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Construction of a linkage map based on retrotransposon insertion polymorphisms in sweetpotato via high-throughput sequencing.

Monden Y, Hara T, Okada Y, Jahana O, Kobayashi A, Tabuchi H, Onaga S, Tahara M - Breed. Sci. (2015)

Bottom Line: Sweetpotato (Ipomoea batatas L.) is an outcrossing hexaploid species with a large number of chromosomes (2n = 6x = 90).Using a pseudo-testcross strategy, 43 and 47 linkage groups were generated for PSL and 90IDN-47, respectively.Additionally, our approach led to savings of time and labor for genotyping.

View Article: PubMed Central - PubMed

Affiliation: Graduate School of Environmental and Life Science, Okayama University , 1-1-1 Tsushimanaka, Kita-ku, Okayama, Okayama 700- 8530 , Japan.

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.

No MeSH data available.


Related in: MedlinePlus

Linkage map of ‘PSL’ based on Rtsp-1 markers (P01–P43). The linkage groups were integrated with JoinMap 4.1 at an LOD of 5.0. The name of each marker is derived from the name of the insertion site (Cl* or pattern) and s (representing simplex marker) or ds (representing double-simplex). The number corresponding to each marker indicates the genetic distance between markers (cM). Of these linkage groups, P01–P10 are homologous to I01–I10.
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f1-65_145: Linkage map of ‘PSL’ based on Rtsp-1 markers (P01–P43). The linkage groups were integrated with JoinMap 4.1 at an LOD of 5.0. The name of each marker is derived from the name of the insertion site (Cl* or pattern) and s (representing simplex marker) or ds (representing double-simplex). The number corresponding to each marker indicates the genetic distance between markers (cM). Of these linkage groups, P01–P10 are homologous to I01–I10.

Mentions: The genetic linkage map for each parent was constructed at an LOD score of 5.0 using JoinMap 4.1 software (Kyazma). The molecular markers were grouped into 43 and 47 linkage groups for PSL and 90IDN-47, respectively (Table 4, Figs. 1 and 2). In the linkage map for PSL, the entire length was estimated as 931.5 cM, with an average distance between markers of 11.6 cM and an average length per linkage group of 21.2 cM. The number of mapped markers totaled 124, ranging from 2 to 8 markers per linkage group (Table 4 and Supplemental Table 4). In the map for 90IDN-47, the entire length was estimated as 734.3 cM, with an average distance between markers of 9.8 cM and an average length per linkage group of 15.6 cM. The number of mapped markers totaled 122, ranging from 2 to 5 per linkage group (Table 4 and Supplemental Table 4). Double-simplex markers were used to investigate the homology of the linkage groups between both parent maps. A total of 20 double-simplex markers revealed homologous relationships between 10 linkage groups of PSL (P01–P10) and 10 of 90IDN-47 (I01–I10) (Figs. 1 and 2, and Supplemental Fig. 3).


Construction of a linkage map based on retrotransposon insertion polymorphisms in sweetpotato via high-throughput sequencing.

Monden Y, Hara T, Okada Y, Jahana O, Kobayashi A, Tabuchi H, Onaga S, Tahara M - Breed. Sci. (2015)

Linkage map of ‘PSL’ based on Rtsp-1 markers (P01–P43). The linkage groups were integrated with JoinMap 4.1 at an LOD of 5.0. The name of each marker is derived from the name of the insertion site (Cl* or pattern) and s (representing simplex marker) or ds (representing double-simplex). The number corresponding to each marker indicates the genetic distance between markers (cM). Of these linkage groups, P01–P10 are homologous to I01–I10.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4430505&req=5

f1-65_145: Linkage map of ‘PSL’ based on Rtsp-1 markers (P01–P43). The linkage groups were integrated with JoinMap 4.1 at an LOD of 5.0. The name of each marker is derived from the name of the insertion site (Cl* or pattern) and s (representing simplex marker) or ds (representing double-simplex). The number corresponding to each marker indicates the genetic distance between markers (cM). Of these linkage groups, P01–P10 are homologous to I01–I10.
Mentions: The genetic linkage map for each parent was constructed at an LOD score of 5.0 using JoinMap 4.1 software (Kyazma). The molecular markers were grouped into 43 and 47 linkage groups for PSL and 90IDN-47, respectively (Table 4, Figs. 1 and 2). In the linkage map for PSL, the entire length was estimated as 931.5 cM, with an average distance between markers of 11.6 cM and an average length per linkage group of 21.2 cM. The number of mapped markers totaled 124, ranging from 2 to 8 markers per linkage group (Table 4 and Supplemental Table 4). In the map for 90IDN-47, the entire length was estimated as 734.3 cM, with an average distance between markers of 9.8 cM and an average length per linkage group of 15.6 cM. The number of mapped markers totaled 122, ranging from 2 to 5 per linkage group (Table 4 and Supplemental Table 4). Double-simplex markers were used to investigate the homology of the linkage groups between both parent maps. A total of 20 double-simplex markers revealed homologous relationships between 10 linkage groups of PSL (P01–P10) and 10 of 90IDN-47 (I01–I10) (Figs. 1 and 2, and Supplemental Fig. 3).

Bottom Line: Sweetpotato (Ipomoea batatas L.) is an outcrossing hexaploid species with a large number of chromosomes (2n = 6x = 90).Using a pseudo-testcross strategy, 43 and 47 linkage groups were generated for PSL and 90IDN-47, respectively.Additionally, our approach led to savings of time and labor for genotyping.

View Article: PubMed Central - PubMed

Affiliation: Graduate School of Environmental and Life Science, Okayama University , 1-1-1 Tsushimanaka, Kita-ku, Okayama, Okayama 700- 8530 , Japan.

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.

No MeSH data available.


Related in: MedlinePlus