Simple sequence repeat (SSR) variations were investigated in the Japanese barnyard millet, Echinochloa esculenta, its wild relative, E. crus-galli var. crus-galli and the rice-mimicking weed E. crus-galli var. formosensis. E. esculenta showed less average gene diversity (H) based on observed SSR allele frequency (0.37) than either E. crus-galli var. crus-galli (0.56) or E. crus-galli var. formosensis (0.55). Accessions of the three Echinochloa taxa were categorized into 13 phenotypes from the combinations of SSR alleles. Only two phenotypes, phenotypes 1 and 4, were detected in 49 accessions of E. esculenta, whereas 12 phenotypes were observed in 94 accessions of E. crus-galli var. crus-galli, and six phenotypes in 12 accessions of E. crus-galli var. formosensis. The H′ value (Shannon’s information index) for SSR phenotypes was 0.69 in E. esculenta, 1.47 in E. crus-galli var. formosensis and 1.90 in E. crus-galli var. crus-galli respectively. In cultivated barnyard millet, two phenotypes aggregated in particular areas of Japan; phenotype 4 was found in the central and northeastern part of Japan, while phenotype 1 in the northern and southern parts of Japan.
An advanced backcross line, WH29001, was produced from a single plant from BC5F3 families derived from a cross between Oryza minuta (2n = 48, BBCC, Acc. No. 101141) as a donor parent and the O. sativa subsp. japonica cv. Hwaseongbyeo as a recurrent parent. Although WH29001 resembled Hwaseongbyeo, several traits were different from those of Hwaseongbyeo, including awn length and heading date. These differences between Hwaseongbyeo and WH29001 could be attributed to the introgressed O. minuta chromosome segments into WH29001. SSR analysis enabled to identify thirteen O. minuta-specific chromosome segments in WH29001 genome. To map and characterize QTLs for awn length and heading date, an F2:3 population from the Hwaseongbyeo/WH29001 cross was developed. The 197 F2 plants and 197 F3 families were evaluated for the two traits and the genotypes of the 197 F2 plants were determined using eighteen SSR markers located in the introgressed segments from O. minuta. QTL analysis identified two QTLs each for days to heading and awn length on chromosomes 6 and 9, respectively. The total phenotypic variance explained by these four QTLs ranged from 8.1% to 51.0% in the F3 population. Interestingly, QTLs for heading date and awn length were colocalized on chromosomes 6 and 9, respectively. Among these QTLs identified, the QTLs for heading date (dth9) and awn length (awn6) had not been detected in previous QTL studies between Oryza cultivars, indicating the existence of potentially novel alleles from O. minuta. The QTLs detected in the present study could become a valuable source of natural genetic variation underlying the evolution of rice.
The production and isolation of a wheat—Aegilops geniculata disomic addition line and of monosomic substitution line resistant to powdery mildew at the seedling and adult plant stages are described. Cytological analysis revealed the presence of an acrocentric chromosome in the resistant derivatives. Polyacrylamide gel electrophoretic analysis indicated differences in the β-zone of the reduced by mercaptoethanol treatment seed protein pattern between the wheat parent cv. Trakya and the resistant derivatives. A component with a high staining intensity in the β-zone was assumed to be a marker for the chromosome 6 of Ae. geniculata. The isoenzyme activity at the Got-1 and Est-4 loci of the lines was lower than that of wheat. By analyzing the isoenzymes of the Amp-1 locus of the addition plants, a quantitative marker of Ae. geniculata 6U chromosome was identified. The progeny of the plants with the 2n = 43 and 2n = 42 chromosomes carrying the chromosome 6U added or mono-substituted for the wheat 6D chromosome segregated for powdery mildew resistance. The mono-and/or double conditions for this chromosome could be maintained by selecting resistant plants in the segregated populations.
The effects of two quantitative trait loci (QTLs) controlling the resistance to rice stripe virus (RSV) identified in a Japanese upland rice line, Kanto 72, (URK 72) were evaluated using near-isogenic lines (NILs). Two NILs carrying a single QTL (QTL-NILs) on chromosomes 2 and 11, respectively, were developed by marker-assisted selection (MAS). The target QTL regions were introduced from the donor parent, Chugoku 40, which was bred from URK 72, into the genetic background of Koshihikari. Another line, which was a combined QTL-NIL, was developed from the cross between the two QTL-NILs to analyze the interaction of the two QTLs. Investigation of RSV resistance using the three NILs revealed that the effects of the two QTLs clearly differed in the reaction to RSV. The QTL on chromosome 11 exerted a major effect on reducing the infection rate of RSV. Although the QTL on chromosome 2 did not affect the infection rate, the symptoms of the diseased plants were milder. The combined QTL-NIL displayed a high level of resistance to RSV, while the infection rate and the symptom types of the diseased plants were similar to those of URK 72 or Chugoku 40. Since the major agronomic characters of the three QTL-NILs were the same as those of Koshihikari, these QTL-NILs were considered to be useful gene sources for RSV resistance rice breeding.
Acetaldehyde is oxidized from anaerobically accumulated ethanol during re-aeration in plants and may cause post-anoxic (post-hypoxic) injury. Aldehyde dehydrogenase (ALDH) can metabolize acetaldehyde to acetate, which is much less toxic. To understand the role of ALDH in alleviating post-anoxic injury of plants, we analyzed the expression of the mitochondrial ALDH genes, rf2a and rf2b, and determined the ethanol and acetaldehyde contents under submergence and subsequent re-aeration in a submergence-intolerant plant, maize (Zea mays L., inbred line B73). The level of rf2a mRNA decreased, whereas that of rf2b mRNA increased under submerged conditions. When the submerged plants were re-aerated, the transcript levels returned to the original levels. The level of mitochondrial ALDH proteins decreased under submergence and remained unchanged under re-aeration. The ALDH activity decreased under submergence and, during re-aeration, recovered to the original level much more slowly than in the case of rice (Oryza sativa L.). The content of acetaldehyde, which was produced under submergence, further increased following re-aeration. These results suggest that the lower submergence tolerance of maize compared to that of rice is partly due to a weaker ALDH activity during re-aeration.
High-throughput assay of molecular markers enables to utilize large amounts of markers in linkage mapping. To incorporate numerous markers into a linkage map, the development of a highly efficient method for linkage mapping is indispensable. When the number of loci is large, locus ordering is a major difficulty in linkage mapping, since the number of possible orders becomes very large. To address this problem, we developed a new algorithm for locus ordering and used it in a newly developed computer program called AntMap. The algorithm is based on ant colony optimization, which is a set of metaheuristic algorithms inspired by the cooperative behavior of real ants in finding the shortest path from their nest to a food source. Using this algorithm, AntMap seeks the linear order of loci that minimizes the sum of adjacent recombination fractions or that maximizes the log likelihood of locus order. Analyses based on simulated data sets indicated that our algorithm displayed a high efficiency level. The high performance of the algorithm enabled to save time and labor, and also to validate an estimated order by bootstrap tests. Our algorithm and AntMap should enable to construct high-throughput systems for linkage mapping. AntMap is available under a GNU general public license at http://cse.naro.affrc.go.jp/iwatah/antmap/index.html. Source codes and executables of AntMap can be obtained there.
Genetic diversity and genetic structure of East Asian wheat populations were studied based on the analysis of five isozymes using 324 wheat landraces. Gene diversity value calculated from the frequency of 31 isozyme bands varied within China, being higher in the western part than in the eastern part. Twenty populations of wheat landraces were classified into three major groups by cluster analysis, and wheat populations from the neighboring areas were clustered together. The first group comprised most of the populations from China (West), though two populations from Xinjiang and Gansu & Ningxia were rather distantly related to the populations from Tibet, Sichuan (West) and Yunnan. These results indicated the transmission of wheat from Nepal to the Tibetan area of China. The second group included the northern populations, from Mongolia to Japan (Northeast), indicating the transmission of wheat through the northern route of the “Silk road”. The third group consisted of wheat populations from Shaanxi, China (Southeast) and Japan (Southwest). Wheat population from Shaanxi was also related to the population from Hebei and Gansu & Ningxia, strongly suggesting the transmission of wheat through the “Silk road”: Xinjiang–Gansu & Ningxia–Shaanxi–Shandong. In addition, in the eastern part of China, genetic differentiation among wheat populations from northern and southern parts was observed, and a similar geographical differentiation was also recorded in Korea and Japan.
The major floral pigment of petunia, which is either a cyanidin-series (cyanidin and peonidin derivatives) or a delphinidin-series anthocyanin (delphinidin, petunidin and malvidin derivatives), is determined by the function of a flavonoid-3′,5′-hydroxylase that is encoded by two independent loci, Hf1 and Hf2. At the Hf2 locus, the recessive allele hf2-1 had a deletion of about 200 base pairs in the first intron and eight missense mutations by base substitution in the exons. The transcript level of hf2-1 was markedly lower than that of Hf2. We developed PCR-based markers to determine genotypes of the Hf1 and Hf2 loci. This technique allows amplified fragments from the Hf1, hf1-2 and hf1-3 alleles, as well as from the Hf2 and hf2-1 alleles, to be distinguished from one another. These PCR-based analyses showed no discrepancy between the Hf1/Hf2 loci genotypes and the major floral anthocyanidin phenotypes in the 129 commercial petunias we examined. Another reported recessive mutant allele at the Hf1 locus, caused by the insertion of an Spm-like transposable element in the second exon (hf1-1), was not found in the commercial petunias.
Near-infrared (NIR) spectroscopy and Fourier-transform infrared (FT-IR) spectroscopy were applied for the discrimination of genomic DNAs from different genotypes of plants. From the results of NIR and FT-IR analyses for the detection of genetically modified (GM) maize, GM and non-GM maize genotypes were distinguished based on the absorbance wavelength or wave number. Statistical analysis of the data obtained suggested that FT-IR gave clearer and more reproducible results than NIR for the discrimination of a GM maize line from a non-GM one. Based on these findings, FT-IR was used to discriminate much smaller variation such as allelic differences at one locus in isogenic lines of rice, and was also applied to the characterization of higher levels of genomic variation using typical indica and japonica rice varieties. In the case of isogenic lines, no obvious difference was observed. On the other hand, indica and japonica varieties could be clearly distinguished, and two varieties belonging to the indica varietal group could also be separated. It was concluded that this method may enable to discriminate among different varieties, and could become an easy and effective method of plant genotyping.