ArticleBMC genomics2016
Marker development using SLAF-seq and whole-genome shotgun strategy to fine-map the semi-dwarf gene ari-e in barley.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed.
- Genetic diversity and structure of the 4Frontiers in plant science · 2023Article
- Discovery of DNA polymorphisms via genome-resequencing and development of molecular markers between two barley cultivars.Plant cell reports · 2022Article
- Investigation of genetic relationships within three Miscanthus species using SNP markers identified with SLAF-seq.BMC genomics · 2022Article
- Discovery of Single Nucleotide Polymorphisms for Resistance to Abnormal Vertical Growth in Macadamia.Frontiers in plant science · 2021Article
- Genome-wide association mapping reveals novel genes associated with coleoptile length in a worldwide collection of barley.BMC plant biology · 2020Article
- Genetic dissection of the interactions between semi-dwarfing genesMolecular breeding : new strategies in plant improvement · 2020Article
- Construction of a high-density genetic map and fine mapping of a candidate gene locus for a novel branched-spike mutant in barley.PloS one · 2020Article
- Fine mapping of qGL5H, a major grain length locus in barley (Hordeum vulgare L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2019Article
- A high density SLAF-SNP genetic map and QTL detection for fibre quality traits in Gossypium hirsutum.BMC genomics · 2018Article
- Physical mapping of the blue-grained gene from Thinopyrum ponticum chromosome 4Ag and development of blue-grain-related molecular markers and a FISH probe based on SLAF-seq technology.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2018Article
- Development of Thinopyrum ponticum-specific molecular markers and FISH probes based on SLAF-seq technology.Planta · 2018Article
- Rapid identification of a stripe rust resistant gene in a space-induced wheat mutant using specific locus amplified fragment (SLAF) sequencing.Scientific reports · 2018Article
- Mutations in the gene of the Gα subunit of the heterotrimeric G protein are the cause for theHereditas · 2018Article
- A Quantitative Profiling Method of Phytohormones and Other Metabolites Applied to Barley Roots Subjected to Salinity Stress.Frontiers in plant science · 2016Article
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11 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundBarley 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.
resultsWe 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.
conclusionsThe 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.
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