44. Microsatellite diversity for chromosome number 8 in Basmati rice

1) Department of Biotechnology and Molecular Biology, CCS Haryana Agricultural University, Hisar 125 004, India.
2) Department of Biochemistry, CCS Haryana Agricultural University, Hisar, 125 004, India.

Basmati rice commands premium price due to its superfine grain qualities, distinct aroma and extra-elongation during cooking. Basmati rice aroma is controlled by a single recessive gene (fgr) closely linked to RFLP clone RG28 on chromosome number 8 (Ahn et al. 1992). Ahn et al. (1993) also mapped the RFLP locus linked to kernel elongation to chromosome number 8. PCR-based markers, such as microsatellite DNA (Simple Sequence Repeats, SSRs) markers, have been successfully used for varietal identification in rice, but they have yet to be exploited for mapping genes/QTLs for important grain/cooking quality traits. The use of already-mapped SSR markers in rice breeding also provides insight as to which putative chromosomal segments have been introgressed from specific parental genomes and to determine if a particular segregant has the desired chromosomal regions/QTLs/alleles from each parent or not. In this paper, we report DNA analysis of some commercially important Basmati rice varieties using 15 SSR markers mapped on chromosome number 8 (Temnykh et al. 2000), including an SSR marker (SCU-rice-SSR1) developed for the RG28 locus (Figure 1, Garland et al., 2000). A total of twelve rice genotypes were evaluated, which included five traditional Basmati (Taraori HBC 19, Basmati 370, Dehradun Basmati Type III, Ambemohar 157, Ranbir Basmati), five cross-bred Basmati (Pusa Basmati 1, Kernel, Super, Basmati 385, Kasturi) developed from indica x Basmati crosses, an indica (IR 36) and a japonica (Azucena). DNA was isolated from 0.5 g leaf tissue collected from five plants of each variety using the modified CTAB method (Saghai-Maroof et al., 1984). SSR marker analysis was carried out using the silver-staining procedure as described by Chen et al. (1997).

A total of 47 alleles were detected using 15 SSR markers. The number of alleles per

locus ranged between 1 (RM325) and 5 (RM310 and RM210), with an average of 3.13 alleles per locus. The overall size of PCR products ranged from 98 to 312 bp. Basmati, indica and japonica rice varieties displayed substantial genetic diversity for chromosome number 8. To give an example, IR 36 and Azucena had different alleles than those in Basmati 370 at 14 and 10 of the 15 SSR loci, respectively. In comparison, IR 36 and Azucena had different alleles at 7 of the15 SSR loci. Among the traditional Basmati varieties, Basmati 370 and Type III were similar at all the15 SSR loci, while Ambemohar 157, HBC 19 and Ranbir Basmati had different alleles respectively at one (RM195), two (RM44, RM195) and five (RM152, RM310, RM42, RM223 and RM210) loci. Ranbir Basmati had three alleles similar to those in either IR 36 or Azucena, and two unique alleles, which were absent in all other genotypes. The cross-bred Basmati rice varieties, Super, Kernel, Basmati 385, Pusa Basmati 1 and Kasturi, had different alleles than those in Basmati 370 at one (RM339), four (RM152, RM44, RM331 and RM195), five (RM152, RM310, RM44, RM331 and RM195), six (RM152, RM310, RM44, RM331, RM210, and RM256) and eight (RM310, RM44, RM137, RM331, RM339, RM42, SCU-rice- SSR1, RM284) of the 15 SSR loci.

The major gene controlling the grain aroma in rice has been located between the RG1 and RG28 RFLP markers (Lorieux et al. 1996). A total of three alleles were detected at the SCUrice-SSR1 locus in 12 rice genotypes; one allele was specifically present in all the Basmati varieties except Kasturi; another allele was present in both IR 36 and Azucena, and Kasturi had an altogether different allele. The SSRs (RM342, RM42, RM195, RM223 and RM284), which lie within the RG1-RG28 region, showed a high degree of polymorphism between Basmati and non-Basmati rice genotypes. In comparison to Basmati 370, IR 36 had different alleles at all the five SSR loci, and Azucena had different alleles at four of them. All the traditional Basmati rice varieties had similar alleles, except in the cases of HBC 19 and Ambemohar 157, which had a different allele at RM195, and Ranbir Basmati harboring different alleles at RM42 and RM223. Among the cross-bred Basmati varieties, Super and Pusa Basmati had similar alleles to those in Basmati 370 at all the five SSR loci, while Basmati 385 and Kernel had a different allele at RM195, and Kasturi had different alleles at two loci (RM42, RM284).

Genetic relationships among the 12 rice genotypes as obtained by cluster tree analysis (NTSYS-PC; version 2.02) using the allelic diversity data at 15 SSR loci, are shown in Figure 2. The rice genotypes were clustered into two major groups at 0.50 similarity coefficient. Group I comprised all five traditional Basmati rice varieties and four of the five crossbred Basmati rice varieties. Group II included IR 36, Azucena and Kasturi. Basmati 370 and Type III showed 100% similarity, and the other traditional/ cross-bred rice varieties merged with the above sub-group at different levels of similarity coefficient in the following order: Super, Ambemohar 157, HBC 19, Basmati 385/Kernel, Pusa Basmati 1 and Ranbir Basmati.

These results indicate that Basmati rice varieties are quite divergent from indica and japonica rice varieties. The close relationship between the traditional Basmati rice varieties suggests that these cultivars may have been derived from within a single population, which is consistent with their breeding histories and known pedigrees. The crossbred varieties, which had been developed from crosses/backcrosses between indica and Basmati rice varieties, had varying levels of similarity with the traditional Basmati group. This may be indicative of differential levels of genetic content from their respective indica and Basmati rice parents. All the traditional and cross-bred Basmati rice varieties, except Kasturi, used in this study share the same alleles at the aroma locus and adjoining loci on chromosome 8, which indicates that the aroma locus remained distinct and intact during the breeding process. The results also demonstrate the need to map genes/QTLs for Basmati grain-quality traits and application of molecular markers to improve the precision and efficiency in Basmati rice breeding.


This work was supported by the Rockefeller Foundation (RF Grant # 2000 FS 023).


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