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12 pages, 2514 KiB

Open AccessArticle

Meta-Analysis of Genetic Factors for Potato Starch Phosphorylation

by Vadim Khlestkin, Tatyana Erst, Alexander Igoshin, Irina Rozanova and Elena Khlestkina

Agronomy 2022, 12(6), 1343; https://doi.org/10.3390/agronomy12061343 - 31 May 2022

Cited by 2 | Viewed by 1765

Abstract

Starch is one of the most demanded renewable feedstock in the world. The degree of phosphorylation of native potato (Solanum tuberosum L.) starch is a practically important quantitative trait, significantly influencing its physical and chemical properties. In this study, we evaluated the [...] Read more.

Starch is one of the most demanded renewable feedstock in the world. The degree of phosphorylation of native potato (Solanum tuberosum L.) starch is a practically important quantitative trait, significantly influencing its physical and chemical properties. In this study, we evaluated the genetic diversity of the population of potato varieties and quantified phosphorus content in potato tuber starch harvested in 2017, 2018, and 2019. With the statistical methods, the most promising varieties for the next generation of breeding were identified for the first time. Genotyping and chemotyping data were utilized for genome-wide associations study (GWAS) in order to reveal genetic factors underlying the trait. GWAS based on a general linear model (GLM) with principal component analysis (PCA) was performed. The approach allowed us to identify two new, and confirm two previously found, significant SNPs on chromosome 5 associated with phosphorus content in starch. A search for the protein products coded in the genome regions carrying the significant SNPs revealed a cluster of genes that code glycoside and protein kinases, thus forming an operon-like structure. The genetic markers can be used for marker-assisted selection or to be considered as potential targets for genome editing to improve the industrially important properties of potato native starch via “intravital modification”. Full article

(This article belongs to the Special Issue Molecular Genetic Studies in Potato Breeding)

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9 pages, 1474 KiB

Open AccessCommunication

The Use of Long-Read Sequencing to Study the Phylogenetic Diversity of the Potato Varieties Plastome of the Ural Selection

by Georgiy A. Lihodeevskiy and Elena P. Shanina

Agronomy 2022, 12(4), 846; https://doi.org/10.3390/agronomy12040846 - 30 Mar 2022

Cited by 1 | Viewed by 2186

Abstract

Plastid DNA holds a substantial amount of plant genetic information, including maternal ancestry information. It helps to uncover interrelations between a wide variety of tuberous species of the genus Solanum to search for promising sources of high-yielding potato varieties resistant to bio- and [...] Read more.

Plastid DNA holds a substantial amount of plant genetic information, including maternal ancestry information. It helps to uncover interrelations between a wide variety of tuberous species of the genus Solanum to search for promising sources of high-yielding potato varieties resistant to bio- and abiotic stressors. This paper demonstrated the opportunities of de novo assembly of potato plastid DNA and its phylogenetic and genome type identification based only on Oxford Nanopore Technologies (ONT) long reads. According to our results, of 28 potato varieties developed at the Ural Research Institute of Agriculture, 16 varieties had one of the most primitive W-type plastomes. Ten varieties’ plastomes belonged to the T-type of cultivated Solanum tuberosum subsp. tuberosum. The varieties Legenda and 15-27-1 were the closest to the wild species Solanum chacoense plastome. Using long-sequencing reads, we confirmed the presence of two isoforms of the plastid genome differing in the orientation of SSC region. We should note that irrespective of sequencing depth and improvements in software for working with ONT reads, a correct de novo plastome assembly and its annotation using only long-reads is impossible. The most problematic regions are homopolymers longer than 5 bp—they account for all detected indels, leading to a change in the reading frame or the deletion of entire genes. Full article

(This article belongs to the Special Issue Molecular Genetic Studies in Potato Breeding)

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12 pages, 2004 KiB

Open AccessArticle

GISH Analysis of the Introgression of the B Subgenome Genetic Material of Wild Allotetraploid Species Solanum stoloniferum into Backcrossing Progenies with Potato

by Tatjana A. Gavrilenko, Galina I. Pendinen and Alexander P. Yermishin

Agronomy 2022, 12(4), 787; https://doi.org/10.3390/agronomy12040787 - 25 Mar 2022

Cited by 3 | Viewed by 1996

Abstract

Wild relatives of cultivated potato are used in breeding to increase the genetic diversity of Solanum tuberosum (AAAA genome) varieties. Wild Mexican allotetraploid species Solanum stoloniferum (AABB genome) was used in breeding for extreme resistance to viruses and late blight. In this study, [...] Read more.

Wild relatives of cultivated potato are used in breeding to increase the genetic diversity of Solanum tuberosum (AAAA genome) varieties. Wild Mexican allotetraploid species Solanum stoloniferum (AABB genome) was used in breeding for extreme resistance to viruses and late blight. In this study, genomic in situ hybridization (GISH) was used for visualization of introgression of genetic material of the B subgenome of S. stoloniferum into the genome of backcross hybrids. The fertile hexaploid hybrid had 48 chromosomes of the A genome and 24 chromosomes of the B subgenome. Plants of the BC₁ generation were pentaploid having the AAAAB genome constitution and three selected BC₂ hybrids were aneuploid, containing one to six chromosomes of the B subgenome and 48 chromosomes of the A genome. The B subgenome of S. stoloniferum was inherited in the backcross generations as single chromosomes and in rare cases as recombinant chromosomes. GISH showed that chromosome pairing in the backcross hybrids was predominantly intragenomic. Most chromosomes of the B subgenome remained as univalents in backcross hybrids. Rare homeologous A/B chromosome pairing was detected in all analyzed hybrids. The obtained data indicate that the B subgenome of S. stoloniferum was able to recombine with the A genome. Full article

(This article belongs to the Special Issue Molecular Genetic Studies in Potato Breeding)

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19 pages, 1689 KiB

Open AccessArticle

by Alex V. Kochetov, Dmitry A. Afonnikov, Nikolay Shmakov, Gennady V. Vasiliev, Olga Y. Antonova, Natalja V. Shatskaya, Anastasiya Y. Glagoleva, Salmaz M. Ibragimova, Aleksander Khiutti, Olga S. Afanasenko and Tatjana A. Gavrilenko

Agronomy 2021, 11(12), 2426; https://doi.org/10.3390/agronomy11122426 - 28 Nov 2021

Cited by 2 | Viewed by 2135

Abstract

The long history of potato breeding includes the numerous introgressions of resistance genes from many wild species of South and Central America as well as from cultivated species into the breeding genepool. Most R genes belong to the NLR family with nucleotide-binding site–leucine-rich [...] Read more.

The long history of potato breeding includes the numerous introgressions of resistance genes from many wild species of South and Central America as well as from cultivated species into the breeding genepool. Most R genes belong to the NLR family with nucleotide-binding site–leucine-rich repeat. The aim of this research concerns an evaluation of NLR genes expression in transcriptomes of three potato cultivars (Evraziya, Siverskij, Sudarynya), which combine genetic material from wild and cultivated potato species, and each bears intragenic markers of RB/Rpi-blb1/Rpi-sto1 genes conferring broad-range resistance to late blight. The transcriptomes of the cultivars were compared before and 24 h after the Phytophthora infestans inoculation. The induction of RB/Rpi-blb1/Rpi-sto1 transcript after 24 h of inoculation was detected in the resistant cultivars Siverskij and Sudarynya but not in susceptible cv. Evraziya. This demonstrates the importance of transcriptomic assay for understanding the results of marker-assisted selection and phenotyping. Interestingly, assembling the transcriptomes de novo and analysis with NLR-parser tool revealed significant fractions of novel NLR genes with no homology to the reference genome from 103 (cv. Siverskij) to 160 (S. stoloniferum, 30514/15). Comparison of novel NLRs demonstrated a relatively small intersection between the genotypes that coincided with their complex pedigrees with several interspecific hybridization events. These novel NLRs may facilitate the discovery of new efficient R genes. Full article

(This article belongs to the Special Issue Molecular Genetic Studies in Potato Breeding)

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20 pages, 353 KiB

Open AccessArticle

Phenotypic and DNA Marker-Assisted Characterization of Russian Potato Cultivars for Resistance to Potato Cyst Nematodes

by Tatjana A. Gavrilenko, Aleksander V. Khiutti, Natalia S. Klimenko, Olga Y. Antonova, Natalia A. Fomina and Olga S. Afanasenko

Agronomy 2021, 11(12), 2400; https://doi.org/10.3390/agronomy11122400 - 25 Nov 2021

Cited by 2 | Viewed by 2104

Abstract

Potato is one of the most important food crops in the world and also in the Russian Federation. Among harmful organisms reducing potato yield potential, the potato cyst nematodes (PCN) are considered to be ones of the most damaging pests. Information on PCN [...] Read more.

Potato is one of the most important food crops in the world and also in the Russian Federation. Among harmful organisms reducing potato yield potential, the potato cyst nematodes (PCN) are considered to be ones of the most damaging pests. Information on PCN resistant cultivars is important for potato breeding and production. Russian potato cultivars are characterized in the state-bio-test program for resistance to only one PCN species Globodera rostochiensis and one pathotype Ro1 which is reported to be present in the country. This study aimed to find domestic cultivars with multiple resistances to different PCN species and different pathotypes using phenotyping coupled with molecular marker analysis due to the risk of the occasional introduction of new pests. The phenotypic response was determined by the inoculation of plants with pathotypes Ro5 of G. rostochiensis and Pa3 of G. pallida. The obtained results were supplemented by the state-bio-test data on resistance to Ro1 of G. rostochiensis. Nine of 26 Russian cultivars were resistant both to Ro5 and Ro1 pathotypes and two cultivars possess multiple resistances to both PCN species. Most tested molecular markers associated with the Gpa2, GpaV_vrn, GpaV^s_spl, Grp1 loci showed discrepancies with phenotyping. However, a predictive haplotype and epistatic effect were detected. Full article

(This article belongs to the Special Issue Molecular Genetic Studies in Potato Breeding)

10 pages, 2420 KiB

Open AccessCommunication

Structural Variations in the Genome of Potato Varieties of the Ural Selection

by Georgiy A. Lihodeevskiy and Elena P. Shanina

Agronomy 2021, 11(9), 1703; https://doi.org/10.3390/agronomy11091703 - 26 Aug 2021

Cited by 4 | Viewed by 1825

Abstract

Potato (Solanum tuberosum L.) is the third most common plant crop in the world. Many studies, such as those using marker-assisted selection (MAS), are devoted to the genomic evaluation of potato. However, the nucleotide composition of some markers has not been described [...] Read more.

Potato (Solanum tuberosum L.) is the third most common plant crop in the world. Many studies, such as those using marker-assisted selection (MAS), are devoted to the genomic evaluation of potato. However, the nucleotide composition of some markers has not been described yet, and some regions of the genome remain unknown. Thus, the development of new marker systems for further genetic selection is required. Whole-genome sequencing and the search for structural variants (SVs) should further develop molecular genetic studies of the potato crop. In this paper, we will show the first results of our studies of the three backcrossed varieties Alaska, Argo, and Shah, which were selected for sequencing. Alaska is a patented variety with confirmed resistance to pathogens, while Argo and Shah are new perspective varieties. We sequenced genomes of these varieties using a nanopore platform. As a result, we identified more than 24,000 authentic structural variants with lengths varying from 4 bp to 100 Mbp. Deletion was found to be the most common type of structural variant in the genome and the genes. The majority of SVs are located in non-coding regions, including introns. However, a quarter of the genes of the sequenced varieties have some chromosomal mutations. Some genes responsible for resistance to abiotic stress and pathogens were duplicated, while genes of nucleic acid polymerization and few metabolic proteins were deleted. Full article

(This article belongs to the Special Issue Molecular Genetic Studies in Potato Breeding)

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11 pages, 1580 KiB

Open AccessArticle

CLAVATA3/EMBRYO SURROUNDING REGION (CLE) Gene Family in Potato (Solanum tuberosum L.): Identification and Expression Analysis

by Maria Gancheva, Irina Dodueva, Maria Lebedeva and Ludmila Lutova

Agronomy 2021, 11(5), 984; https://doi.org/10.3390/agronomy11050984 - 15 May 2021

Cited by 4 | Viewed by 2694

Abstract

CLE genes encode a group of small secretory peptides, which regulate cell proliferation and differentiation in plants. CLE genes have been studied in many plants; however, little is known about this gene family in potato. In this study, we characterized members of the [...] Read more.

CLE genes encode a group of small secretory peptides, which regulate cell proliferation and differentiation in plants. CLE genes have been studied in many plants; however, little is known about this gene family in potato. In this study, we characterized members of the CLE gene family in potato Solanum tuberosum (StCLE) and comprehensively analyzed their phylogenetic relationships, structure, and expression patterns. Using available transcriptomic data, we found a relative high expression level of StCLE8, StCLE12, and StCLE13 in stolons and tubers. Real-time PCR analysis showed that the StCLE23 gene was upregulated by water deficiency, whereas the expression of StCLE4 and StCLE10 was induced by nitrogen supply. Besides that, using data from transcriptomic studies obtained previously for plants with the induction the StBEL5 gene, a positive regulator of tuber development, we found that StCLE4 was among genes upregulated in response to StBEL5 induction, suggesting that StCLE4 could be a target of StBEL5 transcription factor. However, we did not reveal a direct binding of StBEL5 to the regulatory sequences of StCLE4 using yeast one-hybrid assay. Taken together, our data provide basic information for future functional studies of CLE peptides in potato growth and tuberization and in response to various environmental stimuli. Full article

(This article belongs to the Special Issue Molecular Genetic Studies in Potato Breeding)

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Review

Jump to: Research

13 pages, 622 KiB

Open AccessReview

De Novo Domestication Concept for Potato Germplasm Enhancement

by Anastasiya A. Egorova, Nadezhda A. Chalaya, Ivan N. Fomin, Alisa I. Barchuk and Sophia V. Gerasimova

Agronomy 2022, 12(2), 462; https://doi.org/10.3390/agronomy12020462 - 12 Feb 2022

Cited by 5 | Viewed by 2852

Abstract

Wild potato germplasm serves as a natural pool of agronomically valuable traits for potato breeding, such as resistance to pathogens and abiotic stresses, quality, and consumer-oriented traits. The introgression of these traits into cultivated potato is hampered by the different kinds of incompatibility [...] Read more.

Wild potato germplasm serves as a natural pool of agronomically valuable traits for potato breeding, such as resistance to pathogens and abiotic stresses, quality, and consumer-oriented traits. The introgression of these traits into cultivated potato is hampered by the different kinds of incompatibility and linkages between desirable and undesirable features in hybrid progeny. The trait donor improvement via correction of negative characteristics prior to hybridization to domestic potato can be a solution to the linkage drag problem. The de novo domestication concept for developing new crops using gene editing technologies was previously proposed and performed for tomato and physalis. In this review, we collected information about donor properties of different wild potato species and developed a strategy for potato germplasm enhancement using the de novo domestication approach. The possible modifications of several candidate genes responsible for undesirable traits in wild potato, including high steroidal glycoalkaloid content, self-incompatibility, tuberization under short day conditions, and long stolons are proposed. The current challenges and future prospects of implementing the de novo domestication strategy for potato are discussed. Full article

(This article belongs to the Special Issue Molecular Genetic Studies in Potato Breeding)

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