Linkage and QTL mapping for tuber shape and specific gravity in a tetraploid mapping population of potato representing the russet market class

Harnessing the health benefits of purple and yellow-fleshed sweet potatoes: Phytochemical composition, stabilization methods, and industrial utilization- A review

Purple-fleshed sweet potato (PFSP) and yellow-fleshed sweet potato (YFSP) are crops highly valued for their nutritional benefits and rich bioactive compounds. These compounds include carotenoids, flavonoids (including anthocyanins), and phenolic acids etc. which are present in both the leaves and roots of these sweet potatoes. PFSP and YFSP offer numerous health benefits, such as antioxidant, anti-inflammatory, anti-cancer, and neuroprotective properties. The antioxidant activity of these sweet potatoes holds significant potential for various industries, including food, pharmaceutical, and cosmetics. However, a challenge in utilizing PFSP and YFSP is their susceptibility to rapid oxidation and color fading during processing and storage. To address this issue and enhance the nutritional value and shelf life of food products, researchers have explored preservation methods such as co-pigmentation and encapsulation. While YFSP has not been extensively studied, this review provides a comprehensive summary of the nutritional value, phytochemical composition, health benefits, stabilization techniques for phytochemical, and industrial applications of both PFSP and YFSP in the food industry. Additionally, the comparison between PFSP and YFSP highlights their similarities and differences, shedding light on their potential uses and benefits in various food products.

Genotyping-by-sequencing targets genic regions and improves resolution of genome-wide association studies in autotetraploid potato

KEY MESSAGE

De novo genotyping in potato using methylation-sensitive GBS discovers SNPs largely confined to genic or gene-associated regions and displays enhanced effectiveness in estimating LD decay rates, population structure and detecting GWAS associations over 'fixed' SNP genotyping platform. Study also reports the genetic architectures including robust sequence-tagged marker-trait associations for sixteen important potato traits potentially carrying higher transferability across a wider range of germplasm. This study deploys recent advancements in polyploid analytical approaches to perform complex trait analyses in cultivated tetraploid potato. The study employs a 'fixed' SNP Infinium array platform and a 'flexible and open' genome complexity reduction-based sequencing method (GBS, genotyping-by-sequencing) to perform genome-wide association studies (GWAS) for several key potato traits including the assessment of population structure and linkage disequilibrium (LD) in the studied population. GBS SNPs discovered here were largely confined (~ 90%) to genic or gene-associated regions of the genome demonstrating the utility of using a methylation-sensitive restriction enzyme (PstI) for library construction. As compared to Infinium array SNPs, GBS SNPs displayed enhanced effectiveness in estimating LD decay rates and discriminating population subgroups. GWAS using a combined set of 30,363 SNPs identified 189 unique QTL marker-trait associations (QTL-MTAs) covering all studied traits. The majority of the QTL-MTAs were from GBS SNPs potentially illustrating the effectiveness of marker-dense de novo genotyping platforms in overcoming ascertainment bias and providing a more accurate correction for different levels of relatedness in GWAS models. GWAS also detected QTL 'hotspots' for several traits at previously known as well as newly identified genomic locations. Due to the current study exploiting genome-wide genotyping and de novo SNP discovery simultaneously on a large tetraploid panel representing a greater diversity of the cultivated potato gene pool, the reported sequence-tagged MTAs are likely to have higher transferability across a wider range of potato germplasm and increased utility for expediting genomics-assisted breeding for the several complex traits studied.

Genotyping-by-sequencing and weighted gene co-expression network analysis of genes responsive against Potato virus Y in commercial potato cultivars

Potato is considered a key component of the global food system and plays a vital role in strengthening world food security. A major constraint to potato production worldwide is the Potato Virus Y (PVY), belonging to the genus Potyvirus in the family of Potyviridae. Selective breeding of potato with resistance to PVY pathogens remains the best method to limit the impact of viral infections. Understanding the genetic diversity and population structure of potato germplasm is important for breeders to improve new cultivars for the sustainable use of genetic materials in potato breeding to PVY pathogens. While, genetic diversity improvement in modern potato breeding is facing increasingly narrow genetic basis and the decline of the genetic diversity. In this research, we performed genotyping-by-sequencing (GBS)-based diversity analysis on 10 commercial potato cultivars and weighted gene co-expression network analysis (WGCNA) to identify candidate genes related to PVY-resistance. WGCNA is a system biology technique that uses the WGCNA R software package to describe the correlation patterns between genes in multiple samples. In terms of consumption, these cultivars are a high rate among Iranian people. Using population structure analysis, the 10 cultivars were clustered into three groups based on the 118343 single nucleotide polymorphisms (SNPs) generated by GBS. Read depth ranged between 5 and 18. The average data size and Q30 of the reads were 145.98 Mb and 93.63%, respectively. Based on the WGCNA and gene expression analysis, the StDUF538, StGTF3C5, and StTMEM161A genes were associated with PVY resistance in the potato genome. Further, these three hub genes were significantly involved in defense mechanism where the StTMEM161A was involved in the regulation of alkalization apoplast, the StDUF538 was activated in the chloroplast degradation program, and the StGTF3C5 regulated the proteins increase related to defense in the PVY infected cells. In addition, in the genetic improvement programs, these hub genes can be used as genetic markers for screening commercial cultivars for PVY resistance. Our survey demonstrated that the combination of GBS-based genetic diversity germplasm analysis and WGCNA can assist breeders to select cultivars resistant to PVY as well as help design proper crossing schemes in potato breeding.

QTL identified that influence tuber length-width ratio, degree of flatness, tuber size, and specific gravity in a russet-skinned, tetraploid mapping population

Potato tuber shape, size, and specific gravity are important agronomic traits in the russet market class of potatoes with an impact on quality, consistency, and product recovery of processed foods such as French fries. Therefore, identifying genetic regions associated with the three traits through quantitative trait locus/loci (QTL) analysis is a crucial process in the subsequent development of marker-assisted selection for use in potato breeding programs. QTL analysis was conducted on a tetraploid mapping population consisting of 190 individuals derived from the cross between two russet-skinned parents, Palisade Russet and the breeding clone ND028673B-2Russ. Field data collected over a 2-year period and used in the QTL analyses included tuber length-width and width-depth ratios that were obtained using a digital caliper. The width-depth ratio provided an assessment of the "flatness" of a tuber, which is of importance in potato processing. To cross-validate the accuracy and differences among tuber shape measurement methods, a trained evaluator also assessed the identical tubers based on 1-5 scale (compressed to long) visual assessment method. Furthermore, the weights of analyzed tubers and specific gravities were also collected during the phenotyping process for each mapping clone. A major tuber shape QTL was consistently observed on chromosome 10 with both the length-width ratio and visual assessments. On chromosome 4, a significant QTL for tuber shape from the visual assessment phenotypic data was also detected. Additionally, a tuber shape-related QTL on chromosome 6 was also detected from the length-width ratio data from 2020. Chromosome 2 was also identified as having a significant QTL for the width-depth ratio, which is of importance in influencing the flatness of a tuber. One significant QTL for tuber weight (i.e., tuber size) was observed on chromosome 5, and a significant QTL for specific gravity was found on chromosome 3. These significant and major QTL should be useful for developing marker-assisted selection for more efficient potato breeding.

The effect of marker types and density on genomic prediction and GWAS of key performance traits in tetraploid potato

Genomic prediction and genome-wide association studies are becoming widely employed in potato key performance trait QTL identifications and to support potato breeding using genomic selection. Elite cultivars are tetraploid and highly heterozygous but also share many common ancestors and generation-spanning inbreeding events, resulting from the clonal propagation of potatoes through seed potatoes. Consequentially, many SNP markers are not in a 1:1 relationship with a single allele variant but shared over several alleles that might exert varying effects on a given trait. The impact of such redundant "diluted" predictors on the statistical models underpinning genome-wide association studies (GWAS) and genomic prediction has scarcely been evaluated despite the potential impact on model accuracy and performance. We evaluated the impact of marker location, marker type, and marker density on the genomic prediction and GWAS of five key performance traits in tetraploid potato (chipping quality, dry matter content, length/width ratio, senescence, and yield). A 762-offspring panel of a diallel cross of 18 elite cultivars was genotyped by sequencing, and markers were annotated according to a reference genome. Genomic prediction models (GBLUP) were trained on four marker subsets [non-synonymous (29,553 SNPs), synonymous (31,229), non-coding (32,388), and a combination], and robustness to marker reduction was investigated. Single-marker regression GWAS was performed for each trait and marker subset. The best cross-validated prediction correlation coefficients of 0.54, 0.75, 0.49, 0.35, and 0.28 were obtained for chipping quality, dry matter content, length/width ratio, senescence, and yield, respectively. The trait prediction abilities were similar across all marker types, with only non-synonymous variants improving yield predictive ability by 16%. Marker reduction response did not depend on marker type but rather on trait. Traits with high predictive abilities, e.g., dry matter content, reached a plateau using fewer markers than traits with intermediate-low correlations, such as yield. The predictions were unbiased across all traits, marker types, and all marker densities >100 SNPs. Our results suggest that using non-synonymous variants does not enhance the performance of genomic prediction of most traits. The major known QTLs were identified by GWAS and were reproducible across exonic and whole-genome variant sets for dry matter content, length/width ratio, and senescence. In contrast, minor QTL detection was marker type dependent.

Identification of QTL associated with plant vine characteristics and infection response to late blight, early blight, and Verticillium wilt in a tetraploid potato population derived from late blight-resistant Palisade Russet

Potato late blight (causal agent Phytophthora infestans) is a disease of potatoes with economic importance worldwide. Control is primarily through field monitoring and the application of fungicides. Control of late blight with fungicides and host plant resistance is difficult, with documented cases of such control measures failing with the advent of new pathotypes of P. infestans. To better understand host plant resistance and to develop more durable late blight resistance, Quantitative Trait Locus/Loci (QTL) analysis was conducted on a tetraploid mapping population derived from late blight-resistant potato cultivar Palisade Russet. Additionally, QTL analyses for other traits such as Verticillium wilt and early blight resistance, vine size and maturity were performed to identify a potential relationship between multiple traits and prepare genetic resources for molecular markers useful in breeding programs. For this, one hundred ninety progenies from intercrossing Palisade Russet with a late blight susceptible breeding clone (ND028673B-2Russ) were assessed. Two parents and progenies were evaluated over a two-year period for response to infection by the US-8 genotype of P. infestans in inoculated field screenings in Corvallis, Oregon. In Aberdeen, Idaho, the same mapping population was also evaluated for phenotypic response to early blight and Verticillium wilt, and vine size and maturity in a field over a two-year period. After conducting QTL analyses with those collected phenotype data, it was observed that chromosome 5 has a significant QTL for all five traits. Verticillium wilt and vine maturity QTL were also observed on chromosome 1, and vine size QTL was also found on chromosomes 3 and 10. An early blight QTL was also detected on chromosome 2. The QTL identified in this study have the potential for converting into breeder-friendly molecular markers for marker-assisted selection.

Application of SolCAP Genotyping in Potato (Solanum tuberosum L.) Association Mapping

Potato variety development entails a number of breeding steps, as well as testing and, finally, commercialization. Historically, phenotypic assesment were carried out to select and germplasm development. The US Department of Agriculture (USDA) funded the Solanaceae Coordinated Agricultural Project (SolCAP) to decode genomic resources into tools that breeders and geneticists can use. This project resulted in the creation of a genome-wide single-nucleotide polymorphism (SNP) array that can be used to evaluate elite potato-breeding germplasm. This array was used to genotype a diverse panel of Solanum species, as well as numerous biparental, diploid, and tetraploid populations. It has high marker density to generate genetic maps that can be used to identify numerous quantitative trait loci (QTLs) for agronomic, quality, biotic, and abiotic resistance traits. Up to now, numerous QTLs for important traits have been identified using new diploid and tetraploid genetic maps. SNP markers were used to assess germplasm relationships and fingerprint varieties and identify candidate genes. The Infinium 8303 SolCAP Potato array offers a common set of SNP markers that can be used for mapping, germplasm assessment, and fingerprinting with confidence. This array has also been helpful in furthering our understanding of the potato genome. Furthermore, some other Infinium potato arrays (i.e., 12 K, 20 K, and 25 K) have been genotyped, and breeders can map quantitative trait loci (QTLs) across multiple populations to improve our understanding of economically important traits and lead to marker-assisted selection (MAS) and breeding and, ultimately, improved varieties.

Recent Advances in Molecular Improvement for Potato Tuber Traits

Potato is an important crop due to its nutritional value and high yield potential. Improving the quality and quantity of tubers remains one of the most important breeding objectives. Genetic mapping helps to identify suitable markers for use in the molecular breeding, and combined with transgenic approaches provides an efficient way for gaining desirable traits. The advanced plant breeding tools and molecular techniques, e.g., TALENS, CRISPR-Cas9, RNAi, and cisgenesis, have been successfully used to improve the yield and nutritional value of potatoes in an increasing world population scenario. The emerging methods like genome editing tools can avoid incorporating transgene to keep the food more secure. Multiple success cases have been documented in genome editing literature. Recent advances in potato breeding and transgenic approaches to improve tuber quality and quantity have been summarized in this review.