Genetic and Geographic Profiling of Fragrance-Associated BADH2 Mutations in Rice from China, Laos, and Vietnam

Fragrant Rice Genetics Across East and Southeast Asia

Abstract

Fragrance in rice is a culturally and economically significant trait in Asia and around the world. This study aimed to develop a genetic and geographic profile of the fragrance-associated BADH2 mutations (badh2.1 and badh2.11) in 1,067 rice varieties from China, Laos, and Vietnam, which are part of the International Rice Genebank Collection. Seventy-three varieties were found to carry the common eight-base pair (bp) deletion in exon 7 of the genes (badh2.1, also known as badh2.7), primarily from indica varieties, with some belonging to japonica, javanica, and intermediate varieties. Conversely, 59 varieties possess the recently identified badh2 allele, badh2.11 (also known as badh2.4-5). Diversity analysis of a selected subset of these 1,067 varieties using 377 nucleotide polymorphisms revealed that most badh2.1 alleles clustered in Groups A.2, B.1.1, B2.1, B2.2a1, B2.2b1, and B2.2b, B2.2b3, whereas rice varieties carrying the badh2.11 allele clustered in Group B2.2a2. This study provides a genetic and geographic profile of the fragrance-associated badh2 alleles in rice from China, Laos, and Vietnam, offering additional evidence of the domestication, geographical isolation, and introgression or gene flow of fragrance alleles across different rice subgroups.