ArticlePloS one2017
Single Marker and Haplotype-Based Association Analysis of Semolina and Pasta Colour in Elite Durum Wheat Breeding Lines Using a High-Density Consensus Map.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
- Mining rare haplotypes to accelerate precision breeding in rice.The plant genome · 2026Article
- Future of durum wheat research and breeding: Insights from early career researchers.The plant genome · 2025Review
- Genome-Wide Association Integrating a Transcriptomic Meta-Analysis Suggests That Genes Related to Fat Deposition and Muscle Development Are Closely Associated with Growth in Huaxi Cattle.Veterinary sciences · 2025Article
- Review
- Integrated Assays of Genome-Wide Association Study, Multi-Omics Co-Localization, and Machine Learning Associated Calcium Signaling Genes with Oilseed Rape Resistance toInternational journal of molecular sciences · 2024Article
- Genomic wide association study and selective sweep analysis identify genes associated with improved yield under drought in Turkish winter wheat germplasm.Scientific reports · 2024Article
- Identification of superior and rare haplotypes to optimize branch number in soybean.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Association of mannose binding lectin with chronic obstructive pulmonary disease susceptibility and its clinical outcomes.Molecular biology reports · 2023Article
- Towards carotenoid biofortification in wheat: identification of XAT-7A1, a multicopy tandem gene responsible for carotenoid esterification in durum wheat.BMC plant biology · 2023Article
- Genome-wide survey identified superior and rare haplotypes for plant height in the north-eastern soybean germplasm of China.Molecular breeding : new strategies in plant improvement · 2023Article
- Genome-wide association study of agronomical and root-related traits in spring barley collection grown under field conditions.Frontiers in plant science · 2023Article
- Multi-model genome-wide association studies for appearance quality in rice.Frontiers in plant science · 2023Article
- Multi-locus genome-wide association studies reveal the genetic architecture ofFrontiers in plant science · 2023Article
- Breeding effects on durum wheat traits detected using GWAS and haplotype block analysis.Frontiers in plant science · 2023Article
- Haplotype mining panel for genetic dissection and breeding in Eucalyptus.The Plant journal : for cell and molecular biology · 2023Article
- Genome-wide association mapping for component traits of drought tolerance in dry beans (Phaseolus vulgaris L.).PloS one · 2023Article
- Population structure, allelic variation at Rht-B1 and Ppd-A1 loci and its effects on agronomic traits in Argentinian durum wheat.Scientific reports · 2022Article
- Allele expression biases in mixed-ploid sugarcane accessions.Scientific reports · 2022Article
- Meta-analysis reveals consensus genomic regions associated with multiple disease resistance in wheat (Molecular breeding : new strategies in plant improvement · 2022Article
- An LTR retrotransposon in the promoter of aHorticulture research · 2022Article
Corrections and comments
- Erratum issued
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Association mapping is usually performed by testing the correlation between a single marker and phenotypes. However, because patterns of variation within genomes are inherited as blocks, clustering markers into haplotypes for genome-wide scans could be a worthwhile approach to improve statistical power to detect associations. The availability of high-density molecular data allows the possibility to assess the potential of both approaches to identify marker-trait associations in durum wheat. In the present study, we used single marker- and haplotype-based approaches to identify loci associated with semolina and pasta colour in durum wheat, the main objective being to evaluate the potential benefits of haplotype-based analysis for identifying quantitative trait loci. One hundred sixty-nine durum lines were genotyped using the Illumina 90K Infinium iSelect assay, and 12,234 polymorphic single nucleotide polymorphism (SNP) markers were generated and used to assess the population structure and the linkage disequilibrium (LD) patterns. A total of 8,581 SNPs previously localized to a high-density consensus map were clustered into 406 haplotype blocks based on the average LD distance of 5.3 cM. Combining multiple SNPs into haplotype blocks increased the average polymorphism information content (PIC) from 0.27 per SNP to 0.50 per haplotype. The haplotype-based analysis identified 12 loci associated with grain pigment colour traits, including the five loci identified by the single marker-based analysis. Furthermore, the haplotype-based analysis resulted in an increase of the phenotypic variance explained (50.4% on average) and the allelic effect (33.7% on average) when compared to single marker analysis. The presence of multiple allelic combinations within each haplotype locus offers potential for screening the most favorable haplotype series and may facilitate marker-assisted selection of grain pigment colour in durum wheat. These results suggest a benefit of haplotype-based analysis over single marker analysis to detect loci associated with colour traits in durum wheat.
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