Genetic dissection of an allotetraploid interspecific CSSLs guides interspecific genetics and breeding in cotton
Abstract Background The low genetic diversity of Upland cotton limits the potential for genetic improvement. Making full use of the genetic resources of Sea-island cotton will facilitate genetic improvement of widely cultivated Upland cotton varieties. The chromosome segments substitution lines (CSS...
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2020-06-01
|
| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12864-020-06800-x |
| _version_ | 1818693533262938112 |
|---|---|
| author | De Zhu Ximei Li Zhiwei Wang Chunyuan You Xinhui Nie Jie Sun Xianlong Zhang Dawei Zhang Zhongxu Lin |
| author_facet | De Zhu Ximei Li Zhiwei Wang Chunyuan You Xinhui Nie Jie Sun Xianlong Zhang Dawei Zhang Zhongxu Lin |
| author_sort | De Zhu |
| collection | DOAJ |
| description | Abstract Background The low genetic diversity of Upland cotton limits the potential for genetic improvement. Making full use of the genetic resources of Sea-island cotton will facilitate genetic improvement of widely cultivated Upland cotton varieties. The chromosome segments substitution lines (CSSLs) provide an ideal strategy for mapping quantitative trait loci (QTL) in interspecific hybridization. Results In this study, a CSSL population was developed by PCR-based markers assisted selection (MAS), derived from the crossing and backcrossing of Gossypium hirsutum (Gh) and G. barbadense (Gb), firstly. Then, by whole genome re-sequencing, 11,653,661 high-quality single nucleotide polymorphisms (SNPs) were identified which ultimately constructed 1211 recombination chromosome introgression segments from Gb. The sequencing-based physical map provided more accurate introgressions than the PCR-based markers. By exploiting CSSLs with mutant morphological traits, the genes responding for leaf shape and fuzz-less mutation in the Gb were identified. Based on a high-resolution recombination bin map to uncover genetic loci determining the phenotypic variance between Gh and Gb, 64 QTLs were identified for 14 agronomic traits with an interval length of 158 kb to 27 Mb. Surprisingly, multiple alleles of Gb showed extremely high value in enhancing cottonseed oil content (SOC). Conclusions This study provides guidance for studying interspecific inheritance, especially breeding researchers, for future studies using the traditional PCR-based molecular markers and high-throughput re-sequencing technology in the study of CSSLs. Available resources include candidate position for controlling cotton quality and quantitative traits, and excellent breeding materials. Collectively, our results provide insights into the genetic effects of Gb alleles on the Gh, and provide guidance for the utilization of Gb alleles in interspecific breeding. |
| first_indexed | 2024-12-17T13:15:12Z |
| format | Article |
| id | doaj.art-fd4a02160ba747468ecd6bafee270adf |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-17T13:15:12Z |
| publishDate | 2020-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-fd4a02160ba747468ecd6bafee270adf2022-12-21T21:47:01ZengBMCBMC Genomics1471-21642020-06-0121111610.1186/s12864-020-06800-xGenetic dissection of an allotetraploid interspecific CSSLs guides interspecific genetics and breeding in cottonDe Zhu0Ximei Li1Zhiwei Wang2Chunyuan You3Xinhui Nie4Jie Sun5Xianlong Zhang6Dawei Zhang7Zhongxu Lin8National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural UniversityNational Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural UniversityNational Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural UniversityCotton Research Institute, Shihezi Academy of Agriculture ScienceKey Laboratory of Oasis Ecology Agricultural of Xinjiang Bingtuan, Agricultural College, Shihezi UniversityKey Laboratory of Oasis Ecology Agricultural of Xinjiang Bingtuan, Agricultural College, Shihezi UniversityNational Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural UniversityInstitute of Industrial Crops, Xinjiang Academy of Agricultural SciencesNational Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural UniversityAbstract Background The low genetic diversity of Upland cotton limits the potential for genetic improvement. Making full use of the genetic resources of Sea-island cotton will facilitate genetic improvement of widely cultivated Upland cotton varieties. The chromosome segments substitution lines (CSSLs) provide an ideal strategy for mapping quantitative trait loci (QTL) in interspecific hybridization. Results In this study, a CSSL population was developed by PCR-based markers assisted selection (MAS), derived from the crossing and backcrossing of Gossypium hirsutum (Gh) and G. barbadense (Gb), firstly. Then, by whole genome re-sequencing, 11,653,661 high-quality single nucleotide polymorphisms (SNPs) were identified which ultimately constructed 1211 recombination chromosome introgression segments from Gb. The sequencing-based physical map provided more accurate introgressions than the PCR-based markers. By exploiting CSSLs with mutant morphological traits, the genes responding for leaf shape and fuzz-less mutation in the Gb were identified. Based on a high-resolution recombination bin map to uncover genetic loci determining the phenotypic variance between Gh and Gb, 64 QTLs were identified for 14 agronomic traits with an interval length of 158 kb to 27 Mb. Surprisingly, multiple alleles of Gb showed extremely high value in enhancing cottonseed oil content (SOC). Conclusions This study provides guidance for studying interspecific inheritance, especially breeding researchers, for future studies using the traditional PCR-based molecular markers and high-throughput re-sequencing technology in the study of CSSLs. Available resources include candidate position for controlling cotton quality and quantitative traits, and excellent breeding materials. Collectively, our results provide insights into the genetic effects of Gb alleles on the Gh, and provide guidance for the utilization of Gb alleles in interspecific breeding.http://link.springer.com/article/10.1186/s12864-020-06800-xCottonChromosome substituted segments lines (CSSLs)Quantitative trait loci (QTL)Whole genome re-sequencingCottonseed oil content (SOC) |
| spellingShingle | De Zhu Ximei Li Zhiwei Wang Chunyuan You Xinhui Nie Jie Sun Xianlong Zhang Dawei Zhang Zhongxu Lin Genetic dissection of an allotetraploid interspecific CSSLs guides interspecific genetics and breeding in cotton BMC Genomics Cotton Chromosome substituted segments lines (CSSLs) Quantitative trait loci (QTL) Whole genome re-sequencing Cottonseed oil content (SOC) |
| title | Genetic dissection of an allotetraploid interspecific CSSLs guides interspecific genetics and breeding in cotton |
| title_full | Genetic dissection of an allotetraploid interspecific CSSLs guides interspecific genetics and breeding in cotton |
| title_fullStr | Genetic dissection of an allotetraploid interspecific CSSLs guides interspecific genetics and breeding in cotton |
| title_full_unstemmed | Genetic dissection of an allotetraploid interspecific CSSLs guides interspecific genetics and breeding in cotton |
| title_short | Genetic dissection of an allotetraploid interspecific CSSLs guides interspecific genetics and breeding in cotton |
| title_sort | genetic dissection of an allotetraploid interspecific cssls guides interspecific genetics and breeding in cotton |
| topic | Cotton Chromosome substituted segments lines (CSSLs) Quantitative trait loci (QTL) Whole genome re-sequencing Cottonseed oil content (SOC) |
| url | http://link.springer.com/article/10.1186/s12864-020-06800-x |
| work_keys_str_mv | AT dezhu geneticdissectionofanallotetraploidinterspecificcsslsguidesinterspecificgeneticsandbreedingincotton AT ximeili geneticdissectionofanallotetraploidinterspecificcsslsguidesinterspecificgeneticsandbreedingincotton AT zhiweiwang geneticdissectionofanallotetraploidinterspecificcsslsguidesinterspecificgeneticsandbreedingincotton AT chunyuanyou geneticdissectionofanallotetraploidinterspecificcsslsguidesinterspecificgeneticsandbreedingincotton AT xinhuinie geneticdissectionofanallotetraploidinterspecificcsslsguidesinterspecificgeneticsandbreedingincotton AT jiesun geneticdissectionofanallotetraploidinterspecificcsslsguidesinterspecificgeneticsandbreedingincotton AT xianlongzhang geneticdissectionofanallotetraploidinterspecificcsslsguidesinterspecificgeneticsandbreedingincotton AT daweizhang geneticdissectionofanallotetraploidinterspecificcsslsguidesinterspecificgeneticsandbreedingincotton AT zhongxulin geneticdissectionofanallotetraploidinterspecificcsslsguidesinterspecificgeneticsandbreedingincotton |