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Agronomy
Special Issues
Potato Genetics and Breeding in the Genomics Era
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Potato Genetics and Breeding in the Genomics Era

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

Deadline for manuscript submissions: closed (31 July 2019) | Viewed by 17369

Special Issue Editors

Dr. Xianzhou Nie

E-Mail
Guest Editor
Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB 3B 4Z7, Canada
Interests: plant virology; plant viruses and viroids; plant-virus interactions; potato diseases and management
Dr. David De Koeyer

E-Mail Website
Guest Editor
Agriculture and Agri-Food Canada, Fredericton, NB E3B 4Z7, Canada
Interests: genetics; breeding; genomics; potato; marker-assisted selection; crop bioinformatics; breeding values; population improvement
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Potato is—and has long been—one of the major food crops grown worldwide and, with the human population increasing, it will no doubt continue to help feed the masses. In present day, the majority of potato cultivars are tetraploid and propagated vegetatively, with the breeding strategy being primarily based on phenotypic selection. As such, eliminating deleterious alleles and improving crops has proven laborious and difficult. Furthermore, over the years, potato has been no stranger to disease agents of all kinds, and the continual appearance of potato pests will not likely soon cease. As we stand, in the genomics era, breakthroughs and technologies that have come about in the last quarter-century provide us brand-new approaches to studying potato genetics and breeding, and the time has never been better to work on this important crop species. In this Special Issue, we welcome original research, reviews and opinions concerning recent insights, approaches, and advances in potato genetics and the optimization of potato breeding; we hope this will serve as a cache of up-to-date knowledge for researchers, farmers, and industry.

Dr. Xianzhou Nie
Dr. David De Koeyer
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
  • Genetics
  • Breeding
  • Genomics

Published Papers (4 papers)

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Research

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16 pages, 10797 KiB  
Article
Genome-Wide Association and Genomic Prediction for Fry Color in Potato
by Stephen Byrne, Fergus Meade, Francesca Mesiti, Denis Griffin, Colum Kennedy and Dan Milbourne
Agronomy 2020, 10(1), 90; https://doi.org/10.3390/agronomy10010090 - 09 Jan 2020
Cited by 24 | Viewed by 4456
Abstract
Potatoes destined for crisping are normally stored above 8 degrees; below this glucose accumulates leading to very dark fry colors and potential acrylamide build up. Unfortunately, sprouting occurs above 4 degrees and impacts product quality, necessitating the use of sprout suppressant chemicals. Therefore, [...] Read more.
Potatoes destined for crisping are normally stored above 8 degrees; below this glucose accumulates leading to very dark fry colors and potential acrylamide build up. Unfortunately, sprouting occurs above 4 degrees and impacts product quality, necessitating the use of sprout suppressant chemicals. Therefore, a goal of breeders is to develop potatoes with excellent fry color, which is maintained under storage below 8 degrees. Genomic or marker-assisted selection offers an opportunity to improve the efficiency of potato breeding and thereby assist breeders in achieving this goal. In this study, we have accumulated fry-color data on a large population of potato lines and combined this with genotypic data to carry out a GWAS and to evaluate accuracy of genomic prediction. We were able to identify a major QTL on chromosome 10 for fry color, and predict fry color with moderate accuracy using genome-wide markers. Furthermore, our results provide evidence that it is possible to identify a small subset of SNPs for processing characteristics that can give moderate predictive ability, albeit lower than that achieved with genome-wide markers. Full article
(This article belongs to the Special Issue Potato Genetics and Breeding in the Genomics Era)
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18 pages, 3258 KiB  
Article
Transcriptome Profiles of Contrasting Potato (Solanum tuberosum L.) Genotypes Under Water Stress
by Macarena Barra, Claudio Meneses, Stephanie Riquelme, Manuel Pinto, Martin Lagüe, Charlotte Davidson and Helen H. Tai
Agronomy 2019, 9(12), 848; https://doi.org/10.3390/agronomy9120848 - 04 Dec 2019
Cited by 5 | Viewed by 3478
Abstract
The potato is susceptible to water stress at all stages of development. We examined four clones of tetraploid potato, Cardinal, Desirée, Clone 37 FB, and Mije, from the germplasm bank of the National Institute of Agricultural Research (INIA) in Chile. Water stress was [...] Read more.
The potato is susceptible to water stress at all stages of development. We examined four clones of tetraploid potato, Cardinal, Desirée, Clone 37 FB, and Mije, from the germplasm bank of the National Institute of Agricultural Research (INIA) in Chile. Water stress was applied by suspending irrigation at the beginning of tuberization. Stomatal conductance, and tuber and plant fresh and dry weight were used to categorize water stress tolerance. Cardinal had a high susceptibility to water stress. Desirée was less susceptible than Cardinal and had some characteristics of tolerance. Mije had moderate tolerance and Clone 37 FB had high tolerance. Differential gene expression in leaves from plants with and without water stress were examined using transcriptome sequencing. Water stress-susceptible Cardinal had the fewest differentially expressed genes at 101, compared to Desirée at 1867, Clone 37 FB at 1179, and Mije at 1010. Water stress tolerance was associated with upregulation of the expression of transcription factor genes and genes involved in osmolyte and polyamine biosynthesis. Increased expression of genes encoding late embryogenesis abundant (LEA) and dehydrin proteins along with decreased expression of genes involved in nitrate assimilation and amino acid metabolism were found for clones showing water stress tolerance. The results also show that a water deficit was associated with reduced biotic stress responses. Additionally, heat shock protein genes were differentially expressed in all clones except for highly susceptible Cardinal. Together, the gene expression study demonstrates variation in the molecular pathways and biological processes in response to water stress contributing to tolerance and susceptibility. Full article
(This article belongs to the Special Issue Potato Genetics and Breeding in the Genomics Era)
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13 pages, 975 KiB  
Article
Chromosomes I and X Harbor Consistent Genetic Factors Associated with the Anthocyanin Variation in Potato
by María-Angélica Parra-Galindo, Clara Piñeros-Niño, Johana Carolina Soto-Sedano and Teresa Mosquera-Vasquez
Agronomy 2019, 9(7), 366; https://doi.org/10.3390/agronomy9070366 - 10 Jul 2019
Cited by 17 | Viewed by 3439
Abstract
Potatoes are an important staple food worldwide and are the third main source of antioxidants in the human diet. One of the most important antioxidant compounds in potatoes is the anthocyanin pigments. Some reports indicate a high positive correlation between color intensity, anthocyanins [...] Read more.
Potatoes are an important staple food worldwide and are the third main source of antioxidants in the human diet. One of the most important antioxidant compounds in potatoes is the anthocyanin pigments. Some reports indicate a high positive correlation between color intensity, anthocyanins content, and antioxidant level in potato tubers. The variation in anthocyanins composition and content in potato tubers among diverse germplasm sources has important nutritional and health implications and constitutes an interesting trait for potato breeding programs focused on enhancing the anthocyanin and antioxidant contents of potato materials. We identified and quantified five anthocyanidins (delphinidin, cyanidin, petunidin, pelargonidin, and peonidin) on tubers from the Colombian germplasm collection of Solanum tuberosum L. Group Phureja. The phenotypic data were merged into a genome-wide association study in order to identify genomic regions associated with the nutritional compounds’ variation in potatoes. The association was conducted using a 7520 single nucleotide polymorphisms markers matrix. Seven quantitative trait loci were identified. Chromosomes I and X harbored the most stable quantitative trait loci (QTL). Three quantitative trait loci were identified close to previously reported genes involved in the regulation of anthocyanins in potato tubers. The genomic regions of these QTL reveal presumptive candidate genes as genetic factors that are the basis for a better understanding of the genetic architecture of the regulation of nutritional compounds in potatoes. Full article
(This article belongs to the Special Issue Potato Genetics and Breeding in the Genomics Era)
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Review

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20 pages, 956 KiB  
Review
Potato Germplasm Enhancement Enters the Genomics Era
by Paul C. Bethke, Dennis A. Halterman and Shelley H. Jansky
Agronomy 2019, 9(10), 575; https://doi.org/10.3390/agronomy9100575 - 23 Sep 2019
Cited by 32 | Viewed by 5393
Abstract
The goal of germplasm enhancement is to introgress traits from wild crop relatives into cultivated material and eventually cultivars. It seeks to restore genetic diversity that has been lost over time or to augment cultivated material with novel alleles that improve parents in [...] Read more.
The goal of germplasm enhancement is to introgress traits from wild crop relatives into cultivated material and eventually cultivars. It seeks to restore genetic diversity that has been lost over time or to augment cultivated material with novel alleles that improve parents in breeding programs. This paper discusses potato germplasm enhancement efforts in the past, focusing on effective examples such as disease resistance and processing quality. In addition, it outlines new strategies for enhancement efforts, shifting the focus from evaluating phenotypes to tracking and manipulating specific DNA sequences. In the genomics era, germplasm enhancement will increasingly be focused on identifying and introgressing alleles rather than traits. Alleles will come from a broad pool of genetic resources that include wild species relatives of potato, landraces, cultivated potato itself, and distantly-related species. Genomics tools will greatly increase the efficiency of introgressing multi-genic traits and will make it possible to identify rare alleles and utilize recessive alleles. Full article
(This article belongs to the Special Issue Potato Genetics and Breeding in the Genomics Era)
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