Fine mapping of genes controlling intermediate amylose content in rice using bulked segregant analysis
2003
Lanceras, J. | Tragoonrung, S. | Vanavichit, A. | Naivikul, O.
Amylose content (AC) is an important trait determining cooking and eating quality of rice. Bulked segregant analysis was used to identify markers in the region of chromosome 6 containing the quantitative trait locus (QTL) for AC. Two DNA pools based on the parental genotype for both markers defining the target interval and two pools produced from the phenotypic data were constructed. The genotype pools composed of 10 individuals per pool were homozygous for the opposing alleles for the region of the QTL defined by R1962 and RZ588. The phenotype-based pools were also composed of 10 individuals. The low-AC pool contained individuals with ACs ranging from 11% to 16%, whereas the high-AC pool had 23-24% AC. The pools were screened using 85 AFLP PCR II combinations . Two polymorphic markers were identified to be linked to chromosome 6: AC11 and AC12. A waxy microsatellite marker flanking (CT)n repeats at the 5' regulatory region of the waxy gene was also used and mapped 7.2 cM from R1962. AC QTLs were reanalyzed and four QTLs were detected on chromosomes 3, 4, 6, and 7. The QTL detected on chromosome 6 near the waxy microsatellite marker explained 58.7% of the phenotypic variation as part of the 80% variation explained by the four QTLs. Marker AC12 on chromosome 6 was found 0.1 cM from the waxy marker. KDML105 contributed low-AC QTLs on chromosomes 6 and 7, and CT9993 contributed QTLs on chromosomes 3 and 4. AC is positively correlated with gelanitization temperature (GT) (0.3194) and negatively correlated with gel consistency (GC) (0.8011). The KDML105 x CT9993 population favored low to intermediate AC with high GT and hard GC. AC12 and the waxy microsatellite marker will be useful for marker-assisted breeding.
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