Scientia Agricultura Sinica ›› 2026, Vol. 59 ›› Issue (12): 2537-2550.doi: 10.3864/j.issn.0578-1752.2026.12.001

• CROP GENETICS & BREEDING· GERMPLASM RESOURCES· MOLECULAR GENETICS • Previous Articles     Next Articles

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. 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 Online:2026-06-16 Published:2026-06-16
  • Contact: ZHU SuSong

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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

Table 1

A list of nine primer pairs used for sequencing the complete badh2/Badh2 alleles"

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

Table 2

The number and proportion of SNP markers on chromosomes"

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

Fig. 1

Minor allele frequency (MAF) distribution of 131 fragrant rice materials"

Fig. 2

Polymorphism information content (PIC) distribution of 131 fragrant rice materials"

Table 3

Analysis of genetic diversity of 131 fragrant rice resources"

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

Fig. 3

Genetic distance distribution of 131 fragrant rice materials"

Fig. 4

Population structure analysis of 131 fragrant rice germplasm resources A: K value plot of 131 fragrant rice accessions; B: Population structure of 131 fragrant rice accessions (K=4-6). Colors denote different subpopulations, and color proportions show individual ancestral components"

Fig. 5

Genetic relatedness analysis of 131 fragrant rice accessions A: Phylogenetic tree. CK1: Nipponbare; CK2: 9311. The numbers in the figure are variety codes, which are consistent with Supplementary Table 1; B: PCA clustering scatter plot"

Fig. 6

Sequence alignment of the mutant seventh exon in partial fragrant rice materials"

Fig. 7

Mutation analysis and amino acid sequence alignment of Bidaxiang No.6"

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