Home | Vol. 19 >B. Research Notes>VI. Gene and genome structure |
44. | Microsatellite diversity for chromosome number 8 in Basmati rice |
NEELU JAIN1, NAVINDER SAINI1, POONAM RANA, SUNITA
JAIN2, and RAJINDER K. JAIN1 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). 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. |
Home | Vol. 19 >B. Research Notes>VI. Gene and genome structure |