Badh2 of rice is considered to be the major gene responsible for the fragrance in rice. The wild type badh2 allele encodes betaine aldehyde dehydrogenase 2 (BADH2) enzyme while the mutated version of badh2 gene encodes non-functional BADH2 enzyme that leads to the accumulation of 2-acetyl-1-pyrroline (2AP), the principal fragrant compound in rice. There are many mutated recessive alleles causing fragrance in global rice germplasm, although the badh2.1 allele present in Basmati type rice is the most well-known among breeders. In this study, we attempted to reveal potential fragrance causing mutations, and the respective varieties carrying them, through in silico analysis based on the sequences available in the Rice SNP-Seek-Database of International Rice Research Institute. The sequences of 1878 rice accessions from 22 countries were analysed to identify mutations in each exon of badh2 comparatively with the non-fragrant ‘wildtype’ GenBank sequence in Nanjing11, Oryza sativa indica (EU770319.1). Results revealed that 63 varieties from 12 countries possessed the most prevalent allele, badh2.1 having an 8 bp deletion and three single nucleotide polymorphisms in the 7th exon. The second most prevalent allele in genotypes from Asia was badh2.7 having a ‘G’ insertion in the 14th exon. A novel allele with a T deletion in 9th exon was detected in a Thai rice accession. Rice varieties containing either badh2.1 or badh2.7 alleles could be identified with DNA markers for badh2.1 (frg) and badh2.7 (Bad2.7CAPS). The marker, Bad2.7CAPS, co-segregated with the fragrance phenotype in two crosses, confirming the possibility of employing it in marker assisted breeding.

中文翻译：

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亚洲水稻（Oryza sativa L.）种质中香味基因（badh2）的计算机分析和等位基因特异性标记的验证

巴德2大米的香味被认为是造成大米香味的主要基因。野生型坏2等位基因编码甜菜碱醛脱氢酶 2 (BADH2)，而突变型坏2基因编码非功能性 BADH2 酶，该酶导致 2-乙酰基-1-吡咯啉 (2AP) 的积累，2AP 是水稻中主要的芳香化合物。全球水稻种质中有许多引起香味的隐性等位基因突变，尽管badh2.1等位基因存在于巴斯马蒂类型水稻是育种者中最知名的。在这项研究中，我们试图通过计算机基于国际水稻研究所水稻 SNP-Seek-Database 中可用的序列进行分析。对来自 22 个国家的 1878 份水稻种质的序列进行了分析，以确定每个外显子的突变。坏2与南京的非芳香“野生型”基因库序列相比，籼稻(EU770319.1)。结果显示，来自 12 个国家的 63 个品种拥有最普遍的等位基因，badh2.1在第 7 个外显子中具有 8 bp 缺失和三个单核苷酸多态性。亚洲基因型中第二常见的等位基因是badh2.7在第 14 个外显子中有一个“G”插入。在泰国水稻种质中检测到第 9 个外显子 T 缺失的新型等位基因。水稻品种含有badh2.1要么badh2.7等位基因可以用 DNA 标记鉴定badh2.1(框架） 和badh2.7(坏2.7CAPS）。标记，坏2.7CAPS，在两个杂交中与香味表型共同分离，证实了将其用于标记辅助育种的可能性。