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To find new QTLs responsible for kernel cracking resistance, we screened 50 CSSLs derived from the moderately resistant cultivar ‘Itadaki’ (O. sativa L.) and the donor O. rufipogon. Two lines, IRSL 30 and IRSL 37, were selected as resistant. QTL analyses of the percentage of cracked kernels (PCK) in F4 individuals derived from “Itadaki/IRSL 30” and “Itadaki/IRSL 37” identified a major QTL, qCR (Cracking Resistance) 8-2, at the same position on chromosome 8 in both populations. ‘IRSL 30’ and ‘IRSL 37’ had a reduced PCK. These results show that qCR8-2 is likely to be an important QTL for kernel cracking resistance. Both lines had long awns, linked to qCR8-2, but the awnless line ‘Chukei 19301’ was also derived from “Itadaki/IRSL 37”, so qCR8-2 is distinct from the gene for awn development. We consider that qCR8-2 will help in the breeding of new rice cultivars with high cracking resistance and in elucidating the physiological mechanism of kernel cracking.

This manuscript reports the fine mapping of a novel QTL, qAC2 controlling the low amylose in rice. The action mechanism of the qAC2 is also investigated by the analysis of genetic interactions to Wx a , Wx b , du1, du2 and du3. Amylose content of the rice (Oryza sativa L.) endosperm greatly affects starch properties and eating quality of cooked rice. Seeds of japonica rice cultivar Kuiku162 have low amylose content (AC) and good eating quality. Our analysis revealed a novel QTL, designated as qAC2 that contributed to the low AC of Kuiku162. qAC2 was fine mapped within a 74.9-kb region between two insertion and deletion markers, KID3001 and KID5101, on the long arm of chromosome 2. Seven genes are predicted in this region, but none of them is known to be related to the regulation of AC. The AC of a near-isogenic line (NIL110) carrying qAC2 Kuiku , the Kuiku162 allele of qAC2, in the genetic background of japonica cultivar Itadaki was lower by 1.1 % points than that of Itadaki. The chain length distributions of amylopectin were similar in NIL110 and Itadaki; therefore, the low AC of NIL110 was caused by a decrease in the actual AC, but not by a difference in the amylopectin structure. The interaction analyses revealed that qAC2 Kuiku has epistatic interaction with Wx a . The qAC2 Kuiku has epistatic interactions with two loci, du1 and du2, on Wx b , whereas the genetic effect of qAC2 Kuiku has additive to that of du3 on Wx b . Thus, similar to du1 and du2, qAC2 may have a function related to Wx b mRNA splicing.

A promising new cultivar of rice (Oryza sativa L.) ‘Tachisuzuka’ has been developed for silage use with improved feeding value due to a radical decrease in spikelets. However, ‘Tachisuzuka’ has the problem of inefficient seed production. We investigated the effect of planting density on the spikelet number in ‘Tachisuzuka’ to find out how seed yields of this cultivar can be increased by means of cultivation methods. ‘Tachisuzuka’ was cultivated at six different planting densities, in the range of 7.4–22.2 hills m−2. Unlike in ordinary cultivars, there was a negative correlation between the spikelet number per unit area and hills per unit area. Moreover, the spikelet number increased by 67% under the low planting density. This result implies that the efficiency of seed production of ‘Tachisuzuka’ could be improved by low planting density through an increase in spikelet number per unit area.

It is essential to elucidate genetic diversity and relationships among even related individuals and populations for plant breeding and genetic analysis. Since Japanese rice breeding has improved agronomic traits such as yield and eating quality, modern Japanese rice cultivars originated from narrow genetic resource and closely related. To resolve the population structure and genetic diversity in Japanese rice population, we used a total of 706 alleles detected by 134 simple sequence repeat markers in a total of 114 cultivars composed of 94 improved varieties and 20 landraces, which are representative and important for Japanese rice breeding. The landraces exhibit greater gene diversity than improved lines, suggesting that landraces can provide additional genetic diversity for future breeding. Model-based Bayesian clustering analysis revealed six subgroups and admixture situation in the cultivars, showing good agreement with pedigree information. This method could be superior to phylogenetic method in classifying a related population. The leading Japanese rice cultivar, Koshihikari is unique due to the specific genome constitution. We defined Japanese rice diverse sets that capture the maximum number of alleles for given sample sizes. These sets are useful for a variety of genetic application in Japanese rice cultivars.

In the breeding of rice cultivars for use for whole-crop silage, accurate evaluation of shattering is important because its characteristics affect the digestibility of grains by animals. However, measurements of the rice grain pedicel breaking tensile strength (BTS) using a conventional shattering testing device, such as the TR-II, are laborious. We tested a universal testing machine (UTM), a device used for physical analysis, as a labor-saving technique for measuring rice grain pedicel BTS. A simple attachment consisting of a holding clip and a polyethylene string to the coupler was prepared to adapt the UTM for BTS measurement. There were significant (P

The rice cultivar ‘Chumroo’ is commonly cultivated in the mid- and high-altitude areas of Bhutan. This cultivar has shown durable blast resistance in that area, without evidence of breakdown, for over 20 years. Chumroo was inoculated with 22 blast isolates selected from the race differential standard set of Japan. The cultivar showed resistance to all the isolates. To identify the resistance gene(s), Chumroo was crossed with a susceptible rice cultivar, Koshihikari. The F1 plants of the cross showed resistance. Segregation analyses of 300 F3 family lines fitted the segregation ratio of 1:2:1 and indicated that a single dominant gene controls the resistance to a blast isolate Ao 92-06-2 (race 337.1). The Chumroo resistance locus (termed Pi46(t)) was mapped between two SSR markers, RM6748 and RM5473, on the terminal region of the long arm of chromosome 4, using linkage analysis with SSR markers. The nearest marker, RM5473, was linked to the putative resistance locus at a map distance of 3.2 cM. At the chromosomal region, no true resistance genes were identified, whereas two field resistance genes were present. Therefore, we designated Pi46(t) as a novel blast resistance locus.

‘Tachisuzuka’ is a new rice (Oryza sativa L.) cultivar for whole-crop silage (WCS) use. Agronomic characters were recorded from 2007 to 2009. The culm length of Tachisuzuka was 11 cm longer than that of Kusanohoshi. The short panicle of Tachisuzuka was morphologically similar to that of the short panicle 1 (sp1) mutant. Tachisuzuka exhibited high lodging resistance in the yellow ripening stage, the optimal period for harvesting, and a month after yellow ripening. The straw yield of Tachisuzuka was remarkably higher than that of Kusanohoshi but its grain yield was lower. A portion of grains are undigested and excreted in feces by cattle fed with rice WCS, and this loss of nutrients should not be disregarded. The low grain/straw ratio of Tachisuzuka indicates that the loss of nutrients in cattle fed with Tachisuzuka WCS should be lower than with Kusanohoshi WCS. Low sugar content of rice plants is considered a cause of silage deterioration. The sugar content of Tachisuzuka was markedly higher than that of Kusanohoshi.

Genotypic variation in stomatal density and size has been reported but little is known of the genetic mechanisms behind these leaf traits. Using 101 recombinant inbred lines derived from a cross between a tropical japonica, IR69093-41-3-2-2 and an indica variety, IR72, we conducted a field study to determine stomatal density and size and identify quantitative trait loci (QTL) controlling these traits under lowland conditions. Ten QTLs for stomatal density and four QTLs for size were identified across growth stages and leaf surfaces (adaxial and abaxial). The contribution of each QTL to total phenotypic variation ranged from 9.3 to 15.2% for stomatal density and 9.7 to 14.3% for size. The allele from IR72 increased stomatal density and that from IR69093-41-3-2-2 increased size. The expression of the QTLs for stomatal density and size differed by growth stage indicating that these traits might be genetically controlled depending on growth stage or that each QTL had a different function by growth stage. Significant negative genetic correlations between stomatal density and size at both vegetative (r = −0.308**) and heading (r = −0.484**) stages were observed but no common QTL for these traits was detected across growth stages and leaf surfaces. These results indicate that the QTLs for density and size may neither be genetically linked nor pleiotropically controlled and findings can be used as basis for selection at the leaf level on the balance of carbon and water uptake. Further study is needed to fully understand the mechanism underlying the observed genetic association and to elucidate the function of the QTLs involved.

To identify the chromosomal regions controlling the eating quality of cooked rice, we performed a quantitative trait locus (QTL) analysis using 93 backcross inbred lines (BILs) and 39 chromosome segment substitution lines (CSSLs) derived from crosses between a japonica rice cultivar Koshihikari (glossier appearance, tasty, sticky and soft eating quality of rice when cooked) and an indica cultivar Kasalath (less glossy appearance, less sticky and hard eating quality of rice when cooked). We evaluated the eating quality of rice including overall evaluation (OE), glossiness (GL), taste (TA), stickiness (ST) and hardness (HA) in each line based on the sensory test of cooked rice. Twenty-one QTLs for eating quality were mapped to eight regions on chromosomes 1, 2, 3 (two regions), 6, 7, 9 and 10. The Koshihikari alleles at 19 out of 21 QTLs increased the eating quality, while the Kasalath alleles at the other two QTLs increased the eating quality. We also mapped the QTLs for chemical properties, such as amylose content (AC) and protein content (PC), which affected the eating quality. Four QTLs in the terminal region of the short arm of chromosome 3 and five QTLs on chromosome 6 for eating quality were mapped to the same region as that of the QTLs for AC. Three QTLs on chromosome 1 for eating quality were also mapped to the same region as that of a QTL for PC. The chromosome positions of the other QTLs for eating quality did not coincide with those of the QTLs for AC and PC. Six out of 21 QTLs for eating quality, qTA3, qOE6, qGL6, qTA6, qST6 and qHA6, were commonly identified by analysis using both BILs and CSSLs. One QTL, qTA3, was not a locus of AC, PC or known eating genes. Thus the QTL was mapped in the interval between the SSR markers RM1332 and RM6676 in the middle region of the short arm of chromosome 3 by fine mapping of three sub-CSSLs. Five QTLs, qOE6, qGL6, qTA6, qST6 and qHA6, seemed to be associated with the Waxy (Wx) gene located on chromosome 6.

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.

A transgenic amylose-free sweet potato has been obtained by introduction of granule-bound starch synthase I (GBSSI) cDNA of sweet potato in sense orientation (Plant Cell Reports (2001)). In this study, starches from 6 transgenic sweet potatoes produced by introduction of GBSSI cDNA, including the amylose-free transformant, were analyzed for their physicochemical properties, granule-size distribution, enzymatic digestibility, amylopectin structure, gelatinization properties and pasting properties. We observed little difference in granule size distribution between amylose-free starch and control starch. Amylose-free starch was more susceptible to glucoamylase digestion than control starch. The amylopectin of the amylose-free transformant was found to have a slightly lower content of short chains. Amylose-free starch showed higher gelatinization temperature and gelatinization enthalpy and lower setback in comparison with control starch. Thus, it was found that the starch from the amylose-free transgenic sweet potato possessed unique physicochemical properties.

Our simulation results clarify the areas of applicability of nine prediction methods and suggest the factors that affect their accuracy at predicting empirical traits. Whole-genome prediction is used to predict genetic value from genome-wide markers. The choice of method is important for successful prediction. We compared nine methods using empirical data for eight phenological and morphological traits of Asian rice cultivars (Oryza sativa L.) and data simulated from real marker genotype data. The methods were genomic BLUP (GBLUP), reproducing kernel Hilbert spaces regression (RKHS), Lasso, elastic net, random forest (RForest), Bayesian lasso (Blasso), extended Bayesian lasso (EBlasso), weighted Bayesian shrinkage regression (wBSR), and the average of all methods (Ave). The objectives were to evaluate the predictive ability of these methods in a cultivar population, to characterize them by exploring the area of applicability of each method using simulation, and to investigate the causes of their different accuracies for empirical traits. GBLUP was the most accurate for one trait, RKHS and Ave for two, and RForest for three traits. In the simulation, Blasso, EBlasso, and Ave showed stable performance across the simulated scenarios, whereas the other methods, except wBSR, had specific areas of applicability; wBSR performed poorly in most scenarios. For each method, the accuracy ranking for the empirical traits was largely consistent with that in one of the simulated scenarios, suggesting that the simulation conditions reflected the factors that affected the method accuracy for the empirical results. This study will be useful for genomic prediction not only in Asian rice, but also in populations from other crops with relatively small training sets and strong linkage disequilibrium structures.

The cDNA and genomic clones from sweet potato encoding granule-bound starch synthase I (GBSSI) were isolated and characterized. The sequence analysis of the cDNA shows that the sweet potato GBSSI mature protein is comprised of 531 amino acids and that the precursor has a transit peptide of 77 amino acids. A comparison of the cDNA and genomic sequences suggested that the sweet potato GBSSI gene has 14 exons and 13 introns, the first of which is located in the untranslated region. This gene is considered to be a low-copy gene based on genomic Southern analysis.

Four aneuhaploids (2n = 13) and 5 tetrasomics (2n = 26) of rice (Oryza sativa L.), which were obtained through anther culture of trisomics (2n = 25), were examined by Southern hybridization analysis to identify their extra chromosomes, to test their genetic stability, and to demonstrate their utility in genome alaysis. Twenty-one RFLP markers located on 9 chromosomes were used as probes. Extra chrounosome identification was conducted by observing dosage changes of the probes in the aneuhaploids and tetrasomics. The results indicated that the extra chromosomes of the aneuhaploids and tetrasomics were identical to their parental trisomics. The aneuhaploids and tetrasomics used in the study are genetically stable, except the aneuhaploid plant derived from the trisomic with an extra chromosome 5. This plant showed clear DNA variation. Chromosome assignment of unnrapped DNA clones was tried by using the identified aneuploids. The result showed that aneuhaploids and tetrasomics are useful materials for genome analysis in rice to assign cloned DNA fragments to specific chromosomes.

Although quantitative traits loci (QTL) analysis has been widely performed to isolate agronomically important genes, it has been difficult to obtain molecular markers between individuals with similar phenotypes (assortative mating). Recently, the miniature inverted-repeat transposable element mPing was shown to be active in the japonica strain Gimbozu EG4 where it had accumulated more than 1000 copies. In contrast, most other japonicas, including Nipponbare, have 50 or fewer mPing insertions in their genome. In this study we have exploited the polymorphism of mPing insertion sites to generate 150 PCR markers in a cross between the closely related japonicas, Nipponbare × Gimbozu (EG4). These new markers were distributed in genic regions of the whole genome and showed significantly higher polymorphism (150 of 183) than all other molecular markers tested including short sequence repeat markers (46 of 661). In addition, we performed QTL analysis with these markers using recombinant inbred lines derived from Nipponbare × Gimbozu EG4, and successfully mapped a locus involved in heading date on the short arm of chromosome 6. Moreover, we could easily map two novel loci involved in the culm length on the short arms of chromosomes 3 and 10.

We have constructed a genetic map of the nuclear genome in rice (Oryza sativa L.), utilizing 322 restriction fragment length polymorphism (RFLP) DNA markers and nine morphologlcal and biochemical genetlc markers. The RFLP map is based on the segregation of 144 F2 plants from a cross between Indica and Japonica varieties. The map covers a total of 1, 836 cM with 347 loci and exceeds the data recorded in the classical genetic map of rice by 58.5% and the current RFLP map (McCOUCH et al. 1988) by 32.2%. The RFLP linkage groups were assigned to the twelve chromosomes of rice using trisomic mutants andseveral genetic markers. This map should provide the basis for the mapping of genes controlling agronomic traits of rice.

The results from linkage mapping activities at Kyushu University during the last 10 years are summarized in this paper. The present paper concisely reveals present situation on linkage map of phenotype markers, the integration linkage map of phenotype and RFLP markers and the genetic stocks available. Some of the problems in this field, in addition, are pointed out and discussed.

To furnish significant information to genome study of rice, we have studied on integration of conventional linkage map in chromosomes 1, 2, 3 and 4 onto the RFLP linkage map. The orientation of both the linkage maps in the four chromosomes was completely understood and some RFLP markers were detected closely linked to conventional markers. In addition, the low degree of saturation of the RFLP linkage map on chromosomes 2 and 4 was found out. The RFLP map lacked the regions corresponding to d-29 — bl-1 and 1g — d-2 regions on chromosomes 2 and 4 in the conventional linkage map, respectively.