Genome-wide expression analysis of a rice mutant line under salt stress.

Salinity is a major environmental stress to plants. In this study, the ability of plants to tolerate salt was investigated by studying growth, physiological characteristics, and expression levels of genes related to the salt-stress response in the salt-tolerant rice mutant (Till-II-877), which was derived from γ-ray irradiation. Compared to plants grown under normal conditions, the height and root length of wild type (WT) were reduced by approximately 40 and 29% following exposure to salt stress for 3 weeks, whereas Till-II-877 line showed 29 and 23% reductions in plant height and root length, respectively. No significant changes were observed in total chlorophyll content, and the malondialdehyde content of the mutant increased less than that of the WT under salt treatment. Gene expression was compared between the WT and mutant lines using microarray analysis. An unbiased analysis of the gene expression datasets allowed us to identify the pathways involved in salt-stress responses. Among the most significantly affected pathways, changes in gene expression were observed in α-linolenic acid and linoleic acid metabolism (in lipid metabolism), fructose and mannose metabolism and glycolysis-gluconeogenesis (in carbohydrate metabolism), cysteine and methionine metabolism (in amino acid metabolism), and carbon fixation (in the energy metabolism of photosynthetic organisms) under salt stress. These results show that the differential response of plants subjected to salt stress was due to changes in multiple metabolic pathways. These findings increase our understanding of the effects of salt stress in rice and may aid in the development of salt-tolerant rice cultivars.

Development of a transposon-based marker system for mutation breeding in sorghum (Sorghum bicolor L.).

Under certain circumstances, transposable elements (TE) can create or reverse mutations and alter the genome size of a cell. Sorghum (Sorghum bicolor L.) is promising for plant transposon tagging due to its small genome size and its low content of repetitive DNA. We developed a marker system based on targeted region amplification polymorphisms (TE-TRAP) that uses the terminal inverted repeats (TIRs) of transposons. A total of 3816 class 2 transposons belonging to the PIF/Harbinger family were identified from the whole sorghum genome that produced five primers, including eight types of TIRs. To define the applicability and utilization of TE-TRAP, we used 21 individuals that had been bred after ɤ-ray irradiation. In total, 31 TE-TRAP, 16 TD, and 21 AFLP primer combinations generated 1133, 223, and 555 amplicons, respectively. The percent polymorphic marker was 62.8, 51.1, and 59.3% for the TE-TRAP, TD, and AFLP markers, respectively. Phylogenetic and principal component analyses revealed that TE-TRAP divided the 21 individuals into three groups. Analysis of molecular variance suggested that TE-TRAP had a higher level of genetic diversity than the other two marker systems. After verifying the efficiency of TE-TRAP, 189 sorghum individuals were used to investigate the associations between the markers and the ɤ-ray doses. Two significant associations were found among the polymorphic markers. This TE-based method provides a useful marker resource for mutation breeding research.

Comparative genomic hybridization analysis of rice dwarf mutants induced by gamma irradiation.

Comparative genomic hybridization (CGH) is a powerful tool used to analyze changes in copy number, polymorphisms, and structural variations in the genome. Gene copy number variation (CNV) is a common form of natural diversity in the genome, which can create new genes and alter gene structure. Thus, CNVs may influence phenotypic variation and gene expression. In this study, to detect CNVs, we irradiated rice seeds with gamma rays (300 Gy) and selected two dwarf mutagenized plants, GA-III-189 and -1052, in the M3 generation. These plants were subjected to CGH analysis using Agilent's RICE CGH array. Most of the CNVs identified were less than 10 kb in length. We detected 90 amplified and 18 deleted regions in GA-III-189, and 99 amplified and 11 deleted regions in GA-III-1052. Of note, CNVs were located on chromosome 12 in both GA-III-189 and -1052, which contained 39 commonly amplified regions in 29 genes. The commonly amplified genes included six genes encoding F-box domain-containing proteins. Alterations in these F-box domain-containing genes were confirmed by quantitative RT-PCR. Integration of CGH and gene expression data identified copy number aberrations and novel genes potentially involved in the dwarf phenotype. These CGH and gene expression data may be useful for uncovering the mechanisms underlying the dwarf phenotype.

Genetic characterization of hatchery populations of Korean spotted sea bass (Lateolabrax maculatus) using multiplex polymerase chain reaction assays.

The spotted sea bass, Lateolabrax maculatus, is an important commercial and recreational fishery resource in Korea. Aquacultural production of this species has increased because of recent resource declines, growing consumption, and ongoing government-operated stock release programs. Therefore, the genetic characterization of hatchery populations is necessary to maintain the genetic diversity of this species and to develop more effective aquaculture practices. In this study, the genetic diversity and structure of three cultured populations in Korea were assessed using multiplex assays with 12 highly polymorphic microsatellite loci; 144 alleles were identified. The number of alleles per locus ranged from 6 to 28, with an average of 13.1. The mean observed and expected heterozygosities were 0.724 and 0.753, respectively. Low levels of inbreeding were detected according to the inbreeding coefficient (mean FIS = 0.003-0.073). All hatchery populations were significantly differentiated from each other (overall fixation index (FST) = 0.027, P < 0.01), and no population formed a separate cluster. Pairwise multilocus FST tests, estimates of genetic distance, mantel test, and principal component analyses did not show a consistent relationship between geographic and genetic distances. These results could reflect the exchange of breeds and eggs between hatcheries and/or genetic drift due to intensive breeding practices. For optimal resource management, the genetic variation of hatchery stocks should be monitored and inbreeding controlled within the spotted sea bass stocks that are being released every year. This genetic information will be useful for the management of both L. maculatus fisheries and the aquaculture industry.