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Grain yield-related traits and grain quality-related traits are important for rice cultivars. The quantitative trait loci (QTLs) involved in controlling the natural variation in these traits among closely related cultivars are still unclear. The present study describes the development of a novel chromosome segment substitution line (CSSL) population derived from a cross between the temperate japonica cultivars Yukihikari and Kirara397, which are grown in Hokkaido, the northernmost limit for rice cultivation. Days to heading, culm length, panicle length, panicle number, brown grain weight per plant, thousand brown grain weight, brown grain length, brown grain width, brown grain thickness, apparent amylose content, and protein content were evaluated. Panicle length, brown grain length and amylose content differed significantly in the parental cultivars. Thirty-five significant changes in the evaluated traits were identified in the CSSLs. A total of 28 QTLs were located on chromosomes 1, 2, 3, 4, 5, 6, 8, 9, 10, 11 and 12. These findings could be useful for breeding rice cultivars in the northernmost limit for rice cultivation.

Hybrid breakdown (HB) is an important type of post-zygotic reproductive barrier that inhibits hybrid production during the process of cross-breeding. A novel low temperature-dependent HB was identified in a chromosomal segment substitution line (CSSL) library derived from a cross of two rice (Oryza sativa L. japonica) cultivars, Yukihikari and Kirara397. A set of weakness symptoms in a target CSSL was observed at 23°C, but was rescued at 27°C and/or 30°C. Genetic analysis of HB using an F2:3 population of a cross between a target CSSL and Kirara397 found that a recessive temperature sensitive hybrid breakdown1 (thb1) gene from Yukihikari caused HB in the genetic background of Kirara397. Molecular mapping showed that thb1 was located within a 199-kb fragment on chromosome 6. A genetic study of F2 populations of reciprocal crosses between Yukihikari and Kirara397 confirmed that this HB was induced by the interaction of two recessive genes. These results provide important clues to further dissect the mechanism of generation of a novel temperature sensitive HB in rice intrasubspecific crosses and suggest that these linked markers will useful in rice breeding.

Epicotyl length (ECL) of adzuki bean (Vigna angularis) affects the efficiency of mechanized weeding and harvest. The present study investigated the genetic factors controlling ECL. An F2 population derived from a cross between the breeding line 'Tokei1121' (T1121, long epicotyls) and the cultivar 'Erimo167' (common epicotyls) was phenotyped for ECL and genotyped using simple sequence repeats (SSRs) and single-nucleotide polymorphism (SNP) markers. A molecular linkage map was generated and fifty-two segregating markers, including 27 SSRs and 25 SNPs, were located on seven linkage groups (LGs) at a LOD threshold value of 3.0. Four quantitative trait loci (QTLs) for ECL, with LOD scores of 4.0, 3.4, 4.8 and 6.4, were identified on LGs 2, 4, 7 and 10, respectively; together, these four QTLs accounted for 49.3% of the phenotypic variance. The segregation patterns observed in F5 residual heterozygous lines at qECL10 revealed that a single recessive gene derived from T1121 contributed to the longer ECL phenotype. Using five insertion and deletion markers, this gene was fine mapped to a ~255 kb region near the end of LG10. These findings will facilitate marker-assisted selection for breeding in the adzuki bean and contribute to an understanding of the mechanisms associated with epicotyl elongation.

Oryza sativa L. subsp. japonica cultivar Yuhikikari is proposed to alleviate atopic dermatitis, although its mechanism is unclear. To clarify this issue, we evaluated the effect of Yukihikari on the immune system in vitro and in vivo by comparison with another Japanese cultivar Kirara397. A DNA microarray analysis of mouse spleen cells cultured with either Yukihikari or Kirara397 showed that Yukihikari-added spleen cells exhibited significantly reduced expression of pro-inflammatory genes. Furthermore, another transcriptome analysis of the cultivars by RNA sequencing showed a similar result to the DNA microarray analysis. Mice fed with Yukihikari had less germinal center B cells, fewer autoantibodies, and less weight than those fed with Kirara397. These results suggest that Yukihikari has immune-regulatory functions and accounts for its allergy-ameliorating effects.

Epicotyl length (ECL) of adzuki bean (Vigna angularis) affects the efficiency of mechanized weeding and harvest. The present study investigated the genetic factors controlling ECL. An F2 population derived from a cross between the breeding line ‘Tokei1121’ (T1121, long epicotyls) and the cultivar ‘Erimo167’ (common epicotyls) was phenotyped for ECL and genotyped using simple sequence repeats (SSRs) and single-nucleotide polymorphism (SNP) markers. A molecular linkage map was generated and fifty-two segregating markers, including 27 SSRs and 25 SNPs, were located on seven linkage groups (LGs) at a LOD threshold value of 3.0. Four quantitative trait loci (QTLs) for ECL, with LOD scores of 4.0, 3.4, 4.8 and 6.4, were identified on LGs 2, 4, 7 and 10, respectively; together, these four QTLs accounted for 49.3% of the phenotypic variance. The segregation patterns observed in F5 residual heterozygous lines at qECL10 revealed that a single recessive gene derived from T1121 contributed to the longer ECL phenotype. Using five insertion and deletion markers, this gene was fine mapped to a ~255 kb region near the end of LG10. These findings will facilitate marker-assisted selection for breeding in the adzuki bean and contribute to an understanding of the mechanisms associated with epicotyl elongation.

Quantitative trait loci (QTLs) associated with eating quality, grain appearance quality and yield-related traits were mapped in recombinant inbred lines (RILs) derived from closely related rice (Oryza sativa L. subsp. japonica) cultivars, Yukihikari (good eating quality) and Joiku462 (superior eating quality and high grain appearance quality). Apparent amylose content (AAC), protein content (PC), brown grain length (BGL), brown grain width (BGWI), brown grain thickness (BGT), brown grain weight per plant (BGW) and nine yield-related traits were evaluated in 133 RILs grown in four different environments in Hokkaido, near the northernmost limit for rice paddy cultivation. Using 178 molecular markers, a total of 72 QTLs were detected, including three for AAC, eight for PC, two for BGL, four for BGWI, seven for BGT, and six for BGW, on chromosomes 1, 2, 3, 4, 6, 7, 8, 9, 11 and 12. Fifteen intervals were found to harbor multiple QTLs affecting these different traits, with most of these QTL clusters located on chromosomes 4, 6, 8, 9 and 12. These QTL findings should facilitate gene isolation and breeding application for improvement of eating quality, grain appearance quality and yield of rice cultivars.

In roots of gramineous plants, lysigenous aerenchyma is created by the death and lysis of cortical cells. Rice (Oryza sativa) constitutively forms aerenchyma under aerobic conditions, and its formation is further induced under oxygen-deficient conditions. However, maize (Zea mays) develops aerenchyma only under oxygen-deficient conditions. Ethylene is involved in lysigenous aerenchyma formation. Here, we investigated how ethylene-dependent aerenchyma formation is differently regulated between rice and maize. For this purpose, in rice, we used the reduced culm number1 (rcn1) mutant, in which ethylene biosynthesis is suppressed. Ethylene is converted from 1-aminocyclopropane-1-carboxylic acid (ACC) by the action of ACC oxidase (ACO). We found that OsACO5 was highly expressed in the wild type, but not in rcn1, under aerobic conditions, suggesting that OsACO5 contributes to aerenchyma formation in aerated rice roots. By contrast, the ACO genes in maize roots were weakly expressed under aerobic conditions, and thus ACC treatment did not effectively induce ethylene production or aerenchyma formation, unlike in rice. Aerenchyma formation in rice roots after the initiation of oxygen-deficient conditions was faster and greater than that in maize. These results suggest that the difference in aerenchyma formation in rice and maize is due to their different mechanisms for regulating ethylene biosynthesis.

Seed germination rates and plant development and growth under abiotic stress are important aspects of crop productivity. Here, our characterization of the rice (Oryza sativa L.) mutant reduced culm number11 (rcn11) showed that RCN11 controls growth of plants exposed to abnormal temperature, salinity and drought conditions. RCN11 also mediates root aerenchyma formation under oxygen-deficient conditions and ABA sensitivity during seed germination. Molecular studies showed that the rcn11 mutation resulted from a 966-bp deletion that caused loss of function of β1,2-xylosyltransferase (OsXylT). This enzyme is located in the Golgi apparatus where it catalyzes the transfer of xylose from UDP-xylose to the core β-linked mannose of N-glycans. RCN11/OsXylT promoter activity was observed in the basal part of the shoot containing the shoot and axillary meristems and in the base of crown roots. The level of RCN11/OsXylT expression was regulated by multiple phytohormones and various abiotic stresses suggesting that plant specific N-glycosylation is regulated by multiple signals in rice plants. The present study is the first to demonstrate that rice β1,2-linked xylose residues on N-glycans are critical for seed germination and plant development and growth under conditions of abiotic stress.

Seed coat colour is an important agronomic trait in adzuki bean (Vigna angularis). Here, we identified four genes controlling seed coat colour in this species. We conducted a quantitative trait locus (QTL) study of 133 recombinant inbred lines (F6) derived from a cross between V. angularis Shumari (red) and landrace Acc2265 (olive buff), by using simple sequence repeat (SSR) markers. We identified a strong QTL, designated OLB1, which explained 54, 43, and 56 % of the total variance in the L* (lightness), a* (redness), and b* (yellowness) values, respectively. In addition, we identified a minor QTL, designated OLB2, which explained 6 % of the total variance in redness. OLB1 and OLB2 were located on linkage group (LG) 1, >80 cM apart. The F1 phenotype was olive buff, implying that the red colour trait was recessive. Next, we crossed two spontaneous mutants, ‘Shiro-shouzu’ (ivory yellow) and ‘TA230002’ (pale olive buff), to the red-seeded ‘Beni-shouzu’. Genetic analysis of the F1, F2, and F3 progenies derived from each parental cross revealed that the ivory yellow and pale olive buff traits were recessive to the red trait. Molecular mapping studies indicated that the ivory yellow trait was controlled by a single Mendelian gene, designated IVY, located on LG 8. The pale olive buff trait was also controlled by a single Mendelian gene, designated POB, located on LG 10. Our findings will facilitate the development of novel red seed cultivars and the introgression of ivory yellow genes into desirable cultivars, via marker-assisted selection.

Mineral balance and salt stress are major factors affecting plant growth and yield. Here, we characterized the effects of rice ( Oryza sativa L.) reduced culm number1 ( rcn1 ), encoding a G subfamily ABC transporter (OsABCG5) involved in accumulation of essential and nonessential minerals, the Na/K ratio, and salt tolerance. Reduced potassium and elevated sodium in field-grown plants were evident in rcn1 compared to original line ‘Shiokari’ and four independent rcn mutants, rcn2 , rcn4 , rcn5 and rcn6 . A high Na/K ratio was evident in the shoots and roots of rcn1 under K starvation and salt stress in hydroponically cultured plants. Downregulation of SKC1/OsHKT1;5 in rcn1 shoots under salt stress demonstrated that normal function of RCN1/OsABCG5 is essential for upregulation of SKC1/OsHKT1;5 under salt stress. The accumulation of various minerals in shoots and roots was also altered in the rcn1 mutant compared to ‘Shiokari’ under control conditions, potassium starvation, and salt and d -sorbitol treatments. The rcn1 mutation resulted in a salt-sensitive phenotype. We concluded that RCN1/OsABCG5 is a salt tolerance factor that acts via Na/K homeostasis, at least partly by regulation of SKC1/OsHKT1;5 in shoots.

Single nucleotide polymorphisms (SNPs) and insertions–deletions (InDels) are valuable molecular markers for molecular breeding among genetically closely related cultivars. Rice (Oryza sativa L. subsp. japonica) cultivars grown in Hokkaido (45–42°N), the northernmost region of rice paddy cultivation in Japan, have been bred for over 100 years for adaptation to low summer temperatures together with high yield and good eating quality. In this study, for 10 closely related rice cultivars released in Hokkaido and cultivar Koshihikari, we identified genome-wide SNPs and InDels by next-generation sequencing. More than 29 million reads from the Hokkaido cultivars, each 101 nucleotides long, were uniquely mapped to the Nipponbare reference genome. The average of the total nucleotide length of all uniquely mapped reads corresponded to 10.9 times (3,978 Mb with genome coverage of 90.7 %) the Nipponbare reference genome. An average of 99,955 putative SNPs (1.8 times the number in Koshihikari) and 14,617 putative InDels (also 1.8 times the number in Koshihikari) were detected in Hokkaido cultivars relative to the Nipponbare genome, which enabled analyses of the inheritance of pedigree haplotypes of four cultivars, SNPs and InDels among closely related Hokkaido cultivars, and haplotype blocks unique to Hokkaido cultivars. The comprehensive SNP and InDel data provide DNA marker resources and will facilitate quantitative trait locus analysis of biparental mapping of very closely related Hokkaido cultivars. Furthermore, the haplotype blocks unique to Hokkaido cultivars represent ideal genetic regions for improvement of cultivars to be grown near the northern and southern limits of rice cultivation.

The roles of the proteins encoded by half-size adenosine triphosphate-binding cassette transporter subgroup G (ABCG) genes in abiotic stress responses are starting to be established in the dicot model Arabidopsis thaliana. In the monocot model rice, the functions of most half-size ABCG proteins in abiotic stress responses are unknown. Rcn1/OsABCG5 is an essential transporter for growth and development under abiotic stress, but its molecular function remains largely unclear. Here, we present a comprehensive overview of all 30 half-size ABCG genes in rice, including their gene structures, phylogeny, chromosome locations, and conserved motifs. Phylogenetic analysis revealed that the half-size OsABCG proteins were divided to four classes. All seven rice intronless genes, including Rcn1/OsABCG5, were in Class III, like the 12 intronless ABCG genes of Arabidopsis. The EST and FL-cDNA databases provided expression information for 25 OsABCG genes. Semi-quantitative and quantitative RT-PCR analyses demonstrated that seven OsABCG genes were up-regulated in seedlings, shoots or roots following treatments with abiotic stresses (6, 17, 42 °C, NaCl, or mannitol) and abscisic acid. Another 15 OsABCG genes were up-regulated under at least one of the abiotic stress conditions and other phytohormones besides abscisic acid. Hierarchical clustering analysis of gene expression profiles showed that expression of the OsABCG genes could be classified into four clusters. The Rcn1/OsABCG5 cluster was up-regulated by abscisic acid and included OsABCG2, 3, 13, and 27. The present study will provide a useful reference for further functional analysis of the ABCGs in monocots.

application/pdf, Plants constantly sense changes in their environment. When nutrient elements are scarce, plants often allocate a greater proportion of their biomass to the root system. In the present study, we characterized the early root development of rice reduced culm number (rcn) mutants under standard growth conditions. Short lateral root length was consistent in five rcn mutants, and the remaining root traits varied between the rcn mutants. Subsequently, we characterized the effects of rcn1 mutation in response to nutrient shortage. Root development, involving the elongation of seminal, crown, and lateral roots and branching of the lateral roots, was promoted in wild type in response to nutrient shortage. However, in rcn1 mutants, crown root elongation was constant and lateral root branching was reduced in response to nutrient shortage. The present results indicate that RCN1/OsABCG5 is associated with root development in response to nutrient shortage.

Soybean [Glycine max (L.) Merr.] is self-pollinated. To produce large quantities of hybrid seed, insect-mediated cross-pollination is necessary. An efficient nuclear male-sterile system for hybrid seed production would benefit from molecular and/or phenotypic markers linked to male fertility/sterility loci to facilitate early identification of phenotypes. Nuclear male-sterile, female-fertile ms3 mutant is a single recessive gene and displays high outcrossed seed set with pollinators. Our objective was to map the ms3 locus. A segregating population of 150 F(2) plants from Minsoy (PI 27890) x T284H, Ms3ms3 (A00-68), was screened with 231 simple sequence repeat markers. The ms3 locus mapped to molecular linkage group (MLG) D1b (Gm02) and is flanked by markers Satt157 and Satt542, with a distance of 3.7 and 12.3 cM, respectively. Female-partial sterile-1 (Fsp1) and the Midwest Oilseed male-sterile (msMOS) mutants previously were located on MLG D1b. msMOS and Fsp1 are independent genes located very close to each other. All 3 genes are located in close proximity of Satt157. We believe that this is the first report of clustering of fertility-related genes in plants. Characterization of these closely linked genes may help in understanding the evolutionary relationship among them.

Shoot branching is a major factor in plant architecture and an important agronomic trait for productivity. In the present study, we characterized reduced culm number 4 (rcn4) mutants in rice, namely rcn4-1 and rcn4-2. rcn4 developed axillary buds precisely at each leaf node, but the outgrowth of these buds was inhibited. To determine whether rcn4 is involved in a branch-inhibiting strigolactone pathway, we characterized the double mutant of rcn4 and a tillering dwarf mutant, dwarf10 (d10), which is defective in strigolactone synthesis. The axillary bud activity of rcn4d10 double mutant was between that of the rcn4 and d10 mutants suggesting that Rcn4 controls axillary bud activity and is independent of D10 in the strigolactone associated branching inhibition pathway. Molecular mapping study demonstrated that Rcn4 is located between simple sequence repeat markers RM6581 and RM6608 on the long arm of rice chromosome 1. We suggest that Rcn4 is a good candidate for further investigation of the strigolactone independent branching pathway.

application/pdf, P23k is a monocot-unique protein that is highly expressed in barley. Our previous loss-of-function studies in barley leaves indicated that P23k, localized to tissues where cell wall polysaccharides accumulate, might contribute to secondary wall formation in the leaf. However, the P23k loss-of-function analysis was limited to the leaf, which is a vegetative organ. Considering the involvement of P23k in secondary wall formation, a dramatically altered phenotype is expected in the stem of P23k gene-silenced barley, where marked secondary wall deposition occurs during the reproductive growth stage. To test this hypothesis, barley striped mosaic virus-based virus-induced gene silencing of P23k was performed. Abnormal tiller formation and arrested intercalary elongation were observed in P23k-silenced barley. From these results, we speculated that cell wall architecture was altered by P23k gene silencing. Consistent with this idea, we observed a marked decrease in the amount of cell wall polysaccharides stained with calcofluor and down-regulation of the cellulose synthase-like CslF6 gene involved in (1,3;1,4)-β-D-glucan synthesis. Taken together, these results suggest that P23k is possibly involved in determining secondary wall architecture and contributes to tiller formation and intercalary elongation in barley.

Markers linked to male-sterile, female-fertile loci on the soybean [Glycine max (L.) Merr.] molecular map would facilitate early identification of male-sterile plants. The objectives were to verify the chromosome location of the ms2 (A00-63) mutation, to determine the allelism and the chromosome location of the suspected ms2 [ms? (A00-39)] mutation, and to determine the chromosome location of the ms9 (T359) mutation. Simple sequence repeat (SSR) markers were used to molecularly map the male-sterile, female-fertile loci reported in this study. Segregating F 2 populations were developed from crosses of ms?ms? (A00-39) x 'Minsoy' (PI 278901), ms2ms2 (A00-63) x Minsoy, and Minsoy X Ms9ms9 (T359H). The ms? (A00-39) locus was positioned on MLG O at 9.9 centiMorgans (cM) distance from the marker Sat_190. The ms2 (A00-63) locus was positioned on molecular linkage group (MLG) O between markers Sat_190 and Scaa001, with a distance of 6.9 and 9.0 cM, respectively. The ms9 locus was located on MLG N between markers Satt521 and Satt237, with a distance of 8.5 and 16.2 cM, respectively. Classical allelism tests confirmed that mutant ms? (A00-39) was allelic to ms2 (A00-63). The A00-39 mutant line was assigned Genetic Type Collection number T375H and gene symbol Ms2ms2 (Ames 2). Thus Genetic Type T360H, previously identified at Ames, Iowa, becomes Ms2ms2 (Ames 1).

In roots of gramineous plants, lysigenous aerenchyma is created by the death and lysis of cortical cells. Rice (Oryza sativa) constitutively forms aerenchyma under aerobic conditions, and its formation is further induced under oxygen-deficient conditions. However, maize (Zea mays) develops aerenchyma only under oxygen-deficient conditions. Ethylene is involved in lysigenous aerenchyma formation. Here, we investigated how ethylene-dependent aerenchyma formation is differently regulated between rice and maize. For this purpose, in rice, we used the reduced culm number1 (rcn1) mutant, in which ethylene biosynthesis is suppressed. Ethylene is converted from 1-aminocyclopropane-1-carboxylic acid (ACC) by the action of ACC oxidase (ACO). We found that OsACO5 was highly expressed in the wild type, but not in rcn1, under aerobic conditions, suggesting that OsACO5 contributes to aerenchyma formation in aerated rice roots. By contrast, the ACO genes in maize roots were weakly expressed under aerobic conditions, and thus ACC treatment did not effectively induce ethylene production or aerenchyma formation, unlike in rice. Aerenchyma formation in rice roots after the initiation of oxygen-deficient conditions was faster and greater than that in maize. These results suggest that the difference in aerenchyma formation in rice and maize is due to their different mechanisms for regulating ethylene biosynthesis.

application/pdf, White-grained wheat cultivars have long been recognized to be less resistant to preharvest sprouting (PHS) than the red-grained ones. Previously two QTLs for grain dormancy, QPhs.ocs-3A.1 (QPhs-3AS) and QPhs.ocs-4A.1 (QPhs-4AL) were identified in a highly dormant Japanese red wheat, Zenkoujikomugi (Zen). Aiming at improvement of PHS tolerance in white-grained wheat, the introgression effect of these two QTLs in a white-grained population consisting of 40 recombinant inbred lines (RILs) developed from a cross between Zen and white-grained Spica was examined here. Random 20 RILs with red grains were also developed from the same cross and used as a control population. The RILs were grown in the field and in the glasshouse to evaluate the grain dormancy by germination test. Several SSR markers closely linked to the QPhs-3AS and QPhs-4AL were used to estimate the alleles at the QTLs. Dormancy variation in the RILs was significantly associated with the differences for grain color and the alleles at QPhs-3AS over several years. Although allelic variation was detected in a SSR marker closely linked to QPhs-4AL there was no difference in germination data between the Zen-allele and the Spica-allele groups. As expected, the red-grained RILs with the Zen allele at QPhs-3AS were the most dormant. Some white-grained RILs with the Zen allele at QPhs-3AS showed higher dormancy compared to the red-grained RILs with the alternative allele. These results demonstrated that introgression of the QPhs-3AS gene could contribute to the increased grain dormancy in white-grained wheat.

We identified a 23 kDa protein expressed abundantly in young barley seedlings; this protein was named P23k. P23k was shown to have evolved in barley and its allied species such as wheat, oat and rye, suggesting that P23k might be closely related to a specific biological trait of winter cereals. To determine the function of P23k, we examined the expression and localization of P23k and its mRNA in barley seedlings. P23k mRNA was markedly expressed in the scutellum of imbibed barley seeds, and was synchronously down-regulated with consumption of the starchy endosperm. In addition, ABA and sugar treatment of the scutellum showed that expression of P23k is highly dependent on the supply of glucose or sucrose, both of which are starch catabolites. Furthermore, immunocytochemical analysis showed that P23k is primarily localized around the membranes, where sugar translocation is active. These results indicate that P23k plays a role in sugar translocation in young barley seedlings.

Three lethal-yellow mutants have been identified in soybean (Glycine max (L.) Merr.), and assigned genetic type collection numbers T218H, T225H, and T362H. Previous genetic evaluation of T362H indicated allelism with T218H and T225H and duplicate-factor inheritance. Our objectives were to confirm the inheritance and allelism of T218H and T225H and to molecularly map the locus and (or) loci conditioning the lethal-yellow phenotype. The inheritance of T218H and T225H was 3 green : 1 lethal yellow in their original parental source germplasm of Glycine max 'Illini' and Glycine max 'Lincoln', respectively. In crosses to unrelated germplasm, a 15 green : 1 lethal yellow was observed. Allelism tests indicated that T218H and T225H were allelic. The molecular mapping population was Glycine max 'Minsoy' × T225H and simple sequence repeat (SSR) markers were used. The first locus, designated y18_1, was located on soybean molecular linkage group B2, between SSR markers Satt474 and Satt534, and linked to each by 4.4 and 13.4 cM, respectively. The second locus, designated y18_2, was located on soybean molecular linkage group D2, between SSR markers Satt543 and Sat_001, and linked to each by 2.2 and 4.4 cM, respectively.Key words: duplicate gene, Glycine max, homoeologous genomic segment, genome evolution, lethal-yellow mutant.

We report here the genetic identification of a female partial-sterile mutant derived from soybean mutant L67-3483. L67-3483, which originated from the cultivar Clark after X-ray irradiation, is male and female fertile. All F1plants in reciprocal pollinations of L67-3483 with 'Clark', 'Minsoy', or 'BSR 101' were female partial sterile. Partial sterility is expressed in the heterozygous condition at a single locus and upon self-pollination this locus exhibits a 1:1 segregation pattern. This locus is located on the terminus of the soybean molecular linkage group D1b+W, between simple sequence repeat (SSR) markers Satt157 and Satt266, and is linked to each by 5.3 and 1.2 cM, respectively. This gene is transmitted through both female and male gametes and there was no segregation distortion of SSR markers linked to this gene. We concluded that this female partial-sterile gene is a new mutation class, and differs from the previously reported mutation classes in soybean, i.e., sporophytic mutation, gametophytic female-specific mutation, and general gametophytic mutation. Restriction of recombination around the mutant gene suggested that this gene is located near or within (a) small inversion(s) or adjacent to (a) chromosomal deletion(s).Key words: Glycine max, simple sequence repeat marker, recombination restriction.

Water stress is one of the major environmental stresses that affect agricultural production worldwide. Water loss from plants occurs primarily through stomatal pores. Here, we report that an Oryza sativa half-size ATP-binding cassette (ABC) subfamily G protein, RCN1/OsABCG5, is involved in stomatal closure mediated by phytohormone abscisic acid (ABA) accumulation in guard cells. We found that the GFP-RCN1/OsABCG5-fusion protein was localized at the plasma membrane in guard cells. The percentage of guard cell pairs containing both ABA and GFP-RCN1/OsABCG5 increased after exogenous ABA treatment, whereas they were co-localized in guard cell pairs regardless of whether exogenous ABA was applied. ABA application resulted in a smaller increase in the percentage of guard cell pairs containing ABA in rcn1 mutant (A684P) and RCN1-RNAi than in wild-type plants. Furthermore, polyethylene glycol (drought stress)-inducible ABA accumulation in guard cells did not occur in rcn1 mutants. Stomata closure mediated by exogenous ABA application was strongly reduced in rcn1 mutants. Finally, rcn1 mutant plants had more rapid water loss from detached leaves than the wild-type plants. These results indicate that in response to drought stress, RCN1/OsABCG5 is involved in accumulation of ABA in guard cells, which is indispensable for stomatal closure.

Summary Suberin is a complex polymer composed of aliphatic and phenolic compounds. It is a constituent of apoplastic plant interfaces. In many plant species, including rice (Oryza sativa), the hypodermis in the outer part of roots forms a suberized cell wall (the Casparian strip and/or suberin lamellae), which inhibits the flow of water and ions and protects against pathogens. To date, there is no genetic evidence that suberin forms an apoplastic transport barrier in the hypodermis. We discovered that a rice reduced culm number1 (rcn1) mutant could not develop roots longer than 100 mm in waterlogged soil. The mutated gene encoded an ATP-binding cassette (ABC) transporter named RCN1/OsABCG5. RCN1/OsABCG5 gene expression in the wild type was increased in most hypodermal and some endodermal roots cells under stagnant deoxygenated conditions. A GFP-RCN1/OsABCG5 fusion protein localized at the plasma membrane of the wild type. Under stagnant deoxygenated conditions, well suberized hypodermis developed in wild types but not in rcn1 mutants. Under stagnant deoxygenated conditions, apoplastic tracers (periodic acid and berberine) were blocked at the hypodermis in the wild type but not in rcn1, indicating that the apoplastic barrier in the mutant was impaired. The amount of the major aliphatic suberin monomers originating from C28 and C30 fatty acids or ω-OH fatty acids was much lower in rcn1 than in the wild type. These findings suggest that RCN1/OsABCG5 has a role in the suberization of the hypodermis of rice roots, which contributes to formation of the apoplastic barrier.

Chromosome 5A of wheat carries several major genes of agronomic importance, including Vrn1 controlling spring/winter wheat difference, Q determining spike morphology and B1 inhibiting awn development. A population of single-chromosome recombinant lines from the cross between two chromosome substitution lines, 'Chinese Spring' (Cappelle-Desprez 5A) and 'Chinese Spring' (Triticum spelta 5A) was developed to map these genes on the long arm of chromosome 5A relative to RFLP markers. Using 120 recombinant lines, a map of approximately 230 cM in length was constructed. The gene order was centromere– Vrn1– Q– B1. The Vrn1 locus was tightly linked to two RFLP markers, Xbcd450 and Xrz395 with 0.8 cM, and to Xpsr426 with 5.0 cM. The Vrn1-adjacent region was located in the central of the long arm, approximately 90 cM from the centromere. The chromosome region around Q and the 5A/4A translocation break-point were mapped by three RFLP markers, and their order was found to be Q– Xpsr370– Xcdo457–4A/5A break-point– Xpsr164. The B1 locus was located on the most distal portion of the long arm.

Seed weight (weight per seed) is an important trait in soybean [Glycine max (L) Merr.] that affects its production, processing, marketing and consumer preferences. To determine the effects of nitrogen fertilizers and climatic conditions on seed weight, a five-year field experiment was conducted by growing four nodulating cultivars and 13 non-nodulating lines at 4 levels of nitrogen fertilizer (0, 2, 10 and 20 g m–2). The variation in seed weight due to the difference in the fertilizer level and climatic condition of the year was greater in non-nodulating lines than in nodulating cultivars. This resulted in a lower heritability estimate in non-nodulating lines (0.49) than in the nodulating cultivars (0.85). Nitrogen fertilizer increased the seed weights of non-nodulating lines but did not affect the seed weights of the nodulating cultivars. The high response of the non-nodulating lines to nitrogen fertilizer may be attributed to their strong dependence on fertilizer and soil nitrogen due to their lack of ability to fix nitrogen in symbiosis. The small seeds produced during the years with low temperatures and early onset of frost may have been caused by the slow seed growth rate and short seed filling duration.

Improved grain quality is a major breeding target in rice (Oryza sativa L. subsp. japonica), owing to market demand. Rice cultivars grown in Hokkaido (42-45°N), the northernmost region of rice paddy cultivation in Japan and near the northern limit of rice cultivation, have been bred for over 100 years for adaptation to low temperature together with high yield and grain quality. In this study, for seven closely related rice cultivars released in Hokkaido in the last 70 years, we investigated the transcriptome profiles of developing seeds 8 days after flowering (DAF, middle stage) and 15 DAF (late stage) under natural conditions in Hokkaido (42.52°N) using a whole-genome oligonucleotide microarray. The transcriptome profiles were divided into two groups depending on stage and were more variable at the late than that at the middle stage. The genome-wide transcriptome data revealed the features of differentially expressed genes in two first-generation cultivars compared to that in the parental cultivars. Starch properties were varied and correlated with the expression of starch biosynthesis genes among Hokkaido cultivars. Apparent amylose content was positively correlated with Waxy gene expression at the late stage. The expression of starch biosynthesis genes and starch properties were varied among Hokkaido cultivars. The transcriptomes of the most recent cultivars reveal the expression of ideal genes for the development of cultivars with high grain yield, grain quality, and grain traits essential for rice production near the northern and southern limits of rice cultivation.

We characterized a spontaneous dwarf mutant showing extremely short internodes and dark green leaves originating from azuki bean (Vigna angularis (Willd.) Ohwi & Ohashi) cultivar "Erimo-shouzu." F(1) plants of 3 cross combinations between the dwarf mutant and several representative wild-type plants, Erimo-shouzu, V. angularis accession Acc2265 and wild relative V. riukiuensis accession Acc2482, supported the dwarf genotype being recessive. In a total of 3328 F(2) progeny of these 3 crosses, 65 dwarfs (2.0%) and 5 chimeric dwarfs (0.2%) segregated and the remainder were wild-type plants (97.8%). In F(3) progeny derived from self-pollinated dwarf F(2) plants, we observed wild type (54.3%), dwarf (39.1%), and chimeric dwarf (6.5%) plants. Two types of chimeric plants were observed: dwarf branches on the axils of wild-type plant stems and wild-type branches on the axils of dwarf stems. In 21 dwarf F(2) plants, the dwarf trait cosegregated with simple sequence repeat marker CEDG154 on chromosome 4. Conversely, homozygote F(2) plants at this chromosomal segment from the dwarf mutant frequently (>90%) expressed the wild-type phenotype. We concluded that the dwarf phenotype is mitotically and meiotically inheritable and controlled by a single genetically unstable locus, designated Azuki Dwarf1 (AD1), which converts between 2 phenotypic states bidirectionally.

White-grained wheat is usually more susceptible to preharvest sprouting than red-grained wheat. Identification of QTLs affecting grain dormancy is one of the promising ways of developing PHS tolerant white grained-wheat. A white-grained recombinant inbred line (RIL) population was developed from a cross between highly dormant Japanese red-grained wheat cultivar, 'Zenkoujikomugi' ('Zen'), and a low dormant white-grained wheat cultivar 'Spica'. The 3B chromosome was assessed with SSR and EST markers covering most of the chromosomal areas. A highly significant quantitative trait locus (QTL) associated with grain dormancy on chromosome 3B was identified in this cross and the allele contributed to higher dormancy was derived from 'Zen'. Linkage map of 3B short arm was developed showing the location of the QTL linked with Xwocs207 marker. The results of the t -test revealed that the QTL was significant in 5 environments in the field and 3 environments in the glasshouse. This QTL was detected only in the white-grained RIL population and it was not detected if the phenotypic variation of the population was affected by major red color genes. Mapping of the QTL with QGENE also proved that this QTL, located close to the centromere region of 3B, can be a major influential factor for the total dormancy variation of this cross in the field. Keywords : grain dormancy; pre-harvest sprouting; QTLs; SSR markers; white-grained wheat DOI: 10.4038/jfa.v1i2.1794 Journal of Food and Agriculture Vol.1(2) 2008 pp.1-10

* Shoot branching is important for the establishment of plant architecture and productivity. * Here, characterization of rice (Oryza sativa) reduced culm number 1 (rcn1) mutants revealed that Rcn1 positively controls shoot branching by promoting the outgrowth of lateral shoots. Molecular studies revealed that Rcn1 encodes a novel member of ATP-binding cassette protein subfamily G (ABCG subfamily), also known as the white-brown complex (WBC) subfamily, and is designated OsABCG5. * Rcn1 is expressed in leaf primordia of main and axillary shoots, and in the vascular cells and leaf epidermis of older leaves. In addition, Rcn1 is expressed in the crown root primordia, endodermis, pericycle and stele in the root. No effect on Rcn1 expression in shoots or roots was seen when the roots were treated with auxins. Phenotypic analyses of rcn1 and tillering dwarf 3 (d3) double mutants at the seedling stage clarified that Rcn1 works independently of D3 in the branching inhibitor pathway. * Rcn1 is the first functionally defined plant ABCG protein gene that controls shoot branching and could thus be significant in future breeding for high-yielding rice.

P23k is a 23 kDa protein involved in sugar translocation in the scutellum of germinating barley seeds. The present study was carried out to provide the genomic characterization for P23k gene in terms of copy number, chromosome mapping, genetic mapping and expression analysis in germinating sculletum in two major Triticeae crops, barley and wheat, and their relatives. Southern blotting showed that a variable copy number with different restriction fragment sizes was found among 15 Hordeum accessions, while low copy number were found to be conserved in 23 Triticum and 3 Aegilops accessions. Genetic and physical mapping study identified that the P23k gene is duplicated in wild and cultivated barley on chromosomes 1H, 2H, and 3H, and further tandem duplication on chromosomes 1H and 3H. In contrast, the wheat P23k is located on chromosome 3A of durum wheat and at the distal portion of the long arms of 3A and 3D chromosomes of bread wheat. Northern blotting showed remarkably high accumulation of P23k transcript in the germinating scutellum in cultivated and wild barley, whereas very few or no accumulation was detected in diploid, tetraploid, and hexaploid wheat accessions. The present study suggests a simple scenario where the ancestral P23k is encoded on the distal portion of an ancestral chromosome of homoeologous chromosome 3. Beside of polyploidy, dispersed and tandem duplications could trigger generation of the P23k family in the Hordeum lineage, while an ancestral P23k has been conserved in homoeologous 3A and 3D chromosomes in the wheat lineage.

Casein kinase 2 (CK2) is a ubiquitous, highly pleiotropic, constitutively active, and messenger-independent Ser/Thr protein kinase. It is found in two different forms: the heterotetrameric CK2, composed of two alpha catalytic subunits and two beta regulatory subunits, and the monomeric CK2 alpha, consisting of the alpha catalytic subunit. In the present study, we isolated barley cDNA clones of the CK2 alpha and beta subunit genes, designated HvCK2A and HvCK2B, respectively. Chromosome assignment, using a set of wheat–barley disomic chromosome addition lines, and RFLP mapping, using two doubled haploid populations, showed that HvCK2A was duplicated on the short arm of chromosome 2H and the long arm of chromosome 5H (designated HvCK2a-2H and HvCK2a-5H, respectively), and a single copy of HvCK2B was located on the long arm of chromosome 1H (designated HvCK2b). A PCR-Southern hybridization experiment demonstrated that the HvCK2A sequence originated from the HvCK2a-5H locus, showing that at least HvCK2a-5H was expressed. The present cDNA sequences and genomic organization of the two subunits will facilitate further functional analysis of CK2 in barley.

Mutant genes, reduced culm number 1 (rcn1) and bunketsuwaito tillering dwarf (d3), affect tiller number in rice (Oryza sativa L.) in opposite directions. The d3 mutant was reported to increase tiller number and reduce plant stature. Our objective was to compare the phenotype of the d3rcn1 double mutant with each single mutant and parental rice cultivar "Shiokari" and to clarify whether the Rcn1 gene interacted with the D3 gene. We recovered a new rcn1 mutant from Shiokari and developed d3rcn1 double mutant with Shiokari genetic background. A new rcn1 mutant, designated as "S-97-61" exhibited a reduction in tiller number and plant stature to about the same level as the previously reported original rcn1 mutant. Three near-isogenic lines, rcn1 mutant, d3 mutant, and d3rcn1 double mutant, were grown together with the parental Shiokari. The reduction in tillering by the rcn1 mutation was independent of the d3 genotype, and tillering number of d3rcn1 double mutant was between those of the d3 and rcn1 mutants. These results demonstrated that the Rcn1 gene was not involved in the D3-associated pathway in tillering control.

Soybean male-sterile, female-sterile mutant genes have been identified by genetic and cytological studies. The St8 gene has been identified as an asynaptic mutation resulting in male and female sterility. This mutant gene was derived from a gene-tagging study using the soybean w4-mutable line. In this report we identified the genetic map position of st8 via restriction fragment length polymorphism (RFLP) and simple sequence repeat (SSR) markers. The St8 gene mutation was located between RFLP marker E107 and SSR markers Satt132, Sct_065, and Satt414 on molecular linkage group J and linked to each by 7.8 cM and 3.4 cM, respectively.

White-grained wheat is usually more susceptible to preharvest sprouting (PHS). Accumulation of color independent grain dormancy QTLs is one of the promising ways of developing PHS tolerance in white-grained wheat. A white grained recombinant inbred line (RIL) population was developed from a cross between high dormant Japanese red grained wheat, 'Zenkoujikomugi' ('Zen'), and a white cultivar 'Spica'. White-grained RILs demonstrated a severe variation proving that many genes have involved in maintaining grain dormancy. Hence, to identify those dormancy QTLs of 'Zen' x 'Spica', whole genome was assessed with SSR and EST markers. Five novel grain dormancy QTLs, linked with Xwocs207 , Xcfa2163 , Xbarc243 , Xbarc44 and Xgwm577 markers were detected located on chromosomal arms 3BS, 5AL, 5BL, 5DL and 7BL, respectively. In all instances, allele contributed to comparatively higher dormancy was derived from 'Zen'. The QTL linked with Xwocs207 marker appeared to be extremely effective, stable and reliable. Usually QTLs rendering minor effects were difficult to be detected if the phenotypic variation of the population was affected by major red color genes. In the present study, since only the white-grained RILs were used, minor QTLs were also able to be investigated. Key words : Grain dormancy QTLs; EST markers; SSR markers; Preharvest sprouting; White-grained wheat DOI: 10.4038/tare.v11i0.1768 Tropical Agricultural Research and Extension Vol.11 2008 pp.1-6