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

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.

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.

Genome-wide scanning was performed on 131 aromatic rice accessions. After stringent quality filtering, a total of 39580 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.

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.