Soybean (Glycine max (L.) Merrill) is the most important leguminous crop in the world due to its highest content of high-quality protein for food and feed, and its capacity of oil production for food and industrial materials. Physiologically functional constituents in soybean seeds contribute significantly to human health, and because of its characteristic symbiosis with root bacteroids, soybean supplies nitrogen to soil. Although soybean has a relatively large and complex genome, several methods for genome analysis have been applied to obtain improved genotypes and to elucidate the special function of soybean. Research activities undertaken to analyze soybean genome structure and function include the construction of high density linkage maps, integration of trait loci into linkage maps, development of bacterial artificial chromosome libraries, physical mapping, large collection of expressed sequence tags, development of large populations of mutagenized plants and large-scale sequencing of gene-rich regions.

View full abstract

Three soybean [Glycine max (L.) Merr.] germplasms were previously developed for unique fatty acid content: LPKKC-3 has fap1 and sop1 alleles for reduced palmitic acid, HPKKC-7 has fap2 and fapx alleles for elevated palmitic acid and DHL has the ol allele for elevated oleic acid, and fan and fanx^a alleles for reduced linolenic acid. If these loci are independently inherited, soybean germplasms with useful combinations of these fatty acids could be developed that would result in a novel oil quality of great value for the food industry. Crosses were made between DHL and LPKKC-3, and DHL and HPKKC-7. The data from F₂ seed and F₂ progeny of DHL X LPKKC-3 indicated that the loci controlling reduced palmitic acid (fap1 and sop1) were independently inherited from the locus controlling elevated oleic acid (ol), and the loci controlling reduced linolenic acid (fan and fanx^a). Thus, the germplasm (LPDHL) with 4.0% palmitic, 51.0% oleic and 2.9% linolenic acids was easily developed. The data from F₂ seeds and F₂ progeny of DHL X HPKKC-7 indicated that the loci controlling elevated palmitic acid (fap2 and fapx), and reduced linolenic acid (fan and fanx^a) were independently inherited. The locus controlling elevated oleic acid (ol) was also distinctly segregated but the contents of oleic acid were found to be reduced due to the presence of loci for elevated palmitic acid. Thus, one germplasm (HPLL) with 22.5% palmitic acid and 2.7% linolenic acid, and another germplasm (MHPDHL) with 17.1% palmitic acid, 41.8% oleic and 2.9% linolenic acids were developed.

View full abstract

We used RFLP analysis with phenylalanine ammonia-lyase (PAL) cDNA as a probe to evaluate the genetic diversity of the Korean tea plant (Camellia sinensis var. sinensis). We analyzed 297 plants collected from the grounds of 6 old temples and from 1 tea farm. The patterns of DNA fragments in plants from the 6 temples were variable and differed from those of Japanese teas. In Japanese teas the PAL locus is composed of 3 multi-fragment alleles, but at least 10 fragment alleles were apparent in the Korean teas. The Korean teas showed greater genetic diversity than Japanese teas. The RFLP patterns of all 12 samples taken from the tea farm, where Japanese tea seeds had been introduced historically, were the same as those of the Japanese teas. The Korean teas were divided into 2 different genetic groups; one group was found around old temples and was probably derived from China. The other originated from Japanese teas that were introduced 50 to 100 years ago. RFLP analysis using PAL cDNA was very useful for the detection of genetic diversity in Korean teas, because the results of this analysis were similar to those of previous RAPD and morphological studies and were able to reveal the existence of the 2 tea groups. Our results showed that not only several morphological characters, but also the genetic background of Korean teas, differed from those of Japanese teas. Although further evaluation of Korean teas as genetic resources is required, it is possible that Korean teas will prove useful in Japanese tea breeding.

View full abstract

Cross-genus application of SSR markers developed in pear and apple was examined for quince (Cydonia oblonga) in order to conduct a genetic characterization. It was revealed that 77 out of 118 SSR markers producing 1 or more reproducible amplified bands could be used in quince, including 20 SSRs from pear and 57 SSRs from apple. Twenty quince varieties, including 15 accessions, 3 clones of ‘Smyrna’ and 2 clones of ‘Kaori’, were analyzed by using 39 polymorphic SSRs. A total of 122 polymorphic amplified fragments were obtained by using 39 SSR markers, which could divide 20 varieties into 12 genotypes. Cultivars vegetatively propagated and maintained in different areas showed identical SSR genotypes. Parentage of ‘Kaori’ was confirmed because all the putative alleles of ‘Kaori’ were transmitted from its parents ‘Smyrna’ and ‘Zairaishu’ without any discrepancy at tested SSR markers. A phenogram based on genetic similarity was constructed, showing major groups corresponding to the purposes of fruit production and rootstocks. Nine cultivars including almost all the varieties used as rootstocks showed only 0 to 4 differences in SSR fragments, suggesting that these cultivars were genetically very close. The SSR markers could be utilized as a reliable tool for the identification of quince varieties.

View full abstract

To convert RFLP markers of Italian ryegrass to sequence-tagged site (STS) markers, we end-sequenced 93 previously mapped single or low-copy RFLP probes. Eighty-seven clones gave acceptable results from both forward and reverse directions, and 71 contigs were detected, while other clones could not be sequenced completely because their fragments were too long. BLAST search results showed that 16 clones matched sequences reported in rice and other plants. STS primers were designed for all the 93 clones by using Oligo software, and 66 primers amplified a single band with the expected size. Of the 2 SSR primers designed from the 2 clones containing (AT)_n or (TTA)_n repeats, 1 amplified an SSR. Fifty-seven (85%) of the 67 STS (and SSR) primer pairs could amplify products in perennial ryegrass, 47 (70%) in meadow fescue, and 55 (82%) in tall fescue—species closely related to Italian ryegrass. Forty percent of the STS primers detected within-cultivar length or presence /absence of polymorphisms.

View full abstract

This study focused on a Yunnan landrace of rice, Kunmingxiaobaigu, to identify quantitative trait loci (QTLs) controlling cold tolerance at the reproductive stage using DNA markers. A linkage map with 16 linkage groups covering 1,354.4 cM with a total of 122 markers was constructed based on an F₂ population consisting of 250 individuals of a cross between Kunmingxiaobaigu and a Japanese variety, Towada. Nine QTLs were detected by interval mapping in the F₂ population. The nine QTLs were distributed on chromosomes 1 (2 QTLs), 3, 4, 6 (2 QTLs), 7, 10 and 12. The total variance explained by these nine QTLs was 54.2%, while the variance explained by a single QTL ranged from 5.0% to 37.8%. The validity of four QTLs on chromosomes 3, 6 (2 QTLs) and 7 was confirmed by single-marker analysis in the F₃ population and they were designated as qRCT3, qRCT6a, qRCT6b and qRCT7, respectively. The QTLs qRCT3, qRCT6a and qRCT6b were reported here for the first time. The QTL qRCT7 displayed the largest effect, reaching a value of 20.6%.

View full abstract

A near isogenic line T65-LH1 was developed from an upland rice variety R300 (Thailand) through eight successive backcrossing with Thaichung 65 (T65) as a recurrent parent. Previously unpublished study indicated T65-LH1 may harbor a recessive lateness gene which was likely located on the sixth chromosome. The present study was aimed at further identifying the lateness gene of this newly bred line by linkage study and allelism test. Linkage study was conducted using seven kinds of interchange homozygotes involved with the sixth chromosome. Individual interchange homozygous lines were crossed with T65-LH1, then, each F₁ population was backcrossed to T65-LH1. Segregations for heading times in all B₁F₁ populations showed early and late types fitted to the 1: 1 expected ratio, suggesting that T65-LH1 carried a recessive lateness gene. Chi-square values for independence between the present gene and four breakpoints, 2-6, 6-7b, 6-7c and 6-10 were insignificant. However, those to three breakpoints, 4-6, 6-7 and 6-8 were significant at 1% level and the respective recombination values were estimated as 3.2%, 4.3% and 3.4%. This suggested the gene under study was located on the sixth chromosome. Subsequently, allelism test between the present gene and other three lateness genes, ef2(t), ef3(t) and ef4(t) was carried out. Crosses of T65-LH1 and three testers having each of those lateness genes were made. Segregations for heading times in F₂ populations of those crosses fitted to the 9: 3: 3: 1, 12: 3: 1 and 9: 3: 3: 1 expected ratios. It suggested the present gene was independent from the lateness genes, ef2(t), ef3(t) and ef4(t). In conclusion, the lateness gene harbored by T65-LH1 was a new gene and designated as ef5. It was carried by the sixth chromosome.

View full abstract

The rice line WSS2 which was derived from the Vietnamese indica variety Tetep, displays a high partial resistance to sheath blight. Quantitative trait locus (QTL) analysis of the resistance using simple sequence repeat (SSR) and sequence-tagged site (STS) markers was conducted in a BC₁F₁ population derived from the cross Hinohikari/WSS2//Hinohikari. Sheath blight resistance in this population and its cross-parents was studied using syringe inoculation. Two QTLs for sheath blight resistance (qSB-3 and qSB-12) were identified on chromosomes 3 and 12. Their resistance alleles were derived from the resistant parent WSS2. These QTLs totally explained 29.6% of the phenotypic variation. Sheath blight resistance was significantly correlated with culm length and heading date. Among the QTLs for culm length and heading date, qCL-3 for culm length was located in the same region as qSB-3, and the remaining QTLs were not linked to qSB-12. Thus, it was reasonable to assume that qSB-12 would enable to breed a rice variety resistant to sheath blight.

View full abstract

To investigate the molecular basis for the phenotypic diversity and evolutionary relationships within Oryza sativa, we performed large-scale end sequencing and chromosomal in silico mapping (mapping by sequence homology) of rice BAC (bacterial artificial chromosome) clones derived from an indica rice cultivar, ‘Kasalath’. In total, 78,427 high-quality BAC-end sequences (BESs) showing an average read-length of 482 bp with a total of 37.8 Mb of genomic sequences were obtained from 47,194 BAC clones. After removal of those BESs containing repetitive sequences and use of the high-quality genomic sequence of the japonica rice cultivar ‘Nipponbare’ as a reference standard, 12,170 clones with paired BESs were mapped in silico to the 12 chromosomes. These clones consisted of 450 contigs and showed a total physical length of 308.5 Mb, indicating a coverage of the rice genome of about 80%. Confirmation of the chromosomal positions of the Kasalath BAC clones mapped on chromosome 1 using specific DNA markers revealed that the map accuracy was extremely high: at least 94.8%. In general, the genomic composition and structure of all the chromosomes were highly conserved between the two subspecies. However, we still found evidence suggesting the existence of different components in the genome of the two subspecies within large chromosomal fragments, especially on chromosomes 11 and 12. Extensive analysis of the genomic sequences of Nipponbare and Kasalath revealed a frequency of 0.71% for single nucleotide polymorphisms (SNPs) and 1.23 sites per kilobase for indels (1–16 bp length), respectively. The BAC-based Kasalath map could become an invaluable resource, not only for the isolation of genes, but also for conducting extensive analyses of genomic sequences for comparative genomic studies within or between species.

View full abstract

Starch is the major component of the bread wheat (Triticum aestivum L.) grain and its properties affect the quality of wheat flour and flour products. The amylose content is a principle factor influencing starch properties. K107Afpp4 is a low-amylose mutant line induced from cv. Kanto 107 showing an altered flour-pasting profile on measurement with a Rapid Visco Analyzer (RVA). Its RVA profile is characterized by a markedly increased viscosity at a lower temperature and a decreased peak time. The allelic state of the Wx-D1 locus in K107Afpp4 was clarified by assuming Mendelian segregation of the trait. The RVA profile of the mutant was governed by a single major gene, which was partially dominant to that of its wild type, Kanto 107, and also to that of the backcrossed waxy line with the genetic background of Kanto 107. These results indicated that the gene responsible for the characteristic RVA profile of the mutant is located on the Wx-D1 locus and other loci are unrelated to the trait, suggesting a new allele on the Wx-D1 locus, which is designated Wx-D1g. Since the band intensity of the waxy protein (GBSSI) from K107Afpp4 starch was unaltered from that of the wild type, the waxy protein of the mutant presumably has a structure different from that of Kanto 107 and is probably less functional than that of the wild type.

View full abstract

The last name of the third author in the above-referenced article was misspelled on page 1. It should have appeared as “Osawa” and not “Ohsawa”. Wrong:Ohsawa
Right:Osawa

View full abstract

Also, “RAa” and “RAb” on page 4, should read “RAα” and “RAβ”, respectively. Wrong:RAa, RAb
Right:RAα, RAβ

View full abstract