skip to main content

DOE PAGESDOE PAGES

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

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.
Authors:
 [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)
Publication Date:
Grant/Contract Number:
AR0000535
Type:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 7; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Research Org:
Univ. of California, San Diego, CA (United States)
Sponsoring Org:
USDOE Advanced Research Projects Agency - Energy (ARPA-E)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Agricultural genetics; Plant breeding; Polyploidy in plants
OSTI Identifier:
1424915

Shirasawa, Kenta, Tanaka, Masaru, Takahata, Yasuhiro, Ma, Daifu, Cao, Qinghe, Liu, Qingchang, Zhai, Hong, Kwak, Sang-Soo, Cheol Jeong, Jae, Yoon, Ung-Han, Lee, Hyeong-Un, Hirakawa, Hideki, and Isobe, Sachiko. A high-density SNP genetic map consisting of a complete set of homologous groups in autohexaploid sweetpotato (Ipomoea batatas). United States: N. p., Web. doi:10.1038/srep44207.
Shirasawa, Kenta, Tanaka, Masaru, Takahata, Yasuhiro, Ma, Daifu, Cao, Qinghe, Liu, Qingchang, Zhai, Hong, Kwak, Sang-Soo, Cheol Jeong, Jae, Yoon, Ung-Han, Lee, Hyeong-Un, Hirakawa, Hideki, & Isobe, Sachiko. A high-density SNP genetic map consisting of a complete set of homologous groups in autohexaploid sweetpotato (Ipomoea batatas). United States. doi:10.1038/srep44207.
Shirasawa, Kenta, Tanaka, Masaru, Takahata, Yasuhiro, Ma, Daifu, Cao, Qinghe, Liu, Qingchang, Zhai, Hong, Kwak, Sang-Soo, Cheol Jeong, Jae, Yoon, Ung-Han, Lee, Hyeong-Un, Hirakawa, Hideki, and Isobe, Sachiko. 2017. "A high-density SNP genetic map consisting of a complete set of homologous groups in autohexaploid sweetpotato (Ipomoea batatas)". United States. doi:10.1038/srep44207. https://www.osti.gov/servlets/purl/1424915.
@article{osti_1424915,
title = {A high-density SNP genetic map consisting of a complete set of homologous groups in autohexaploid sweetpotato (Ipomoea batatas)},
author = {Shirasawa, Kenta and Tanaka, Masaru and Takahata, Yasuhiro and Ma, Daifu and Cao, Qinghe and Liu, Qingchang and Zhai, Hong and Kwak, Sang-Soo and Cheol Jeong, Jae and Yoon, Ung-Han and Lee, Hyeong-Un and Hirakawa, Hideki and Isobe, Sachiko},
abstractNote = {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.},
doi = {10.1038/srep44207},
journal = {Scientific Reports},
number = ,
volume = 7,
place = {United States},
year = {2017},
month = {3}
}

Works referenced in this record:

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species
journal, May 2011