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



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.



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.
College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, China. jiaqj@zstu.edu.cn.|Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Hangzhou, 310018, China. jiaqj@zstu.edu.cn.
Qiaojun
Q
Jia
Western Barley Genetics Alliance, Murdoch University, Murdoch, WA, 6150, Australia.
Cong
C
Tan
Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
Junmei
J
Wang
Western Barley Genetics Alliance, Murdoch University, Murdoch, WA, 6150, Australia.
Xiao-Qi
XQ
Zhang
Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
Jinghuan
J
Zhu
Western Barley Genetics Alliance, Murdoch University, Murdoch, WA, 6150, Australia.
Hao
H
Luo
Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
Jianming
J
Yang
Department of Agriculture and Food Government of Western Australia, South Perth, WA, 6155, Australia.
Sharon
S
Westcott
Department of Agriculture and Food Government of Western Australia, South Perth, WA, 6155, Australia.
Sue
S
Broughton
InterGrain Pty Ltd, 19 Ambitious Link, Bibra Lake, WA, 6163, Australia.
David
D
Moody
Western Barley Genetics Alliance, Murdoch University, Murdoch, WA, 6150, Australia. c.li@murdoch.edu.au.
Chengdao
C
Li
D002874:Chromosome Mapping; D018744:DNA, Plant / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism; D008040:Genetic Linkage; D005819:Genetic Markers; D018745:Genome, Plant; D006238:Haploidy; D059014:High-Throughput Nucleotide Sequencing; D001467:Hordeum / Q000235:genetics*; D054643:INDEL Mutation; D010641:Phenotype; D018515:Plant Leaves / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D017422:Sequence Analysis, DNA
D018744:DNA, Plant; D005819:Genetic Markers
Barley; Fine-map; SLAF; Semi-dwarf; Whole-genome sequence