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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.
Highlights
Aroma is an important grain quality trait in rice, controlled by mutations within the Betaine aldehyde dehydrogenase gene (BADH2) gene
The objectives of this research were to 1) characterize the haplotype diversity of the BADH2 gene across O. sativa, 2) determine which BADH2 haplotypes/alleles are present in U.S rice germplasm, and 3) develop and validate a Single nucleotide polymorphism (SNP)-based kompetitive allele specific polymerase chain reaction (KASP) assay (LGC Group, 2016) informative across U.S breeding germplasm and useful for high-throughput genotypic selection for fragrance in U.S breeding programs
Haplotype Variation in BADH2 in the 3 K Genomes Dataset Single nucleotide polymorphism variation across the BADH2 (LOC_Os08g32870) gene was obtained from the International Rice Informatics Consortium (IRIC) SNPSeek database, from the “3kAll” SNP dataset (Mansueto et al, 2017)
Summary
Aroma is an important grain quality trait in rice, controlled by mutations within the BADH2 gene. Aromatic varieties account for a significant portion of the export market and include widely recognized types, including Jasmine and Basmati rice. These two types account for the majority of. Rice (Oryza sativa) was domesticated roughly 10,000 years ago from predifferentiated gene pools of the wild grass species Oryza rufipogon (Kovach et al, 2007). These gene pools, Indica and Japonica, are hypothesized to have diverged between
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