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      Potato soup: analysis of cultivated potato gene bank populations reveals high diversity and little structure

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          Abstract

          Cultivated potatoes are incredibly diverse, ranging from diploid to pentaploid and encompass four different species. They are adapted to disparate environments and conditions and carry unique alleles for resistance to pests and pathogens. Describing how diversity is partitioned within and among these populations is essential to understanding the potato genome and effectively utilizing landraces in breeding. This task is complicated by the difficulty of making comparisons across cytotypes and extensive admixture within section petota. We genotyped 730 accessions from the US Potato genebank including wild diploids and cultivated diploids and tetraploids using Genotype-by-sequencing. This data set allowed us to interrogate population structure and diversity as well as generate core subsets which will support breeders in efficiently screening genebank material for biotic and abiotic stress resistance alleles. We found that even controlling for ploidy, tetraploid material exhibited higher observed and expected heterozygosity than diploid accessions. In particular group chilotanum material was the most heterozygous and the only taxa not to exhibit any inbreeding. This may in part be because group chilotanum has a history of introgression not just from wild species, but landraces as well. All group chilotanum, exhibits introgression from group andigenum except clones from Southern South America near its origin, where the two groups are not highly differentiated. Moving north, we do not observe evidence for the same level of admixture back into group andigenum. This suggests that extensive history of admixture is a particular characteristic of chilotanum.

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          Fast gapped-read alignment with Bowtie 2.

          As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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            Cutadapt removes adapter sequences from high-throughput sequencing reads

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              The variant call format and VCFtools

              Summary: The variant call format (VCF) is a generic format for storing DNA polymorphism data such as SNPs, insertions, deletions and structural variants, together with rich annotations. VCF is usually stored in a compressed manner and can be indexed for fast data retrieval of variants from a range of positions on the reference genome. The format was developed for the 1000 Genomes Project, and has also been adopted by other projects such as UK10K, dbSNP and the NHLBI Exome Project. VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API. Availability: http://vcftools.sourceforge.net Contact: rd@sanger.ac.uk
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                Author and article information

                Contributors
                URI : https://loop.frontiersin.org/people/2767939Role: Role: Role: Role: Role: Role:
                URI : https://loop.frontiersin.org/people/1679416Role: Role: Role: Role: Role:
                URI : https://loop.frontiersin.org/people/2635186Role: Role: Role: Role: Role:
                URI : https://loop.frontiersin.org/people/542530Role: Role: Role: Role: Role:
                Journal
                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                1664-462X
                18 July 2024
                2024
                : 15
                : 1429279
                Affiliations
                [1] 1 Department of Horticultural Science, University of Minnesota , St. Paul, MN, United States
                [2] 2 U.S. Department of Agriculture (USDA)/Agricultural Research Service, Potato Genebank , Sturgeon Bay, WI, United States
                Author notes

                Edited by: Daniel Pinero, National Autonomous University of Mexico, Mexico

                Reviewed by: Diego Hojsgaard, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Germany

                Isabel Marques, Laboratorio TERRA. Universidade de Lisboa, Portugal

                *Correspondence: Laura M. Shannon, lmshannon@ 123456umn.edu
                Article
                10.3389/fpls.2024.1429279
                11291250
                39091313
                042ac0bf-30bf-43ef-b014-40167363f3c3
                Copyright © 2024 Tuttle, Del Rio, Bamberg and Shannon

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 07 May 2024
                : 27 June 2024
                Page count
                Figures: 6, Tables: 3, Equations: 0, References: 107, Pages: 15, Words: 7482
                Funding
                Funded by: National Institute of Food and Agriculture , doi 10.13039/100005825;
                Award ID: 2020-51181-32156, 2021–34141-3544
                Funded by: Minnesota Department of Agriculture , doi 10.13039/100004952;
                The author(s) declare financial support was received for the research, authorship, and/or publication of this article. GBS genotyping was funded by Pepsi Co under the guidance of Dr. David Eickholt. We made use of the new Polyploid tools and were funded to attend trainings in them by USDA NIFA Specialty Crop Research Initiative Award # 2020-51181-32156. This work was also funded by Minnesota Department of Agriculture through AGREETT and USDA-NIFA Grants # 2021–34141-3544 and # 2019-34141-30284.
                Categories
                Plant Science
                Original Research
                Custom metadata
                Plant Systematics and Evolution

                Plant science & Botany
                core subsets,autopolyploidy,ploidy detection,admixture,heterozygosity,multiploidy populations

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