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The construction of banks and surface soil cutting involved in newly reclaiming orchards may cause spatial variability in soil properties, which could cause poor fruit tree productivity. This study examined spatial relationships between variations in peach tree properties and soil properties around each tree and assessed the possibility of site-specific field management for individual trees in a newly reclaimed orchard. Three and four years after reclamation in 2016, the 0.1-ha field located in Kyoto, Japan was divided into 32 grid cells at 5-m intervals for all individual peach trees and 128 grid cells at 2.5-m intervals for measuring soil properties around each tree (field scale). The 128 grid cells were each further divided into five positions at 0.71-m intervals for assessing selected soil properties (grid-cell scale). The soil data were geostatistically analyzed by calculating the nugget/sill ratios and anisotropy ratios (degree of variation in relation to direction) and drawing kriged maps. Coefficients of variation of soil properties at the grid-cell scale were much higher than those at the field scale. Pearson’s correlation analysis at the field scale indicated that the tree productivity was most strongly correlated with relative altitude, followed by the degree of soil reduction, time-domain reflectometry electrical conductivity (TDR-EC), subsoil pH (H2O), and TDR-volumetric water content. Tree productivity tended to be lower at lower elevations, where the degree of soil reduction, TDR-EC, subsoil pH (H2O), and soil water content tended to be high. Poor productivity appeared to be related to wet injury. Semivariograms of the soil properties related to soil water showed strong spatial dependence and had nugget/sill ratios of ≤24.0%. Kriged maps and anisotropy ratios further indicated that most tree property values decreased from southeast to northwest and showed variations similar to those of the soil properties related to soil water. Fine-scale mapping of soil properties in the orchard could reveal spatial soil-property variations around individual peach trees, and the result would imply the importance of soil management practices on a per-tree basis. Our findings could help to improve tree productivity in the northwestern area by increasing soil drainage for individual trees.

“Autonomous fruit set” refers to self-pollination and fruit set without pollen vectors such as vibration or insects. Autonomous fruit set under high-temperature stress is an important breeding goal as climate change can reduce fruit yields in Capsicum. We screened Capsicum cultivars for autonomous fruit set ability in a greenhouse environment and investigated pollen germination, viability, pollen grains number, chlorophyll fluorescence (Fv/Fm), style length, anther cone length, and anthesis stage under high temperatures in order to identify indicator traits for screening more genotypes with autonomous fruit set ability. The fruit set of the ‘Takanotsume’ (57.7 ± 20.6%) and ‘Goshiki Kyokko’ (52.2 ± 14.2%) cultivars (both C. annuum) were higher than those of other cultivars. Correlation analysis showed that pollen germination had the highest correlation with fruit set in C. annuum cultivars (r = 0.63). These results indicate that ‘Takanotsume’ and ‘Goshiki Kyokko’ are useful cultivars for novel breeding programs focusing on autonomous fruit sets under high temperatures, and pollen germination in C. annuum was a convincing candidate for an indicator trait of autonomous fruit set ability under high temperatures.

SummaryMultiplexed inter-simple sequence repeats genotyping by sequencing (MIG-seq) is an next-generation sequencing library construction method developed for the analysis of DNA in ecology. Although MIG-seq can generate libraries from low-quality DNA, few polymorphisms can be obtained in species with small genomes. In this study, we developed degenerate oligonucleotide primer MIG-seq (dpMIG-seq) as an effective polymorphism discovery method that allows for variation in the number of polymorphisms while retaining the advantages of MIG-seq, including independence from DNA quality. In dpMIG-seq, a proportion of the simple sequence repeats in the primer sequence of the first PCR in MIG-seq was changed to degenerate oligonucleotides to enable annealing to a wider range of sequences. In tests of several crop species other than wheat, the number of loci that could be sequenced using dpMIG-seq with a data volume of 0.3 gigabases (Gb) was increased compared with that sequenced using MIG-seq. In wheat, the number of polymorphisms obtained via dpMIG-seq was higher than that obtained via MIG-seq when a data volume of about ≥2 Gb was obtained. In dpMIG-seq, different loci could be sequenced by changing the positions of the degenerate oligonucleotides. By applying dpMIG-seq, we constructed a linkage map consisting of 5,142 markers for the rice inter-subspecies F2 population, and we detected quantitative trait loci for heading date in the regions where known heading-related genes were located. Overall, our results show that dpMIG-seq is a useful tool for the genetic analysis of crop species.

Increasing the yield potential of rice (Oryza sativa) is the main objective of breeders and cultivators engaged in rice improvement programs. Erect panicle (EP) rice is generally high-yielding with panicles that remain non-curved until maturation. The aim of our study was to evaluate the association of agronomic traits with rice productivity in EP rice. Here, we used the recombinant inbred lines (RILs), crosses between Liaojing5 (erect panicle japonica type) and Wanlun422 (high-yielding indica type). The yield varied among the RILs, and the flag leaf length of EP RILs was negatively correlated with the yield; however, the correlation was not significant in the non-EP RILs. The flag leaf length of the EP RILs was also negatively correlated with biomass increase during the late ripening stage. This may reflect the canopy structure of the EP RILs with short flag leaves which had a larger leaf area index in the lower strata. Additionally, the chlorophyll content in the lower leaf significantly differed among the EP RILs with flag leaves of different lengths, resulting in a higher photosynthetic ability of the lower leaf of EP RILs with short flag leaves. In the present study, an EP line, which has the shortest flag leaf, showed a higher yield than Wanlun422 in both years. EP RILs with short flag leaves might show a higher canopy photosynthetic rate in the later ripening stage; therefore, this trait could be a potential phenotypic marker for achieving high yield of EP rice.

Grafting-induced flowering is a key phenomenon to understand systemic floral induction caused by florigen. It can also be used as a breeding technique enabling rapid seed production of crops with long generation times. However, the degree of floral induction in grafted plants is often variable. Moreover, it is difficult in some crop species. Here, we explored the factors promoting variability in the grafting-induced flowering of cabbage (Brassica oleracea L. var. capitata), an important vegetable crop with a long generation time, via the quantitative analysis of florigen accumulation. Significant variability in the flowering response of grafted cabbage was observed when rootstocks of different genotypes were used. As reported previously, B. oleracea rootstocks did not induce the flowering of grafted cabbage plants, but radish (Raphanus sativus L.) rootstocks unstably did, depending on the accessions used. Immunoblotting analysis of the FLOWERING LOCUS T (FT) protein, a main component of florigen, revealed that floral induction was quantitatively correlated with the level of accumulated FT protein in the grafted scion. To identify rootstock factors that cause variability in the floral induction of the grafted scion, we investigated FT protein accumulation and flowering response in grafted scions when the transcription levels of FT and the leaf area of rootstocks were altered by vernalization, daylength and leaf trimming treatments. We concluded that increasing the total amount of FT protein produced in the rootstock is important for the stable floral induction of the grafted cabbage, and this can be accomplished by increasing FT transcription and the leaf area of the rootstock.

Bread wheat is a major crop that has long been the focus of basic and breeding research. Assembly of its genome has been difficult because of its large size and allohexaploid nature (AABBDD genome). Following the first reported assembly of the genome of the experimental strain Chinese Spring (CS), the 10+ Wheat Genomes Project was launched to produce multiple assemblies of worldwide modern cultivars. The only Asian cultivar in the project is Norin 61, a representative Japanese cultivar adapted to grow across a broad latitudinal range, mostly characterized by a wet climate and a short growing season. Here, we characterize the key aspects of its chromosome-scale genome assembly spanning 15 Gb with a raw scaffold N50 of 22 Mb. Analysis of the repetitive elements identified chromosomal regions unique to Norin 61 that encompass a tandem array of the pathogenesis-related 13 family. We report novel copy-number variations in the B homeolog of the florigen gene FT1/VRN3, pseudogenization of its D homeolog and the association of its A homeologous alleles with the spring/winter growth habit. Furthermore, the Norin 61 genome carries typical East Asian functional variants different from CS, ranging from a single nucleotide to multi-Mb scale. Examples of such variation are the Fhb1 locus, which confers Fusarium head-blight resistance, Ppd-D1a, which confers early flowering, Glu-D1f for Asian noodle quality and Rht-D1b, which introduced semi-dwarfism during the green revolution. The adoption of Norin 61 as a reference assembly for functional and evolutionary studies will enable comprehensive characterization of the underexploited Asian bread wheat diversity.

Mesophyll (M) chloroplasts in finger millet are known to aggregate to the bundle sheath side when leaves are constantly irradiated with extremely high-intensity light. This aggregative movement of M chloroplasts is also observed in natural environment, but whether a natural light regime is effective in inducing the response remains unclear. Abscisic acid is reported to trigger not only the aggregative movement but also stomatal closure, but photosynthetic responses accompanying the aggregative movement also remain unknown.We investigated changes in chloroplast positioning and photosynthetic traits under diurnal patterns of light, mimicking the natural light environment. M chloroplasts showed the aggregative movement with increasing light intensity whether it frequently fluctuated or not, and kept their aggregative positions in the midday. With decreasing light intensity, M chloroplasts returned to the random position in the evening. These results suggest that M chloroplasts often rearrange their intracellular positions during the daytime and that the chloroplast aggregative movement can be induced by a natural regime of light. The chloroplast aggregative movement was observed with increasing stomatal conductance, suggesting that stomatal closure is not crucial to trigger the chloroplast response.

Plants are exposed to high light intensity, high leaf temperatures and high air-to-leaf water vapor pressure deficit (ALVPD) during the day. These environmental stresses cause stomatal closure and photoinhibitory damage, leading to midday depression of photosynthesis. Chloroplast positioning is essential for the efficient operation of photosynthesis. However, chloroplast behavior before, during, and even after the midday depression of photosynthesis remains unknown. We investigated changes in the intracellular positioning of chloroplasts and photosynthetic traits under a diurnal pattern of light. Sorghum leaves were exposed to a 12-h regime of light mimicking the natural light environment, with constant leaf temperature and ALVPD. Net photosynthetic rate (Pn) showed a diurnal pattern, and midday depression in Pn was observed at 3.8 h of irradiation. Depression in Pn was attributed to stomatal limitation because the decrease in Pn was in accordance with the decrease in stomatal conductance. The maximum efficiency of photosystem II decreased with the increase in light intensity and remained low after 12 h of irradiation. Bundle sheath chloroplasts swelled after 8 h of irradiation, representing the accumulation of starch. Conversely, mesophyll chloroplasts exhibited avoidance response after 4 h of irradiation, and the avoidance position was maintained during the remainder of the daytime. These data suggest that chloroplasts are subject to light stress during and after the midday depression of photosynthesis. The intensity of natural light is excessive for most of the day and this light stress induces chloroplast avoidance response and depression of photosynthesis.

MIG-seq (Multiplexed inter-simple sequence repeats genotyping by sequencing) has been developed as a low cost genotyping technology, although the number of polymorphisms obtained is assumed to be minimal, resulting in the low application of this technique to analyses of agricultural plants. We applied MIG-seq to 12 plant species that include various crops and investigated the relationship between genome size and the number of bases that can be stably sequenced. The genome size and the number of loci, which can be sequenced by MIG-seq, are positively correlated. This is due to the linkage between genome size and the number of simple sequence repeats (SSRs) through the genome. The applicability of MIG-seq to population structure analysis, linkage mapping, and quantitative trait loci (QTL) analysis in wheat, which has a relatively large genome, was further evaluated. The results of population structure analysis for tetraploid wheat showed the differences among collection sites and subspecies, which agreed with previous findings. Additionally, in wheat biparental mapping populations, over 3,000 SNPs/indels with low deficiency were detected using MIG-seq, and the QTL analysis was able to detect recognized flowering-related genes. These results revealed the effectiveness of MIG-seq for genomic analysis of agricultural plants with large genomes, including wheat.

Parthenocarpy, or fruit set and growth without fertilization, is a desirable trait in tomato cultivation as it reduces the cost of tomato production. MPK-1 is a Japanese parthenocarpic tomato cultivar, and the gene responsible for parthenocarpy of MPK-1 is Pat-k. As MPK-1 is a stable parthenocarpic tomato cultivar, we investigated the physiological mechanism of parthenocarpy in this cultivar. Indole-3-acetic acid (IAA) is considered as the main factor contributing to parthenocarpy, as its exogenous application to unpollinated ovaries triggers parthenocarpic fruit development in tomato. In this study, we investigated the level of IAA and its metabolites and the expression of genes involved in IAA metabolism in unpollinated ovaries of MPK-1. We observed an increase in the level of IAA accompanied by an elevated level of expression of an IAA biosynthesis gene, ToFZY5 in parthenocarpic ovaries of MPK-1. Simultaneously, the level of IAA-glutamate (IAA-Glu), one of the IAA conjugates comprising a potential IAA inactivation pathway, was also increased. These results suggest that the increase in IAA levels, driven by the up-regulation of IAA biosynthesis genes, promotes the growth of parthenocarpic fruits in MPK-1, and that the IAA synthesized in parthenocarpic ovaries is primarily metabolized to IAA-Glu. In addition, expression profiles of some genes involved in IAA metabolism were different between pollinated and parthenocarpic ovaries, suggesting that the specific transcriptional regulation of IAA metabolism in parthenocarpic ovaries of MPK-1 differs from that in pollinated ovaries.

Raman spectroscopy was applied to characterize at the molecular scale the nutritional quality of the Japanese Koshihikari rice cultivar in comparison with other renowned rice cultivars including Carnaroli from Italy, Calrose from the USA, Jasmine rice from Thailand, and Basmati from both India and Pakistan. For comparison, two glutinous (mochigome) cultivars were also investigated. Calibrated and validated Raman analytical algorithms allowed quantitative determinations of: (i) amylopectin and amylose concentrations, (ii) fractions of aromatic amino acids, and (iii) protein content and secondary structure. The Raman assessments non-destructively linked the molecular composition of grains to key nutritional parameters and revealed a complex intertwine of chemical properties. The Koshihikari cultivar was rich in proteins (but with low statistical relevance as compared to other investigated cultivars) and aromatic amino acids. However, it also induced a clearly higher glycemic impact as compared to long-grain cultivars from Asian countries. Complementary to genomics and wet-chemistry analyses, Raman spectroscopy makes non-destructively available factual and data-driven information on rice nutritional characteristics, thus providing customers, dietitian nutritionists, and producers with a solid science-consolidated platform.

Analytical algorithms based on Raman spectroscopy are proposed for the determination of amylopectin and amylose concentrations in polished white rice, and applied to characterize and compare linear and branched polysaccharide structures in nine different types of Japanese rice. A selected algorithm used symmetric bending vibrations of the C O C glycosidic linkage from a relatively narrow spectral zone between 830 and 895 cm−1. It specifically compared the intensity of Raman signals from two types of bending common to both starch components (C1-O-C5 and C1-O-C4 at 868 and 855 cm−1, respectively) and that at the branch point peculiar to amylopectin (C1-O-C6 at 844 cm−1). Raman data were confronted with data collected by conventional amylose-iodine colorimetry method. Consistency was found between Raman and colorimetric methods over the entire series of tested rice cultivars, thus validating the newly proposed spectroscopic algorithm. The amylose content of the tested rice species broadly varied between 1.2 and 20.4%. The proposed Raman algorithm allows fast and nondestructive determination of amylose content in rice with minimal sample preparation. These characteristics might be key in the development of portable Raman devices capable to promptly screen polysaccharides in different rice cultivars with respect to their interannual and plantation-related fluctuations.

Bulb scale propagation makes it difficult to obtain a large number of bulblets from disease-free stocks in a short time. The establishment of improved micropropagation procedures by in vitro culture is therefore desirable. Easter lily (Lilium longiflorum Thunb.) filaments with and without anther were excised and cultured in vitro with different media and culture conditions. In cultures of filaments with anther, callus developed and led to bulb, shoot, and root formation, whereas in cultures of filaments lacking anther, callus development did not occur. Among the various media tested, the B5 medium combined with darkness and the N6 medium combined with darkness or light, both supplemented with 9% sucrose, proved to be superior. A total of 1260 plants were regenerated from callus, acclimatized under a mist, and transferred to the greenhouse with a 100% success rate. No morphological abnormalities were observed among plants regenerated from filament-derived callus and all plants displayed isozyme banding patterns identical to the original cultivar. Chromosome observations revealed that all callus-regenerated plantlets tested were diploid (2n=24). The results suggest that in vitro culture of filaments with anther can be cultured for mass propagation.

Physiological fruit drop in citrus is the deeper problem for fruit production and many researches have suggested that decreasing of carbohydrate translocation to fruit involved in fruit abscission. The fruit abscission process requires 3 stages for successful abscission, which include “induction”, “decision”, and “execution”. However, there is almost no information in the molecular mechanism of secondary physiological fruit drop in citrus. Here, anatomical observation and microarray analysis demonstrated the candidate genes involved in the fruit abscission process after induction of fruit abscission by incubating the detached ponkan (Citrus reticulata Blanco) and hyuganatsu (C. tamurana hort. ex Tanaka) fruit on agar medium. In our study, the cumulative ratio of fruit abscission was very high in ponkan, but very low in hyuganatsu. Morphology of abscission zone (AZ) cells was drastically changed in ponkan, but almost not changed in hyuganatsu. From the 60 K microarray analysis at 0, 12, 24, or 36 h after the induction, the specific up-regulated genes in ponkan AZ tissue were identified. The expressions of many cell wall degrading related genes, such as beta-galactosidase, polygalacturonase and beta-glucosidase etc. increased rapidly at 24 h. These results indicated that “execution” stage of fruit abscission process would be initiated until 24 h after the induction of fruit abscission in citrus.

Background Parthenocarpy is a desired trait in tomato because it can overcome problems with fruit setting under unfavorable environmental conditions. A parthenocarpic tomato cultivar, ‘MPK-1’, with a parthenocarpic gene, Pat-k, exhibits stable parthenocarpy that produces few seeds. Because ‘MPK-1’ produces few seeds, seedlings are propagated inefficiently via cuttings. It was reported that Pat-k is located on chromosome 1. However, the gene had not been isolated and the relationship between the parthenocarpy and low seed set in ‘MPK-1’ remained unclear. In this study, we isolated Pat-k to clarify the relationship between parthenocarpy and low seed set in ‘MPK-1’. Results Using quantitative trait locus (QTL) analysis for parthenocarpy and seed production, we detected a major QTL for each trait on nearly the same region of the Pat-k locus on chromosome 1. To isolate Pat-k, we performed fine mapping using an F4 population following the cross between a non-parthenocarpic cultivar, ‘Micro-Tom’ and ‘MPK-1’. The results showed that Pat-k was located in the 529 kb interval between two markers, where 60 genes exist. By using data from a whole genome re-sequencing and genome sequence analysis of ‘MPK-1’, we could identify that the SlAGAMOUS-LIKE 6 (SlAGL6) gene of ‘MPK-1’ was mutated by a retrotransposon insertion. The transcript level of SlAGL6 was significantly lower in ovaries of ‘MPK-1’ than a non-parthenocarpic cultivar. From these results, we could conclude that Pat-k is SlAGL6, and its down-regulation in ‘MPK-1’ causes parthenocarpy and low seed set. In addition, we observed abnormal micropyles only in plants homozygous for the ‘MPK-1’ allele at the Pat-k/SlAGL6 locus. This result suggests that Pat-k/SlAGL6 is also related to ovule formation and that the low seed set in ‘MPK-1’ is likely caused by abnormal ovule formation through down-regulation of Pat-k/SlAGL6. Conclusions Pat-k is identical to SlAGL6, and its down-regulation causes parthenocarpy and low seed set in ‘MPK-1’. Moreover, down-regulation of Pat-k/SlAGL6 could cause abnormal ovule formation, leading to a reduction in the number of seeds. Electronic supplementary material The online version of this article (10.1186/s12870-018-1285-6) contains supplementary material, which is available to authorized users.

We identified a novel allele of the Vrn-A3 gene that is associated with an early flowering trait in wheat. This trait is caused by a cis-element GATA box in Vrn-A3. To identify novel flowering genes in wheat, we investigated days from germination to heading (DGH) in tetraploid wheat accessions. We found that the tetraploid variety Triticum turgidum L. ssp. dicoccum (TN26) harbors unknown genes that surpass the earliness effect of the early flowering allele Ppd-A1a harbored by TN28 (T. turgidum L. ssp. turgidum conv. pyramidale). Using recombinant inbred lines resulting from a cross between TN26 and TN28, we performed a quantitative trait locus (QTL) analysis for DGH. We identified a QTL for earliness in TN26 on chromosome 7AS, the chromosome on which Vrn-A3 is located. By sequence analysis for the Vrn-A3 locus in both TN26 and TN28, we identified a 7-bp insertion that included a cis-element GATA box sequence at the promoter region of the Vrn-A3 locus of TN26. Based on an expression analysis using sister lines for Vrn-A3, we suggest that the early flowering trait of TN26 was caused by the GATA box in Vrn-A3. In addition, we identified tetraploid wheat as a useful genetic resource for wheat breeding.

Green stem disorder (GSD) of soybean reduces harvesting efficiency and negatively impacts seed appearance when mechanical harvesting is employed. Two recombinant inbred populations were investigated for the effects of segregating stem determination and flowering time on GSD at two different locations, Kyoto and Akita, over two years. Although the severity of GSD of each line varied considerably with the location, the scores showed significant correlation with the environment. Quantitative trait locus (QTL) analysis revealed a strong and consistent QTL for GSD severity in one population of recombinant inbred lines (RILs) across the environments at the Dt1 locus, which governs stem growth habits, and the determinate growth genotypes showed evident symptoms of GSD. However, QTLs were not detected near the Dt1 locus in the other population. Thus, it was unclear if the responsible gene was identical to the stem determination gene. The early flowering genotype showed a more severe symptom of GSD in both populations, but this effect was dependent on the allele at the Dt1 locus. The effect of another QTL detected in the latter population also depended on the allele at the Dt1 locus. Our results indicated that the genetic factor at the Dt1 locus and the factor controlling flowering time influenced the severity of GSD at each location and year and that their effects and interaction complicated the genetic control of the occurrence of GSD.

Black soybeans have been used as a food source and also in traditional medicine because their seed coats contain natural phenolic compounds such as proanthocyanidin and anthocyanin. The objective of this research is to reveal the genetic variation in the phenolic compound contents (PCCs) of seed coats in 227 black soybean cultivars, most of which were Japanese landraces and cultivars. Total phenolics were extracted from seed coats using an acidic acetone reagent and the proanthocyanidin content, monomeric anthocyanin content, total flavonoids content, total phenolics content, and radical scavenging activity were measured. The cultivars showed wide genetic variation in PCCs. Each of the contents was highly correlated with one another, and was closely associated with radical scavenging activity. PCCs were also moderately associated by flowering date but not associated by seed weight. Cultivars with purple flowers had a tendency to produce higher PCCs compared with cultivars with white flowers, suggesting that the W1 locus for flower color can affect phenolic compound composition and content. Our results suggest that developing black soybean cultivars with high functional phenolic compounds activity is feasible.

The breeding of japonica varieties with erect-pose panicle (EP) has recently progressed in the northern part of China, because these varieties exhibit a far higher grain yield than the varieties with normal-pose panicle (NP). A genetic analysis using the F(2) population from the cross between Liaojing5, the first japonica EP variety in China, and the Japanese japonica NP variety Toyonishiki revealed that EP is governed by a single dominant gene EP. Based on previous studies, map-based cloning of EP locus was conducted using Liaojing5, Toyonishiki, their F(2) population, and a pair of near-isogenic lines for EP locus (ZF14 and WF14) derived from the cross between the two varieties; consequently, the STS marker H90 was found to completely cosegregate with panicle pose. The H90 is located in the coding sequence AK101247 in the database, and the AK101247 of Liaojing5 has a 12 bp sequence in exon 5 replaced with a 637 bp sequence of its wild type allele. It was therefore considered that the AK101247 encodes the protein of the wild type allele at EP locus, and that the sequence substitution in exon 5 of Liaojing5 is crucial for expression of the EP phenotype. The effects of EP gene on agronomic traits were investigated using two pairs of near-isogenic lines (ZF6 vs. WF6 and ZF14 vs. WF14) derived from the cross between the two varieties. Experimental results showed that EP gene markedly enhanced grain yield, chiefly by increasing number of secondary branches and number of grains on the secondary branch. EP gene also produced a remarkable increase in grain density.

The distribution and proliferation among Oryza species of miniature Ping (mPing), the only miniature inverted-repeat transposable element (MITE) that is active in all organisms, were investigated through analysis of 78 accessions encompassing nine of the 10 genomic constitutions of the genus Oryza. The mPing family transposons, mPing, Ping, and Pong, were detected in only two of the AA genome species, Oryza sativa and its direct ancestor O. rufipogon, whereas the inactive rice MITE Kiddo was detected in the AA, BB, CC, BBCC and CCDD genome species. Furthermore, the insertion sites and copy numbers of mPing were considerably different among O. rufipogon accessions. A phylogenetic analysis showed that the O. rufipogon accessions used in this study could be grouped into four clusters which were not associated with the copy number of mPing or the presence of Ping. These results suggest that the mPing family was present in the ancestor of O. rufipogon and that mPing proliferated independently in each accession. Based on these results, one possible evolutionary history of the distribution and proliferation of mPing family in O. rufipogon is discussed.

Understanding the relationships between leaf photosynthetic activity and physiological and morphological traits of soybeans [Glycine max. (L.) Merr.] with different stem growth habits could be exploited for yield improvement. Leaf photosynthetic rate (P n ), stomatal conductance (g s ), leaf mass per unit area (LMA), and leaf nitrogen content per unit area (LNC) were measured for fi eld-grown progeny of a cross between an indeterminate type, ‘Stressland’, and a determinate type, ‘Tachinagaha’, soybean. The P n of the uppermost fully expanded leaves of Stressland was 19% greater than Tachinagaha during the fi rst 20 d after seed fi lling (growth stage R5) in 2005. Among 18 F 3 lines, P n at 14 d after R5 in 2005 varied from 22.1 to 34.2 μmol CO 2 m –2 s –1 and was more strongly and signifi cantly correlated with g s (P < 0.01) than with LMA (P < 0.05) and LNC (P = 0.11). In 2006, P n of eight selected F 4 genotypes and the parents varied from 27.9 to 35.0 μmol CO 2 m –2 s –1 . Leaf gas exchange activity of the selected lines was represented by two attributes; the maximum of g s (g max ), and functional leaf lifespan (LL). Values of g max were positively correlated with stomatal density (r = 0.91, P < 0.01), and LL was positively correlated with LMA (r = 0.89, P < 0.01). Some indeterminate types had very high g max but exhibited shorter LL. Genetic improvement of maximum leaf photosynthesis appears possible by increasing stomatal density, and the Dt1 locus for stem habit has a positive effect on soybean leaf photosynthesis, both in its maximum and duration.