ArticleFrontiers in plant science2017
Genome-Wide SNP Markers Based on SLAF-Seq Uncover Breeding Traces in Rapeseed (
Article in Frontiers in plant science, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed, 78 citations in OpenAlex.
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- Exploration of the molecular mechanism behind a novel natural genic male-sterile mutation of 1205A in Brassica napus.BMC plant biology · 2025Article
- Genome-wide association studies of root system architecture traits in a broad collection ofFrontiers in plant science · 2024Article
- Genetic Analysis of Potato Breeding Collection Using Single-Nucleotide Polymorphism (SNP) Markers.Plants (Basel, Switzerland) · 2023Article
- Genetic diversity, population structure, and genome-wide association study for the flowering trait in a diverse panel of 428 moth bean (Vigna aconitifolia) accessions using genotyping by sequencing.BMC plant biology · 2023Article
- Genome-wide association mapping for yield-related traits in soybean (Glycine max) under well-watered and drought-stressed conditions.Frontiers in plant science · 2023Article
- Association mapping reveals novel genes and genomic regions controlling grain size architecture in mini core accessions of Indian National Genebank wheat germplasm collection.Frontiers in plant science · 2023Article
- Genome-Wide Association Studies of Salt Tolerance at the Seed Germination Stage and Yield-Related Traits inInternational journal of molecular sciences · 2022Article
- Genetic loci associated with freezing tolerance in a European rapeseed (Plant direct · 2022Article
- Integration of GWAS and transcriptome analyses to identify SNPs and candidate genes for aluminum tolerance in rapeseed (Brassica napus L.).BMC plant biology · 2022Article
- Whole genome re-sequencing reveals the genetic diversity and evolutionary patterns of Eucommia ulmoides.Molecular genetics and genomics : MGG · 2022Article
- Combined GWAS and Transcriptome Analyses Provide New Insights Into the Response Mechanisms of Sunflower Against Drought Stress.Frontiers in plant science · 2022Article
- Linkage disequilibrium and population structure in a core collection of Brassica napus (L.).PloS one · 2022Article
- Advances and Challenges for QTL Analysis and GWAS in the Plant-Breeding of High-Yielding: A Focus on Rapeseed.Biomolecules · 2021Review
- Genome-wide association study and transcriptome of olecranon-type traits in peach (Prunus persica L.) germplasm.BMC genomics · 2021Article
- Integrating a genome-wide association study with transcriptomic data to predict candidate genes and favourable haplotypes influencing Brassica napus seed phytate.DNA research : an international journal for rapid publication of reports on genes and genomes · 2021Article
- Molecular genetic diversity and population structure analyses of rutabaga accessions from Nordic countries as revealed by single nucleotide polymorphism markers.BMC genomics · 2021Article
- Genetic diversity and evolutionary patterns ofEcology and evolution · 2021Article
- SNP detection and population structure evaluation ofPhysiology and molecular biology of plants : an international journal of functional plant biology · 2021Article
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8 authors at 3 institutions in 2 countries.
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Abstract
Single Nucleotide Polymorphisms (SNPs) are the most abundant and richest form of genomic polymorphism, and hence make highly favorable markers for genetic map construction and genome-wide association studies. In this study, a total of 300 rapeseed accessions (278 representative of Chinese germplasm, plus 22 outgroup accessions of different origins and ecotypes) were collected and sequenced using Specific-Locus Amplified Fragment Sequencing (SLAF-seq) technology, obtaining 660.25M reads with an average sequencing depth of 6.27 × and a mean Q30 of 85.96%. Based on the 238,711 polymorphic SLAF tags a total of 1,197,282 SNPs were discovered, and a subset of 201,817 SNPs with minor allele frequency >0.05 and integrity >0.8 were selected. Of these, 30,877 were designated SNP "hotspots," and 41 SNP-rich genomic regions could be delineated, with 100 genes associated with plant resistance, vernalization response, and signal transduction detected in these regions. Subsequent analysis of genetic diversity, linkage disequilibrium (LD), and population structure in the 300 accessions was carried out based on the 201,817 SNPs. Nine subpopulations were observed based on the population structure analysis. Hierarchical clustering and principal component analysis divided the 300 varieties roughly in accordance with their ecotype origins. However, spring-type varieties were intermingled with semi-winter type varieties, indicating frequent hybridization between spring and semi-winter ecotypes in China. In addition, LD decay across the whole genome averaged 299 kb when
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