Leaf Membrane Stability under High Temperatures as an Indicator of Heat Tolerance in Potatoes and Genome-Wide Association Studies to Understand the Underlying Genetics.

High temperatures during the crop growing season are becoming more frequent and unpredictable, resulting in reduced crop productivity and quality. Heat stress disrupts plant metabolic processes that affect cell membrane composition and integrity. Cell membrane permeability, ion leakage, and heat shock proteins have been evaluated to screen for heat tolerance in plants. In potatoes, it is unclear whether leaf membrane stability under heat stress is correlated with underground tuber productivity and quality. The main goal of this study was to evaluate if leaf membrane relative electrolyte conductivity (REC) under high temperatures could be used to identify heat-tolerant potato genotypes. Electrolyte leakage assays, correlation estimations, and genome-wide association studies were carried out in 215 genotypes. Expression levels of small heat shock protein 18 (sHSP18) were evaluated in the heat-sensitive potato variety Russet Burbank and compared with those of the heat-tolerant variety Vanguard Russet using Western blotting. Significant differences were observed among genotypes for leaf membrane REC under extreme heat (50°C); REC values ranged from 47.0-99.5%. Leaf membrane REC was positively correlated with tuber external and internal defects and negatively correlated with yield. REC was negatively correlated with the content of several tuber minerals, such as nitrogen, magnesium, and manganese. Eleven quantitative trait loci (QTLs) were identified for leaf membrane REC, explaining up to 13.8% of the phenotypic variance. Gene annotation in QTL areas indicated associations with genes controlling membrane solute transport and plant responses to abiotic stresses. Vanguard Russet had lower leaf REC and higher expression of sHSP18 under high-temperature stress. Our findings indicate that leaf membrane REC under high temperatures can be used as an indicator of potato heat tolerance.

Assessing heat tolerance in potatoes: Responses to stressful Texas field locations and controlled contrasting greenhouse conditions.

In recent years, heat stress has affected potato production more frequently, resulting in lower marketable yields and reduced tuber quality. In order to develop heat-tolerant potatoes, it is necessary to select under heat-stress conditions and consider traits affected by heat stress. The Texas A&M Potato Breeding Program has selected potatoes under high-temperature stress for several decades. Ten potato cultivars, representing heat tolerant and sensitive clones based on past performance in Texas, were included in field trials for three years at the two main locations used by the Texas Breeding Program (Dalhart and Springlake, TX) to assess if the Texas field locations are suitable for heat tolerance screening. Both locations were confirmed as appropriate for heat stress screening. However, Springlake was a more stressful location since it had significantly lower yields of marketable tubers and increased percentages of tuber defects. Planting time did not have a significant effect at the most stressful location. The same ten potato clones were included in greenhouse experiments with contrasting temperatures (normal versus heat stress). There was confirmation that heat stress conditions resulted in significantly lower marketable yields, specific gravity, dormancy, and significantly higher percentages of tuber defects; however, significant differences existed between potato clones. Under heat stress conditions, Russet Burbank had a high percent of tubers with external defects, whereas Atlantic showed the highest percentage of internal defects (mainly internal heat necrosis). Vanguard Russet produced the highest marketable yield while maintaining a low percentage of external and internal defects. Russet Burbank and Atlantic were heat-sensitive controls for external and internal tuber defects, respectively. In contrast, Vanguard Russet can be used as a reliable heat-tolerant control. Including appropriate controls in heat stress studies will help identify clones with heat tolerance.

Corrigendum: Genomic regions associated with tuber traits in tetraploid potatoes and identification of superior clones for breeding purposes.

[This corrects the article DOI: 10.3389/fpls.2022.952263.].

Genetic Basis of Potato Tuber Defects and Identification of Heat-Tolerant Clones.

Heat stress during the potato growing season reduces tuber marketable yield and quality. Tuber quality deterioration includes external (heat sprouts, chained tubers, knobs) and internal (vascular discoloration, hollow heart, internal heat necrosis) tuber defects, as well as a reduction in their specific gravity and increases in reducing sugars that result in suboptimal (darker) processed products (french fries and chips). Successfully cultivating potatoes under heat-stress conditions requires planting heat-tolerant varieties that can produce high yields of marketable tubers, few external and internal tuber defects, high specific gravity, and low reducing sugars (in the case of processing potatoes). Heat tolerance is a complex trait, and understanding its genetic basis will aid in developing heat-tolerant potato varieties. A panel of 217 diverse potato clones was evaluated for yield and quality attributes in Dalhart (2019 and 2020) and Springlake (2020 and 2021), Texas, and genotyped with the Infinium 22 K V3 Potato Array. A genome-wide association study was performed to identify genomic regions associated with heat-tolerance traits using the GWASpoly package. Quantitative trait loci were identified on chromosomes 1, 3, 4, 6, 8, and 11 for external defects and on chromosomes 1, 2, 3, 10, and 11 for internal defects. Yield-related quantitative trait loci were detected on chromosomes 1, 6, and 10 pertaining to the average tuber weight and tuber number per plant. Genomic-estimated breeding values were calculated using the StageWise package. Clones with low genomic-estimated breeding values for tuber defects were identified as donors of good traits to improve heat tolerance. The identified genomic regions associated with heat-tolerance attributes and the genomic-estimated breeding values will be helpful to develop new potato cultivars with enhanced heat tolerance in potatoes.

Genetic architecture of tuber-bound free amino acids in potato and effect of growing environment on the amino acid content.

Free amino acids in potato tubers contribute to their nutritional value and processing quality. Exploring the natural variation in their accumulation in tubers across diverse genetic backgrounds is critical to potato breeding programs aiming to enhance or partition their distribution effectively. This study assessed variation in the tuber-bound free amino acids in a diversity panel of tetraploid potato clones developed and maintained by the Texas A&M Potato Breeding Program to explore their genetic basis and to obtain genomic-estimated breeding values for applied breeding purposes. Free amino acids content was evaluated in tubers of 217 tetraploid potato clones collected from Dalhart, Texas in 2019 and 2020, and Springlake, Texas in 2020. Most tuber amino acids were not affected by growing location, except histidine and proline, which were significantly lower (- 59.0%) and higher (+ 129.0%), respectively, at Springlake, Texas (a location that regularly suffers from abiotic stresses, mainly high-temperature stress). Single nucleotide polymorphism markers were used for genome-wide association studies and genomic selection of clones based on amino acid content. Most amino acids showed significant variations among potato clones and moderate to high heritabilities. Principal component analysis separated fresh from processing potato market classes based on amino acids distribution patterns. Genome-wide association studies discovered 33 QTL associated with 13 free amino acids. Genomic-estimated breeding values were calculated and are recommended for practical potato breeding applications to select parents and advance clones with the desired free amino acid content.

Raman spectroscopy detects chemical differences between potato tubers produced under normal and heat stress growing conditions.

Potato is the most consumed vegetable worldwide. Potato tubers contain water, starch, proteins, minerals, and vitamins. The amounts of these chemicals depend on the cultivar and growing location. When potatoes are exposed to high temperatures during the growing period, tuber yield and quality are detrimentally affected; however, there is limited knowledge about the influence of high temperatures on tuber chemical composition. With temperatures rising around the globe, the reaction of potato cultivars to high temperatures is increasingly important, and heat-induced changes, including changes in the chemical composition of tubers, should be considered. The Texas A&M University Potato Breeding Program has been selecting potato clones under high-temperature conditions for many years. Several released cultivars are considered heat-tolerant based on high marketable yields and low internal and external tuber defects. In this study, we used Raman spectroscopy (RS), an analytical tool, to determine whether heat stress causes changes in the chemical composition of tubers of ten potato cultivars. RS is a non-invasive method that requires less time and labor than conventional chemical analysis. We found drastic changes in the intensities of vibrational bands that originate from carbohydrates in the spectra acquired from tubers of heat-stressed plants compared to tubers produced by potato plants grown under normal conditions. These results demonstrate that RS could be used as a replacement or complement to conventional chemical analysis to inspect the effect of heat stress on tuber chemical composition.

Genomic selection and genome-wide association studies in tetraploid chipping potatoes.

Potato is a major food crop in the United States and around the world. Most potatoes grown in the United States are destined for processing. Genomic selection can speed up breeding progress for important traits, including those with complex inheritance by guiding the identification of the best parents and guiding selection to advance clones in the breeding program. However, the application of genomic selection in polyploid species has been challenging. In this study, we obtained breeding values of 384 chipping clones evaluated in Texas between 2017 and 2020. The mean reliability of the genomic-estimated breeding values obtained were 0.77, 0.41, 0.61, 0.71, and 0.24 for chip color, chip quality, specific gravity, vine maturity, and total yield, respectively. Potato clones with good chip quality, high yield, high specific gravity, and light-color chips were identified using a multi-trait selection index based on weighted standardized genomic-estimated breeding values. Genome-wide association studies identified quantitative trait loci on chromosome 5 for vine maturity and chromosomes 1, 3, and 7 for chip color. This research has laid the groundwork for implementing genomic selection in tetraploid potato breeding and understanding the genetic basis of chip processing traits in potatoes.

Variation and genetic basis of mineral content in potato tubers and prospects for genomic selection.

Malnutrition is a major public health concern in many parts of the world. Among other nutrients, minerals are necessary in the human diet. Potato tubers are a good source of minerals; they contribute 18% of the recommended dietary allowance of potassium; 6% of copper, phosphorus, and magnesium; and 2% of calcium and zinc. Increased public interest in improving the nutritional value of foods has prompted the evaluation of mineral content in tubers of advanced genotypes from the Texas A&M Potato Breeding Program and the investigation of the genetics underlying mineral composition in tubers. The objectives of this study were to i) assess phenotypic variation for mineral content in tubers of advanced potato genotypes, ii) identify genomic regions associated with tuber mineral content, and iii) obtain genomic-estimated breeding values. A panel of 214 advanced potato genotypes and reference varieties was phenotyped in three field environments in Texas for the content of 12 minerals in tubers and genotyped using the Infinium Illumina 22K V3 single nucleotide polymorphism (SNP) Array. There was significant variation between potato genotypes for all minerals evaluated except iron. As a market group, red-skinned potatoes had the highest amount of minerals, whereas russets had the lowest mineral content. Reds had significantly higher P, K, S, and Zn than russets and significantly higher P and Mg than chippers. Russets had significantly higher Ca, Mg, and Na than chippers. However, the chippers had significantly higher K than the russets. A genome-wide association study for mineral content using GWASpoly identified three quantitative trait loci (QTL) associated with potassium and manganese content on chromosome 5 and two QTL associated with zinc content on chromosome 7. The loci identified will contribute to a better understanding of the genetic basis of mineral content in potatoes. Genomic-estimated breeding values for mineral macro and micronutrients in tubers obtained with StageWise will guide the selection of parents and the advancement of genotypes in the breeding program to increase mineral content in potato tubers.

Genomic regions associated with tuber traits in tetraploid potatoes and identification of superior clones for breeding purposes.

In potato breeding, morphological tuber traits are important selection targets to meet the demands of the fresh and processing markets. Understanding the genetic basis of tuber traits should guide selection and improve breeding efficiencies. However, this is challenging in potato due to the complexity of the traits and the polyploid nature of the potato genome. High-throughput affordable molecular markers and new software specific for polyploid species have the potential to unlock previously unattainable levels of understanding of the genetic basis of tuber traits in tetraploid potato. In this study, we genotyped a diversity panel of 214 advanced clones with the 22 K SNP potato array and phenotyped it in three field environments in Texas. We conducted a genome-wide association study using the GWASpoly software package to identify genomic regions associated with tuber morphological traits. Some of the QTLs discovered confirmed prior studies, whereas others were discovered for the first time. The main QTL for tuber shape was detected on chromosome 10 and explained 5.8% of the phenotypic variance. GWAS analysis of eye depth detected a significant QTL on chromosome 10 and explained 3.9% of the phenotypic variance. Another QTL peak for eye depth on chromosome 5 was located near the CDF1 gene, an important regulator of maturity in potato. Our study found that multiple QTLs govern russeting in potato. A major QTL for flesh color on chromosome 3 that explained 26% of the phenotypic variance likely represents the Y locus responsible for yellow flesh in potato tubers. Several QTLs were detected for purple skin color on chromosome 11. Furthermore, genomic estimated breeding values were obtained, which will aid in the early identification of superior parental clones that should increase the chances of producing progenies with higher frequencies of the desired tuber traits. These findings will contribute to a better understanding of the genetic basis of morphological traits in potato, as well as to identifying parents with the best breeding values to improve selection efficiency in our potato breeding program.

Phased, chromosome-scale genome assemblies of tetraploid potato reveal a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity.

Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous genome. Phased assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity, including altered coding and transcript sequences, preferential allele expression, and structural variation that collectively result in a highly complex transcriptome and predicted proteome, which are distributed across the homologous chromosomes. Wild species contribute to the extensive allelic diversity in tetraploid cultivars, demonstrating ancestral introgressions predating modern breeding efforts. As a clonally propagated autotetraploid that undergoes limited meiosis, dysfunctional and deleterious alleles are not purged in tetraploid potato. Nearly a quarter of the loci bore mutations are predicted to have a high negative impact on protein function, complicating breeder's efforts to reduce genetic load. The StCDF1 locus controls maturity, and analysis of six tetraploid genomes revealed that 12 allelic variants of StCDF1 are correlated with maturity in a dosage-dependent manner. Knowledge of the complexity of the tetraploid potato genome with its rampant structural variation and embedded deleterious and dysfunctional alleles will be key not only to implementing precision breeding of tetraploid cultivars but also to the construction of homozygous, diploid potato germplasm containing favorable alleles to capitalize on heterosis in F1 hybrids.

Development of an in vitro Microtuberization and Temporary Immersion Bioreactor System to Evaluate Heat Stress Tolerance in Potatoes (Solanum tuberosum L.).

High temperature (heat) stress reduces tuber yield and quality of potatoes. Screening potatoes for heat tolerance is increasingly important, considering the climate change scenario and expansion of potatoes to countries where heat stress is an issue. In vitro screening for tolerance to abiotic stresses offers several advantages, including quick evaluation of numerous genotypes (clones) in reduced space, controlled environmental conditions (temperature and photoperiod), and free from confounding variables inherent to greenhouse and field conditions. In this study, we explored the feasibility of using a temporary immersion bioreactor system for heat tolerance screening of potatoes. We determined the best hormone-free microtuberizing media for this system (MSG with 8% sucrose) to enhance microtuber number and size. Comparisons of microtubers produced at 30°C as heat treatment, with 16°C as normal condition, allowed to identify heat tolerant and susceptible potato clones. The use of bioreactors allowed distinguishing well-formed (non-deformed) from deformed microtubers. Heat stress increased the total biomass of plant tissues in all the clones. However, the effect of heat stress on microtuber number and weight varied among the clones. Incubation at 30°C decreased the weight and number of non-deformed microtubers in all the clones except for Reveille Russet in which the weight of non-deformed microtubers was significantly increased and the count of non-deformed microtubers was not affected. The potato variety Reveille Russet, which was selected under high-temperature field conditions in Texas, had many non-deformed microtubers per explant and the highest microtuber weight among four clones evaluated under heat stress. We described a faster and reliable in vitro microtuberization system for abiotic stress tolerance screening, identified Reveille Russet as a promising heat-tolerant potato variety, and confirmed Russet Burbank and Atlantic as susceptible heat-tolerant checks.

Genetic diversity and population structure of advanced clones selected over forty years by a potato breeding program in the USA.

Knowledge regarding genetic diversity and population structure of breeding materials is essential for crop improvement. The Texas A&M University Potato Breeding Program has a collection of advanced clones selected and maintained in-vitro over a 40-year period. Little is known about its genetic makeup and usefulness for the current breeding program. In this study, 214 potato clones were genotyped with the Infinium Illumina 22 K V3 Potato Array. After filtering, a total of 10,106 single nucleotide polymorphic (SNP) markers were used for analysis. Heterozygosity varied by SNP, with an overall average of 0.59. Three groups of tetraploid clones primarily based on potato market classes, were detected using STRUCTURE software and confirmed by discriminant analysis of principal components. The highest coefficient of differentiation observed between the groups was 0.14. Signatures of selection were uncovered in genes controlling potato flesh and skin color, length of plant cycle and tuberization, and carbohydrate metabolism. A core set of 43 clones was obtained using Core Hunter 3 to develop a sub-collection that retains similar genetic diversity as the whole population, minimize redundancies, and facilitates long-term conservation of genetic resources. The comprehensive molecular characterization of our breeding clone bank collection contributes to understanding the genetic diversity of existing potato resources. This analysis could be applied to other breeding programs and assist in the selection of parents, fingerprinting, protection, and management of the breeding collections.

Non-invasive identification of potato varieties and prediction of the origin of tuber cultivation using spatially offset Raman spectroscopy.

High starch content, simplicity of cultivation, and high productivity make potatoes (Solanum tuberosum) a staple in the diet of people around the world. On average, potatoes are composed of 83% water and 12% carbohydrates, and the remaining 4% includes proteins, vitamins, and other trace elements. These proportions vary depending on the type of potato and location where they were cultivated. At the same time, the chemical composition determines the nutritional value of potato tubers and can be proved using various wet chemistry and spectroscopic methods. For instance, gravity measurements, as well as several different colorimetric assays, can be used to investigate the starch content. However, these approaches are indirect, often destructive, and time- and labor-consuming. This study reports on the use of Raman spectroscopy (RS) for completely non-invasive and non-destructive assessment of nutrient content of potato tubers. We also show that RS can be used to identify nine different potato varieties, as well as determine the origin of their cultivation. The portable nature of Raman-based identification of potato offers the possibility to perform such analysis directly upon potato harvesting to enable quick quality evaluation. Graphical abstract.

Systematic bias of correlation coefficient may explain negative accuracy of genomic prediction.

Accuracy of genomic prediction is commonly calculated as the Pearson correlation coefficient between the predicted and observed phenotypes in the inference population by using cross-validation analysis. More frequently than expected, significant negative accuracies of genomic prediction have been reported in genomic selection studies. These negative values are surprising, given that the minimum value for prediction accuracy should hover around zero when randomly permuted data sets are analyzed. We reviewed the two common approaches for calculating the Pearson correlation and hypothesized that these negative accuracy values reflect potential bias owing to artifacts caused by the mathematical formulas used to calculate prediction accuracy. The first approach, Instant accuracy, calculates correlations for each fold and reports prediction accuracy as the mean of correlations across fold. The other approach, Hold accuracy, predicts all phenotypes in all fold and calculates correlation between the observed and predicted phenotypes at the end of the cross-validation process. Using simulated and real data, we demonstrated that our hypothesis is true. Both approaches are biased downward under certain conditions. The biases become larger when more fold are employed and when the expected accuracy is low. The bias of Instant accuracy can be corrected using a modified formula.

Resistance of potato germplasm to the potato tuberworm (Lepidoptera: Gelechiidae).

The evaluation of potato germplasm for resistance to potato tuberworm, Phthorimaea operculella (Zeller) (Lepidoptera: Gelechiidae), is a valuable component of integrated pest management; however, few attempts have been made to identify natural genetic tuber resistance to tuberworm on potato germplasm. The objective of this study was to screen potato germplasm with potential tuberworm resistance for tuber resistance under field and laboratory conditions. Experiments were conducted over a 2-yr period at the Hermiston Agricultural Research and Extension Center, Hermiston, OR. Of 125 germplasm that were tested in 2006, q13 were selected for further screening in 2007. These germplasm were: A0008-1TE, A97066LB, NY123, PA00N10-5, PA99N2, PA99N82, Paciencia, Q174-2, Russet Burbank, Rubi, Ranger Russet, Spunta G2, and T88-4. Tuber resistance of potato germplasm was determined based on the number of mines per tuber and the number of live larvae. Tubers of transgenic clone Spunta G2 were resistant to tuberworm damage. All other germplasm tested in this study, including Russet Burbank and Ranger Russet, were susceptible to tuberworm in the field and laboratory experiments. Incorporation of host plant resistance to tuber penetration by larvae together with appropriate cultural practices including limiting exposure time of tubers in the field may provide the best management option in the future.

Genetic structure of Aegilops cylindrica Host in its native range and in the United States of America.

Chloroplast and nuclear microsatellite markers were used to study genetic diversity and genetic structure of Aegilops cylindrica Host collected in its native range and in adventive sites in the USA. Our analysis suggests that Ae. cylindrica, an allotetraploid, arose from multiple hybridizations between Ae. markgrafii (Greuter) Hammer. and Ae. tauschii Coss. presumably along the Fertile Crescent, where the geographic distributions of its diploid progenitors overlap. However, the center of genetic diversity of this species now encompasses a larger area including northern Iraq, eastern Turkey, and Transcaucasia. Although the majority of accessions of Ae. cylindrica (87%) had D-type plastomes derived from Ae. tauschii, accessions with C-type plastomes (13%), derived from Ae. markgrafii, were also observed. This corroborates a previous study suggesting the dimaternal origin of Ae. cylindrica. Model-based and genetic distance-based clustering using both chloroplast and nuclear markers indicated that Ae. tauschii ssp. tauschii contributed one of its D-type plastomes and its D genome to Ae. cylindrica. Analysis of genetic structure using nuclear markers suggested that Ae. cylindrica accessions could be grouped into three subpopulations (arbitrarily named N-K1, N-K2, and N-K3). Members of the N-K1 subpopulation were the most numerous in its native range and members of the N-K2 subpopulation were the most common in the USA. Our analysis also indicated that Ae. cylindrica accessions in the USA were derived from a few founder genotypes. The frequency of Ae. cylindrica accessions with the C-type plastome in the USA (approximately 24%) was substantially higher than in its native range of distribution (approximately 3%) and all C-type Ae. cylindrica in the USA except one belonged to subpopulation N-K2. The high frequency of the C-type plastome in the USA may reflect a favorable nucleo-cytoplasmic combination.

Radiation hybrid (RH) and HAPPY mapping in plants.

Radiation hybrid (RH) and HAPPY mapping are two technologies used in animal systems that have attracted the attention of the plant genetics community because they bridge the resolution gap between meiotic and BAC-based physical mapping that would facilitate the analysis of plant species lacking substantial genomics resources. Research has shown that the essence of these approaches can be applied and that a variety of strategies can be used to produce mapping panels. Mapping panels composed of live plants, protoplast fusion cultures, and sub-genomic DNA samples have been described. The resolution achievable by RH mapping panels involving live-plant derivatives of a monosomic maize (Zea mays) chromosome 9 addition in allohexaploid oat (Avena sativa), a monosomic chromosome 1D addition in allotetraploid durum wheat (Triticum turgidum), and interspecific hybrids between two tetraploid cotton species (G. hirsutum and G. barbadense), has been estimated to range from 0.6 to 6 Mb. On the other hand, a more comprehensive evaluation of one panel from durum wheat suggests that a higher mapping resolution (approximately 200 kb) is possible. In cases involving RH mapping panels based on barley (Hordeum vulgare)-tobacco (Nicotiana tabacum) protoplast fusions or a HAPPY mapping panel based on genomic DNA from Arabidopsis thaliana, the potential mapping resolution appears to be higher (50 to 200 kb). Despite these encouraging results, the application of either RH or HAPPY mapping in plants is still in the experimental phase and additional work is clearly needed before these methods are more routinely utilized.

Maize centromere mapping: a comparison of physical and genetic strategies.

Centromere positions on 7 maize chromosomes were compared on the basis of data from 4 to 6 mapping techniques per chromosome. Centromere positions were first located relative to molecular markers by means of radiation hybrid lines and centric fission lines recovered from oat-maize chromosome addition lines. These centromere positions were then compared with new data from centric fission lines recovered from maize plants, half-tetrad mapping, and fluorescence in situ hybridizations and to data from earlier studies. Surprisingly, the choice of mapping technique was not the critical determining factor. Instead, on 4 chromosomes, results from all techniques were consistent with a single centromere position. On chromosomes 1, 3, and 6, centromere positions were not consistent even in studies using the same technique. The conflicting centromere map positions on chromosomes 1, 3, and 6 could be explained by pericentric inversions or alternative centromere positions on these chromosomes.