Genetic analysis of seed-shattering genes in rice using an F3:4 population derived from an Oryza sativa x Oryza rufipogon cross.

Seed shattering of wild plant species is thought to be an adaptive trait to facilitate seed dispersal. For rice breeding, seed shatter-ing is an important trait for improving breeding strategies, particularly when developing lines use interspecific hybrids and introgression of genes from wild species. We developed F3:4 recombinant inbred lines from an interspecific cross between Oryza sativa cv. Ilpoombyeo and Oryza rufipogon. In this study, we genetically analyzed known shat-tering-related loci using the F3:4 population of O. sativa/O. rufipogon. CACTA-AG190 was significantly associated with the shattering trait CACTA-TD according to bulked segregant analysis results, and was found in the qSH-1 region of chromosome 1. Fine genetic mapping of the flanking regions around qSH-1 based on CACTA-AG190 revealed multiple-sequence variations. The highest limit of detection based on quantitative trait locus analysis was observed between shaap-7715 and a 518-bp insertion site. Two other quantitative trait locus analyses of seed-shattering-related loci, qSH-4 and sh-h, were performed using simple sequence repeat and allele-pecific single nucleotide polymor-phism markers. Our results can be applied for rice-breeding research, such as marker-assisted selection between cultivated and wild rice.

Analysis of genetic diversity and trait correlations among Korean landrace rice (Oryza sativa L.).

This study analyzed 394 Korean rice landrace accessions, including 93 waxy varieties, for polymorphisms using 29 simple sequence repeat (SSR) markers. In total, 381 alleles served as raw data for estimating the genetic diversity (GD) and population structure. The number of alleles per locus ranged from 3 to 44 (average = 13.14). The expected heterozygosity and polymorphism information content (PIC) ranged from 0.0341 to 0.9358 (mean = 0.5623) and from 0.0783 to 0.9367 (mean = 0.5839), respectively. The mean GDs in waxy, low amylose content, intermediate amylose content, and high amylose content (HAC) varieties were 0.6014, 0.5922, 0.5858, and 0.7232, respectively, whereas the mean PIC values for each SSR locus were 0.5701, 0.5594, 0.5550, and 0.6926, respectively. HAC varieties had the highest GD and PIC. Consistent with clustering by genetic distances, a model-based structural analysis revealed 3 subpopulations. Analysis of molecular variance revealed that the between-population component of genetic variance was 22.35%, and that of the within-population component was 77.65%. Significant correlations were observed between eating quality and protein content (r = -0.262), K(+) (r = -0.655), Mg(2+) (r = -0.680), 1000-GW (r = 0.159), and amylose content (r = -0.134). The overall FST value was 0.2235, indicating moderate differentiation among the groups. Analysis of variance of the 3 genetic groups (mean of 9 phenotypic and 5 physicochemical traits) by the Duncan multiple range test showed significant differences in 10 traits. This preliminary study represents a first step toward more efficient conservation and greater utilization of rice landraces to broaden the genetic bases of commercially grown varieties.

Phylogenetic relationships of chrysanthemums in Korea based on novel SSR markers.

Chrysanthemums are well known for their esthetic and medicinal values. Characterization of chrysanthemums is vital for their conservation and management as well as for understanding their genetic relationships. We found 12 simple sequence repeat markers (SSRs) of 100 designed primers to be polymorphic. These novel SSR markers were used to evaluate 95 accessions of chrysanthemums (3 indigenous and 92 cultivated accessions). Two hundred alleles were identified, with an average of 16.7 alleles per locus. KNUCRY-77 gave the highest polymorphic information content value (0.879), while KNUCRY-10 gave the lowest (0.218). Similar patterns of grouping were observed with a distance-based dendrogram developed using PowerMarker and model-based clustering with Structure. Three clusters with some admixtures were identified by model-based clustering. These newly developed SSR markers will be useful for further studies of chrysanthemums, such as taxonomy and marker-assisted selection breeding.

Updates and perspectives on the utilization of molecular makers of complex traits in rice.

After complete sequencing of its genome and annotation of the majority of its ~32,000 genes, rice genome has become the model genome among the cereal genomes, and the focus has shifted from structural to functional genomics and application of genomic-derived information in rice breeding. During the past 2 decades, intensive worldwide efforts have led to significant improvements in rice. An abundance of molecular markers and information related to many genes/quantitative trait loci that control agronomically important traits such as yield, quality, and biotic and abiotic stress tolerance have been identified. Bridging the application gap between quantitative trait locus identification and marker-assisted selection breeding is an urgent, arduous, and long-term task. Marker development, allele mining, gene discovery, and molecular breeding have progressed to a great extent because of the rapid development of next-generation sequencing, large-scale high-density genotyping, and genome-wide selection strategies. The availability of high-density markers and the rapidly decreasing cost of genotyping have facilitated marker-assisted selection of many traits that were previously not possible.

SCAR markers for discriminating species of two genera of medicinal plants, Liriope and Ophiopogon.

The development of DNA markers that can closely discriminate between Liriope and Ophiopogon species is vital for efficient and accurate identification of these species, and to ensure the quality, safety, and efficacy of medicines made from these plants. We developed species-specific molecular markers for these two genera. Forty RAPD primers were tested to detect polymorphism; species-specific RAPD bands were gel-purified, cloned, and sequenced. Primers for sequence-characterized amplified regions (SCARs) were then designed, based on nucleotide sequences of specific RAPD primers. SCAR markers SA06 and SB05, specific to Ophiopogon japonicus, amplified 460- and 553-bp DNA fragments, respectively. The marker SA12 amplified a 485-bp fragment specific to Liriope platyphylla. This is the first report of a species-specific SCAR marker for this group. These markers will be useful for rapid identification of closely related Liriope and Ophiopogon species.