2023 Recorded Presentations

Training Presentations

Introduction Website Reads2Map Multiparental QTL analysis haplotype assembly  
MAPpoly and QTLpoly Genetic marker imputation Software comparisons polyHaplotyper Genomic selection with R package StageWise Comparisons of hybrid breeding

User Presentations

Construction of a strawberry breeding core collection Genetic mapping in tetraploid kiwiberry root-knot nematodes in sweetpotato marker-assisted selection in sweetpotato hidecan package
breeding modernization in yam breeding GWAS and genomic prediction in blueberries chromosome synteny and legume evolution Genome-wide association mapping in blueberries building polyploid statistical genetics workflows

Poster Presentations and Abstracts

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.