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Agronomy
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Molecular Genetic Studies in Potato Breeding — Series II
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Molecular Genetic Studies in Potato Breeding — Series II

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Crop Breeding and Genetics".

Deadline for manuscript submissions: closed (15 January 2024) | Viewed by 7748

Special Issue Editors

Dr. Tatjana Gavrilenko

E-Mail Website
Guest Editor
Federal Research Center, Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia
Interests: potato genetics and biotechnology; molecular cytogenetics; germplasm collection
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Alex V. Kochetov

E-Mail Website
Guest Editor
Institute of Cytology and Genetics, SB RAS, 630090 Novosibirsk, Russia
Interests: plant molecular genetics; gene engineering; resistance to pathogens
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Potato is most important non-cereal food crop. Traditional potato breeding is complicated by autotetraploidy, a high level of heterozygosity, tetrasomic inheritance, sterility of many forms, and inbred depression.

Molecular breeding studies integrate the results of molecular genetic and genomic research and translate them into practical breeding programs. The information generated from molecular markers and QTL loci, genomes and pangenomes, variety-specific SNPs, and transcriptome profiling significantly facilitates breeding research in potato.

The objectives of the proposed Issue are to review advances in the application of molecular data in breeding, and to present recent research in potato molecular genetics.

Particular attention will be given to the opportunities of using molecular approaches to address the current challenges in potato breeding.

Submissions on the following topics (but not limited to these) are invited:

(1) Molecular mechanisms of potato tolerance to abiotic stresses and their relation to perspectives of climate changes.

(2) Molecular breeding toward durable resistance to potato diseases and pests, with special attention to new aggressive strains and to quarantine objects.

(3) Improving the nutritional value of tubers using a genomics approach.

(4) Developing new breeding techniques to improve potato cultivars—gene pyramiding, GWAS, genetic transformation, gene editing, and diploid hybrid breeding with true seeds.

Dr. Tatjana Gavrilenko
Prof. Dr. Alex V. Kochetov
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Agronomy is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • potato
  • molecular breeding
  • transcriptomes profiling
  • MAS
  • QTL
  • genomic selection
  • GWAS
  • genome editing

Published Papers (7 papers)

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Research

15 pages, 10426 KiB  
Article
Genome-Wide Identification of Phytochrome-Interacting Factor (PIF) Gene Family in Potatoes and Functional Characterization of StPIF3 in Regulating Shade-Avoidance Syndrome
by Yuwen Han, Jiangwei Yang, Ning Zhang, Yating Gong, Mei Liu, Run Qiao, Xinhong Jiao, Fengjiao Zhu, Xinxia Li and Huaijun Si
Agronomy 2024, 14(4), 873; https://doi.org/10.3390/agronomy14040873 - 22 Apr 2024
Viewed by 437
Abstract
The phytochrome-interacting factor (PIF) proteins are part of a subfamily of basic helix–loop–helix (bHLH) transcription factors that integrate with phytochromes (PHYs) and are known to play important roles in adaptive changes in plant architecture. However, the characterization and function of PIFs in potatoes [...] Read more.
The phytochrome-interacting factor (PIF) proteins are part of a subfamily of basic helix–loop–helix (bHLH) transcription factors that integrate with phytochromes (PHYs) and are known to play important roles in adaptive changes in plant architecture. However, the characterization and function of PIFs in potatoes are currently poorly understood. In this study, we identified seven PIF members in potatoes and named them StPIF01-1, StPIF01-2, StPIF03, StPIF06-1, StPIF06-2, StPIF07, and StPIF09 based on their location in potato chromosomes. The chromosomal location, gene structures, physicochemical characteristics, phylogenetic tree, and tissue-specific expression of StPIFs were also analyzed. RT-qPCR analysis revealed that the StPIF3 gene was highly induced by shade and may play a crucial regulatory role in potato responses to shade stress. Also, multiple cis-regulatory elements involved in light response were detected in the promoter of the StPIF genes. Subcellular localization analysis indicated that the StPIF3-encoding protein is mainly localized in the nucleus. Transgenic overexpression of StPIF3 in potatoes increased stem length, chlorophyll accumulation, and enhanced shade-avoidance symptoms, whereas the StPIF3-interfering lines had a lower plant height and more chlorophyll accumulation. These findings enhance our comprehension of StPIF gene roles, potentially advancing potato yield and quality research. This study provides detailed information about StPIFs and identifies the function of StPIF3, which is involved in shade-avoidance syndrome. Full article
(This article belongs to the Special Issue Molecular Genetic Studies in Potato Breeding — Series II)
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18 pages, 5291 KiB  
Article
Comparative Study of Small-RNA and Degradome Sequencing Reveals Role of Novel stu-miR8006 in Regulating Root Development in Solanum tuberosum L.
by Xiaoqin Duan, Jiangwei Yang, Feiyan Zhang, Yuwen Han, Yating Gong, Mei Liu, Ning Zhang and Huaijun Si
Agronomy 2023, 13(12), 2942; https://doi.org/10.3390/agronomy13122942 - 29 Nov 2023
Viewed by 634
Abstract
MicroRNAs are a class of endogenous, non-coding, small-RNA molecules with important functions in plant development and stress response processes. Root systems are important because they allow plants to absorb nutrients and water from the soil and are fundamental for anchoring the plant and [...] Read more.
MicroRNAs are a class of endogenous, non-coding, small-RNA molecules with important functions in plant development and stress response processes. Root systems are important because they allow plants to absorb nutrients and water from the soil and are fundamental for anchoring the plant and responding to environmental signals. However, the roles of miRNAs underlying root development remain poorly investigated in potato. In this research, small-RNA sequencing was performed to thoroughly detect underlying miRNAs and their roles in regulating root development between the early root (ER) stage and the mature root (MR) stage of potato roots. A total of 203 known and 137 novel miRNAs were obtained, and 64 differentially expressed miRNAs (DEMs) were identified between the ER and MR stages. The expression patterns of 12 DEMs were also determined via qRT-PCR. In addition, a mixed degradome library was constructed from the ER and the MR stages to identify the targets of the identified miRNAs, and 2400 target genes were verified to be the targets of 131 miRNAs. Based on target annotation, we identified that nine target genes of six DEMs were probably involved in potato root development, and eight targets of six DEMs were validated via 5’-RLM-RACE assays. These targets may participate in root development by regulating cell proliferation, root cultures (PGSC0003DMT400013837), root meristem growth (PGSC0003DMT400079970), root morphogenesis (PGSC0003DMT400040282), post-embryonic root development (PGSC0003DMT400021612), root hair elongation (PGSC0003DMT400034518), cell wall repair (PGSC0003DMT400074930), and auxin polar transport (PGSC0003DMT400079970), and by negatively regulating cell proliferation (PGSC0003DMT400009997) and cell growth (PGSC0003DMT400003464). The qRT-PCR analysis indicated that most miRNAs have opposing expression patterns to their targets. It is widely accepted that potato root development is regulated by miRNAs, among which stu-miR8006-p5-1ss9AT is substantially down-regulated during root development. We show here that the suppression of stu-miR8006-p5-1ss9AT led to an alteration in the potato root architecture and that it targeted auxin induction in the root culture protein 12-encoding gene that is potentially involved in the regulation of root development. In addition, the suppression of stu-miR8006-p5-1ss9AT led to a significant alteration in the potato root architecture. Altogether, our results might provide some useful insights into stu-miR8006-p5-1ss9AT and the crucial role that it plays in potato root development; they could also facilitate the molecular genetic breeding of potato. Full article
(This article belongs to the Special Issue Molecular Genetic Studies in Potato Breeding — Series II)
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23 pages, 5561 KiB  
Article
Homoeologous Chromosome Pairing and Alien Introgression in Backcrossing Progenies Derived from Hybrids Solanum tuberosum (+) Mexican 2x (1 EBN) B-Genome Potato Species
by Tatjana Gavrilenko, Galina Pendinen, Olga Antonova, Tamara Makarova and Ramona Thieme
Agronomy 2023, 13(7), 1809; https://doi.org/10.3390/agronomy13071809 - 07 Jul 2023
Viewed by 1186
Abstract
We applied a genomic in situ hybridization (GISH) to analyze the genomic constitution of and meiotic pairing in interspecific somatic hybrids, and in a wide subset of backcrossing derivatives (BC1–BC5), from three interspecific combinations involving the cultivated potato, Solanum [...] Read more.
We applied a genomic in situ hybridization (GISH) to analyze the genomic constitution of and meiotic pairing in interspecific somatic hybrids, and in a wide subset of backcrossing derivatives (BC1–BC5), from three interspecific combinations involving the cultivated potato, Solanum tuberosum (AAAA genome), and three diploid (1 EBN) wild Mexican potato species (genome BB)—S. tarnii, S. pinnatisectum, and S. bulbocastanum. The theoretically expected genomic composition was detected in the somatic hybrids (AAAABB) and in the BC1 progeny (AAAAB), whereas in the subsequent BC2–BC4 generations, the partial loss of alien chromosomes was observed and almost all the BC5 genotypes showed a complete chromosome elimination of wild species. GISH revealed a homoeologous pairing between the chromosomes of the A- and the B-genomes in each of the hybrid progenies. Using GISH, we selected introgression lines with a single chromosome of the wild species in a potato genome background, as well as introgression lines with intergenomic recombinant chromosomes. Moreover, via molecular screening, BC hybrids with diagnostic markers for the R-genes conferring resistance to late blight disease and to the quarantine pest of the potato–Columbia root-knot nematode—were selected. The potential application of the results obtained for the planning of introgressive schemes directed to the breeding of advanced lines with multiple disease and pest resistance is discussed. Full article
(This article belongs to the Special Issue Molecular Genetic Studies in Potato Breeding — Series II)
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18 pages, 28070 KiB  
Article
Combined Small RNA and Degradome Sequencing Reveals Important Roles of Light-Responsive microRNAs in Wild Potato (Solanum chacoense)
by Yan Qiao, Fang Yang, Qian Li, Panrong Ren, Peipei An, Dan Li and Junfei Xiao
Agronomy 2023, 13(7), 1763; https://doi.org/10.3390/agronomy13071763 - 29 Jun 2023
Viewed by 753
Abstract
The accumulation of chlorophyll and antinutritional glycoalkaloids in potato tubers resulting from exposure to light has been widely recognized as a cause of unpredictable quality loss of potato tuber. While transcriptional regulation of light-induced chlorophyll and glycoalkaloids accumulation has been extensively investigated, the [...] Read more.
The accumulation of chlorophyll and antinutritional glycoalkaloids in potato tubers resulting from exposure to light has been widely recognized as a cause of unpredictable quality loss of potato tuber. While transcriptional regulation of light-induced chlorophyll and glycoalkaloids accumulation has been extensively investigated, the mechanisms of post-transcriptional regulation through miRNA remain largely unexplored. An experimental model, the tubers of Solanum chacoense, were used to identify light-responsive miRNA–target interactions (MTIs) related to tuber greening and glycoalkaloid biosynthesis by employing multi-omics approaches (miRNA-seq and degradome-seq). A total of 732 unique mature miRNAs have been identified in S. chacoense. In total, 6335 unique target transcripts were cleaved by 489 known miRNAs and 153 novel miRNAs. The results revealed that light-responsive miRNAs can be grouped into eight temporally related clusters and play important roles in various physiological processes such as plant growth, stress responses, and primary and secondary metabolism. Multi-omics analyses have revealed that the modulation of transcript abundance of MYB59, HSPs, and EBF1/EBF2 by light-responsive miRNAs is pivotal for their function in cross-tolerance responses to both abiotic and biotic stresses. Furthermore, our findings suggest that many light-responsive miRNAs are crucial regulators in various biosynthetic pathways, including tetrapyrrole biosynthesis, suberin biosynthesis, and steroid biosynthesis. These findings highlight the significant role of light-responsive miRNAs in secondary metabolic pathways, particularly in isoprenoid, terpenoid, and glycoalkaloid biosynthesis, and have implications for the precise manipulation of metabolic pathways to produce new potato varieties with improved resistance to greening and lower glycoalkaloid levels. Full article
(This article belongs to the Special Issue Molecular Genetic Studies in Potato Breeding — Series II)
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12 pages, 1069 KiB  
Article
Assembly and Analysis of Plastomes for 15 Potato Cultivars Grown in Russia
by Dmitry I. Karetnikov, Elena A. Salina, Alex V. Kochetov and Dmitry A. Afonnikov
Agronomy 2023, 13(6), 1454; https://doi.org/10.3390/agronomy13061454 - 24 May 2023
Viewed by 1022
Abstract
Chloroplasts are important organelles in a plant cell, having their own DNA (cpDNA), transmitted only through the female line, and performing the function of photosynthesis. The determination of chloroplast DNA is of interest in the study of the genetic diversity and phylogeny of [...] Read more.
Chloroplasts are important organelles in a plant cell, having their own DNA (cpDNA), transmitted only through the female line, and performing the function of photosynthesis. The determination of chloroplast DNA is of interest in the study of the genetic diversity and phylogeny of potatoes, and of cytoplasmic sterility, as well as for applications in biotechnology and genetic engineering. Here, we reconstructed the complete plastomes of 15 S. tuberosum potato cultivars grown in Russia. Our analysis allowed us to determine the composition and location of genes for these plastid DNAs. It was shown that the plastid genome contains both highly and low-variable regions. The region at position 63,001–68,000 nt has the highest variability. We determined the types of cpDNA based on in silico approaches: 10 cultivars have cpDNA of the W-type and 5 cultivars have cpDNA of the T-type. The genetic diversity of the plastid DNA for these potato cultivars was analyzed alongside the previously reconstructed plastomes of South American accessions, European/North American commercial cultivars and potato cultivars bred in the Ural region. The results show that plastid DNAs of the same type form clusters by sequence similarity, in agreement with previous studies. Full article
(This article belongs to the Special Issue Molecular Genetic Studies in Potato Breeding — Series II)
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13 pages, 1209 KiB  
Article
Three Cycles of Continuous Propagation of a Severe PSTVd Strain NicTr-3 in Solanum lycopersicum cv. Rutgers Resulted in Its Attenuation and Very Mild Disease Symptoms in Potato
by Alex V. Kochetov, Nikolay Shmakov, Dmitry A. Afonnikov, Gennady V. Vasiliev, Natalja V. Shatskaya, Anastasiya A. Egorova, Nina V. Mironenko, Nina M. Lashina, Alexander V. Khiutti and Olga S. Afanasenko
Agronomy 2023, 13(3), 684; https://doi.org/10.3390/agronomy13030684 - 26 Feb 2023
Viewed by 1143
Abstract
Potato spindle tuber viroid (PSTVd) is a small infectious non-coding circular RNA causing diseases of important crops, including tomato and potato. The symptoms vary from mild to severe depending on the viroid strain, the host plant variety, and the environmental conditions. The molecular [...] Read more.
Potato spindle tuber viroid (PSTVd) is a small infectious non-coding circular RNA causing diseases of important crops, including tomato and potato. The symptoms vary from mild to severe depending on the viroid strain, the host plant variety, and the environmental conditions. The molecular mechanisms underlying the development of particular disease phenotypes remain elusive. The PSTVd strain NicTr-3 causes severe disease symptoms on Solanum lycopersicum cv. Rutgers and Solanum tuberosum cv. Colomba. It was found that after three cycles of propagation in tomato cv. Rutgers, infection of potato cv. Colomba with NicTr-3 resulted in very mild symptoms including smaller size of tubers and delayed leaf senescence. Sequence analysis of PSTVd clones isolated from tomato inoculum revealed the presence of mutated variants of genomic RNA. Transcriptome analysis carried out on leaves showed a considerable difference between infected and healthy plants at 14 dpi and 30 dpi. Interestingly, the response of potato plants to the attenuated PSTVd strain revealed a large number of DEGs associated with initiation of dormancy with a considerable increase in the vegetation period. The second vegetative generation (tuber-derived plantlets from control healthy and PSTVd-infected plants) was characterized by similar phenotypes and transcriptomes. Thus, here we describe a case of attenuation of a severe PSTVd strain after continuous propagation in tomato. It would be of interest to consider the attenuated viroid strains as a potential biocontrol agent or vaccine against this type of pathogenic RNA. Full article
(This article belongs to the Special Issue Molecular Genetic Studies in Potato Breeding — Series II)
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17 pages, 11871 KiB  
Article
Evaluation of Responses of Potato Cultivars to Potato Spindle Tuber Viroid and to Mixed Viroid/Viral Infection
by Olga S. Afanasenko, Nina M. Lashina, Nina V. Mironenko, Elena I. Kyrova, Elena V. Rogozina, Natalia G. Zubko and Aleksander V. Khiutti
Agronomy 2022, 12(12), 2916; https://doi.org/10.3390/agronomy12122916 - 23 Nov 2022
Cited by 3 | Viewed by 1999
Abstract
Potato spindle tuber viroid (PSTVd) is a harmful quarantine disease with wide geographic distribution. To date, experimentally proved resistance or tolerance of potato cultivars to PSTVd has not been reported. The aim of this study was to evaluate responses to four PSTVd strains [...] Read more.
Potato spindle tuber viroid (PSTVd) is a harmful quarantine disease with wide geographic distribution. To date, experimentally proved resistance or tolerance of potato cultivars to PSTVd has not been reported. The aim of this study was to evaluate responses to four PSTVd strains of 39 modern potato cultivars of different origin. Four PSTVd strains of different origin, the intermediate VP35, VP87, and two sever strains FP10-13 and NicTr-3, deposited in GenBank, were used. Transcripts of these strains were used to inoculate tomato plants of the cv. Rutgers. Before PSTVd inoculation with tomato sap, all plants were tested for viral infection by ELISA. The presence of PSTVd in infected plants was verified by RT-PCR as well as by RT-qPCR at sixty days post-inoculation (dpi). The strain-specificity in the response of cultivars to viroid infection was revealed. Five cultivars were identified in which, after the first inoculation of plants with all PSTVd strains, normal in shape tubers were formed. All plants of the next generation derived from infected but normally shaped tubers showed strong symptoms of disease. PSTVd and mixed viroid/viral infection (PVY + PSTVd, PVM + PSTVd, and PVY + PVS + PSTVd) led to a significant decrease in the number and weight of tubers in most of the cultivars studied. Full article
(This article belongs to the Special Issue Molecular Genetic Studies in Potato Breeding — Series II)
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