Marker development using SLAF-seq and whole-genome shotgun strategy to fine-map the semi-dwarf gene ari-e in barley

Authors

Qiaojun Jia, Zhejiang Sci-Tech University, China
Cong Tan, Murdoch University
Junmei Wang, Zhejiang Academy of Agricultural Sciences, China
Xiao-Qi Zhang, Murdoch University
Jinghuan Zhu, Zhejiang Academy of Agricultural Sciences, China
Hao Luo, Murdoch University
Jianming Yang, Zhejiang Academy of Agricultural Sciences, China
Sharon Westcott, Department of Agriculture and Food, WAFollow
Sue Broughton, Department of Agriculture and Food, WAFollow
David Moody, InterGrain Pty Ltd
Chengdao Li, Department of Agriculture and Food, WAFollow

Document Type

Article

Publication Date

11-11-2016

Journal Title

BMC Genomics

ISSN

1471-2164

Keywords

Barley, Semi-dwarf, SLAF, Whole-genome sequence, Fine-map

Disciplines

Agricultural Science | Agriculture | Agronomy and Crop Sciences | Plant Breeding and Genetics

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.

Recommended Citation

Jia, Q, Tan, C, Wang, J, Zhang, X, Zhu, J, Luo, H, Yang, J, Westcott, S, Broughton, S, Moody, D, and Li, C. (2016), Marker development using SLAF-seq and whole-genome shotgun strategy to fine-map the semi-dwarf gene ari-e in barley. BMC Genomics, 17 (911).
https://library.dpird.wa.gov.au/fc_researchart/55