基于高密度SNP标记的贵州香稻资源遗传多样性分析及其Badh2等位变异分析

doi:10.3864/j.issn.0578-1752.2026.12.001

中国农业科学 ›› 2026, Vol. 59 ›› Issue (12): 2537-2550.doi: 10.3864/j.issn.0578-1752.2026.12.001

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

基于高密度SNP标记的贵州香稻资源遗传多样性分析及其Badh2等位变异分析

官亚东¹^,²(), 龙武华², 吴娴², 王倩², 刘雪薇², 王学良⁵, 王忠妮², 宫彦龙², 姚元勋⁴, 朱速松³()

¹ 贵州师范大学生命科学学院，贵阳 550001
² 贵州省水稻研究所，贵阳 550006
³ 贵州省农作物品种资源研究所，贵阳 550006
⁴ 贵州兆丰种业有限公司，贵州黔东南 556000
⁵ 黔东南苗族侗族自治州农业科学院水稻研究所，贵州黔东南 556000

收稿日期:2026-03-23 接受日期:2026-05-01 出版日期:2026-06-16 发布日期:2026-06-16
通信作者:
朱速松，E-mail：susongzhu@139.com
联系方式: 官亚东，E-mail：758638996@qq.com。
基金资助:
贵州省后补助计划(黔科合平台人才[2018]5263号); 贵州省后补助计划(黔农科院种质资源[2023]11号); 贵州省科技计划(黔科合支撑[2022]重点028); 贵州省育种科研基础平台创新能力建设(黔科合服企[2022]014)

Analysis of Genetic Diversity and Allelic Variation of the Badh2 Gene in Guizhou Aromatic Rice Germplasm Based on High-Density SNP Markers

GUAN YaDong¹^,²(), LONG WuHua², WU Xian², WANG Qian², LIU XueWei², WANG XueLiang⁵, WANG ZhongNi², GONG YanLong², YAO YuanXun⁴, ZHU SuSong³()

¹ School of Life Sciences, Guizhou Normal University, Guiyang 550001
² Guizhou Rice Research Institute, Guiyang 550006
³ Guizhou Crop Germplasm Resources Research Institute, Guiyang 550006
⁴ Guizhou Zhaofeng Seed Industry Co., Ltd., Qiandongnan 556000, Guizhou
⁵ Rice Research Institute, Qiandongnan Miao and Dong Autonomous Prefecture Academy of Agricultural Sciences, Qiandongnan 556000, Guizhou

Received:2026-03-23 Accepted:2026-05-01 Published:2026-06-16 Online:2026-06-16

摘要/Abstract

摘要：

【目的】分析贵州香稻（包含贵州香禾、贵州香稻育种材料、除贵州香禾外的贵州地方香稻）种质资源的遗传多样性，评估其遗传背景的差异性，并分析其Badh2等位变异类型，为改善香稻育种遗传基础狭窄的问题提供理论基础和材料支撑。【方法】供试材料共131份，其中有87份贵州香稻，此外还收集广东、福建、江苏等省份香稻材料共40份，泰国香稻3份，印度香稻1份。利用50K液相基因芯片对131份香稻材料进行全基因组扫描并经过滤获得高质量SNP位点。基于最小等位基因频率、多态性信息含量、有效等位基因数等遗传参数进行遗传多样性评估，结合群体结构与聚类分析探究不同香稻群体遗传背景差异性；利用香味基因Badh2的全长引物对87份贵州香稻材料进行基因分型，明确等位变异类型。【结果】全基因组扫描131份香稻资源并经严格过滤后共获得39 580个高质量SNP位点，最小等位基因频率为0.05—0.50，多态性信息含量为0.091—0.634，有效等位基因数为2.000—10.526，Nei’s遗传多样性指数为0.095—0.500，Shannon指数为0.199—0.693，表明香稻群体整体位点遗传多样性较高。且131份香稻材料可划分为4个遗传亚群，亚群间基因交流匮乏、遗传分化显著，大部分贵州香禾材料集中归属于2个遗传亚群，且有13份材料未表现出明确群体归属。比较有趣的是，与其他省份及国外香稻群体相比，贵州香禾群体呈现出独特的遗传构成。等位变异分析结果表明，有4份香稻材料的香味性状调控机制不依赖Badh2，可能为新型香稻种质资源；1份香稻材料为Badh2第六外显子39 bp处单碱基G的插入；82份香稻属于badh2-E7突变类型。【结论】贵州香稻群体的位点遗传多样性较高，且贵州香禾具有独特的遗传结构；badh2-E7是贵州香稻的主导等位变异，且发现了新型Badh2第六外显子突变的材料和非Badh2依赖型的突变材料。

关键词: 贵州香禾, 遗传多样性, 群体结构, 遗传多样性, 50K液相基因芯片, Badh2

Abstract:

【Objective】The genetic diversity of fragrant rice germplasm resources in Guizhou (including Guizhou scented glutinous rice, breeding materials of Guizhou scented rice and Guizhou local scented rice excluding Guizhou scented glutinous rice) was analyzed, the differences in their genetic background were evaluated, and the allelic variation of the Badh2 gene was identified. This study provides theoretical basis and material support for addressing the problem of narrow genetic basis in fragrant rice breeding. 【Method】A total of 131 test materials were collected in this study, including 87 Guizhou fragrant rice accessions. In addition, 40 fragrant rice materials were obtained from Guangdong, Fujian, Jiangsu and other provinces, together with 3 Thai fragrant rice accessions and 1 Indian fragrant rice accession. A 50K liquid-phase gene chip was used for genome-wide scanning of the 131 fragrant rice materials, and high-quality SNP loci were acquired after data filtering. Genetic diversity was evaluated based on genetic parameters including minor allele frequency, polymorphism information content and effective number of alleles. Combined with population structure analysis and cluster analysis, the genetic background differences among different fragrant rice populations were explored. Gene typing was performed on 87 Guizhou fragrant rice accessions using full-length primers of the fragrance gene Badh2 to clarify allelic variation types.【Result】Genome-wide scanning was performed on 131 aromatic rice accessions. After stringent quality filtering, a total of 39 580 high-quality SNP loci were obtained. The minor allele frequency (MAF) ranged from 0.05 to 0.50, the polymorphism information content (PIC) varied between 0.091 and 0.634, and the number of effective alleles ranged from 2.000 to 10.526. The Nei’s genetic diversity index and Shannon’s information index ranged from 0.095 to 0.500 and 0.199 to 0.693, respectively, indicating a relatively high level of overall genetic diversity at the loci in the aromatic rice population. Population structure analysis revealed that the 131 aromatic rice accessions could be divided into four genetic subgroups, with limited gene flow and significant genetic differentiation among subgroups. Most Guizhou aromatic He rice accessions were clustered into two genetic subgroups, while 13 accessions showed no clear population assignment. Notably, the Guizhou aromatic He rice population exhibited a unique genetic structure compared with aromatic rice populations from other provinces and abroad. Allelic variation analysis showed that the aroma formation of 4 accessions was independent of the Badh2 gene, potentially representing novel aromatic rice germplasm. 1 accession carried a single-base G insertion at the 39 bp position of the sixth exon of Badh2, and 82 aromatic rice accessions belonged to the badh2-E7 mutation type.【Conclusion】The genetic parameter results revealed high locus genetic diversity in the Guizhou fragrant rice population. Based on allelic variation analysis, badh2-E7 was identified as the dominant allelic variant in Guizhou fragrant rice, and novel materials with a new mutation in the sixth exon of Badh2 as well as new Badh2-independent mutant materials were also found.

Key words: Guizhou fragrant rice resources, genetic diversity, group structure, genetic diversity, 50K liquid gene chip, Badh2

官亚东, 龙武华, 吴娴, 王倩, 刘雪薇, 王学良, 王忠妮, 宫彦龙, 姚元勋, 朱速松. 基于高密度SNP标记的贵州香稻资源遗传多样性分析及其Badh2等位变异分析[J]. 中国农业科学, 2026, 59(12): 2537-2550.

GUAN YaDong, LONG WuHua, WU Xian, WANG Qian, LIU XueWei, WANG XueLiang, WANG ZhongNi, GONG YanLong, YAO YuanXun, ZHU SuSong. Analysis of Genetic Diversity and Allelic Variation of the Badh2 Gene in Guizhou Aromatic Rice Germplasm Based on High-Density SNP Markers[J]. Scientia Agricultura Sinica, 2026, 59(12): 2537-2550.

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引物名称Primer name	引物序列Primer sequence (5′-3′)	退火温度Annealing temperature (℃)	PCR产物PCR product (bp)
Badh2P2	F: CCGAAGTCCGTACCAACTGC R: CAATCAGCCATGCTTCCAAC	56.8	972
Badh2P3	F: GTGCGTATCCTCTGTTCTGG R: CAAGCGTCTCTAGTCTAGCC	58.9	855
Badh2P4	F: CTGAGCTGGCTAGACTAGAG R: CCATCAGGAGAGGATAGTTTC	59.6	1025
Badh2P5	F: CCTCCGTGTTAATGCAGCTC R: CATAGCAAGTGGCATGTACC	61.6	1026
Badh2P6	F: GGTTGGTCTTCCTTCAGGTTG R: GTTCCTTCCTAACTGCCTTCC	56.4	926
Badh2P7	F: CCAGACGAGCAGGATGCAAG R: CATGGTCAGGAGCAAGAAGC	53.1	984
Badh2P8	F: GTGGCAAGGAAGGCAGTTAG R: GCAAATAAGGCTTGGAAGGAC	54.1	912
Badh2P9	F: TTTCAGTTCTCTTGCTCCTGA R: CAGTTAATCTCTGGCATCGC	57.5	1023
Badh2P10	F: GGCCAACGATACTCAGTTGAG R: CCGGTCATCAGCTAACCTTCC	57.5	1083

染色体 Chromosome	SNP数量 Number of SNPs	所占比例 Proportion (%)
Chr.01	5336	13.5
Chr.02	4821	12.2
Chr.03	4321	10.9
Chr.04	3166	8.0
Chr.05	2719	6.9
Chr.06	3764	9.5
Chr.07	3276	8.3
Chr.08	2748	6.9
Chr.09	2384	6.0
Chr.10	2533	6.4
Chr.11	2430	6.1
Chr.12	2082	5.3

参数 Parameter	最小等位基因频率 MAF	多态性信息含量 PIC	观测杂合度 Observed heterozygosity	期望杂合度 Expected heterozygosity	有效等位基因数 Effective number of alleles	Shannon信息指数 Shannon’s diversity index	Nei′s遗传多样性指数 Nei’s genetic diversity index
最大值Maximum	0.500	0.634	0.797	0.500	10.526	0.693	0.500
最小值Minimum	0.050	0.091	0.000	0.095	2.000	0.199	0.095
平均值Average	0.300	0.310	0.007	0.389	3.118	0.570	0.389

基于高密度SNP标记的贵州香稻资源遗传多样性分析及其Badh2等位变异分析

Analysis of Genetic Diversity and Allelic Variation of the Badh2 Gene in Guizhou Aromatic Rice Germplasm Based on High-Density SNP Markers

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