title: Construction of a linkage map based on retrotransposon insertion polymorphisms in sweetpotato via high-throughput sequencing.
abstract: Sweetpotato (Ipomoea batatas L.) is an outcrossing hexaploid species with a large number of chromosomes (2n = 6x = 90). Although sweetpotato is one of the world's most important crops, genetic analysis of the species has been hindered by its genetic complexity combined with the lack of a whole genome sequence. In the present study, we constructed a genetic linkage map based on retrotransposon insertion polymorphisms using a mapping population derived from a cross between 'Purple Sweet Lord' (PSL) and '90IDN-47' cultivars. High-throughput sequencing and subsequent data analyses identified many Rtsp-1 retrotransposon insertion sites, and their allele dosages (simplex, duplex, triplex, or double-simplex) were determined based on segregation ratios in the mapping population. Using a pseudo-testcross strategy, 43 and 47 linkage groups were generated for PSL and 90IDN-47, respectively. Interestingly, most of these insertions (~90%) were present in a simplex manner, indicating their utility for linkage map construction in polyploid species. Additionally, our approach led to savings of time and labor for genotyping. Although the number of markers herein was insufficient for map-based cloning, our trial analysis exhibited the utility of retrotransposon-based markers for linkage map construction in sweetpotato.
authors.affiliation: Graduate School of Environmental and Life Science, Okayama University , 1-1-1 Tsushimanaka, Kita-ku, Okayama, Okayama 700- 8530 , Japan.
authors.forename: Yuki
authors.initials: Y
authors.lastname: Monden
authors.affiliation: Graduate School of Environmental and Life Science, Okayama University , 1-1-1 Tsushimanaka, Kita-ku, Okayama, Okayama 700- 8530 , Japan.
authors.forename: Takuya
authors.initials: T
authors.lastname: Hara
authors.affiliation: National Agriculture and Food Research Organization, Itoman Resident Office, Kyushu Okinawa Agricultural Research Center , 820 Makabe, Itoman, Okinawa 901-0336 , Japan.
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Okada
authors.affiliation: Okinawa Prefectural Agricultural Research Center , 820 Makabe, Itoman, Okinawa 901-0336 , Japan.
authors.forename: Osamu
authors.initials: O
authors.lastname: Jahana
authors.affiliation: National Agriculture and Food Research Organization, Kyushu Okinawa Agricultural Research Center , 6651-2 Yokoichi-machi, Miyakonojo, Miyazaki 885-0091 , Japan.
authors.forename: Akira
authors.initials: A
authors.lastname: Kobayashi
authors.affiliation: National Agriculture and Food Research Organization, Kyushu Okinawa Agricultural Research Center , 6651-2 Yokoichi-machi, Miyakonojo, Miyazaki 885-0091 , Japan.
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Tabuchi
authors.affiliation: Okinawa Prefectural Agricultural Research Center , 820 Makabe, Itoman, Okinawa 901-0336 , Japan.
authors.forename: Shoko
authors.initials: S
authors.lastname: Onaga
authors.affiliation: Graduate School of Environmental and Life Science, Okayama University , 1-1-1 Tsushimanaka, Kita-ku, Okayama, Okayama 700- 8530 , Japan.
authors.forename: Makoto
authors.initials: M
authors.lastname: Tahara
keywords: high-throughput sequencing; linkage map; polyploidy; pseudo-testcross; retrotransposon; sweetpotato