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.

Genetic Variance Partitioning and Genome-Wide Prediction with Allele Dosage Information in Autotetraploid Potato.

As one of the world's most important food crops, the potato (Solanum tuberosum L.) has spurred innovation in autotetraploid genetics, including in the use of SNP arrays to determine allele dosage at thousands of markers. By combining genotype and pedigree information with phenotype data for economically important traits, the objectives of this study were to (1) partition the genetic variance into additive vs. nonadditive components, and (2) determine the accuracy of genome-wide prediction. Between 2012 and 2017, a training population of 571 clones was evaluated for total yield, specific gravity, and chip fry color. Genomic covariance matrices for additive (G), digenic dominant (D), and additive × additive epistatic (G#G) effects were calculated using 3895 markers, and the numerator relationship matrix (A) was calculated from a 13-generation pedigree. Based on model fit and prediction accuracy, mixed model analysis with G was superior to A for yield and fry color but not specific gravity. The amount of additive genetic variance captured by markers was 20% of the total genetic variance for specific gravity, compared to 45% for yield and fry color. Within the training population, including nonadditive effects improved accuracy and/or bias for all three traits when predicting total genotypic value. When six F1 populations were used for validation, prediction accuracy ranged from 0.06 to 0.63 and was consistently lower (0.13 on average) without allele dosage information. We conclude that genome-wide prediction is feasible in potato and that it will improve selection for breeding value given the substantial amount of nonadditive genetic variance in elite germplasm.

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.

Global gene expression in two potato cultivars in response to 'Candidatus Liberibacter solanacearum' infection.

BACKGROUND: Transcriptomic analyses were performed to compare the molecular responses of two potato varieties previously shown to differ in the severity of disease symptoms due to infection by "Candidatus Liberibacter solanacearum" (Lso), the causative agent of Zebra Chip in potato. A factorial design utilizing the two varieties and psyllids either harboring Lso or without bacteria was used to discriminate varietal responses to pathogen infection versus psyllid feeding. Plant response was determined from leaf samples 3 weeks after infection. RESULTS: In response to Lso infection, 397 genes were differentially expressed in the variety Atlantic (most susceptible) as compared to 1027 genes in Waneta. Over 80% of the transcriptionally-changed genes were down-regulated in both varieties, including genes involved in photosynthesis or primary and secondary metabolism. Many of the Lso-responsive genes involved in stress responses or hormonal pathways were regulated differently in the two potato varieties. CONCLUSIONS: This study focused on the time point just prior to the onset of symptom development and provides valuable insight into the mechanisms of Liberibacter pathogenicity, especially the widespread suppression of plant gene expression, including genes involved in plant defenses.

The bioactive compounds alpha-chaconine and gallic acid in potato extracts decrease survival and induce apoptosis in LNCaP and PC3 prostate cancer cells.

We recently reported that colored potato extracts and an anthocyanin rich fraction suppressed lymph-node carcinoma of the prostate (LNCaP) and prostate cancer-3 (PC-3) prostate cancer cell proliferation and induced apoptosis via caspase-dependent and caspase-independent pathways. Chlorogenic acid, caffeic acid, gallic acid, catechin, malvidin, and glycoalkaloids (alpha-chaconine and solanine) have now been identified as the major bioactive components of potato, and their effects on LNCaP and PC-3 cell proliferation and apoptosis have been investigated. alpha-chaconine (5 microg/ml) and gallic acid (15 microg/ml) exhibited potent antiproliferative properties and increased cyclin-dependent kinase inhibitor p27 levels in both cell lines. Both alpha-chaconine and gallic acid induced poly [adenosine diphosphate (ADP)] ribose polymerase cleavage and caspase-dependent apoptosis in LNCaP cells; however, caspase-independent apoptosis through nuclear translocation of endonuclease G was observed in both LNCaP and PC-3 cells. alpha-chaconine and gallic acid activated c-Jun N-terminal protein kinase (JNK), and this response played a major role in induction of caspase-dependent apoptosis in LNCaP cells; whereas modulation of JNK and mitogen-activated protein kinase did not affect alpha-chaconine- and gallic acid-induced caspase-independent apoptosis. These results suggest that apoptosis induced by whole potato extracts in prostate cancer cell lines may be in part due to alpha-chaconine and gallic acid.

Antiproliferative activity and cytotoxicity of Solanum jamesii tuber extracts on human colon and prostate cancer cells in vitro.

Some tuber-bearing wild potato species are reportedly higher in potential health-promoting traits, such as antioxidant activity (AOA) and total phenolic content (TP), than commercial cultivars; therefore, they could be used as parental material in breeding for high AOA and TP. However, using wild species might result in progenies that are toxic for human consumption because of the presence of high total glycoalkaloids (TGAs) and other unknown compounds. Therefore, wild potato accessions should be screened for cytotoxicity before their introduction into breeding programs. The objective of this study was to investigate antiproliferative activity and cytotoxicity of tuber extracts from 15 Solanum jamesii accessions on human HT-29 colon and LNCaP prostate cancer cell lines in vitro. Also, correlations among AOA, TP, TGA, and antiproliferative activity were determined. The tuber extracts significantly inhibited proliferation of HT-29 and LNCaP cell lines and were not cytotoxic to the cells compared to the control (DMSO). The antiproliferative activity exhibited by tuber extracts was not due to necrosis, because the amount of lactate dehydrogenase (LDH) released from cells incubated with the extracts was not significantly different from that released from cells incubated without extracts (control). Colon cancer cells were more responsive to tuber extract treatment than prostate cancer cells. In both HT-29 and LNCaP cells, there were no observable significant correlations between antioxidant activity (DPPH and ABTS) and inhibition of cell proliferation or between TP and cell proliferation inhibition. Also, glycoalkaloids did not exhibit significant correlations with the inhibition of cancer cell proliferation. Findings of this study show that S. jamesii accessions probably pose no cytotoxic effects when used as parental material in improving the nutritional value of potato cultivars. Correlation results, along with cell proliferation data, suggest that not only the compounds measured in this study but also other bioactive compounds present in the matrix acting additively or synergistically may be more responsible for the antiproliferative effects of potato tuber extracts than higher concentrations of a single or group of compounds.

Genotype, location, and year influence antioxidant activity, carotenoid content, phenolic content, and composition in specialty potatoes.

The influence of genotype, location, and year on antioxidant activity (AOA), total phenolics (TP), total carotenoids (TC), and phenolic composition was studied using specialty (colored) potatoes ( Solanum tuberosum L.) from the Texas Potato Variety Development Program. Twenty-five potato genotypes were grown at two Texas locations (McCook and Dalhart) and in two years (2003 and 2004). The AOA, TP, and TC differed significantly with genotype (G), location (L), and year (Y). Phenolic composition differed significantly among genotypes and between locations. The AOA, TP, and chlorogenic acid content were significantly correlated with one another. Genotypic effects were significant for all parameters measured and were larger than location and year effects. Interaction effects (G x L and G x L x Y) were significant for most parameters, but were relatively smaller than genotypic effects. Lutein and violaxanthin were the major carotenoids identified, and genotypes differed significantly in their carotenoid content. Genotypes CO112F2-2P/P and ATTX98013-1R/R were stable between locations and years with high AOA and TP, suggesting that they could be used as parents in breeding varieties with improved health benefits.

Anthocyanin fraction from potato extracts is cytotoxic to prostate cancer cells through activation of caspase-dependent and caspase-independent pathways.

Polyphenols from fruits and vegetables exhibit anticancer properties both in vitro and in vivo and specialty potatoes are an excellent source of dietary polyphenols, including phenolic acids and anthocyanins. This study investigated the effects of specialty potato phenolics and their fractions on LNCaP (androgen dependent) and PC-3 (androgen independent) prostate cancer cells. Phenolic extracts from four specialty potato cultivars CO112F2-2, PATX99P32-2, ATTX98462-3 and ATTX98491-3 and organic acid, phenolic acid and anthocyanin fractions (AF) were used in this study. CO112F2-2 cultivar extracts and their AF at 5 mug chlorogenic acid eq/ml were more active and inhibited cell proliferation and increased the cyclin-dependent kinase inhibitor p27 levels in both LNCaP and PC-3 cells. Potato extract and AF induced apoptosis in both the cells and, however, the effects were cell context dependent. Cell death pathways induced by potato extract and AF were associated with mitogen-activated protein kinase and c-jun N-terminal kinase activation and these kinases activated caspase-independent apoptosis through nuclear translocation of endonuclease G (Endo G) and apoptosis-inducing factor in both cell lines. Induction of caspase-dependent apoptosis was also kinase dependent but was observed only in LNCaP cells. Kinase inhibitors reversed this nuclear translocation of endonuclease G and apoptosis-inducing factor. This is the first report showing that the cytotoxic activities of potato extract/AF in cancer cells were due to activation of caspase-independent apoptosis. Current studies are focused on identifying individual components of the AF responsible for the induction of cell death pathways in prostate and other cancer cell lines and developing potato cultivars that overexpress these active compounds.