Rice Recombinant Inbred Lines Research Articles

Genetic mapping of hypervariable minisatellite sequences in rice (Oryza sativa L.)

Minisatellites, or DNA fingerprinting sequences, have been utilized in animal linkage studies for several years but have not been used as markers for plant genome mapping. In animal genome mapping they have resulted in limited success because they are evenly dispersed in some species but are often clustered near telomeric regions, as observed on human chromosomes. The purpose of the present study was to generate DNA fingerprints utilizing several rice-derived minisatellites containing different core sequences and numbers of repeat units, followed by assessing their potential for use as genetic markers when mapped to a rice recombinant inbred line (RIL) population. Sites of segregating minisatellite loci were mapped onto 11 of the 12 rice RIL linkage maps. The implications for the use of rice minisatellite core sequences as genetic markers on linkage maps in rice are discussed.

Mapping of Quantitative Trait Loci of Ovicidal Response to Brown Planthopper (Nilaparvata lugens Stal) in Rice (Oryza sativa L.).

The brown planthopper(BPH), Nilaparvata lugens Stal, is a serious pest of rice(Oryza sativa L.) in Asia. The rice ovicidal response to BPH is characterized by the formation of watery lesions which result in the death of the eggs. It is one of the factors affecting the suppression of the multiplication of BPH. To detect quantitative trait loci(QTLs) for this ovicidal response, a set of 71 rice recombinant inbred lines(F11) derived from a cross between a Japonica variety Asominori with ovicidal response and an Indica variety IR24 without ovicidal response were phenotyped for grade of watery lesions(GWL) and egg mortality(EM) of BPH. GWL and EM showed a significant positive correlation(P<0.001) and transgressive segregation was observed for EM. In composite interval mapping for GWL and EM with 293 RFLP marker loci, two QTLs each on the long arm of chromosome 1(1L) and the short arm of chromosome 6(6S) were detected for both GWL and EM. The 6S QTL explained 72.1% and 85.1% of the phenotypic variantions for GWL and EM, respectively. The QTL on 1L explained 19.8% and 17.8% of the phenotypic variations for GWL and EM, respectively. Both alleles from Asominori increased GWL and EM. The Asominori allele at the 6S QTL was essential for the ovicidal response to BPH and the Asominori allele at 1L QTL could increase the EM of BPH in the presence of the Asominori allele at the 6S QTL. It is concluded that two RFLP loci, R1954 linked to 6S QTL and C112 linked to 1L QTL can be used for marker-assisted selection.

Quantitative Trait Locus Mapping of Ovicidal Responsein Rice (Oryza sativa L.) against Whitebacked Planthopper (Sogatella furcifera Horváth)

The ovicidal response in rice (Oryza sativa L.) to whitebacked planthopper (WBPH), Sogatella furcifera Horváth, is characterized by the formation of watery lesions which result in the death of WBPH eggs. To determine the genetic mechanism of this ovicidal response, a set of 71 rice recombinant inbred (RI) lines (F8, F9, and F10) derived from a cross of japonica cultivar Asominori and indica cultivar IR24, the two parents, and the F1 were phenotyped for percentage of watery lesions (PWL) and WBPH egg mortality (EM). PWL and EM showed significant positive correlations (P &lt; 0.001) and transgressive segregation was observed for both traits. A total of 10 quantitative trait loci (QTLs) for ovicidal response were detected with 292 RFLP markers in the F6 and F7 populations by composite interval mapping (LOD ≥ 1.5). Four of 10 QTLs coincided for PWL and EM and each three QTLs were only detected for PWL and EM. The QTL on chromosome 6 (R1954‐L688) was most significantly associated with the ovicidal response and accounted for 69.9% of phenotypic variance for PWL (F8) and 46.0% of phenotypic variance for EM (F8). Positive alleles for ovicidal response came from Asominori on chromosomes 1, 3, 6S (short arm), 8, and 12 and from IR24 on chromosomes 2, 6L (long arm), and 10. QTL accumulation from both parents was the genetic basis of the transgressive segregation in the RI population. No epistatic interaction was detected. The Asominori allele on the chromosome 6S QTL was essential to the ovicidal response, and R1954 was found to be a target marker for marker assisted selection.

Detection of a highly heterozygous locus in recombinant inbred lines of rice and its possible involvement in heterosis

Forty-seven recombinant inbred (RI) lines derived from a cross between two indica rices, cv 'Phalguna' and the Assam land race ARC 6650, were subjected to restriction fragment length polymorphism (RFLP) analysis using cloned probes defining 150 single-copy loci uniformly dispersed on the 12 chromosomes of rice. Of the probes tested, 47 detected polymorphism between the parents. Heterozygosity was calculated for each line and for each of the polymorphic loci. Average heterozygosity per line was 9.6% but was excessive (>20%) in the 5 lines that seemed to have undergone outcrossing immediately prior to harvest. Average heterozygosity detected by each probe across the 47 RI lines was 9.7%. The majority of probes revealed the low level of heterozygosity (<8%) expected for F5-F6 lines in a species showing about 5% outbreeding. On the other hand, 7 probes exhibited heterozygosity in excess of 15%, while with a eighth probe (RG2 from chromosome 11) heterozygosity varied according to the restriction enzyme employed, ranging from 2% with SaII to 72% with EcoRV. The presence of 34 recombination sites in a segment of the genome as short as 24 kb indicates a strong selection for recombination between two neighbouring loci, one required as homozygous for the 'Phalguna' allele, and the other heterozygous. Since selection was principally for yield advantage over that of the high-yielding parent, 'Phalguna', one or both of these loci may be important for heterosis in this cross. The results also indicate that heterozygosity as measured by RFLP can depend on the particular restriction endonuclease employed.