Analysis Of Recombinant Inbred Lines Research Articles

English

The aroma or fragrance of Basmati rice is associated with the presence and content of the chemical compound, 2-acetyl-1-pyrroline and the trait is monogenic recessive. Several polymerase chain reaction (PCR)-based co-dominant markers based on RG28 locus were developed, which can differentiate between fragrant and non-fragrant rice cultivars. For molecular and biochemical analysis of aroma, a mapping population comprising 208 recombinant inbred lines (RILs) derived from a diverse cross between CSR10 and Taraori Basmati through Single seed descent (SSD) method was used. RILs are among the best mapping populations, which provide a novel material for linkage mapping of genes/QTLs marker for various traits. Biochemical analysis of aroma was performed with the 1.7% KOH solution and molecular analysis of aroma was carried out with microsatellite markers present on chromosome 8 (BAD2, BADEX7-5, SCUSSR1) to determine the extent of association between trait, marker and chromosome 8. Among these markers, BAD2 amplified aroma specific alleles having 256 bp in 72 lines, BADEX7-5 with 95 bp in 74 lines and SCUSSR1 with 129 bp in 79 lines. Mantel test of significance detected by biochemical analysis of RILs (with 1.7% KOH) and molecular marker study revealed high degree (>90%) of association of aroma with the above mentioned markers, respectively. Some of the F10 lines amplified the heterozygous alleles for two sets of specific markers (BAD2 and SCUSSR-1) but did not show the presence of aroma as analyzed by chemical test. Aromatic and nonaromatic lines were almost common in three markers, indicating association of markers with the trait and chromosome 8. The results reveal that these markers could be used for marker assisted selection and RIL population for mapping of aroma QTLs/genes.

Quantitative trait locus analysis for days-to-heading and morphological traits in an RIL population derived from an extremely late flowering F1 hybrid of sorghum

The hybrid vigor typical of F1 cultivars is used to boost biomass production of sorghum (Sorghum bicolor (L.) Moench). The high dry-matter yielding F1 cultivar Kazetachi uniquely shows extremely late flowering and a long culm, and is greatly different from its parents. We investigated the genetic mechanisms underlying these phenotypes by quantitative trait locus (QTL) analysis of recombinant inbred lines derived from a male-fertile line and a restorer line and grown in 3 years. QTL analysis for six traits (days-to-heading, culm length, culm width, culm number, panicle length, panicle number) revealed that the unique phenotypes of the F1 plants were controlled by the genetic combination of 12 or more QTLs detected in at least 2 years. Two putative QTLs for days-to-heading (qDH1 on SBI-01 and qDH6 on SBI-06) would strongly affect the other phenotypes because of their co-localization with QTLs for other traits, as supported by significant phenotypic correlations. These QTLs would be useful for understanding the association of plant type with biomass production in sorghum.

New broad-spectrum resistance to septoria tritici blotch derived from synthetic hexaploid wheat.

Septoria tritici blotch (STB), caused by the ascomycete Mycosphaerella graminicola, is one of the most devastating foliar diseases of wheat. We screened five synthetic hexaploid wheats (SHs), 13 wheat varieties that represent the differential set of cultivars and two susceptible checks with a global set of 20 isolates and discovered exceptionally broad STB resistance in SHs. Subsequent development and analyses of recombinant inbred lines (RILs) from a cross between the SH M3 and the highly susceptible bread wheat cv. Kulm revealed two novel resistance loci on chromosomes 3D and 5A. The 3D resistance was expressed in the seedling and adult plant stages, and it controlled necrosis (N) and pycnidia (P) development as well as the latency periods of these parameters. This locus, which is closely linked to the microsatellite marker Xgwm494, was tentatively designated Stb16q and explained from 41 to 71% of the phenotypic variation at seedling stage and 28–31% in mature plants. The resistance locus on chromosome 5A was specifically expressed in the adult plant stage, associated with SSR marker Xhbg247, explained 12–32% of the variation in disease, was designated Stb17, and is the first unambiguously identified and named QTL for adult plant resistance to M. graminicola. Our results confirm that common wheat progenitors might be a rich source of new Stb resistance genes/QTLs that can be deployed in commercial breeding programs.

Characterization of the Interaction Between the Bacterial Wilt Pathogen Ralstonia solanacearum and the Model Legume Plant Medicago truncatula

The soilborne pathogen Ralstonia solanacearum is the causal agent of bacterial wilt and attacks more than 200 plant species, including some legumes and the model legume plant Medicago truncatula. We have demonstrated that M. truncatula accessions Jemalong A17 and F83005.5 are susceptible to R. solanacearum and, by screening 28 R. solanacearum strains on the two M. truncatula lines, differential interactions were identified. R. solanacearum GMI1000 infected Jemalong A17 line, and disease symptoms were dependent upon functional hrp genes. An in vitro root inoculation method was employed to demonstrate that R. solanacearum colonized M. truncatula via the xylem and intercellular spaces. R. solanacearum multiplication was restricted by a factor greater than 1 x 10(5) in the resistant line F83005.5 compared with susceptible Jemalong A17. Genetic analysis of recombinant inbred lines from a cross between Jemalong A17 and F83005.5 revealed the presence of major quantitative trait loci for bacterial wilt resistance located on chromosome 5. The results indicate that the root pathosystem for M. truncatula will provide useful traits for molecular analyses of disease and resistance in this model plant species.

Dot-blot Analysis for Identification of <i>japonica</i> Rice Cultivars and Genotyping of Recombinant Inbred Lines

Dot-blot analysis of rice cultivars was performed using 14 cultivar-specific sequences identified previously by AFLP and PCR-RF-SSCP analyses as probes. DNA samples prepared from leaves by a simple method without the use of organic solvent were found to be usable for dot-blot analysis. Although more than a single grain of rice was needed as material for direct dot-blotting of genomic DNA, PCR amplification of DNA enabled detection of cultivar-specific signals in a DNA sample from a single grain by dot-blot analysis. All 31 rice cultivars examined could be distinguished from each other by analysis using ten cultivar-specific probes. Dot-blot analysis was also applied to genotyping of recombinant inbred lines (RILs), the results of which corresponded to those by electrophoretic analysis of PCR products amplified with specific primer sequences. The probe sequences deleted in ‘Nipponbare’ were mapped on the rice chromosome by BlastN search using all the Kasalath BAC-end sequences and by analysis of RILs and chromosome segment substitution lines (CSSLs). Dot-blot analysis using cultivar-specific sequences was found to be applicable for the identification of cultivars and genotyping of plants in rice.

Enhanced fitness conferred by naturally occurring variation in the circadian clock.

Natural variation in clock parameters is necessary for the circadian clock to contribute to organismal fitness over a broad geographic range. Considerable variation is evident in the period, phase, and amplitude of 150 Arabidopsis accessions, and the period length is correlated with the day length at the latitude of origin, implying the adaptive significance of correctly regulated circadian timing. Quantitative trait loci analysis of recombinant inbred lines indicates that multiple loci interact to determine period, phase, and amplitude. The loss-of-function analysis of each member of the ARABIDOPSIS PSEUDO-RESPONSE REGULATOR family suggests that they are candidates for clock quantitative trait loci.

Genetics of aliphatic glucosinolates. III. Side chain structure of aliphatic glucosinolates in Arabidopsis thaliana

The inheritance of aliphatic glucosinolates in Arabidopsis thaliana was studied. Analysis of F3 families from a cross between the ecotype Limburg-5 and the accession H51 (an inbred line derived from the ecotype Stockholm) suggested that alleles at a single locus regulate the conversion of methylsulphinylalkyl glucosinolates into alkenyl (and hydroxyalkenyl) glucosinolates. Likewise, analysis of recombinant inbred lines derived from a cross between the ecotypes Columbia and Landsberg erecta suggested that alleles at a single locus regulate the conversion of methylsulphinylpropyl glucosinolate into hydroxypropyl glucosinolate. Both loci mapped to a similar position on chromosome 4 and it is suggested that these alleles occur at the same locus. A genetic model is proposed in which the aliphatic glucosinolates of A. thaliana are determined by alleles at three loci. The ecological significance of variation in aliphatic glucosinolates is discussed.

Analysis of recombinant inbred lines derived from "autoimmune" (NZB) and "high leukemia" (C58) strains: independent multigenic systems control B cell hyperactivity, retrovirus expression, and autoimmunity.

The relationship of B cell hyperactivity and retrovirus expression to other autoimmune traits were examined in recombinant inbred (N X 8 RI) lines derived from NZB and C58 progenitor strains. Although both NZB and C58 mice expressed high levels of xenotropic virus, the RI lines segregated in virologic phenotype, as high or low expressors of the endogenous virus. The expression of the C58-derived ecotropic virus occurred in only one-half of the RI lines, and its expression in the remaining lines of mice appeared to be suppressed by the NZB-derived allele at the Fv-1 locus. The inheritance of B lymphocyte abnormalities of the NZB progenitor strain was investigated by studying spontaneous and SRBC-induced production of IgM by the spleen cells of the RI lines. These two phenotypes of B cell hyperactivity were found to be determined by independently segregating genes and they were not linked to immunoglobulin structural gene loci. The strain distribution patterns of virus expression and B cell hyperactivity in the RI lines did not match with each other or with the inheritance patterns of other immunologic abnormalities, such as defective AMLR and production of autoantibodies.

Genetic studies in NZB mice. V. Recombinant inbred lines demonstrate that separate genes control autoimmune phenotype.

The genetic basis for autoimmunity in NZB mice has been investigated through analysis of recombinant inbred lines produced by mating NZB mice with two different non-autoimmune strains. Several genes (at least six) were found to be necessary for the production of eight traits characteristic of the NZB mice that were studied. No fundamental genetic defect (an "autoimmunity gene") was identified that could give rise to the various autoimmune traits studied. This study strongly suggests that NZB disease results from the actions of several separate genes that together result in the characteristic manifestations of autoimmunity.