M University, College Station, TX.

Rose rosette disease (RRD) caused by Rose rosette emaravirus is one of the major diseases on roses (Rosa sp.) which threatens the $168 million rose industry. The virus is transmitted by eriophyid mites, and symptomatic roses are generally destroyed to reduce further spread. The disease symptoms include elongated shoots, excessive branching of shoots, leaf distortion, red or yellow leaves, excessive prickles, and increased susceptibility to other stresses or diseases. Little is known about the genetics of RRD resistance, but recent quantitative trait mapping studies have revealed quantitative trait loci (QTL) for reduced susceptibility to RRD in linkage group (LG) 5, 6, and 7 in tetraploid, and LG 1, 3, 5, and 6 in diploid populations. In this study, we seek to better understand the relationship between QTL on LG 5 and 6 identified in both diploid and tetraploid populations and to better localize QTL by performing a meta-analysis using data from these reports. For this, we compiled and aligned genetic maps and projected meta-QTL. This analysis revealed that the peaks and intervals for QTL in LG 5 and 6 using diploid and tetraploid populations co-localized, suggesting that these may be the same QTL. The analysis also led to a narrowing of QTL intervals, which will guide the search for candidate genes. Results from this study may be used in the design of strategies to manipulate and use these genetic factors in a plant breeding context.