ArticleBMC plant biology2016
SNP-markers in Allium species to facilitate introgression breeding in onion.
Article in BMC plant biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed.
- Proportion of parental genomes in hybrids Allium cepa × A. roylei determines which one becomes dominant.The plant genome · 2025Article
- Harnessing chloroplast SSRs to decipher genetic diversity in underutilizedFrontiers in plant science · 2025Article
- Deciphering genetic diversity phylogeny and assembly ofHeliyon · 2024Article
- Conservation and Global Distribution of Onion (Plants (Basel, Switzerland) · 2023Review
- Development of SNP markers linked to purple blotch resistance for marker-assisted selection in onion (3 Biotech · 2023Article
- Integrating Genetic and Chromosome Maps ofInternational journal of molecular sciences · 2022Article
- Development of a genome-wide marker design workflow for onions and its application in target amplicon sequencing-based genotyping.DNA research : an international journal for rapid publication of reports on genes and genomes · 2022Article
- Cytotoxic activity of Nep1-like proteins on monocots.The New phytologist · 2022Article
- Article
- Detecting major introgressions in wheat and their putative origins using coverage analysis.Scientific reports · 2022Article
- Genome Dominance inFrontiers in plant science · 2022Article
- Genetic diversity and population structure in onion (Physiology and molecular biology of plants : an international journal of functional plant biology · 2021Article
- Insights from the first genome assembly of Onion (Allium cepa).G3 (Bethesda, Md.) · 2021Article
- Simulation-based optimization of genomic selection scheme for accelerating genetic gain while preventing inbreeding depression in onion breeding.Breeding science · 2020Article
- Construction of an Onion (Plants (Basel, Switzerland) · 2020Article
- Omics approaches inPeerJ · 2020Article
- High-density SNP linkage map construction and QTL mapping for flavonoid-related traits in a tea plant (Camellia sinensis) using 2b-RAD sequencing.BMC genomics · 2018Article
- Development of a Genetic Map for Onion (Frontiers in plant science · 2017Article
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9 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundWithin onion, Allium cepa L., the availability of disease resistance is limited. The identification of sources of resistance in related species, such as Allium roylei and Allium fistulosum, was a first step towards the improvement of onion cultivars by breeding. SNP markers linked to resistance and polymorphic between these related species and onion cultivars are a valuable tool to efficiently introgress disease resistance genes. In this paper we describe the identification and validation of SNP markers valuable for onion breeding.
resultsTranscriptome sequencing resulted in 192 million RNA seq reads from the interspecific F1 hybrid between A. roylei and A. fistulosum (RF) and nine onion cultivars. After assembly, reliable SNPs were discovered in about 36 % of the contigs. For genotyping of the interspecific three-way cross population, derived from a cross between an onion cultivar and the RF (CCxRF), 1100 SNPs that are polymorphic in RF and monomorphic in the onion cultivars (RF SNPs) were selected for the development of KASP assays. A molecular linkage map based on 667 RF-SNP markers was constructed for CCxRF. In addition, KASP assays were developed for 1600 onion-SNPs (SNPs polymorphic among onion cultivars). A second linkage map was constructed for an F2 of onion x A. roylei (F2(CxR)) that consisted of 182 onion-SNPs and 119 RF-SNPs, and 76 previously mapped markers. Markers co-segregating in both the F2(CxR) and the CCxRF population were used to assign the linkage groups of RF to onion chromosomes. To validate usefulness of these SNP markers, QTL mapping was applied in the CCxRF population that segregates for resistance to Botrytis squamosa and resulted in a QTL for resistance on chromosome 6 of A. roylei.
conclusionsOur research has more than doubled the publicly available marker sequences of expressed onion genes and two onion-related species. It resulted in a detailed genetic map for the interspecific CCxRF population. This is the first paper that reports the detection of a QTL for resistance to B. squamosa in A. roylei.
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