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Behn A, Lizana C, Zapata F, Gonzalez A, Reyes-Díaz M, Fuentes D. Phenolic and anthocyanin content characterization related to genetic diversity analysis of Solanum tuberosum subsp. tuberosum Chilotanum Group in southern Chile. FRONTIERS IN PLANT SCIENCE 2023; 13:1045894. [PMID: 36704150 PMCID: PMC9872146 DOI: 10.3389/fpls.2022.1045894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/16/2022] [Indexed: 06/18/2023]
Abstract
The potato (Solanum tuberosum L) is one of the four most important crops worldwide in production and consumption. It originated from South America along the Andes, where six hotspots of diversity known as subcenters of origin are described from Venezuela to Chiloe Island in Chile, and where the greatest diversity of potatoes in the world is found. Today, the use of ancestral genetic resources has gained significant relevance, recovering and producing foods with a greater nutrient content and beneficial to human health. Therefore, native potatoes possess a set of characteristics with great potential for use in potato breeding guided primarily to produce better feed, especially potatoes of the Chilotanum Group that are easily crossed with conventional varieties. The primary objective of this study was to evaluate 290 accessions of S. tuberosum subsp tuberosum belonging to the Chilotanum Group using a set of molecular markers and correlate them to its phenotypic traits for future use in breeding programs. For this purpose, 290 accessions were analysed through 22 specific microsatellites described previously, correlating them with flesh and skin colour, total phenolic content, and anthocyanin content. A division into groups considering all the 290 accessions resulted in two clusters using STRUCTURE analysis and seven different genetic clusters using UPGMA. The latter exhibited common phenotypic characteristics as well as anthocyanin content, strongly supporting a correlation between phenotypic traits and the genetic fingerprint. These results will enable breeders to focus on the development of potatoes with high polyphenol and anthocyanin content.
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Affiliation(s)
- Anita Behn
- Instituto de Producción y Sanidad Vegetal, Facultad de Ciencias Agrarias y Alimentarias, Universidad Austral de Chile, Valdivia, Chile
| | - Carolina Lizana
- Instituto de Producción y Sanidad Vegetal, Facultad de Ciencias Agrarias y Alimentarias, Universidad Austral de Chile, Valdivia, Chile
| | - Felipe Zapata
- Biocomputing and Applied Genetics, Center for Systems Biotechnology, Fraunhofer Chile Research Foundation, Santiago, Chile
| | - Alvaro Gonzalez
- Biocomputing and Applied Genetics, Center for Systems Biotechnology, Fraunhofer Chile Research Foundation, Santiago, Chile
| | - Marjorie Reyes-Díaz
- Departamento de Ciencias Químicas y Recursos Naturales, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Temuco, Chile
| | - Derie Fuentes
- Biocomputing and Applied Genetics, Center for Systems Biotechnology, Fraunhofer Chile Research Foundation, Santiago, Chile
- Centro de Biotecnología de Sistemas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
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Wilson S, Malosetti M, Maliepaard C, Mulder HA, Visser RGF, van Eeuwijk F. Training Set Construction for Genomic Prediction in Auto-Tetraploids: An Example in Potato. FRONTIERS IN PLANT SCIENCE 2021; 12:771075. [PMID: 34899794 PMCID: PMC8651708 DOI: 10.3389/fpls.2021.771075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 10/20/2021] [Indexed: 06/14/2023]
Abstract
Training set construction is an important prerequisite to Genomic Prediction (GP), and while this has been studied in diploids, polyploids have not received the same attention. Polyploidy is a common feature in many crop plants, like for example banana and blueberry, but also potato which is the third most important crop in the world in terms of food consumption, after rice and wheat. The aim of this study was to investigate the impact of different training set construction methods using a publicly available diversity panel of tetraploid potatoes. Four methods of training set construction were compared: simple random sampling, stratified random sampling, genetic distance sampling and sampling based on the coefficient of determination (CDmean). For stratified random sampling, population structure analyses were carried out in order to define sub-populations, but since sub-populations accounted for only 16.6% of genetic variation, there were negligible differences between stratified and simple random sampling. For genetic distance sampling, four genetic distance measures were compared and though they performed similarly, Euclidean distance was the most consistent. In the majority of cases the CDmean method was the best sampling method, and compared to simple random sampling gave improvements of 4-14% in cross-validation scenarios, and 2-8% in scenarios with an independent test set, while genetic distance sampling gave improvements of 5.5-10.5% and 0.4-4.5%. No interaction was found between sampling method and the statistical model for the traits analyzed.
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Affiliation(s)
- Stefan Wilson
- Biometris, Wageningen University & Research, Wageningen, Netherlands
| | - Marcos Malosetti
- Biometris, Wageningen University & Research, Wageningen, Netherlands
| | - Chris Maliepaard
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Han A. Mulder
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, Netherlands
| | | | - Fred van Eeuwijk
- Biometris, Wageningen University & Research, Wageningen, Netherlands
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Tillault A, Yevtushenko DP. Simple sequence repeat analysis of new potato varieties developed in Alberta, Canada. PLANT DIRECT 2019; 3:e00140. [PMID: 31245780 PMCID: PMC6551368 DOI: 10.1002/pld3.140] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 04/26/2019] [Accepted: 04/28/2019] [Indexed: 06/09/2023]
Abstract
The worldwide demand for potato production requires the constant development of new potato varieties with improved yield, quality, disease resistance, and abiotic tolerance. However, cultivar registration is preceded by a long process to morphologically and physiologically characterize the plants. Notably, this process can be expedited by DNA marker analysis. Simple sequence repeats (SSRs), also known as microsatellites, are the most common reliable DNA markers used to discriminate between genotypes. In this study, 20 potato varieties, including five new genotypes developed in Alberta, Canada, were fingerprinted using 10 SSR markers selected for their high discriminatory power. Different SSRs were amplified from potato DNA using specific primers, and the DNA fragment sizes were analyzed by denaturing polyacrylamide gel electrophoresis. The number of alleles per locus ranged from two for the SSR marker STPoAc58 to six for STM0030 and STM0037 with an average of 4.4. In addition, a total of 77 unique patterns were observed for the 10 SSR markers. The polymorphic information content ranged from 0.477 to 0.802 with an average of 0.675 per locus. In this study, STM0037, STM1016, and STM1104 were found to be the best SSR markers to detect genetic differences between potato varieties. A minimum of two markers was required to distinguish between all 20 genotypes. Most importantly, this highly informative molecular tool confirmed that the developed potato varieties were genetically different from their respective maternal lines and potentially constituted new cultivars.
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Affiliation(s)
- Anne‐Sophie Tillault
- Department of Biological SciencesUniversity of LethbridgeLethbridgeAlbertaCanada
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Li Y, Colleoni C, Zhang J, Liang Q, Hu Y, Ruess H, Simon R, Liu Y, Liu H, Yu G, Schmitt E, Ponitzki C, Liu G, Huang H, Zhan F, Chen L, Huang Y, Spooner D, Huang B. Genomic Analyses Yield Markers for Identifying Agronomically Important Genes in Potato. MOLECULAR PLANT 2018; 11:473-484. [PMID: 29421339 DOI: 10.1016/j.molp.2018.01.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 01/02/2018] [Accepted: 01/22/2018] [Indexed: 05/24/2023]
Abstract
Wild potato species have substantial phenotypic and physiological diversity. Here, we report a comprehensive assessment of wild and cultivated potato species based on genomic analyses of 201 accessions of Solanum section Petota. We sequenced the genomes of these 201 accessions and identified 6 487 006 high-quality single nucleotide polymorphisms (SNPs) from 167 accessions in clade 4 of Solanum section Petota, including 146 wild and 21 cultivated diploid potato accessions with a broad geographic distribution. Genome-wide genetic variation analysis showed that the diversity of wild potatoes is higher than that of cultivated potatoes, and much higher genetic diversity in the agronomically important disease resistance genes was observed in wild potatoes. Furthermore, by exploiting information about known quantitative trait loci (QTL), we identified 609 genes under selection, including those correlated with the loss of bitterness in tubers and those involved in tuberization, two major domesticated traits of potato. Phylogenetic analyses revealed a north-south division of all species in clade 4, not just those in the S. brevicaule complex, and further supported S. candolleanum as the progenitor of cultivated potato and the monophyletic origin of cultivated potato in southern Peru. In addition, we analyzed the genome of S. candolleanum and identified 529 genes lost in cultivated potato. Collectively, the molecular markers generated in this study provide a valuable resource for the identification of agronomically important genes useful for potato breeding.
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Affiliation(s)
- Yangping Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, China; Joint International Research Laboratory of Crop Resources and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Chengdu, China
| | | | - Junjie Zhang
- Joint International Research Laboratory of Crop Resources and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Chengdu, China; College of Life Science, Sichuan Agricultural University, Chengdu, China
| | - Qiqi Liang
- Novogene Bioinformatics Institute, Beijing, China
| | - Yufeng Hu
- College of Agronomy, Sichuan Agricultural University, Chengdu, China; Joint International Research Laboratory of Crop Resources and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Chengdu, China
| | - Holly Ruess
- Vegetable Crops Research Unit, USDA-Agricultural Research Service, Department of Horticulture, University of Wisconsin, Madison, WI, USA
| | - Reinhard Simon
- Integrated IT and Computational Research Unit, International Potato Center, Lima, Peru
| | - Yinghong Liu
- Joint International Research Laboratory of Crop Resources and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Chengdu, China; Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Hanmei Liu
- Joint International Research Laboratory of Crop Resources and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Chengdu, China; College of Life Science, Sichuan Agricultural University, Chengdu, China
| | - Guowu Yu
- College of Agronomy, Sichuan Agricultural University, Chengdu, China; Joint International Research Laboratory of Crop Resources and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Chengdu, China
| | - Eric Schmitt
- University of Lille, CNRS, UMR 8198 Evo Eco-Paleo, Lille, France
| | - Chloé Ponitzki
- University of Lille, CNRS, UMR 8198 Evo Eco-Paleo, Lille, France
| | | | - Huanhuan Huang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Feilong Zhan
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Lin Chen
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Yubi Huang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - David Spooner
- Vegetable Crops Research Unit, USDA-Agricultural Research Service, Department of Horticulture, University of Wisconsin, Madison, WI, USA.
| | - Binquan Huang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China; Joint International Research Laboratory of Crop Resources and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Chengdu, China; Department of Plant Sciences, University of Oxford, Oxford, UK.
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