ArticleRice (New York, N.Y.)2020
Characterization of Haplotype Diversity in the BADH2 Aroma Gene and Development of a KASP SNP Assay for Predicting Aroma in U.S. Rice.
Article in Rice (New York, N.Y.), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 1 of them a synthesis that pooled it.
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16 citing papers in PubMed, 1 synthesis or guideline pooled it, 33 citations in OpenAlex.
- Meta-QTL s and haplotypes for efficient zinc biofortification of rice.The plant genome · 2023Pooled it
- Analysis of volatile organic compounds in ten types of tribute Rice based on headspace-gas chromatography-ion mobility spectrometry technology.Food chemistry: X · 2025Article
- Thousands of trait-specific KASP markers designed for diverse breeding applications in rice (Oryza sativa).G3 (Bethesda, Md.) · 2025Article
- Development and Validation of Kompetitive Allele-Specific Polymerase Chain Reaction Markers for Seed Protein Content in Soybean.Plants (Basel, Switzerland) · 2024Article
- KASP: a high-throughput genotyping system and its applications in major crop plants for biotic and abiotic stress tolerance.Molecular biology reports · 2024Review
- Investigation of Imidazolinone Herbicide Resistance Gene with KASP Markers forPlants (Basel, Switzerland) · 2024Article
- Development of KASP markers, SNP fingerprinting and population genetic analysis ofFrontiers in plant science · 2024Article
- A non-synonymous SNP in homolog ofGenetic resources and crop evolution · 2023Article
- Multi-omics analysis reveals the genetic basis of rice fragrance mediated by betaine aldehyde dehydrogenase 2.Journal of advanced research · 2022Article
- Selection and Validation of 48 KASP Markers for Variety Identification and Breeding Guidance in Conventional and Hybrid Rice (Oryza sativa L.).Rice (New York, N.Y.) · 2022Article
- Development and validation of an optimized marker set for genomic selection in southern U.S. rice breeding programs.The plant genome · 2022Article
- Post-genomics revolution in the design of premium quality rice in a high-yielding background to meet consumer demands in the 21st century.Plant communications · 2022Review
- Applications of Genomic Tools in Plant Breeding: Crop Biofortification.International journal of molecular sciences · 2022Review
- A SNP of betaine aldehyde dehydrogenase (BADH) enhances an aroma (2-acetyl-1-pyrroline) in sponge gourd (Luffa cylindrica) and ridge gourd (Luffa acutangula).Scientific reports · 2022Article
- Discovery and Validation of Grain Shape Loci in U.S. Rice Germplasm Through Haplotype Characterization.Frontiers in genetics · 2022Article
- Aroma, Quality, and Consumer Mindsets for Shelf-Stable Rice Thermally Processed by Reciprocal Agitation.Foods (Basel, Switzerland) · 2020Article
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundAroma is an important grain quality trait in rice, controlled by mutations within the BADH2 gene. The trait is simply inherited, and its importance in variety development makes it a practical target for marker-assisted selection in applied breeding programs. The predominant functional mutation within BADH2, an 8-bp indel, can be reliably detected using a PCR-based assay, but the available assays and associated genotyping platforms are insufficient for large-scale applied molecular breeding applications and are not compatible with outsourcing genotyping services.
resultsWe first characterized SNP diversity across the BADH2 gene in a collection of 2932 rice varieties to determine the number of gene haplotypes in O. sativa. Using 297 gene-based SNPs, 11 haplotype groups were detected, and subsequently identified a minimal set of nine informative SNPs that uniquely identified the BADH2 haplotypes. These nine SNPs were developed into KASP assays and used to examine a panel of 369 U.S. rice accessions. The panel represented modern breeding germplasm and included all known aroma pedigree sources in U.S. rice. Six haplotypes were detected within the U.S. panel, of which two were found in majority (85%) of varieties. A representative set of 39 varieties from all haplotype groups was evaluated phenotypically to distinguish aromatic from non-aromatic lines.
conclusionOne haplotype (Hap 6) was found to be perfectly associated with the aromatic phenotype. A single KASP SNP unique to Hap 6 was demonstrated to reliably differentiate aromatic from non-aromatic rice varieties across U.S. germplasm.
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