A high-density genetic map constructed using specific length amplified fragment (SLAF) sequencing and QTL mapping of seed-related traits in sesame (Sesamum indicum L.)
Abstract Background Sesame (Sesamum indicum L., 2n = 2x = 26) is an important oilseed crop with high oil content but small seed size. To reveal the genetic loci of the quantitative seed-related traits, we constructed a high-density single nucleotide polymorphism (SNP) linkage map of an F2 population...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2019-12-01
|
| Series: | BMC Plant Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12870-019-2172-5 |
| _version_ | 1818565140175388672 |
|---|---|
| author | Hua Du Haiyang Zhang Libin Wei Chun Li Yinghui Duan Huili Wang |
| author_facet | Hua Du Haiyang Zhang Libin Wei Chun Li Yinghui Duan Huili Wang |
| author_sort | Hua Du |
| collection | DOAJ |
| description | Abstract Background Sesame (Sesamum indicum L., 2n = 2x = 26) is an important oilseed crop with high oil content but small seed size. To reveal the genetic loci of the quantitative seed-related traits, we constructed a high-density single nucleotide polymorphism (SNP) linkage map of an F2 population by using specific length amplified fragment (SLAF) technique and determined the quantitative trait loci (QTLs) of seed-related traits for sesame based on the phenotypes of F3 progeny. Results The genetic map comprised 2159 SNP markers distributed on 13 linkage groups (LGs) and was 2128.51 cM in length, with an average distance of 0.99 cM between adjacent markers. QTL mapping revealed 19 major-effect QTLs with the phenotypic effect (R2) more than 10%, i.e., eight QTLs for seed coat color, nine QTLs for seed size, and two QTLs for 1000-seed weight (TSW), using composite interval mapping method. Particularly, LG04 and LG11 contained collocated QTL regions for the seed coat color and seed size traits, respectively, based on their close or identical locations. In total, 155 candidate genes for seed coat color, 22 for seed size traits, and 54 for TSW were screened and analyzed. Conclusions This report presents the first QTL mapping of seed-related traits in sesame using an F2 population. The results reveal the location of specific markers associated with seed-related traits in sesame and provide the basis for further seed quality traits research. |
| first_indexed | 2024-12-14T01:37:24Z |
| format | Article |
| id | doaj.art-4785169d32134f4aa4c6119fa3259c2c |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-12-14T01:37:24Z |
| publishDate | 2019-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-4785169d32134f4aa4c6119fa3259c2c2022-12-21T23:21:51ZengBMCBMC Plant Biology1471-22292019-12-0119112010.1186/s12870-019-2172-5A high-density genetic map constructed using specific length amplified fragment (SLAF) sequencing and QTL mapping of seed-related traits in sesame (Sesamum indicum L.)Hua Du0Haiyang Zhang1Libin Wei2Chun Li3Yinghui Duan4Huili Wang5Henan Sesame Research Center, Henan Academy of Agricultural SciencesHenan Sesame Research Center, Henan Academy of Agricultural SciencesHenan Sesame Research Center, Henan Academy of Agricultural SciencesHenan Sesame Research Center, Henan Academy of Agricultural SciencesHenan Sesame Research Center, Henan Academy of Agricultural SciencesHenan Sesame Research Center, Henan Academy of Agricultural SciencesAbstract Background Sesame (Sesamum indicum L., 2n = 2x = 26) is an important oilseed crop with high oil content but small seed size. To reveal the genetic loci of the quantitative seed-related traits, we constructed a high-density single nucleotide polymorphism (SNP) linkage map of an F2 population by using specific length amplified fragment (SLAF) technique and determined the quantitative trait loci (QTLs) of seed-related traits for sesame based on the phenotypes of F3 progeny. Results The genetic map comprised 2159 SNP markers distributed on 13 linkage groups (LGs) and was 2128.51 cM in length, with an average distance of 0.99 cM between adjacent markers. QTL mapping revealed 19 major-effect QTLs with the phenotypic effect (R2) more than 10%, i.e., eight QTLs for seed coat color, nine QTLs for seed size, and two QTLs for 1000-seed weight (TSW), using composite interval mapping method. Particularly, LG04 and LG11 contained collocated QTL regions for the seed coat color and seed size traits, respectively, based on their close or identical locations. In total, 155 candidate genes for seed coat color, 22 for seed size traits, and 54 for TSW were screened and analyzed. Conclusions This report presents the first QTL mapping of seed-related traits in sesame using an F2 population. The results reveal the location of specific markers associated with seed-related traits in sesame and provide the basis for further seed quality traits research.https://doi.org/10.1186/s12870-019-2172-5QTL mappingSeed traitsSeed sizeSeed coat colorSesameSLAF |
| spellingShingle | Hua Du Haiyang Zhang Libin Wei Chun Li Yinghui Duan Huili Wang A high-density genetic map constructed using specific length amplified fragment (SLAF) sequencing and QTL mapping of seed-related traits in sesame (Sesamum indicum L.) BMC Plant Biology QTL mapping Seed traits Seed size Seed coat color Sesame SLAF |
| title | A high-density genetic map constructed using specific length amplified fragment (SLAF) sequencing and QTL mapping of seed-related traits in sesame (Sesamum indicum L.) |
| title_full | A high-density genetic map constructed using specific length amplified fragment (SLAF) sequencing and QTL mapping of seed-related traits in sesame (Sesamum indicum L.) |
| title_fullStr | A high-density genetic map constructed using specific length amplified fragment (SLAF) sequencing and QTL mapping of seed-related traits in sesame (Sesamum indicum L.) |
| title_full_unstemmed | A high-density genetic map constructed using specific length amplified fragment (SLAF) sequencing and QTL mapping of seed-related traits in sesame (Sesamum indicum L.) |
| title_short | A high-density genetic map constructed using specific length amplified fragment (SLAF) sequencing and QTL mapping of seed-related traits in sesame (Sesamum indicum L.) |
| title_sort | high density genetic map constructed using specific length amplified fragment slaf sequencing and qtl mapping of seed related traits in sesame sesamum indicum l |
| topic | QTL mapping Seed traits Seed size Seed coat color Sesame SLAF |
| url | https://doi.org/10.1186/s12870-019-2172-5 |
| work_keys_str_mv | AT huadu ahighdensitygeneticmapconstructedusingspecificlengthamplifiedfragmentslafsequencingandqtlmappingofseedrelatedtraitsinsesamesesamumindicuml AT haiyangzhang ahighdensitygeneticmapconstructedusingspecificlengthamplifiedfragmentslafsequencingandqtlmappingofseedrelatedtraitsinsesamesesamumindicuml AT libinwei ahighdensitygeneticmapconstructedusingspecificlengthamplifiedfragmentslafsequencingandqtlmappingofseedrelatedtraitsinsesamesesamumindicuml AT chunli ahighdensitygeneticmapconstructedusingspecificlengthamplifiedfragmentslafsequencingandqtlmappingofseedrelatedtraitsinsesamesesamumindicuml AT yinghuiduan ahighdensitygeneticmapconstructedusingspecificlengthamplifiedfragmentslafsequencingandqtlmappingofseedrelatedtraitsinsesamesesamumindicuml AT huiliwang ahighdensitygeneticmapconstructedusingspecificlengthamplifiedfragmentslafsequencingandqtlmappingofseedrelatedtraitsinsesamesesamumindicuml AT huadu highdensitygeneticmapconstructedusingspecificlengthamplifiedfragmentslafsequencingandqtlmappingofseedrelatedtraitsinsesamesesamumindicuml AT haiyangzhang highdensitygeneticmapconstructedusingspecificlengthamplifiedfragmentslafsequencingandqtlmappingofseedrelatedtraitsinsesamesesamumindicuml AT libinwei highdensitygeneticmapconstructedusingspecificlengthamplifiedfragmentslafsequencingandqtlmappingofseedrelatedtraitsinsesamesesamumindicuml AT chunli highdensitygeneticmapconstructedusingspecificlengthamplifiedfragmentslafsequencingandqtlmappingofseedrelatedtraitsinsesamesesamumindicuml AT yinghuiduan highdensitygeneticmapconstructedusingspecificlengthamplifiedfragmentslafsequencingandqtlmappingofseedrelatedtraitsinsesamesesamumindicuml AT huiliwang highdensitygeneticmapconstructedusingspecificlengthamplifiedfragmentslafsequencingandqtlmappingofseedrelatedtraitsinsesamesesamumindicuml |