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Cadmium (Cd) is as an extremely toxic metal that can contaminate agricultural soils. To reduce the risk of Cd intake in food cereals, the development of cultivars with low grain Cd concentration (GCC) is an effective countermeasure. We analyzed quantitative trait loci (QTLs) for GCC in a doubled haploid (DH) common wheat (Triticum aestivum L.) population derived from ‘Chugoku 165’ (low GCC) × ‘Chukei 10-22’ (high GCC). We found novel loci for low GCC on the short arm of chromosome 4B and on the long arm of chromosome 6B. These QTLs accounted for 9.4%–25.4% (4B) and 9.0%–17.8% (6B) of the phenotypic variance in the DH population. An association analysis with 43 cultivars identified 3 loci at these QTLs: QCdc.4B-kita, QCdc.6B-kita1, and QCdc.6B-kita2. In contrast to durum wheat and barley, no QTL was detected on the chromosomes of homeologous group 5 for heavy metal P1B-type ATPase 3. These results will contribute to marker-assisted selection for low GCC in breeding of common wheat.

Amylose (AM) and amylopectin (AP) functionality during bread making was unravelled with a temperature-controlled time domain proton nuclear magnetic resonance (TD 1H NMR) toolbox. Fermented doughs from wheat flour containing starches with atypical AP chain length distribution and/or AM to AP ratio, or supplemented with Bacillus stearothermophilus α-amylase (BStA) were analyzed in situ during baking and cooling. The gelatinization temperature of starch logically depended on AP crystal stability. It was lower when starch contained a higher portion of short AP branches and higher when starch had higher AP content. During cooling, the onset temperature and extent of AM crystallization were positively related to starch AM content. BStA use resulted in slightly weakened starch networks and increased the starch polymers' mobility at the end of baking. That proton distributions evolved in a way corresponding to starch characteristics supports the suggested interpretation of NMR profiles during baking and cooling. ispartof: FOOD CHEMISTRY vol:295 pages:110-119 ispartof: location:England status: published

15 Pags.- 5 Figs.- 3 TAbls.- Supp. Mat. Copyright Owner, the Authors. Under LicenceCC BY 4.0., One option to achieving greater resiliency for barley production in the face of climate change is to explore the potential of winter and facultative growth habits: for both types, low temperature tolerance (LTT) and vernalization sensitivity are key traits. Sensitivity to short-day photoperiod is a desirable attribute for facultative types. In order to broaden our understanding of the genetics of these phenotypes, we mapped quantitative trait loci (QTLs) and identified candidate genes using a genome-wide association studies (GWAS) panel composed of 882 barley accessions that was genotyped with the Illumina 9K single-nucleotide polymorphism (SNP) chip. Fifteen loci including 5 known and 10 novel QTL/genes were identified for LTT—assessed as winter survival in 10 field tests and mapped using a GWAS meta-analysis. FR-H1, FR-H2, and FR-H3 were major drivers of LTT, and candidate genes were identified for FR-H3. The principal determinants of vernalization sensitivity were VRN-H1, VRN-H2, and PPD-H1. VRN-H2 deletions conferred insensitive or intermediate sensitivity to vernalization. A subset of accessions with maximum LTT were identified as a resource for allele mining and further characterization. Facultative types comprised a small portion of the GWAS panel but may be useful for developing germplasm with this growth habit., Support was provided by the USDA-NIFA TCAP Project no. 2011-68002-30029.

Influenza encephalopathy is characterized by high fever, disturbance of consciousness following influenza virus infection. We encountered 2 adult patients with influenza-associated acute necrotizing encephalopathy (Case 1, a 70-year-old woman with diabetes; Case 2, a 49-year-old woman with multiple myeloma), showing hemorrhagic lesions in the bilateral thalamus. Case 1 presented with fever and disturbance of consciousness followed by status epilepticus, and Case 2 developed fever and drowsiness as initial manifestation. Influenza type A was positive in Case 1 and influenza type B was positive in Case 2. In the acute phase, 2 patients required respiratory ventilation and were treated with anti-influenza drug, steroid and immunoglobulin. Cognitive impairment remained in the both patients in the chronic phase. When acute necrotizing encephalopathy is suspected, intensive treatment should be started as early as possible to improve clinical outcome of patients.

Wheat flours are used to produce bread, pasta, breakfast cereals, and biscuits; the various properties of these end-products are attributed to the gluten content, produced as seed storage proteins in the wheat endosperm. Thus, genes encoding gluten protein are major targets of wheat breeders aiming to improve the various properties of wheat flour. Here, we describe a novel compensating wheat-Thinopyrum elongatum Robertsonian translocation (T1AS.1EL) line involving the short arm of wheat chromosome 1A (1AS) and the long arm of Th. elongatum chromosome 1E (1EL); we developed this line through centric breakage-fusion. Compared to the common wheat cultivars Chinese Spring and Norin 61, we detected two additional 1EL-derived high-molecular-weight glutenin subunits (HMW-GSs) in the T1AS.1EL plants. Based on the results of an SDS-sedimentation volume to estimate the gluten strength of T1AS.1EL-derived flour, we predict that T1AS.1EL-derived flour is better suited to bread-making than Chinese Spring- and Norin 61-derived flour and that this is because of its greater gluten diversity. Also, we were able to assign 33 of 121 wheat PCR-based Landmark Unique Gene markers to chromosome 1E of Th. elongatum. These markers can now be used for further chromosome engineering of the Th. elongatum segment of T1AS.1EL.

Milling properties and flour color are essential selection criteria in soft wheat breeding. However, high phenotypic screening costs restrict selection to relatively few breeding lines in late generations. To achieve marker-based selection of these traits in early generations, we performed genetic dissection of quality traits using three doubled haploid populations that shared the high-quality soft wheat variety Kitahonami as the paternal parent. An amplicon sequencing approach allowed effective construction of well-saturated linkage maps of the populations. Marker-based heritability estimates revealed that target quality traits had relatively high values, indicating the possibility of selection in early generations. Taking advantage of Chinese Spring reference sequences, joint linkage maps of the three populations were generated. Based on the maps, multifamily quantitative trait locus (QTL) analysis revealed a total of 86 QTLs for ten traits investigated. In terms of target quality traits, 12 QTLs were detected for flour yield, and 12 were detected for flour redness (a* value). Among these QTLs, six for flour yield and nine for flour a* were segregating in more than two populations. Some relationships among traits were explained by QTL collocations on chromosomes, especially group 7 chromosomes. Ten different ideotypes with various combinations of favorable alleles for the flour yield and flour a* QTLs were generated. Phenotypes of derivatives from these ideotypes were predicted to design ideal genotypes for high-quality wheat. Simulations revealed the possibility of breeding varieties with better quality than Kitahonami.

Durum wheat (L.) cultivars can benefit from having some level of seed dormancy to help reduce seed damage and lower grain quality caused by preharvest sprouting (PHS) occurring during wet harvesting conditions. Previously, a single chromosome substitution line carrying chromosome 2B of wild emmer [ L. subsp. (Korn. ex Asch. & Graebn.) Thell.] in the durum cultivar Langdon background was found to have higher levels of seed dormancy and PHS tolerance. In this study, a population of recombinant substitution lines was developed and used to construct a single nucleotide polymorphism (SNP)-based high-density genetic linkage map. Seed germination tests were used to evaluate seed dormancy levels. Multiple interval mapping analysis revealed four quantitative trait loci (QTL) regions affecting seed dormancy. Two regions containing major-effect QTL contributed by wild emmer were consistently expressed in four environments and explained 5.89 to 11.14% of the phenotypic variation. One QTL region was located near the centromere and the other on the long arm of chromosome 2B in Bayes credible intervals of 4 and 7 cM, respectively. Recombinant inbred lines (RILs) carrying both QTL had an average of 35% reduced rate of germination measured by weighted germination index compared with RILs carrying neither QTL. The two QTL regions identified in this study should be useful for improving PHS tolerance in wheat. Efforts to transfer the two QTL into elite durum cultivars are in progress to examine the effects of genetic background and environment on QTL expression and to evaluate the performance of other agronomic traits in the presence of the QTL.

Yellow mosaic disease, caused by wheat yellow mosaic virus (WYMV), is one of the most serious diseases of winter wheat (Triticum aestivum L.) in Japan. The three pathotypes of WYMV are distributed in different geographical areas: pathotype I is found mainly in western and central Japan (Kanto), pathotype II in northern Japan (Tohoku and Hokkaido) and pathotype III on the southern island of Japan (Kyushu). A total of 246 doubled-haploid (DH) lines, derived from a cross between ‘Yumechikara’ (resistant) and ‘Kitahonami’ (susceptible), were evaluated for 2 years for their resistance to WYMV pathotype I. A single major quantitative trait locus, Q.Ymym, mapping to chromosome 2D was associated with resistance to pathotype I in ‘Yumechikara’. This is the first time a QTL responsible for pathotype I resistance has been identified. Fine mapping of Q.Ymym indicated that it was on a tight linkage block originating from ‘Yumechikara’, and the markers associated with this block will accelerate the development of varieties resistant to WYMV pathotype I.

In common wheat, the development of genotyping platforms has been hampered by the large size of the genome, its highly repetitive elements and its allohexaploid nature. However, recent advances in sequencing technology provide opportunities to resolve these difficulties. Using next-generation sequencing and gene-targeting sequence capture, 12,551 nucleotide polymorphisms were detected in the common wheat varieties ‘Hatsumochi’ and ‘Kitahonami’ and were assigned to chromosome arms using International Wheat Genome Sequencing Consortium survey sequences. Because the number of markers for D genome chromosomes in commercially available wheat single nucleotide polymorphism arrays is insufficient, we developed markers using a genome-specific amplicon sequencing strategy. Approximately 80% of the designed primers successfully amplified D genome-specific products, suggesting that by concentrating on a specific subgenome, we were able to design successful markers as efficiently as could be done in a diploid species. The newly developed markers were uniformly distributed across the D genome and greatly extended the total coverage. Polymorphisms were surveyed in six varieties, and 31,542 polymorphic sites and 5,986 potential marker sites were detected in the D genome. The marker development and genotyping strategies are cost effective, robust and flexible and may enhance multi-sample studies in the post-genomic era in wheat.

We report here that the mutation causing fractured starch granules in the barley line “Franubet” results from a point mutation in the barley gene corresponding to the rice FLO6 gene. The “fra” mutation in barley, which was originally isolated and characterized over 30 years ago, results in fractured starch granules and an opaque phenotype. This mutation has been used in breeding programs, since it appears to be useful in the production of pearled barley for human consumption. However, selection for this phenotype is difficult, since wild-type and heterozygous kernels cannot be distinguished phenotypically, and until now, the gene involved in this mutation has not been determined. Here, we used a map-based cloning approach using nanopore sequencing to obtain long reads from a BAC clone carrying markers on either side of the fra locus. By fine mapping followed by aligning RNA-seq reads to four genes within the mapped region, we were able to determine that the fra mutation is caused by the introduction of a stop codon in the barley homologue of the rice FLOURY ENDOSPERM 6 (FLO6) gene. This gene has a CBM48 domain that binds to starch, and may act through interactions with isoamylase1 (ISA1), assisting in the binding of ISA1 to starch granules. Perfect markers able to distinguish all genotypes were designed and tested in several large populations; in all cases, the markers were able to distinguish wild-type, heterozygous, and mutant genotypes.

A 26-year-old, otherwise healthy man presented with visual abnormality followed by loss of consciousness and convulsion. The patient then developed headache and fever 14 days later. Brain MRI showed hyperintensities in the left cingulate cortex. The cerrebrospinal fluid examinations showed mononuclear pleocytosis and positive PCR results for human herpesvirus 6 (HHV-6). A diagnosis of HHV-6 encephalitis and symptomatic epilepsy was made. The patient's clinical symptoms improved promptly following acyclovir treatment. However, 3 months later the patient noticed dysesthesia in the trunk, the left upper limb and the right lower limb. Brain and spine MRI showed multiple brain white matter lesions, the middle cerebellar peduncle and cervical spinal lesions. The symptoms resolved following methylprednisolone pulse therapy only. We report an adult patient with HHV-6 encephalitis followed by acute disseminated encephalomyelitis whose initial presentation was epilepsy. HHV-6 encephalitis should be included in the differential diagnosis of encephalitis of unknown etiology in an immunocompetent adult.

The pathogenicity of Newcastle disease (ND) virus, isolated from ND outbreak in vaccinated chickens, was evaluated through experiments. The pathogenicity indexes (mean death time (MDT); 58 hr, intracerebral pathogenicity index (ICPI); 1.7 and intravenous pathogenicity index (IVPI); 2.51) indicated that the ND virus was velogenic. The ND virus caused lymphocytic necrosis in the spleen with fibrinous exudation and proliferation of macrophages, sinusoidal fibrin exudation in the liver, proliferation of macrophages in the lung, lymphocytic necrosis and depletion in the bursa of Fabricius, cecal tonsils and thymus, necrosis of bone marrow, tracheitis, conjunctivitis and necrosis of feather epithelial cells in specific-pathogen-free chickens. Immunohistochemically, ND virus antigens were seen in the lesions mentioned above. The ND virus could not induce the encephalitis and pancreatitis that were observed in the natural case of ND in vaccinated chickens. There was no clinical disease in vaccinated chickens after the challenge of the ND virus. In diluted ND vaccine experiments, chickens vaccinated with a high dilution of vaccine and then challenged with the ND virus showed clinical sign and mortality with pancreatic focal necrosis. Vaccine diluted with fresh tap water had no effect on protection against the challenge of the ND virus. This study suggests that improper vaccination may be involved in outbreaks of ND in vaccinated chickens.

Based on the similarity in gene structure between rice and wheat, the polymerase chain reaction (PCR)-based landmark unique gene (PLUG) system enabled us to design primer sets that amplify wheat genic sequences including introns. From the previously reported wheat PLUG markers, we chose 144 markers that are distributed on different chromosomes and in known chromosomal regions (bins) to obtain rye-specific PCR-based markers. We conducted PCR with the 144 primer sets and the template of the Imperial rye genomic DNA and found that 131 (91.0%) primer sets successfully amplified PCR products. Of the 131 PLUG markers, 110 (76.4%) markers showed rye-specific PCR amplification with or without restriction enzyme digestion. We assigned 79 of the 110 markers to seven rye chromosomes (1R to 7R) using seven wheat-rye (cv. Imperial) chromosome addition and substitution lines: 12 to 1R, 8 to 2R, 11 to 3R, 8 to 4R, 16 to 5R, 12 to 6R, and 12 to 7R. Furthermore, we located their positions on the short or long (L) chromosome arm, using 13 Imperial rye telosomic lines of common wheat (except for 3RL). Referring to the chromosome bin locations of the 79 PLUG markers in wheat, we deduced the syntenic relationships between rye and wheat chromosomes. We also discussed chromosomal rearrangements in the rye genome with reference to the cytologically visible chromosomal gaps.

Japanese barnyard millet is an important food source in East Asian countries. However its crumbly texture limits desirability and consumption. Controlling amylose level in the endosperm is important to improve the eating quality of the millet. Because it is well known that the waxy gene determines the amylose level in the endosperm, we conducted a molecular analysis of the gene. Segregation analysis revealed that wild-type cultivars had three functional genes while low-amylose cultivars had one. We determined complete sequences of the three homoeologous waxy structural genes, EeWx1, EeWx2 and EeWx3, in a wild-type cultivar. These sequences showed high homology in the exon regions (97 %), and lower homology in the introns (82 %). Two spontaneous mutations were characterized in the low-amylose cultivars. In addition, one induced mutation was found in the fully waxy cultivar, Chojuromochi. Spontaneous mutations are deletions of whole and terminal regions in the EeWx2 and EeWx3 alleles, respectively. The induced mutation is a single-base deletion that led to a premature termination codon in EeWx1. These findings led us to develop useful markers for selecting low-amylose and waxy lines in millet.

The double mutant "sweet wheat" (SW), which produces substantial amounts of sugars in immature seeds, is missing two starch synthases, namely granule-bound starch synthase I (GBSSI) and starch synthase IIa (SSIIa). The lack of these two enzymes causes major changes in the attributes of SW seed, starch, and starch granules. SW seeds appear normal during early stages of development, but become shrunken when seeds begin to mature and dry. However, even in immature seed, starch granules are small and misshapen, and high levels of maltose are present throughout seed development. The crystallinity of SW starch is altered in that a major peak typical of the cereal A-type diffraction pattern is absent, and the gelatinization temperature of SW starch is considerably lower than that of wild-type starch. Amylopectin from SW seed has a substantially lower molecular weight than that from wild-type seed, and a low molecular weight peak with a bimodal distribution is found only in SW starch. This peak contains linear malto-oligosaccharides as well as short, branched glucans. SW starch has an increased proportion of branches with DP10, and chains with DP 2 and 3 are particularly increased. These changes suggest that sweet wheat starch is being modified in an atypical manner by isoamylases and/or β-amylases.

Dibutylphthalate (DBP), di(2-ethylhexyl)phthalate (DEHP), and di(2-ethylhexyl)adipate (DEHA) are used as plasticizers. Their metabolites activate peroxisome proliferator-activated receptor (PPAR) α, which may be related to their toxicities. However, species differences in the receptor functions between rodents and human make it difficult to precisely extrapolate their toxicity from animal studies to human. In this paper, we compared the species differences in the activation of mouse and human hepatic PPARα by these plasticizers using wild-type (mPPARα) and humanizedPPARα (hPPARα) mice. At 12 weeks old, each genotyped male mouse was classified into three groups, and fed daily for 2 weeks per os with corn oil (vehicle control), 2.5 or 5.0 mmol/kg DBP (696, 1392 mg/kg), DEHP (977, 1953 mg/kg), and DEHA (926, 1853 mg/kg), respectively. Generally, hepatic PPARα ofmPPARα mice was more strongly activated than that ofhPPARα mice when several target genes involving β-oxidation of fatty acids were evaluated. Interestingly, all plasticizers also activated hepatic constitutive androstane receptor (CAR) more inhPPARα mice than inmPPARα mice. Taken together, these plasticizers activated mouse and human hepatic PPARα as well as CAR. The activation of PPARα was stronger inmPPARα mice than inhPPARα mice, while the opposite was true of CAR.

It has long been known that a bacterial leaf blight-resistant line in rice obtained from a crossing using ‘Asominori’ as a resistant parent also has resistance to blast, but a blast resistance gene in ‘Asominori’ has not been investigated in detail. In the present study, a blast resistance gene in ‘Asominori’, tentatively named Pias(t), was revealed to be located within 162-kb region between DNA markers YX4-3 and NX4-1 on chromosome 4 and to be linked with an ‘Asominori’ allele of the bacterial leaf blight resistance gene Xa1, tentatively named Xa1-as(t). An ‘Asominori’ allele of Pias(t) was found to be dominant and difference of disease severity between lines having the ‘Asominori’ allele of Pias(t) and those without it was 1.2 in disease index from 0 to 10. Pias(t) was also closely linked with the Ph gene controlling phenol reaction, suggesting the possibility of successful selection of blast resistance using the phenol reaction. Since blast-resistant commercial cultivars have been developed using ‘Asominori’ as a parent, Pias(t) is considered to be a useful gene in rice breeding for blast resistance.

Approximately 70% of wheat endosperm consists of starch, and variations in the quality and quantity of starch affect the processing characteristics of wheat flour. Amylose content in particular has a major effect on Asian noodle quality, and selection of wheat lines with slightly lower amylose levels is an important goal in Japanese wheat breeding programs. Accurately measuring amylose content by direct methods such as colorimetric assays was found to be problematic, suggesting there was a need for a more efficient and accurate method of screening for reduced amylose content. Therefore, we characterized mutations in the wheat waxy genes, which control amylose synthesis, and developed DNA markers for the identification of null waxy alleles. In this review, we describe the development of these markers and outline their utility for wheat breeding programs.

Several species of the genus Aegilops, wild relatives of wheat (Triticum aestivum, 2n = 6x = 42, AABBDD) carry gametocidal (Gc) genes. Gc genes kill the gametes without themselves by causing chromosomal breakage during post-meiotic cell divisions, and therefore are strong segregation distorters. The Gc gene Gc3-C1 derived from chromosome 3C of Ae. triuncialis (2n = 4x = 28, CCUU) induces chromosomal breakage in wheat cultivar 'Chinese Spring' (CS) but not in cultivar 'Norin 26' (N26). This cultivar-specific inhibition of Gc function is caused by a suppressor gene Igc1 located on chromosome 3B of N26. Igc1 is presumed to be a modified Gc gene without breakage function because of its homoeology to Gc3-C1. Here we report the results of linkage and physical mapping of Igc1 to help elucidate the molecular mechanisms underlying Gc action. Segregation analysis of the phenotypic data in BC(1)F(1) mapping population of the cross between (CSxN26)F(1) and CS + 3C" showed a 1:1 segregation ratio indicating that Igc1 is a dominant gene. In the linkage analysis, three molecular marker loci Xgwm285, Xgwm376, and Xcfp1886 cosegregated with the Igc1 locus. Bin mapping assigned the loci Xgwm285 and Xcfp1886 to bin C-3BS1-0.33 and Xgwm376 to bin C-3BL2-0.22. Physical mapping using Gc-induced chromosomal deletion lines of chromosome 3B of N26 revealed that the Igc1 locus resides in 52.0% or 2.1% of bins C-3BS1-0.33 and C-3BL2-0.22, respectively. Pericentromeric localization of Igc1 in chromosome 3B of N26 may have a positive effect to keep the two-component system of the Gc action. Map-based cloning approach to isolate the Igc1 may be difficult because recombination is depleted in the pericentromeric region. As is shown in this study, the combination of genetic and physical mapping offers high efficiency to identify the regions where genes are located especially in regions with low levels of recombination.

Perfluorooctanoic acid (PFOA) is a ligand for peroxisome proliferator-activated receptor (PPAR) alpha, which exhibits marked species differences in expression and function, especially between rodents and humans. We investigated the functional difference in PFOA response between mice and humans, using a humanized PPARalpha transgenic mouse line. Three genotyped mice, 129/Sv wild-type (mPPARalpha), Pparalpha-null mice and humanized PPARalpha (hPPARalpha) mice (8-week-old males) were divided into three groups: the first was treated with water daily for 2 weeks by gavage (control group), and the remaining two groups were treated with 0.1 and 0.3mg/kg ammonium perflurooctanate (APFO), respectively, for 2 weeks by gavage. The APFO dosages used did not influence the plasma triglyceride or total cholesterol levels in any mouse line, but the high dose increased both hepatic lipid levels only in mPPARalpha mice. APFO increased mRNA and/or protein levels of PPARalpha target genes cytochrome P450 Cyp4a10, peroxisomal thiolase and bifunctional protein only in the liver of mPPARalpha mice, but not in Pparalpha-null or hPPARalpha mice. This chemical also increased expression of mitochondrial very long chain acyl-CoA dehydrogenase only in the liver of mPPARalpha mice. Taken together, human PPARalpha may be less responsive to PFOA than that of mice when a relatively low dose is applied. This information may be very valuable in considering whether PFOA influences the lipid metabolism in humans.

Waxy protein (granule-bound starch synthase I) is a key enzyme in the synthesis of amylose in endosperm tissue. The amylose content of wheat flour plays a significant role in determining Japanese udon noodle quality. Most wheat cultivars suitable for producing udon noodles have a low amylose level due to a lack of Wx-B1 protein conditioned by null Wx-B1 alleles. It was previously determined that the entire coding region of the wheat Wx-B1 gene is deleted in the most common null allele. However, the extent and breakpoints of the deletion have not been established. In this study, the position of the 3′ deletion breakpoint was refined by mapping with PCR-based markers. Using information from this analysis, a chromosome walk was initiated and the DNA sequence flanking the deletion breakpoints was obtained. The deletion included a 3,872 bp region downstream from the termination codon of Wx-B1 gene. Based on similarity with T. monococcum sequences, it was estimated that approximately 60 kb upstream of the Wx-B1 gene was also deleted. Using this sequence information, a codominant marker for the identification of the Wx-B1 null allele was developed. This marker can unambiguously identify heterozygous plants, which will accelerate the selection of partial waxy mutants carrying the Wx-B1 null allele.

Rye chromosome 1R contains many agronomically useful genes. Physical dissection of chromosome 1R into segments would be useful in mapping 1R-specific DNA markers and in assembling DNA clones into contig maps. We applied the gametocidal system to produce rearranged 1R chromosomes of Imperial rye (1R(i)) added to common wheat. We identified rearranged 1R(i) chromosomes and established 55 1R(i) dissection lines of common wheat carrying a single rearranged 1R(i) chromosome. Fifty-two of the rearranged 1R(i) chromosomes had single breakpoints and three had double breakpoints. The 58 breakpoints were distributed in the short arm excluding the satellite (12 breakpoints), in the satellite (4), in the long arm (28), and in the centromere (14). Out of the 55 lines, nine were homozygous for the rearranged 1R(i) chromosomes, and the remaining lines were hemizygous. We developed 26 PCR-based EST markers that were specific to the 1R(i) chromosome, and nine of them amplified 1R(i) arm-specific PCR products without restriction-enzyme digestion. Using the nine EST markers and two previously reported 1R-specific markers, we characterized the 55 1R(i) dissection lines, and also proved that we can select critical progeny plants carrying specific rearranged 1R(i) chromosomes by PCR, without cytological screening, in 48 out of the 55 hemizygous dissection lines.

In hexaploid crops, such as bread wheat, it should be possible to fine-tune phenotypic traits by identifying wild-type and null genes from each of the three genomes and combining them in a calculated manner. Here, we demonstrate this with gene combinations for two starch synthesis genes, SSIIa and GBSSI. Lines with inactive copies of both enzymes show a very dramatic change in phenotype, so to create intermediate phenotypes, we used marker-assisted selection to develop near-isogenic lines (NILs) carrying homozygous combinations of null alleles. For both genes, gene dosage effects follow the order BD ≥ A; therefore, we completed detailed analysis of starch characteristics for NIL 3-3, which is null for the B-genome copy of the SSIIa and GBSSI genes, and NIL 5-5, which has null mutations in the B- and D-genome-encoded copies of both of these genes. The effects of the combinations on phenotypic traits followed the order expected on the basis of genotype, with NIL 5-5 showing the largest differences from the wild type, while NIL 3-3 characteristics were intermediate between NIL 5-5 and the wild type. Differences among genotypes were significant for many starch characteristics, including percent amylose, chain length distribution, gelatinization temperature, retrogradation, and pasting properties, and these differences appeared to translate into improvements in end-product quality, since bread made from type 5-5 flour showed a 3 day lag in staling.

Background A complete genome sequence is an essential tool for the genetic improvement of wheat. Because the wheat genome is large, highly repetitive and complex due to its allohexaploid nature, the International Wheat Genome Sequencing Consortium (IWGSC) chose a strategy that involves constructing bacterial artificial chromosome (BAC)-based physical maps of individual chromosomes and performing BAC-by-BAC sequencing. Here, we report the construction of a physical map of chromosome 6B with the goal of revealing the structural features of the third largest chromosome in wheat. Results We assembled 689 informative BAC contigs (hereafter reffered to as contigs) representing 91 % of the entire physical length of wheat chromosome 6B. The contigs were integrated into a radiation hybrid (RH) map of chromosome 6B, with one linkage group consisting of 448 loci with 653 markers. The order and direction of 480 contigs, corresponding to 87 % of the total length of 6B, were determined. We also characterized the contigs that contained a part of the nucleolus organizer region or centromere based on their positions on the RH map and the assembled BAC clone sequences. Analysis of the virtual gene order along 6B using the information collected for the integrated map revealed the presence of several chromosomal rearrangements, indicating evolutionary events that occurred on chromosome 6B. Conclusions We constructed a reliable physical map of chromosome 6B, enabling us to analyze its genomic structure and evolutionary progression. More importantly, the physical map should provide a high-quality and map-based reference sequence that will serve as a resource for wheat chromosome 6B. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1803-y) contains supplementary material, which is available to authorized users.

The soybean cultivar Yumeminori, which lacks the α′- and α-subunits of β-conglycinin, carries both naturally occurring and induced mutations. While the cause of the natural mutation resulting in the α′-subunit deficiency has been determined, the induced mutation in the CG-2 gene encoding the α-subunit has not been characterized at the molecular level. In this study, we identified a four base pair insertion in the first exon of CG-2, which introduced a premature stop codon. The insertion co-segregated with the lack of α-subunit, indicating that this mutation is the cause of the α-subunit deficiency. A multiplex PCR method of testing for the presence or absence of α′- and α-subunits was developed based on the sequences of mutated and wild-type alleles. This PCR-based test was also capable of detecting the presence of wild-type genes when Yumeminori DNA samples were contaminated with wild-type DNA at levels of 0.2% or greater. Thus, this method will be useful both for marker-assisted selection in soybean breeding programs, and for seed purity tests in food industries.

パンコムギ品種「関東107号」におけるWx-B1遺伝子の変異は，麺用コムギに適する「やや低アミロース」形質の要因であり，育種における重要な選抜指標となっている．その変異の原因がコード領域全体の欠失であることは既に報告されているが，そのゲノム上での欠失点はまだ明らかにされていない．そこで，本研究では，コムギEST情報，オオムギおよびヒトツブコムギの waxy遺伝子を含むBACクローン塩基配列情報，さらにはイネゲノム情報を利用してマーカーを作製することにより，1） Wx-B1遺伝子下流の欠失点は，終止コドンから3.3 kbから6 kbの間に存在すること，2）同欠失により， Wx-B1遺伝子の下流に存在する機能未知の遺伝子も同時に欠失していることを明らかにした．

Wheat (Triticum aestivum L.) starch synthase II, which is also known as starch granule protein 1 (SGP-1), plays a major role in endosperm starch synthesis. The three SGP-1 proteins, SGP-A1, B1 and D1, are produced by three homoeologous SSII genes, wSSII-A, B, and D. Lines carrying null alleles for each SGP-1 protein have previously been identified. In this report, the mutations occurring in each wSSII gene were characterized, and PCR-based DNA markers capable of detecting the mutations were developed. In the null wSSII-A allele, a 289 bp deletion accompanied by 8 bp of filler DNA was present near the initiation codon. A 175 bp insertion occurred in exon 8 of the null wSSII-B allele. The insertion represented a recently discovered miniature inverted-repeat transposable element (MITE) named Hikkoshi that was first found in a wheat waxy gene. A 63 bp deletion was found at the region surrounding the junction of the fifth exon and intron of the null wSSII-D allele. Based on this information, we designed primer sets to enable us to conduct allele-specific amplifications for each locus. The applicability of these primer sets for breeding programs was demonstrated by reconstructing a line lacking all three SGP-1 proteins using marker-assisted selection. These markers will also be useful in breeding programs aimed at obtaining partial mutants missing one or two SGP-1 proteins.

Expression profiles of a set of Cor/Lea genes were assessed during early stages of cold acclimation in seedlings of two wheat cultivars, which showed contrasting levels of freezing tolerance. These Cor/Lea family members consisted of three EST clones and 13 previously identified cDNA clones of wheat and rye. Northern blot analysis using RNA extracted from seedling leaves and roots showed that most of the genes exhibited a quite similar time-course of expression, although with different expression levels: They rapidly responded to low temperature and their transcript levels reached high plateaus within 3-5 days. The overall gene expression profiles were correlated with the time-dependent development and the level of freezing tolerance under low temperature in the two cultivars. Western blot analysis of protein accumulation further verified this observation. Abscissic acid response was proved for at least four genes. Light was stimulatory to most of the genes, and this positive light response associated with low temperature occurred not only in leaf-specific genes but also in leaf/root-expressed genes. Taken together, the present results suggest that the Cor/Lea gene family represents a major group of downstream genes involved in the ABA-dependent and -independent signal pathways and that most of them are co-regulated in determining freezing tolerance in wheat seedlings.

In the past two decades, three types of starch mutants, waxy (Wx), high amylose (HA) and sweet type wheat (SW) have been developed in Japan. Each of these lines was obtained by identifying “partial“ mutants with mutations in one or two homeoelogous genes derived from the A, B or D-genomes, followed by crossing to produce fully null mutants. The Wx line lacks the three granule-bound starch synthase I (GBSSI) proteins responsible for amylose synthesis, and HA lacks the three starch synthase IIa (SSIIa) enzymes that are involved in amylopectin synthesis. SW lacks all active GBSSI and SSIIa enzymes. “Partial“ null mutants have also been used to obtain more subtle modifications in starch quality. For example, the GBSSI-B1 single null lines produce starch which is slightly reduced in amylose. This suggested that the identification of other desirable lines using MAS would allow us to further fine-tune starch characteristics. Sixty-four homozygous lines differing in GBSSI and SSIIa composition can be selected from progeny of crosses between HA and Wx. Co-dominant markers for all GBSSI and SSIIa genes enabled us to select all 64 lines quickly and effectively. The modulation of starch characteristics serves as a model that demonstrates the utility of mutation identification in combination with MAS in hexaploid wheat. The availability of genome sequence information, combined with new methods of mutation detection, reduces the amount of work involved in finding single mutations in wheat, and one can easily see the potential for expanding this methodology to other traits.

The soft winter wheat variety, Kitahonami, shows a superior flour yield in comparison to other Japanese soft varieties. In order to map quantitative trait loci (QTL) associated with the flour-yield trait, association mapping was performed using panel lines in Kitahonami’s pedigree, along with leading varieties and advanced breeding lines. Using a mixed linear model corrected for kernel types and familial relatedness, 62 marker-trait associations were identified and classified into 21 QTLs. Five out of eight QTLs tested were validated by linkage analyses using three sets of doubled haploid populations from crosses in which Kitahonami was used as a parent. Among them, QTLs on 3B and 7A chromosome showed highly significant effects and consistency across the three populations. A joint linkage map of 3B showed that the QTL on this chromosome was located at the same interval across the populations. By applying a meta-analysis approach, we have succeeded in identifying QTLs with consistent contributions to high flour yield across various genetic backgrounds.

The ClpB/Hsp104 chaperone solubilizes and reactivates protein aggregates in cooperation with DnaK/Hsp70 and its cofactors. The ClpB/Hsp104 protomer has two AAA+ modules, AAA-1 and AAA-2, and forms a homohexamer. In the hexamer, these modules form a two-tiered ring in which each tier consists of homotypic AAA+ modules. By ATP binding and its hydrolysis at these AAA+ modules, ClpB/Hsp104 exerts the mechanical power required for protein disaggregation. Although ATPase cycle of this chaperone has been studied by several groups, an integrated understanding of this cycle has not been obtained because of the complexity of the mechanism and differences between species. To improve our understanding of the ATPase cycle, we prepared many ordered heterohexamers of ClpB from Thermus thermophilus, in which two subunits having different mutations were cross-linked to each other and arranged alternately and measured their nucleotide binding, ATP hydrolysis, and disaggregation abilities. The results indicated that the ATPase cycle of ClpB proceeded as follows: (i) the 12 AAA+ modules randomly bound ATP, (ii) the binding of four or more ATP to one AAA+ ring was sensed by a conserved Arg residue and converted another AAA+ ring into the ATPase-active form, and (iii) ATP hydrolysis occurred cooperatively in each ring. We also found that cooperative ATP hydrolysis in at least one ring was needed for the disaggregation activity of ClpB.

A 31-year-old man with pontine infarction was referred to our hospital for further evaluation and treatment. At admission, his neurological examination was unremarkable. No lymphadenopathy or skin lesions were found. The Treponema pallidum haemagglutination test, rapid plasma regain test and fluorescent treponemal antibody absorption test of immunoglobulin G were positive in both serum and cerebrospinal fluid (CSF). CSF analysis showed lymphocytic pleocytosis. The patient had male-to-male sexual contact and was found to be HIV positive. Physicians should be aware that acute ischaemic stroke may be the first manifestation of neurosyphilis in a young adult, especially with HIV infection.

Studies of waxy mutations in wheat and other cereals have shown that null mutations in genes encoding granule-bound starch synthase I (GBSSI) result in amylose-free starch in endosperm and pollen grains, whereas starch in other tissues may contain amylose. We have isolated a cDNA from waxy wheat that encodes GBSSII, which is thought to be responsible for the elongation of amylose chains in non-storage tissues. The deduced amino acid sequences of wheat GBSSI and GBSSII were almost 66% identical, while those of wheat GBSSII and potato GBSSI were 72% identical. GBSSIIwas expressed in leaf, culm, and pericarp tissue, but transcripts were not detected in endosperm tissue. In contrast, GBSSIexpression was high in endosperm tissue. The expression ofGBSSII mRNA in pericarp tissue was similar at the midpoints of the day and night periods. The GBSSII genes were mapped to chromosomes 2AL, 2B, and 2D, whereasGBSSI genes are located on group 7 chromosomes. Gel-blot analysis indicated that genes related to GBSSII also occur in barley, rice, and maize. The possible role ofGBSSII in starch synthesis is discussed.

The growth and O2 uptake of roots under low , and the cytochrome c oxidase activities were compared between flooding-tolerant rice (Oryza sativa L. cv. Fujisaka 5) plants and flooding-sensitive wheat (Triticum aestivum L. cv. Chinese Spring) plants. The roots of 2- to 3-week-old seedlings were used. The growth of the roots laid on Murashige and Skoog (MS) medium in a gas incubator at 1, 2, 5, 21% O2 concentrations at 25°C during 30 d was examined. The O2 uptake of the roots laid on MS medium in sealed test tubes filled with gas containing various O2 concentrations (0, 0.5, 1, 2, 5, 10, 21%) was measured by gas chromatography. The crude cytochrome c oxidase was prepared from roots and the O2 uptake was measured with an O2 electrode. The growth reduction and O2 uptake of the roots were observed at a concentration of O2 below 2% in rice, and below 5% in wheat. There was a correlation between the growth and oxygen uptake rate. The O2 uptake activity of cytochrome c oxidase did not differ between rice...

The Waxy (Wx) protein has been identified as granule-bound starch synthase (GBSS; EC 24.1.21), which is involved in amylose synthesis in plants. Although common wheat (Triticum aestivum L.) has three Wx proteins, "partial waxy mutants" lacking one or two of the three proteins have been found. Using such partial waxy mutants, tetra- and hexaploid waxy mutants with endosperms that are stained red-brown by iodine were produced. Both mutants showed loss of Wx protein and amylose. This is the first demonstration of genetic modification of wheat starch.

Near-isogenic lines (NILs) of the eight haplotypes of starch synthase IIa (SSIIa) were used to analyze the effects of SSIIa gene dosage on branch chain length, gelatinization, pasting, retrogradation, and enzymatic hydrolysis of starches. Compared to wild-type, the amylopectin of lines missing one or more active SSIIa enzymes had increases in the proportion of short branch chains (DP6-10) and decreases in midlength chains (DP11-24), and the size of these differences depended on the dosage of active SSIIa enzymes. Of the three loci, SSIIa-A1 had the smallest contribution to amylopectin structure and SSIIa-B1 the largest. The different effects of the three SSIIa enzymes on starch properties were also seen in gelatinization, retrogradation, pasting, and enzymatic hydrolysis properties. Such differences in starch properties might be useful in influencing the texture and shelf life of food products.

Deficiency of the wheat waxy (Wx) proteins (Wx-A1, Wx-B1 and Wx-D1) was studied in 1,960 cultivars derived from several countries. Gel electrophoretic analyses revealed that the null allele for the Wx-A1 protein occurred frequently in Korean, Japanese and Turkish wheats but was relatively rare in cultivars from other countries and regions. About 48% of the wheats deficient for the Wx-B1 protein were from Australia and India. One Chinese cultivar lacked the WxD1 protein. While 9 Japanese cultivars were deficient in both the Wx-A1 and Wx-B1 proteins, no cultivars lacked both the Wx-A1 and Wx-D1 proteins, both the Wx-B1 and Wx-D1 proteins or all three Wx proteins. Two-dimensional gel electrophoresis revealed polymorphisms of the three Wx proteins that varied according to isoelectric points or molecular weight. The Wx-A1 gene coding the Wx-A1 protein and the Wx-B1 gene coding the Wx-B1 protein were localized in the distal regions of chromosome arms 7AS and 4AL, respectively, by deletion mapping using the deletion lines developed in the common wheat cultivar 'Chinese Spring'.

Sweet wheat (SW), which lacks functional granule-bound starch synthase I (GBSSI) and starch synthase IIa (SSIIa), accumulates high levels of free sugars in immature seeds. Here, we examined the effects of the lack of these two enzymes on mature kernel composition. Whole grain flour of SW had higher levels of sugars, particularly maltose, slightly higher ash and protein content, approximately two to three times higher lipid levels, and about twice as much total dietary fiber as parental or wild-type lines. Considerably higher levels of low-molecular-weight soluble dietary fiber (LMW-SDF), largely consisting of fructan, were also detected in SW. Although there were no differences in total amino acid levels, the free amino acid content of SW was approximately 4-fold higher than that of wild type, and the levels of certain free amino acids such as proline were particularly high. Thus, we were able to clearly demonstrate that the lack of GBSSI and SSIIa caused dramatic changes in mature seed composition in SW. These compositional changes suggest that SW flour may provide health benefits when used as a food ingredient.

Maize waxy (Wx) protein, which has been detected as a single protein with a M r 60 000 by sodium dodecylsulphate polyacrylamide gel electrophoresis (SDS-PAGE), was separated into four isoforms by 2D-PAGE. The isoelectric point (p I ) of these isoforms ranged from 6.0 to 6.5. Starch isolation with SDS-buffer and heat-extraction of protein from starch granules had no effect on the 2D electrophoretic patterns of Wx protein. Rice and barley Wx proteins were also analysed by the same method and separated into four and three isoforms, respectively. Rice Wx protein isoforms had a M r of 60 000 as had been reported with a p I range from 6.5 to 7.2 while barley Wx protein isoforms had a M r of 61 000 and p I in the range of 5.8 to 6.3.

A 24-year-old woman presented subdural empyema developing from sinusitis caused by Porphyromonas and Fusobacterium infection. She experienced fever and progressive headache with gradually worsening symptoms. Neurological examination revealed drowsiness and neck stiffness. A CSF examination detected pleocytosis and a low glucose level. Gadolinium-enhanced T1-weighted images from brain MRI showed thickening enhancement at the leptomeninges in the left frontal to temporal lobes and interhemispheric fissure with edema. Based on the diagnosis of bacterial meningoencephalitis and subdural empyema developing from sinusitis primary to odontogenic infection, she received antibacterial chemotherapy with meropenem hydrate and vancomycin hydrochloride, after which motor aphasia and consciousness disturbance occurred. No bacteria were isolated from a trans-sphenoidal biopsy specimen and CSF culture. Molecular typing also was performed by sequencing the 16S ribosomal RNA intergenic spacer region, and Porphyromonas and Fusobacterium were identified. She was given cephalosporin and metronidazol, after which her neurological symptoms and signs gradually lessened. Physicians need to be aware that patients may develop subdural empyema subsequent to sinusitis associated with Porphyromonas and Fusobacterium infection and that amplification and sequence analysis of partial bacterial 16S ribosomal RNA gene should be examined when no bacteria is identified by culture.

The Japanese rice cultivar Asominori shows high bacterial leaf blight resistance (BLBR). The resistance locus is closely linked with the Ph gene on chromosome 4. Japanese rice breeders noticed that lines resistant to both bacterial leaf blight (BLB) and rice leaf blast (LB) segregated from descendants of crosses with Asominori; however, the cause of this cosegregation was unclear. In 2004, we obtained five Asominori backcrossed inbred lines (BILs). Firstly, we evaluated the resistance to LB and BLB in these BILs. The partial resistance to LB was high, similar to criterial varieties such as Ouu320 and Chubu45. The BILs were also resistant to the BLB strain T-7174 (race1). Using 21 PCR-based DNA markers, we analyzed the genotypes of the BILs on chromosome 4, where BLBR and Ph genes are located. All five BILs carried a common Asominori-derived chromosomal segment estimated to be 1336 kbp long. Secondly, segregation of BLBR and LBR was monitored using 118 F3 lines obtained from a cross between Ukei854 and Hitomebore, a BLB- and LB-susceptible cultivar. Most resulting F3 lines showing BLBR also carried LBR; however, several lines showed only BLBR or BLR, indicating that BLBR and LBR were controlled by very closely linked loci. Using RM5473-2, we surveyed the genotypes of the 118 F3 lines located on the common segment. Most F3 lines with a high LBR showed genotypes identical to Asominori. Thus, the LBR locus in Asominori was tightly linked to the BLBR locus on chromosome 4, and the LBR gene was probably located near RM5473-2.

The Cape Ohma region of Shimokita Peninsula, the northernmost point of Honshu Island, Japan, is subject to both the warm Tsugaru Current and the cold Kurile Current. As a result, the Laminarialean flora includes both cold temperature species (Laminaria japonica Areschoug, Kjellmaniella crassifolia Miyabe and Costaria costata (C. Agardh) Saunders) andwarm temperature species (Undaria peterseniana (Kjellman) Okamura, Ecklonia stolonifera Okamura), as well as Undaria pinnatifida (Yendo) Okamura, which is distributed in both waters. The frequency of occurrence (as a measure of distribution) and the biomass of these species were recorded in June 1976 (at 50 points in depths between 8–30 m), July 1988 (192 points, 2.5–25 m) and July 2001 (78 points, 2.5–25 m). Comparison of these data revealed a decrease in cold temperature species and an increase in warm temperature species from 1976 or 1988 to 2001. Long-term data of seawater temperature measured at 5 m depth near the study site showed that mean temperatures in the middle of winter (late January to February) in 1989–2000 were 0.9–1.1 °C higher than those in 1980-1988. Higher seawater temperatures in the last decade appear to have affected the frequency of occurrence and biomass of the Laminarialean species along the coasts of Cape Ohma. This result supported our previous conclusion that 1 °C higher mean seawater temperature in late January caused a decrease in the biomass of L. japonica (by ca. 64%) along the same coast.

A number of cold responsive (Cor)/late embryogenesis abundant (Lea) genes are induced by both low temperature (LT) and dehydration. To understand the molecular basis of cold acclimation and its relationship with drought stress response in wheat seedlings, we isolated a DREB2 homolog Wdreb2, which is the candidate gene for a transcription factor of the Cor/Lea genes. The Wdreb2 expression was activated by cold, drought, salt and exogenous ABA treatment. Detailed expression studies of Wdreb2 indicated the involvement of two distinct pathways of its activation, a drought and salt stress-responsive pathway and a cold-responsive pathway. The transient expression analysis showed that the Wrab19 expression was directly activated by the WDREB2 transcription factor in wheat cells. Three transcript forms of Wdreb2 (Wdreb2alpha, Wdreb2beta and Wdreb2gamma) were produced through alternative splicing. Under drought and salt stress conditions, the amount of the Wdreb2beta form remained fairly constant during 24-hour treatment, while those of the Wdreb2alpha and Wdreb2gamma forms showed transient increases. On the other hand, the LT treatment resulted in increased transcript levels of all three forms of Wdreb2. Thus, under the LT and drought/salt stress conditions the amount of the WDREB2 transcription factors in wheat is differentially controlled by the level of transcription and alternative splicing.

PCR selection markers for the identification of null waxy alleles were used to screen for waxy mutations in 168 common wheat cultivars. In all cultivars where the Wx-B1 protein was absent, the Wx-B1 allele was identical to the previously identified mutation carried by Kanto 107. Although most cultivars missing the Wx-A1 protein also carried the same Wx-A1 mutation as found in Kanto 107, all of the Turkey Wx-A1 mutants produced a different PCR fragment, implying the presence of a different mutation. Sequencing of this fragment indicated the mutation, which consisted of a 173-bp insertion in an exon, was in a different location than the previously identified Wx-A1 mutation. An 8-bp duplication of the Wx-A1 sequence flanked each end of the insertion, and an element with reverse complementary sequences was present at both ends of the insertion. These structures correspond with the features of class II transposable elements. Hence, the Turkey null Wx-A1 mutation was likely caused by the movement of a transposon, and this spontaneous mutation appears to be present in a limited geographical area.

Mutations in the three homeologous waxy loci Wx-A1, Wx-B1, and Wx-D1 of a waxy wheat line have previously been characterized at the molecular level. Using combinations of these mutations, six types of partial waxy wheat plus wild type and waxy wheat (types 1–8) can be produced. Here, we describe primer sets for all three loci that can be used under a single set of conditions, allowing 32 lines to be characterized as types 1–8 in a single PCR run using a 96-well plate. Using multiplex PCR, mutations at the Wx-B1 and Wx-D1 loci can be identified in a single PCR, reducing the number of reactions necessary to identify and select the desired partial waxy wheat line. A single multiplex PCR can be used to detect all three mutations when products are analyzed using capillary electrophoresis on a microchip device. The PCR conditions and primers are effective with a number of cultivars from other countries, indicating that the mutations found at the Wx-A1 and Wx-B1 loci of these cultivars likely have the same origins as the mutations in the corresponding loci of the waxy wheat line used in this study. The PCR selection method described here is an easy and effective alternative to the commonly used SDS–PAGE methods for identification of null alleles.Key words: partial waxy wheat, amylose, PCR, capillary electrophoresis, marker-assisted selection.

The winter wheat variety Kitahonami shows a superior flour yield in comparison to other Japanese soft wheat varieties. To map the quantitative trait loci (QTL) associated with this trait, association mapping was performed using a panel of lines from Kitahonami's pedigree, along with leading Japanese varieties and advanced breeding lines. Using a mixed linear model corrected for kernel types and familial relatedness, 62 marker-trait associations for flour yield were identified and classified into 21 QTLs. In eighteen of these, Kitahonami alleles showed positive effects. Pedigree analysis demonstrated that a continuous pyramiding of QTLs had occurred throughout the breeding history of Kitahonami. Linkage analyses using three sets of doubled haploid populations from crosses in which Kitahonami was used as a parent were performed, leading to the validation of five of the eight QTLs tested. Among these, QTLs on chromosomes 3B and 7A showed highly significant and consistent effects across the three populations. This study shows that pedigree-based association mapping using breeding materials can be a useful method for QTL identification at the early stages of breeding programs.