Biomedical subjects

S R McCouch

Publications and source records attributed to S R McCouch.

24 records · Page 2Linked to original sources

PubMed1995

Comparative mapping in grasses. Oat relationships.

The development of RFLP linkage maps in hexaploid and diploid oat allows us to study genetic relationships of these species at the DNA level. In this report, we present the extension of a previously developed diploid oat map (Avena atlantica x A. hirtula) and its molecular-genetic relationships with wheat, rice and maize. Examination of 92-99% of the length of the oat genome map with probes common to Triticeae species, rice or maize showed that 84, 79 and 71%, respectively, was conserved between these species and oat. Generally, the orders of loci among chromosomes homoelogous to oat chromosomes A and D were the most conserved and those of chromosomes homoeologous to oat chromosome G were the least conserved. Conservation was observed for blocks ranging from whole chromosomes 101 cM long to small segments 2.5 cM long containing two loci. Comparison of the homoeologous segments of Triticeae, rice and maize relative to oat indicated that certain regions have been maintained in all four species. The relative positions of major genes governing traits such as seed storage proteins and resistance to leaf rusts have been conserved between cultivated oat and Triticeae species. Also, the locations of three vernalization/or photoperiod response genes identified in hexaploid oat correspond to the locations of similar genes in homoeologous chromosomes of wheat, rice or maize. The locations of the centromeres for six of the seven oat chromosomes were estimated based on the homoeologous segments between oat and Triticeae chromosomes.

Avena↗

PubMed1995

Comparative mapping in grasses. Wheat relationships.

Conventionally, the genetics of species of the family Gramineae have been studied separately. Comparative mapping using DNA markers offers a method of combining the research efforts in each species. In this study, we developed consensus maps for members of the Triticeae tribe (Triticum aestivum, T. tauschii, and Hordeum spp.) and compared them to rice, maize and oat. The aneuploid stocks available in wheat are invaluable for comparative mapping because almost every DNA fragment can be allocated to a chromosome arm, thus preventing erroneous conclusions about probes that could not be mapped due to a lack of polymorphism between mapping parents. The orders of the markers detected by probes mapped in rice, maize and oat were conserved for 93, 92 and 94% of the length of Triticeae consensus maps, respectively. The chromosome segments duplicated within the maize genome by ancient polyploidization events were identified by homoeology of segments from two maize chromosomes to regions of one Triticeae chromosome. Homoeologous segments conserved across Triticeae species, rice, maize, and oat can be identified for each Triticeae chromosome. Putative orthologous loci for several simply inherited and quantitatively inherited traits in Gramineae species were identified.

Avena↗

PubMed1995

QTL mapping in rice.

In the past 10 years, interest in applying the tools of molecular genetics to the problem of increasing world rice production has resulted in the generation of two highly saturated, molecular linkage maps of rice, and the localization of numerous genes and quantitative trait loci (QTLs). Primary studies have identified QTLs associated with disease resistance, abiotic stress tolerance and yield potential of rice in a range of ecosystems. The ability to identify, manipulate and potentially clone individual genes involved in quantitatively inherited characters, combined with the demonstrated conservation of numerous linkage blocks among members of the grass family, emphasizes the contribution of map-based genetic analyses both to applied and to basic crop research.

Chromosome Mapping↗

PubMed1995

Frequency of microsatellite sequences in rice (Oryza sativa L.).

This study was undertaken to estimate the relative frequencies of 13 microsatellite motifs in the rice genome as a basis for efficient development of a microsatellite map. Two dinucleotide, seven trinucleotide, and four tetranucleotide repeat motifs were end labelled and used as hybridization probes to screen genomic and cDNA libraries of rice, cv. IR36. Optimal washing temperatures for identification of clones containing specific microsatellite motifs were estimated based on washing temperatures near Td (dissociation temperature; Td = Tm - 7.6 degrees C). Sequencing of 20 putatively positive clones corresponding to each of 4 microsatellite motifs suggested that while Td provides a useful predictor of washing stringency for most of the repeats studied, those with a very high GC or AT content were most prone to error. The results from screening the rice genomic library suggest that there are an estimated 1360 poly(GA)n and 1230 poly(GT)n microsatellites in the rice genome, and that the relative frequency of different repeats decreased with increasing size of the motif. The most frequently observed microsatellites in the cDNA library were the same as for genomic library, but no poly(CGG)n, poly(ATC)n, or tetranucleotide motifs were observed among cDNA in this study.

Base Composition↗

PubMed1994

RFLP mapping of genes conferring complete and partial resistance to blast in a durably resistant rice cultivar.

Moroberekan, a japonica rice cultivar with durable resistance to blast disease in Asia, was crossed to the highly susceptible indica cultivar, CO39, and 281 F7 recombinant inbred (RI) lines were produced by single seed descent. The population was evaluated for blast resistance in the greenhouse and the field, and was analyzed with 127 restriction fragment length polymorphism (RFLP) markers. Two dominant loci associated with qualitative resistance to five isolates of the fungus were tentatively named Pi-5(t) and Pi-7(t). They were mapped on chromosomes 4 and 11, respectively. To identify quantitative trait loci (QTLs) affecting partial resistance, RI lines were inoculated with isolate PO6-6 of Pyricularia oryzae in polycyclic tests. Ten chromosomal segments were found to be associated with effects on lesion number (P < 0.0001 and LOD > 6.0). Three of the markers associated with QTLs for partial resistance had been reported to be linked to complete blast resistance in previous studies. QTLs identified in greenhouse tests were good predictors of blast resistance at two field sites. This study illustrates the usefulness of RI lines for mapping a complex trait such as blast resistance and suggests that durable resistance in the traditional variety, Moroberekan, involves a complex of genes associated with both partial and complete resistance.

Chromosome Mapping↗

PubMed1993

Genetic diversity and phylogeny analysis of Azolla based on DNA amplification by arbitrary primers.

The polymerase chain reaction was used to amplify random sequences of DNA from 25 accessions of Azolla to evaluate the usefulness of this technique for identification and phylogenetic analysis of this aquatic fern. Accessions were selected to represent all known species within the genus Azolla and to encompass the world-wide distribution of the fern. Primers of 10 nucleotides with 70% G + C content were used to generate randomly amplified polymorphic DNA from the symbiotic Azolla-Anabaena complex. Twenty-two primers were used and each primer gave 4-10 bands of different molecular weights for each accession. Bands were scored as present or absent for each accession and variation among accessions was quantified using Nei's genetic distances. A dendrogram summarizing phenetic relationships among the 25 accessions was generated using the unweighted pair-group method with arithmetic mean. Principal component analysis was also used to evaluate genetic similarities. Three distinct groups were identified: group 1 contains five species, group 2 contains the pinnata species, and group 3 contains the nilotica species. The analysis demonstrates that the major groups of Azolla species can be easily distinguished from one an other and, in addition, that closely related accessions within species can be identified. We further found that using 10 primers, a phylogeny that is essentially the same as that derived from 22 primers can be constructed. Our results suggest that total DNA extracted from the Azolla-Anabaena symbionts is useful for classification and phylogenetic studies of Azolla.

Base Sequence↗