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Title: A high-density SNP genetic map consisting of a complete set of homologous groups in autohexaploid sweetpotato (Ipomoea batatas)

Journal Article · · Scientific Reports
DOI:https://doi.org/10.1038/srep44207· OSTI ID:1424915
 [1];  [2];  [2];  [3];  [3];  [4];  [4];  [5];  [5];  [6];  [6];  [1];  [1]
  1. Kazusa DNA Research Institute (Japan)
  2. Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization (Japan)
  3. Chinese Academy of Agricultural Science (China)
  4. China Agricultural University (China)
  5. Korea Research Institute of Bioscience & Biotechnology (South Korea)
  6. Rural Development Administration (South Korea)
+ Show Author Affiliations

Sweetpotato (Ipomoea batatas) is an autohexaploid species with 90 chromosomes (2n = 6x = 90) and a basic chromosome number of 15, and is therefore regarded as one of the most challenging species for high-density genetic map construction. Here, we used single nucleotide polymorphisms (SNPs) identified by double-digest restriction site-associated DNA sequencing based on next-generation sequencing technology to construct a map for sweetpotato. We then aligned the sequence reads onto the reference genome sequence of I. trifida, a likely diploid ancestor of sweetpotato, to detect SNPs. In addition, to simplify analysis of the complex genetic mode of autohexaploidy, we used an S1 mapping population derived from self-pollination of a single parent. As a result, 28,087 double-simplex SNPs showing a Mendelian segregation ratio in the S1 progeny could be mapped onto 96 linkage groups (LGs), covering a total distance of 33,020.4 cM. Based on the positions of the SNPs on the I. trifida genome, the LGs were classified into 15 groups, each with roughly six LGs and six small extra groups. The molecular genetic techniques used in this study are applicable to high-density mapping of other polyploid plant species, including important crops.

Research Organization:
Univ. of California, San Diego, CA (United States)
Sponsoring Organization:
USDOE Advanced Research Projects Agency - Energy (ARPA-E)
Grant/Contract Number:
AR0000535
OSTI ID:
1424915
Journal Information:
Scientific Reports, Vol. 7; ISSN 2045-2322
Publisher:
Nature Publishing GroupCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 36 works
Citation information provided by
Web of Science

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Cited By (19)

An ultra-dense integrated linkage map for hexaploid chrysanthemum enables multi-allelic QTL analysis journal August 2017
Genome-Wide Association Studies (GWAS) for Yield and Weevil Resistance in Sweet potato (Ipomoea batatas (L.) Lam) journal July 2019
Current status in whole genome sequencing and analysis of Ipomoea spp. journal August 2019
Recent research on enhanced resistance to parasitic nematodes in sweetpotato journal August 2019
Genome-wide association study overcomes the genome complexity in autohexaploid chrysanthemum and tags SNP markers onto the flower color genes journal September 2019
De novo whole-genome assembly in Chrysanthemum seticuspe, a model species of Chrysanthemums, and its application to genetic and gene discovery analysis journal January 2019
Development of molecular markers associated with resistance to Meloidogyne incognita by performing quantitative trait locus analysis and genome-wide association study in sweetpotato journal August 2019
Genome-wide association studies on the phyllosphere microbiome: Embracing complexity in host-microbe interactions journal January 2019
Identification of QTL for resistance to root rot in sweetpotato (Ipomoea batatas (L.) Lam) with SSR linkage maps journal May 2020
Analyses of single nucleotide polymorphisms identified by ddRAD-seq reveal genetic structure of tea germplasm and Japanese landraces for tea breeding journal August 2019
Unraveling the Hexaploid Sweetpotato Inheritance Using Ultra-Dense Multilocus Mapping journal November 2019
Genotyping Polyploids from Messy Sequencing Data journal September 2018
Tools for Genetic Studies in Experimental Populations of Polyploids journal April 2018
Genetic Mapping With Allele Dosage Information in Tetraploid Urochloa decumbens (Stapf) R. D. Webster Reveals Insights Into Spittlebug (Notozulia entreriana Berg) Resistance journal February 2019
Unraveling the hexaploid sweetpotato inheritance using ultra-dense multilocus mapping posted_content July 2019
Linkage Analysis and Haplotype Phasing in Experimental Autopolyploid Populations with High Ploidy Level Using Hidden Markov Models journal October 2019
Genetic Mapping in Autohexaploid Sweet Potato with Low-Coverage NGS-Based Genotyping Data journal August 2020
Priors for Genotyping Polyploids journal November 2019
Corrigendum: Genetic Mapping With Allele Dosage Information in Tetraploid Urochloa decumbens (Stapf) R. D. Webster Reveals Insights Into Spittlebug (Notozulia entreriana Berg) Resistance journal June 2019

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Agricultural genetics
Plant breeding
Polyploidy in plants