Background: Fragrance is one of the most important quality traits in rice, and the phenotype is attributed to the loss-of-function betaine aldehyde dehydrogenase ( BADH2 ) gene. At least 12 allelic variations of BADH2 have been identified, and some of these have been applied to rice fragrance breeding using traditional molecular markers and Sanger sequencing techniques. However, these traditional methods have several limitations, such as being very expensive, imprecise, inefficient, and having security issues. Thus, a new molecular marker technology must be developed to improve rice fragrance breeding. Results: In this study, more than 95% of the cultivated fragrant rice varieties belonged to a 7-bp deletion in exon 2 ( badh2-E2 ) or an 8-bp deletion and 3-bp variation in exon 7 ( badh2-E7 ). Both allelic variations resulted in the loss of function of the badh2 gene. We developed two novel SNP molecular markers, SNP_badh2-E2 and SNP_badh2-E7, related to the alleles. Their genotype and phenotype were highly cosegregated in the natural variation of rice accessions, with 160 of the 164 fragrant rice varieties detected with the two markers. These markers cosegregated with the fragrance phenotype in the F2 population. Conclusions: Two functional SNP molecular markers of badh2-E2 and badh2-E7 allelic variations were developed. These functional SNP molecular markers can be used for genotype and genetic improvement of rice fragrance through marker-assisted selection and will significantly improve the efficiency of fragrant rice breeding and promote commercial molecular breeding of rice in the future. Normal 0 false false false EN-US X-NONE X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Tabla normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin-top:0cm; mso-para-margin-right:0cm; mso-para-margin-bottom:8.0pt; mso-para-margin-left:0cm; line-height:107%; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri",sans-serif; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;}

中文翻译：

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水稻 BADH2 两种新型功能分子标记的开发与应用

背景：香味​​是水稻最重要的品质性状之一，其表型归因于功能丧失的甜菜碱醛脱氢酶（BADH2）基因。至少有 12 个 BADH2 等位基因变异已被鉴定，其中一些已使用传统分子标记和 Sanger 测序技术应用于水稻香味育种。然而，这些传统方法有一些局限性，例如非常昂贵、不精确、效率低下以及存在安全问题。因此，必须开发一种新的分子标记技术来改善水稻香味育种。结果：本研究中，95%以上的栽培香稻品种属于外显子2（ badh2-E2 ）7 bp缺失或外显子7（ badh2-E7 ）8 bp缺失和3 bp变异. 两种等位基因变异都导致 badh2 基因的功能丧失。我们开发了两个与等位基因相关的新型 SNP 分子标记，SNP_badh2-E2 和 SNP_badh2-E7。它们的基因型和表型在水稻种质的自然变异中高度共分离，164 个香稻品种中有 160 个用这两个标记检测到。这些标记与 F2 种群中的香味表型共分离。结论：开发了 badh2-E2 和 badh2-E7 等位基因变异的两个功能性 SNP 分子标记。这些功能性SNP分子标记可通过标记辅助选择用于水稻香味的基因型和遗传改良，将显着提高香米育种效率，促进未来水稻的商业化分子育种。正常 0 false false false EN-US X-NONE X-NONE /* 样式定义 */ table.MsoNormalTable {mso-style-name:"Tabla normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow：是；mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin-top:0cm; mso-para-margin-right:0cm; mso-para-margin-bottom:8.0pt; mso-para-margin-left:0cm; 行高：107%；mso-分页：寡妇孤儿；字体大小：11.0pt; font-family:"Calibri",sans-serif; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} mso-tstyle-colband-size:0; mso-style-noshow：是；mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin-top:0cm; mso-para-margin-right:0cm; mso-para-margin-bottom:8.0pt; mso-para-margin-left:0cm; 行高：107%；mso-分页：寡妇孤儿；字体大小：11.0pt; font-family:"Calibri",sans-serif; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} mso-tstyle-colband-size:0; mso-style-noshow：是；mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin-top:0cm; mso-para-margin-right:0cm; mso-para-margin-bottom:8.0pt; mso-para-margin-left:0cm; 行高：107%；mso-分页：寡妇孤儿；字体大小：11.0pt; font-family:"Calibri",sans-serif; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} 字体大小：11.0pt; font-family:"Calibri",sans-serif; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} 字体大小：11.0pt; font-family:"Calibri",sans-serif; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;}