Novel Deletion in Exon 7 of Betaine Aldehyde Dehydrogenase 2 (BADH2)
The fragrance of rice is one of the premium characteristics that breeders want to include in rice varieties due to the higher market value. Nucleotide deletions in exons 2 (7 bp) and 7 (8 bp) of Betaine Aldehyde Dehydrogenase 2 (BADH2) are associated with fragrance in rice. In this study, a new 13 b...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2023-03-01
|
| Series: | Rice Science |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1672630823000057 |
| _version_ | 1828046751307661312 |
|---|---|
| author | Van Quoc Giang Huynh Ky Nguyen Chau Thanh Tung Nguyen Loc Hien Nguyen van Manh Nguyen Nhut Thanh Vo Cong Thanh Swee Keong Yeap |
| author_facet | Van Quoc Giang Huynh Ky Nguyen Chau Thanh Tung Nguyen Loc Hien Nguyen van Manh Nguyen Nhut Thanh Vo Cong Thanh Swee Keong Yeap |
| author_sort | Van Quoc Giang |
| collection | DOAJ |
| description | The fragrance of rice is one of the premium characteristics that breeders want to include in rice varieties due to the higher market value. Nucleotide deletions in exons 2 (7 bp) and 7 (8 bp) of Betaine Aldehyde Dehydrogenase 2 (BADH2) are associated with fragrance in rice. In this study, a new 13 bp deletion in exon 7 of the BADH2 gene was discovered in the Nang Thom Cho Dao (NTCD) variety, and the mutation has been closely related to the genetic background of indica subspecies through the Bayesian phylogenetic approach and haplotype network analysis of the 3 000 Rice Genomes Project. In addition, a set of functional markers (EX07-13F, EX07-13RN, and EX07-13RM) identified the 13 bp deletion only within NTCD (no amplified band) compared with both non-aromatic and other aromatic rice varieties (110 bp band). The deletion of 13 bases instead of 8 bases in exon 7 of BADH2 caused a premature stop codon, which down-regulated the expression of the BADH2 transcript while associated with up-regulation of OsP5CS and the high amount of 2-acetyl-1-pyrroline. It is potential to use the deletion in exon 7 of the BADH2 gene as a novel marker for adulteration and breeding of fragrant rice varieties, particularly for NTCD. |
| first_indexed | 2024-04-10T18:30:21Z |
| format | Article |
| id | doaj.art-de43ec919858436b84d90a0d9460c5eb |
| institution | Directory Open Access Journal |
| issn | 1672-6308 |
| language | English |
| last_indexed | 2024-04-10T18:30:21Z |
| publishDate | 2023-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Rice Science |
| spelling | doaj.art-de43ec919858436b84d90a0d9460c5eb2023-02-02T04:47:36ZengElsevierRice Science1672-63082023-03-01302104112Novel Deletion in Exon 7 of Betaine Aldehyde Dehydrogenase 2 (BADH2)Van Quoc Giang0Huynh Ky1Nguyen Chau Thanh Tung2Nguyen Loc Hien3Nguyen van Manh4Nguyen Nhut Thanh5Vo Cong Thanh6Swee Keong Yeap7College of Agriculture, Can Tho University, Can Tho 92000, VietnamCollege of Agriculture, Can Tho University, Can Tho 92000, Vietnam; Corresponding authors: ()College of Agriculture, Can Tho University, Can Tho 92000, VietnamCollege of Agriculture, Can Tho University, Can Tho 92000, VietnamCollege of Agriculture, Can Tho University, Can Tho 92000, VietnamDepartment of Sciences and Technology of Long An Province, Long An 850000, VietnamCollege of Agriculture, Can Tho University, Can Tho 92000, VietnamChina-Association of Southeast Asian Nations College of Marine Sciences, Xiamen University Malaysia, Sepang 49000, Selangor, Malaysia; Corresponding authors: ()The fragrance of rice is one of the premium characteristics that breeders want to include in rice varieties due to the higher market value. Nucleotide deletions in exons 2 (7 bp) and 7 (8 bp) of Betaine Aldehyde Dehydrogenase 2 (BADH2) are associated with fragrance in rice. In this study, a new 13 bp deletion in exon 7 of the BADH2 gene was discovered in the Nang Thom Cho Dao (NTCD) variety, and the mutation has been closely related to the genetic background of indica subspecies through the Bayesian phylogenetic approach and haplotype network analysis of the 3 000 Rice Genomes Project. In addition, a set of functional markers (EX07-13F, EX07-13RN, and EX07-13RM) identified the 13 bp deletion only within NTCD (no amplified band) compared with both non-aromatic and other aromatic rice varieties (110 bp band). The deletion of 13 bases instead of 8 bases in exon 7 of BADH2 caused a premature stop codon, which down-regulated the expression of the BADH2 transcript while associated with up-regulation of OsP5CS and the high amount of 2-acetyl-1-pyrroline. It is potential to use the deletion in exon 7 of the BADH2 gene as a novel marker for adulteration and breeding of fragrant rice varieties, particularly for NTCD.http://www.sciencedirect.com/science/article/pii/S1672630823000057novel deletionBADH2fragrant ricefunctional marker |
| spellingShingle | Van Quoc Giang Huynh Ky Nguyen Chau Thanh Tung Nguyen Loc Hien Nguyen van Manh Nguyen Nhut Thanh Vo Cong Thanh Swee Keong Yeap Novel Deletion in Exon 7 of Betaine Aldehyde Dehydrogenase 2 (BADH2) Rice Science novel deletion BADH2 fragrant rice functional marker |
| title | Novel Deletion in Exon 7 of Betaine Aldehyde Dehydrogenase 2 (BADH2) |
| title_full | Novel Deletion in Exon 7 of Betaine Aldehyde Dehydrogenase 2 (BADH2) |
| title_fullStr | Novel Deletion in Exon 7 of Betaine Aldehyde Dehydrogenase 2 (BADH2) |
| title_full_unstemmed | Novel Deletion in Exon 7 of Betaine Aldehyde Dehydrogenase 2 (BADH2) |
| title_short | Novel Deletion in Exon 7 of Betaine Aldehyde Dehydrogenase 2 (BADH2) |
| title_sort | novel deletion in exon 7 of betaine aldehyde dehydrogenase 2 badh2 |
| topic | novel deletion BADH2 fragrant rice functional marker |
| url | http://www.sciencedirect.com/science/article/pii/S1672630823000057 |
| work_keys_str_mv | AT vanquocgiang noveldeletioninexon7ofbetainealdehydedehydrogenase2badh2 AT huynhky noveldeletioninexon7ofbetainealdehydedehydrogenase2badh2 AT nguyenchauthanhtung noveldeletioninexon7ofbetainealdehydedehydrogenase2badh2 AT nguyenlochien noveldeletioninexon7ofbetainealdehydedehydrogenase2badh2 AT nguyenvanmanh noveldeletioninexon7ofbetainealdehydedehydrogenase2badh2 AT nguyennhutthanh noveldeletioninexon7ofbetainealdehydedehydrogenase2badh2 AT vocongthanh noveldeletioninexon7ofbetainealdehydedehydrogenase2badh2 AT sweekeongyeap noveldeletioninexon7ofbetainealdehydedehydrogenase2badh2 |