Multi-omics analysis reveals the genetic basis of rice fragrance mediated by betaine aldehyde dehydrogenase 2

Chromosome-Level Genome Assembly of a Fragrant Japonica Rice Cultivar ‘Changxianggeng 1813’ Provides Insights into Genomic Variations between Fragrant and Non-Fragrant Japonica Rice

“…The badh2-E2 allele carried by ‘Changxianggeng 1813’ was consistent with that in a number of Chinese fragrant japonica rice cultivars, e.g., ‘Wuxiang 9915’, ‘Xiangjing 111’, ‘Zhenxiangjing 5’, suggesting that this allele is common by descent in Chinese fragrant rice cultivars [ 8 , 13 ]. Phylogenetic analysis of BADH2 haplotype data ( Figure S1b ) further showed that the badh2-E2 allele in ‘Changxianggeng 1813’ clustered together with a previously identified haplotype sequence endemic to two cultivated japonica rice (see [ 2 ] for full details). Taken together, these findings provided additional support for the previous studies indicating that badh2-E2 may arise and become fixed in the japonica gene pool [ 7 , 8 , 13 ].…”

“…The BADH2 gene sequence for ‘Changxianggeng 1813’ was extracted from its genome sequence according to annotation files and then compared to that of the non-fragrant cultivar Nipponbare using the MAFFT multiple sequence alignment program [ 75 ], to verify the presence/absence of the mutations associated with fragrance in ‘Changxianggeng 1813’. The BADH2 protein-coding sequence for ‘Changxianggeng 1813’, was further combined with previously published 38 haplotypes in the BADH2 coding region for phylogenetic analysis [ 2 ]. All 39 BADH2 coding sequences were aligned using ClustalW [ 76 ], and the resulting alignment was used for Neighbor-Joining (NJ) phylogenetic tree construction using MEGA v.11.0.11 [ 77 ], with 1000 bootstrap replicates.…”

“…Fragrant rice ( Oryza sativa L.), well-known for its pleasant and subtle aroma, is widely preferred among rice consumers and fetches a higher price than non-fragrant rice in both domestic and international markets [ 1 , 2 ]. At present, Basmati rice from India and Pakistan and Jasmine rice from Thailand are the two most popular fragrant rice cultivars in the world [ 3 , 4 ].…”

“…Hundreds of volatile compounds have been detected in fragrant rice, but the key compound responsible for the characteristic fragrance is 2-acetyl-1-pyrroline (2AP) [ 2 , 7 ]. Investigations into the genetic basis of rice fragrance have demonstrated that the fragrance phenotype is largely controlled by a recessive betaine aldehyde dehydrogenase 2 ( BADH2 ) gene, which comprises 15 exons and 14 introns with approximately 7 kilobase pairs in length [ 7 , 8 ].…”

Development of an inclusive 580K SNP array and its application for genomic selection and genome-wide association studies in rice

“…We utilized different databases for designing the Axiom rice genotyping chip:1) Resequencing data of Korean World Rice Collection (KRICE) of 475 accessions composed of 417 cultivated and 58 wild accessions ( Phitaktansakul et al., 2021 ), 2) Rice genome project data of 3,000 accessions (3 K-RGP) from the International Rice Research Institute (IRRI) ( ), 3) High-Density Rice Array (HDRA, 700K) array reported from Cornell university ( McCouch et al., 2016 ), 4) Affymetrix 44 K Rice Chip (Affy44K) ( Zhao et al., 2011 ), 5) QTARO database ( ) ( Yonemaru et al., 2010 ), 6) Plant Reactome Gramene Pathways database ( ) 7) Chloroplast ( Tong et al., 2016 ; Cheng et al., 2019 ) and mitochondria ( Tong et al., 2017 ) genomic sequences of japonica and rufipogon and 8) GMO, we used transgenic plants and genomes of various microorganisms as references for GMO marker design. The known GMO events consisted of host and insert regions; we utilized NCBI Primer-BLAST tool to get the full-length products and modified them into Axiom probes for 155 events.…”