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.

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.

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.

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.

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 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.

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.

Transcriptome of Russet Norkotah and its clonal selection, TXNS278

Objectives

Potato has a large genetic diversity. This diversity is in part due to somaclonal variability that appears within potato selections for which tubers are used as seeds. However, the potato tetraploid genome, as well as the use of tubers for crop propagation, does not allow for easy genetic studies. The objective is to gain knowledge at the genomic level from standard Russet Norkotah and a subclonal Russet Norkotah selection TXNS278.

Data description

In this report, we used RNA-seq, which allows genome-wide gene expression analysis to sequence the transcriptomes of the subclonal Russet Norkotah selection TXNS278 with standard Russet Norkotah grown in commercial fields. Among the selections, TXNS278 appeared in a multi-year analysis in Texas as a top No 1 yielding variety. Russet Norkotah and TXNS278 leaf and root transcriptomes were sequenced at two time points during growing season.

Electronic supplementary material

The online version of this article (10.1186/s13104-018-3254-4) contains supplementary material, which is available to authorized users.