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Journal article
Marker development using SLAF-seq and whole-genome shotgun strategy to fine-map the semi-dwarf gene ari-e in barley
BMC Genomics, Vol.17(1)
2016
Abstract
Background: Barley semi-dwarf genes have been extensively explored and widely used in barley breeding programs. The semi-dwarf gene ari-e from Golden Promise is an important gene associated with some agronomic traits and salt tolerance. While ari-e has been mapped on barley chromosome 5H using traditional markers and next-generation sequencing technologies, it has not yet been finely located on this chromosome. Results: We integrated two methods to develop molecular markers for fine-mapping the semi-dwarf gene ari-e: (1) specific-length amplified fragment sequencing (SLAF-seq) with bulked segregant analysis (BSA) to develop SNP markers, and (2) the whole-genome shotgun sequence to develop InDels. Both SNP and InDel markers were developed in the target region and used for fine-mapping the ari-e gene. Linkage analysis showed that ari-e co-segregated with marker InDel-17 and was delimited by two markers (InDel-16 and DGSNP21) spanning 6.8 cM in the doubled haploid (DH) Dash × VB9104 population. The genetic position of ari-e was further confirmed in the Hindmarsh × W1 DH population which was located between InDel-7 and InDel-17. As a result, the overlapping region of the two mapping populations flanked by InDel-16 and InDel-17 was defined as the candidate region spanning 0.58 Mb on the POPSEQ physical map. Conclusions: The current study demonstrated the SLAF-seq for SNP discovery and whole-genome shotgun sequencing for InDel development as an efficient approach to map complex genomic region for isolation of functional gene. The ari-e gene was fine mapped from 10 Mb to 0.58 Mb interval.
Details
- Title
- Marker development using SLAF-seq and whole-genome shotgun strategy to fine-map the semi-dwarf gene ari-e in barley
- Authors/Creators
- Q. Jia (Author/Creator) - Zhejiang Sci-Tech UniversityC. Tan (Author/Creator) - Murdoch UniversityJ. Wang (Author/Creator) - ZheJiang Academy of Agricultural SciencesX-Q Zhang (Author/Creator) - Murdoch UniversityJ. Zhu (Author/Creator) - ZheJiang Academy of Agricultural SciencesH. Luo (Author/Creator) - Murdoch UniversityJ. Yang (Author/Creator) - ZheJiang Academy of Agricultural SciencesS. Westcott (Author/Creator) - Government of Western AustraliaS Broughton (Author/Creator) - Government of Western AustraliaD. Moody (Author/Creator) - InterGrainC. Li (Author/Creator) - Murdoch University
- Publication Details
- BMC Genomics, Vol.17(1)
- Publisher
- BioMed Central
- Identifiers
- 991005541756507891
- Copyright
- © 2016 The Authors.
- Murdoch Affiliation
- School of Veterinary and Life Sciences
- Language
- English
- Resource Type
- Journal article
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- Citation topics
- 3 Agriculture, Environment & Ecology
- 3.4 Crop Science
- 3.4.96 QTL
- Web Of Science research areas
- Biotechnology & Applied Microbiology
- Genetics & Heredity
- ESI research areas
- Molecular Biology & Genetics