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Asian rice (Oryza sativa) was domesticated from O. rufipogon, and reduced seed-shattering behaviour was selected to increase yields. Two seed-shattering loci, qSH3 and sh4, are involved in reducing seed shattering in both japonica and indica rice cultivars, while qSH1 and qCSS3 are likely specific to japonica cultivars. In indica cultivars, qSH3 and sh4 fail to explain the degree of seed shattering, as an introgression line (IL) of O. rufipogon W630 carrying domesticated alleles at qSH3 and sh4 still showed seed shattering. Here we analysed differences in seed-shattering degree between the IL and the indica cultivar IR36. The values for grain detachment in the segregating population between the IL and IR36 were continuous. Based on QTL-seq analysis using the BC1F2 population between the IL and IR36, we detected two novel loci, qCSS2 and qCSS7 (QTLs for the Control of Seed Shattering in rice on chromosomes 2 and 7), which contributed to the reduced seed shattering in IR36. We further investigated the genetic interaction of qCSS2 and qCSS7 under the presence of qSH3 and sh4 mutations in O. rufipogon W630 and found that IL carrying IR36 chromosomal segments covering all four loci are required to explain seed-shattering degree in IR36. Since qCSS2 and qCSS7 were not detected in previous studies on seed shattering in japonica, their control may be specific to indica cultivars. Therefore, they are important to understanding the history of rice domestication as well as to adjusting the seed-shattering degree of indica cultivars to maximise their yield.

The Japanese apricot (Prunus mume) is a culturally and economically important fruit tree in East Asia. ‘Nanko’, the primary cultivar of Japanese apricot well known in Japan, usually suffers from scab, a disease caused by Venturia carpophila. Scabs result in the development of black spots on the fruit surface, which considerably reduce their commercial value. Despite being an economic concern, there have been few reports on phenotypic variation in scab resistance/susceptibility, the underlying genetic factors, and the development of DNA markers. Therefore, in this study, we performed a comprehensive trait analysis for naturally occurring fruit scab resistance and susceptibility over four years. We also conducted a genome-wide association study (GWAS), and significant peaks were detected in 2017 and 2018. Candidate genes associated with disease resistance were located around the nine single-nucleotide polymorphisms (SNPs) detected in 2017 and 2018. These SNPs were thought to be associated with scab susceptibility of ‘Nanko’ lineages. These findings shed light on phenotypic and genetic profiles of scab resistance in P. mume and will assist future breeding programs to improve scab resistance.

Japanese apricot (Prunus mume) is a culturally and economically important fruit tree in East Asia. ‘Nanko’, the primary cultivar of the Japanese apricot well known in Japan, usually suffers from scab, a disease caused by Venturia carpophila. Scab results in the development of black spots on the fruit surface, which considerably reduces its commercial value. Despite being an economic concern for Japanese apricot, there have been few reports on the phenotypic variation in scab resistance/susceptibility, the underlying genetic factors, and the development of DNA markers. Therefore, in this study, we performed a comprehensive trait analysis for scab resistance and susceptibility for four years and conducted a genome-wide association study (GWAS) to identify the associated loci. The results showed that significant GWAS peaks were detected in 2017 and 2018. Promising candidate gene encoding domains associated with disease resistance were found at the nine single-nucleotide polymorphisms (SNPs) identified in 2017 and 2018. These SNPs were thought to be associated with scab susceptibility of ‘Nanko’ lineages. These findings shed light on the mechanisms of scab resistance in P. mume and will assist future breeding programs to improve scab resistance in ‘Nanko’ lineages.

Key message A candidate gene responsible for higher grain zinc accumulation in rice was identified, which was probably associated with a partial defect in anther dehiscence. Abstract Zinc (Zn) is an essential mineral element in many organisms. Zn deficiency in humans causes various health problems; therefore, an adequate dietary Zn intake is required daily. Rice, Oryza sativa, is one of the main crops cultivated in Asian countries, and one of the breeding scopes of rice is to increase the grain Zn levels. Previously, we found that an Australian wild rice strain, O. meridionalis W1627, exhibits higher grain Zn levels than cultivated rice, O. sativa Nipponbare, and identified responsible genomic loci. An increase in grain Zn levels caused by one of the loci, qGZn9a, is associated with fertility reduction, but how this negative effect on grain productivity is regulated remains unknown. In this study, we artificially trimmed spikelets on the flowering day and found that a reduction in number of seeds was associated with an increase in the grain Zn levels. We also found that a partial defect in anther dehiscence correlated with the increase in grain Zn levels in plants carrying the W1627 chromosomal segment at qGZn9a in a Nipponbare genetic background. Among eight candidate genes in the qGZn9a region, three were absent from the corresponding region of W1627; one of these, Os09g0384900, encoding a DUF295 protein with an unknown function, was found to be specifically expressed in the developing anther, thereby suggesting that the gene may be involved in the regulation of anther dehiscence. As fertility and grain Zn levels are essential agronomic traits in rice, our results highlight the importance of balancing these two traits. Supplementary Information The online version contains supplementary material available at 10.1007/s00122-021-03873-4.

Raman spectroscopy is a powerful method for estimating the molecular structure of a target that can be adapted for biomedical analysis given its non-destructive nature. Inflammatory skin diseases impair the skin’s barrier function and interfere with the patient’s quality of life. There are limited methods for non-invasive and objective assessment of skin inflammation. We examined whether Raman spectroscopy can be used to predict skin inflammation with high sensitivity and specificity when combined with artificial intelligence (AI) analysis. Inflammation was chemically induced in mouse ears, and Raman spectra induced by a 785 nm laser were recorded. A principal component (PC) analysis of the Raman spectra was performed to extract PCs with the highest percentage of variance and to estimate the statistical score. The accuracy in predicting inflammation based on the Raman spectra with or without AI analysis was assessed using receiver operating characteristic (ROC) curves. We observed some typical changes in the Raman spectra upon skin inflammation, which may have resulted from vasodilation and interstitial oedema. The estimated statistical scores based on spectral changes correlated with the histopathological changes in the skin. The ROC curve based on PC2, which appeared to include some spectral features, revealed a maximum accuracy rate of 80.0% with an area under the curve (AUC) of 0.864. The AI analysis improved the accuracy rate to 93.1% with an AUC of 0.972. The current findings demonstrate that the combination of Raman spectroscopy with near-infrared excitation and AI analysis can provide highly accurate information on the pathology of skin inflammation.

Cultivated rice (Oryza sativa L.) was domesticated from the Asian wild species O. rufipogon. Compared with cultivated rice, wild rice has spikelets/seeds with long barbed awns. In order to evaluate the role of awns in wild rice, four seed groups with different awn lengths (full, half, quarter and no awns) were prepared, and the following seed dispersal movements were investigated under simulated natural conditions as observed in the tropical Asian habitat: (1) seed detachment from the parent plant; (2) falling angle of mature seed; (3) ability to slip into small spaces; (4) horizontal movement on the ground and (5) horizontal movement in water. As a result, awns were found to enhance the detachment of matured seeds from the panicles in the initial seed dispersal step. They regulated vertical orientation in the air, and the vertical form may enable seeds to squeeze to the ground. The awned seeds also showed advantages in horizontal movements on the ground and in the water. In most of the experiments, seeds with full awns showed the best performance for seed dispersal, suggesting that wild rice keeps long awns to survive under natural conditions. Since seed awning is dominantly controlled by wild functional alleles at several loci, wild rice may be able to prevent a drastic reduction of awn length.

Key message A novel locus, qCSS3, involved in the non-seed-shattering behaviour of Japonica rice cultivar, 'Nipponbare', was detected by QTL-seq analysis using the segregating population with the fixed known seed-shattering loci. Abstract Asian cultivated rice, Oryzasativa, was domesticated from its wild ancestor, O.rufipogon. Loss of seed shattering is one of the most recognisable traits selected during rice domestication. Three quantitative trait loci (QTLs), qSH1, qSH3, and sh4, were previously reported to be involved in the loss of seed shattering of Japonica cultivated rice, O.sativa 'Nipponbare'. However, the introgression line (IL) carrying 'Nipponbare' alleles at these three loci in the genetic background of wild rice, O.rufipogon W630, showed a lower value for detaching a grain from the pedicel than 'Nipponbare'. Here, we investigated abscission layer formation in the IL and found a partially formed abscission layer in the central region between the epidermis and vascular bundles. Based on QTL-seq analysis using the F-2 population obtained from a cross between 'Nipponbare' and the IL, we detected two novel loci qCSS3 and qCSS9 (QTL for the Control of Seed Shattering in rice on chromosomes 3 and 9), which were found to be involved in the difference in seed-shattering degree between 'Nipponbare' and W630. Then, we further focused on qCSS3 in order to understand its potential role on the loss of seed shattering. The candidate region of qCSS3 was found to be located within a 526-kb region using substitution mapping analysis. Interestingly, the qCSS3 candidate region partially overlaps the selective sweep detected for Japonica but not for Indica rice cultivars, suggesting that this region harbours the mutation at a novel seed-shattering locus specifically selected for non-seed-shattering behaviour in Japonica cultivars.

To evaluate genetic diversity and genetic structure of wild rice (Oryza rufipogon) populations in Myanmar, seven research sites were selected based on various ecological conditions. A large number of samples under natural growth conditions were collected and studied using six simple sequence repeats (SSRs) and two chloroplast DNA markers. A total of 77 alleles were detected from 1559 samples over six SSR loci. The mean number of alleles per population ranged from 3.167 to 8.667, and the mean expected heterozygosity ranged from 0.140 to 0.701. Wild rice populations survived under various environmental conditions and retained different levels of genetic diversity. The large number of samples was effective to confirm the spatial genetic structure of wild rice populations in a relatively small area. Regarding chloroplast DNA polymorphisms, four populations possessed only one pattern, while the other three showed two or five combinations of haplotypes, even within the same population. Additionally, the existence of a new genotype was revealed. Considerable variations in chloroplast DNA exist in the wild rice populations of Myanmar. A high proportion of genetic variation was detected within, rather than among, populations. To ensure maintenance of allelic diversity, it is advisable to preserve many individuals from a large population.

Asian rice (Oryza sativa L.) is consumed by more than half of the world’s population. Despite its global importance, the process of early rice domestication remains unclear. During domestication, wild rice (O. rufipogon Griff.) acquired non-seed-shattering behaviour, allowing humans to increase grain yield. Previous studies argued that the sh4 mutation triggered a reduction in seed shattering during rice domestication; but our experiments using wild introgression lines of O. rufipogon show that the domesticated sh4 allele alone is insufficient for shattering loss. Here, we identified the interaction between three key mutations associated with the interruption of abscission layer formation and panicle architecture that were causal in early rice domestication. An interruption of abscission layer formation requires both sh4 and qSH3 mutations, presenting an apparent barrier to the selection of shattering loss. We identified a causal single-nucleotide polymorphism at qSH3 within the seed-shattering gene OsSh1, which is conserved in indica and japonica subspecies but absent in the circum-aus group of rice. Through harvest experiments, we demonstrated that seed shattering alone did not significantly impact yield; rather yield increases were observed with closed panicle formation controlled by SPR3, which is further augmented by the integration of sh4 and qSH3 alleles. Complementary manipulation of seed shattering and panicle shape result in a mechanically stable panicle structure. We propose a stepwise route for the earliest phase of rice domestication, wherein selection of visible SPR3-controlled closed panicle morphology was instrumental in the sequential recruitment of sh4 and qSH3, which led to the loss of shattering.Significance StatementRice is one of the most important crops worldwide. Loss of seed shattering in domesticated rice, previously attributed to single mutations such as those in sh4, is considered the principal genetic change which resulted in yield increases. However, we show that sh4 alone is insufficient and other genes, such as qSH3, are required to cause abscission layer disruption. The evolution of non-seed-shattering therefore required multiple mutations. Furthermore, shattering loss in genetic backgrounds of wild rice does not correspondingly increase yields. We have identified an interaction in which a second trait, closed panicle formation controlled by SPR3, that both increases the yield and facilitates recruitment of sh4 and qSH3, which synergistically augment yield, leading to a stepwise model for rice domestication.

SummaryDomestication and population differentiation in crops involve considerable phenotypic changes. The logs of these evolutionary paths, including natural/artificial selection, can be found in the genomes of the current populations. However, these profiles have been little studied in tree crops, which have specific characters, such as long generation time and clonal propagation, maintaining high levels of heterozygosity.We conducted exon-targeted resequencing of 129 genomes in the genusPrunus, mainly Japanese apricot (Prunus mume), and apricot (P. armeniaca), plum (P. salicina), and peach (P. persica). Based on their genome-wide single nucleotide polymorphisms merged with published resequencing data of 79 ChineseP. mumecultivars, we inferred complete and ongoing population differentiation inP. mume.Sliding window characterization of the indexes for genetic differentiation identified interspecific fragment introgressions betweenP. mumeand related species (plum and apricot). These regions often exhibited strong selective sweeps formed in the paths of establishment or formation of substructures ofP. mume, suggesting thatP. mumehas frequently imported advantageous genes from other species in the subgenusPrunusas adaptive evolution.These findings shed light on the complicated nature of adaptive evolution in a tree crop that has undergone interspecific exchange of genome fragments with natural/artificial selection.

Background Awns are bristle-like organs at the tips of the glumes. Wild rice has maintained long awns for successful seed propagation through seed dispersal. Seed awning is an interesting trait in rice domestication. Long awns might have been beneficial for seed gatherers in the initial phase of domestication; however, awnless phenotypes were preferably selected in a later phase with non-seed-shattering plants. Investigation of domestication loci associated with awnlessness in cultivated rice will be useful in clarifying the process and history of rice domestication. Results Quantitative trait locus (QTL) analysis for seed awning was carried out using a BC3F2 population between Oryza sativa IR36 (a cultivated donor parent with awnless phenotype) and O. rufipogon W630 (a wild recurrent parent with awns). As a result, two QTLs on chromosome 4 (corresponding to An-1 and LABA1) and one on chromosome 2 (designated as qAWNL2) were detected. Gene interaction among three seed-awning QTLs were further examined with the plants having eight different combinations of homozygous genotypes. Their awn length variation indicated that the IR36 alleles at these loci had the additive awnlessness effects in the genetic background of wild rice. The shortest awn length was observed for the plants having IR36 homozygous alleles at all loci, giving about 75% reduction in awn length. By the fine mapping, the candidate region of the novel qAWNL2 locus was delimited in a 157.4-kb region containing 22 predicted genes in Nipponbare genome. Conclusions QTL analysis revealed that three loci, An-1, LABA1 and qAWNL2, were mainly responsible for the awnlessness of O. sativa IR36. In the wild genetic background, loss-of-function alleles at three awning loci showed additive effects on length reduction. In rice domestication, awnless forms may be gradually generated through the accumulation of mutations at awning loci.

Additional file 2: Figure S1. Graphical genotype of the J5 backcross recombinant inbred line. Figure S2. Frequency distributions of awn lengths in the 1st to 5th spikelet positions in BC3F2 population between O. rufipogon W630 and the J5 line. Figure S3. Spikelet morphology of the eight genotypes of BC3F3 plants together with O. rufipogon W630, J5 line and O. sativa IR36. Figure S4. Awn lengths (means ± SD) of the 1st to 4th spikelets of eight homozygous genotypes in the wild genetic background.

Rice (Oryza sativa L.) is widely cultivated around the world and is known to be domesticated from its wild form, O. rufipogon. A loss of seed shattering is one of the most obvious phenotypic changes selected for during rice domestication. Previously, three seed-shattering loci, qSH1, sh4, and qSH3 were reported to be involved in non-shattering of seeds of Japonica-type cultivated rice, O. sativa cv. Nipponbare. In this study, we focused on non-shattering characteristics of O. sativa Indica cv. IR36 having functional allele at qSH1. We produced backcross recombinant inbred lines having chromosomal segments from IR36 in the genetic background of wild rice, O. rufipogon W630. Histological and quantitative trait loci analyses of abscission layer formation were conducted. In the analysis of quantitative trait loci, a strong peak was observed close to sh4. We, nevertheless, found that some lines showed complete abscission layer formation despite carrying the IR36 allele at sh4, implying that non-shattering of seeds of IR36 could be regulated by the combination of mutations at sh4 and other seed-shattering loci. We also genotyped qSH3, a recently identified seed-shattering locus. Lines that have the IR36 alleles at sh4 and qSH3 showed inhibition of abscission layer formation but the degree of seed shattering was different from that of IR36. On the basis of these results, we estimated that non-shattering of seeds in early rice domestication involved mutations in at least three loci, and these genetic materials produced in this study may help to identify novel seed-shattering loci.

Differences in floral morphologies affect pollination behaviour in many flowering plants. In the genus Oryza, several differences in the size of floral organs are known. In this study, we focused on the differences in the size of floral organs between common cultivated rice, Oryza sativa L. and its wild ancestor, O. rufipogon. We compared floral morphologies between cultivated rice O. sativa cv. Nipponbare and O. rufipogon W630. We first evaluated temporal changes in filament and anther lengths. W630 had longer filaments with rapid elongation within 15 min after spikelet opening. W630 also had longer anthers than Nipponbare, and size of anther was consistent throughout all time examined. We also analysed other six floral traits, and found that W630 had higher stigma and style length, as well as lemma and palea length, but lower lemma and palea width. Quantitative trait locus (QTL) analysis was performed to identify the loci controlling these floral traits, using backcross recombinant inbred lines derived from a cross between Nipponbare and W630. A total of 11 significant QTLs were identified. Of these, two pairs of QTLs for lemma and palea length and one pair for lemma and palea width overlapped, suggesting that common genetic factors may be the reason for the differences in these traits. In addition, we performed QTL analysis for grain size, and found that QTLs for grain size coincided with those for lemma and palea size, indicating that grain size is partly controlled by glume capacity. The QTLs identified in this study will be informative for understanding genetic changes associated with rice domestication.

Cultivated rice (Oryza sativa L.) was domesticated from the Asian wild species, Oryza rufipogon Griff. Among morphological differences between them, one of the striking traits specific to cultivated rice is loss of seed shattering. In the early stage of rice domestication, the related traits of this character have been desirable for the ancient seed gatherers because it enhances the efficiency of seed collection. In this chapter, we propose that three morphological traits, closed panicle shape, non-seed shattering, and seed awning, played important roles in controlling the degree of seed dispersal. First, we reviewed domestication loci controlling the three traits. We then evaluated allele effects at these loci using reciprocal backcross populations between O. sativa Nipponbare and our standard wild accession of O. rufipogon W630. In the genetic background of cultivated rice, all the wild functional alleles were responsible for these domestication traits. On the other hand, cultivated non-functional alleles were not always associated with the drastic morphological changes in the genetic background of wild rice. Since ancient humans have selected cultivated-type mutants in natural wild populations, possible domestication process for the emergence of cultivated rice is discussed based on the effects of cultivated non-functional alleles.

A total of 448 samples in five natural populations of wild rice (Oryza rufipogon) were collected in Cambodia. They were examined using 12 SSR and two chloroplast markers to evaluate the degree of variation among populations and the genetic structure within populations. In the two annual populations, the number of plants with homozygous alleles at all 12 SSR loci were high (66.3% and 79.5%), suggesting that these plants propagate mainly through self-pollination. In the three perennial populations, no individuals had all homozygous genotypes, but redundant genotypes resulted from clonal propagation were observed. Percentages of the redundant genotypes were highly varied (3.6%, 29.2% and 86.0%). This may be due to the different stable levels of environmental conditions. As for chloroplast genome, most of the wild plants showed the same chloroplast types as most Indica-type cultivars have. However, plants with different chloroplast types were maintained, even in the same population. In tropical Asian countries, many wild rice populations were observed under similar ecological conditions examined in this study. Therefore, the present results concerning population structure will be important to further elucidate genetic features of wild rice, and will also give strong clues to utilize and conserve wild natural genetic resources.

Loss of seed shattering was one of the key phenotypic changes selected for in the domestication of many crop species. Asian cultivated rice, Oryza sativa L., was domesticated from its wild ancestor, O. rufipogon, and three seed-shattering loci, qSH1, sh4 and qSH3, have been reported to be involved in the loss of seed shattering in cultivated rice. Here, we analysed the seed-shattering behaviour of wild rice using introgression lines carrying the cultivated alleles from O. sativa Nipponbare in the genetic background of wild rice, O. rufipogon W630. We first carried out fine mapping of the qSH3 region and found that the qSH3 locus is localized in an 850-kb region on chromosome 3. We then analysed the effects of the Nipponbare alleles at sh4 and qSH3 on seed-shattering behaviour in wild rice, as a mutation at qSH1 was not commonly found in rice cultivars. Seed-shattering behaviour did not change in the two types of introgression line independently carrying the Nipponbare-homozygous alleles at sh4 or qSH3 in the genetic background of wild rice. However, the introgression lines having the Nipponbare-homozygous alleles at both sh4 and qSH3 showed a reduction in the degree of seed shattering. Histological and scanning electron microscopy analyses revealed that abscission layer formation was inhibited around the vascular bundles in these lines. Since the qSH3 region, as well as sh4, has been shown to be under artificial selection, the interaction of mutations at these two loci may have played a role in the initial loss of seed shattering during rice domestication.

Zinc (Zn) is one of the essential mineral elements for both plants and humans. Zn deficiency in human is one of the major causes of hidden hunger, a serious health problem observed in many developing countries. Therefore, increasing Zn concentration in edible part is an important issue for improving human Zn nutrition. Here, we found that an Australian wild rice O. meridionalis showed higher grain Zn concentrations compared with cultivated and other wild rice species. The quantitative trait loci (QTL) analysis was then performed to identify the genomic regions controlling grain Zn levels using backcross recombinant inbred lines derived from O. sativa 'Nipponbare' and O. meridionalis W1627. Four QTLs responsible for high grain Zn were detected on chromosomes 2, 9, and 10. The QTL on the chromosome 9 (named qGZn9), which showed the largest effect on grain Zn concentration was confirmed with the introgression line, which had a W1627 chromosomal segment covering the qGZn9 region in the genetic background of O. sativa 'Nipponbare'. Fine mapping of this QTL resulted in identification of two tightly linked loci, qGZn9a and qGZn9b. The candidate regions of qGZn9a and qGZn9b were estimated to be 190 and 950 kb, respectively. Furthermore, we also found that plants having a wild chromosomal segment covering qGZn9a, but not qGZn9b, is associated with fertility reduction. qGZn9b, therefore, provides a valuable allele for breeding rice with high Zn in the grains.

Asian cultivated rice Oryza sativa L. was domesticated from its wild ancestor, O. rufipogon. During domestication, the cultivated rice lost its seed-shattering behaviour. Previous studies have shown that two major quantitative trait loci (QTLs; qSH1 and sh4) are responsible for the seed-shattering degree. Here, we produced introgression lines carrying non-functional alleles from O. sativa ‘Nipponbare’ at the two major QTLs in the genetic background of wild rice O. rufipogon W630, and examined the effects of the two QTLs on seed shattering and abscission layer formation. The introgression lines, with Nipponbare alleles at either or both loci, showed complete or partial abscission layer formation, respectively, indicating that other unknown loci might be involved in enhancing seed shattering in wild rice. We detected a single QTL named qSH3 regulating seed-shattering degree using an F2 population between Nipponbare and the introgression line carrying Nipponbare alleles at the two QTLs. Although we generated an introgression line for qSH3 alone, no effects on seed shattering were observed. However, a significant effect on seed-shattering degree was observed for the introgression line carrying Nipponbare alleles at qSH3 and the two QTLs, suggesting an important role of qSH3 on seed shattering in coordination with the two QTLs.

Emmer wheat (Triticum turgidum ssp. dicoccum) was a principal crop in the development and spread of Neolithic agriculture in the Old World. It represents the primitive situation in the domestication of AABB tetraploid wheat. To understand the genetic modifications underlying the early stage of tetraploid wheat domestication, QTL analysis was carried out using 144 F2 plants derived from a cross between the domesticated emmer wheat and the wild emmer wheat (T. turgidum ssp. dicoccoides). To our knowledge, this is the first report of molecular linkage map and QTL analysis of the domestication-related characters in emmer wheat. The linkage map with a total length of 2849.8 cM was constructed using 227 microsatellite (SSR) markers. Chromosomal location and effect of QTLs were estimated for ten domestication-related traits including whole plant and spike characteristics. Seventeen QTLs were detected on chromosomes 1B, 2A, 2B, 3A, 3B, 4A, 5B, and 7B. Two regions on chromosomes 2A and 3B have a large effe...

Seed awning is one of the important traits for successful propagation in wild rice. During the domestication of rice by ancient humans, plants with awnless seeds may have been selected because long awns hindered collection and handling activities. To investigate domestication of awnless rice, QTL analysis for seed awning was first carried out using backcross recombinant inbred lines between Oryza sativa Nipponbare (recurrent parent) and O. rufipogon W630 (donor parent). Two strong QTLs were detected in the same regions as known major seed-awning loci, An-1 and RAE2. Subsequent causal mutation surveying and fine mapping confirmed that O. rufipogon W630 has functional alleles at both loci. The gene effects and interactions at these loci were examined using two backcross populations with reciprocal genetic backgrounds of O. sativa Nipponbare and O. rufipogon W630. As awn length in wild rice varied among seeds even in the same plant, awn length was measured based on spikelet position. In the genetic background of cultivated rice, the wild alleles at An-1 and RAE2 had awning effects, and plants having both wild homozygous alleles produced awns whose length was about 70% of those of the wild parent. On the other hand, in the genetic background of wild rice, the substitution of cultivated alleles at An-1 and RAE2 contributed little to awn length reduction. These results indicate that the domestication process of awnless seeds was complicated because many genes are involved in awn formation in wild rice.

Witchweed, Striga hermonthica (hereafter, referred to as “Striga”), is a major biotic constraint to cereal production in sub-Saharan Africa. The parasitic plant is a socioeconomic problem that has forced some resource-poor farmers to abandon their farms due to high infestation. This study was designed in order to elucidate farmers' perceptions of Striga control measures and to determine their potential adoption in two villages in western Kenya. Participatory rural appraisals and individual interviews were conducted in 2009 and 2010 in a sample of 128 and 120 households in Kaura and Kogweno-Oriang villages in Homabay and Rachuonyo districts, respectively. The results revealed that crop production was the main occupation in most households. The farmers identified Striga as one of the major constraints to maize, sorghum, and finger millet production. According to the farmers, the most popular control measures were hand-pulling, crop rotation, and intercropping, even though rotational systems might need a longer timeframe to reduce the soil seed bank of Striga. Although the level of Striga infestation and damage were increasing in the farmers' fields, the adoption of the control options was limited. The reason for the low adoption level of the control methods by the farmers is because they are “too risky” as there is no guarantee of a direct pay-off in increased crop yield. Farmer-led evaluation and adaptation of the various Striga control technologies in real-life situations will facilitate the choice of appropriate options and facilitate their uptake.

Saikai 35 was bred from a cross between TD0101 as the female, which was created by chromosome-doubling of a good-tasting and bacterial wilt resistant diploid variety, Inca-no-mezame, and Sakurafubuki as the male, the latter of which has H1 and Rychc genes showing resistance to potato cyst nematode (PCN) and Potato virus Y (PVY), respectively. All favorable traits were combined into Saikai 35, although marketable yield in the spring cropping was 20.4–21.0% lower than those of major double-cropping varieties. Saikai 35 is particularly useful for having Solanum phureja-derived cytoplasm (S/e), which resulted in high male and female fertility. In addition, sets of very tightly linked DNA markers sandwiching H1 and Rychc are available. Therefore, Saikai 35 is being released as a breeding line, which can confer efficiently PCN and PVY resistance genes.

To decrease the age at first calving in Holsteins, the effects of average daily body weight gain (ADG) and crude protein (CP) level until first insemination on growth performance and milk production were examined. The MM group had a target ADG of 0.75 kg and received a diet with a CP level of 14%. The HM and HH groups had a target ADG of 1 kg; both these groups received a diet with CP levels 14% and 16%, respectively. The ADG in the HM and HH groups was 1.1 kg, whereas in the MM group it was 0.97 kg (P < 0.01). The HM and HH groups showed no differences in withers height at body weight 350 kg. The ages at first calving in MM, HM and HH groups were 23.1, 21.0 and 21.8 months, respectively. The HM and HH groups had lower milk yield at day 305 than the MM group (P < 0.01). These results suggest that growth performance until first insemination should be maintained at an ADG of 0.97 kg or less with a CP level of approximately 14%, to shorten time until first insemination and prevent the decrease of milk yield.

We investigated the effect of cellooligosaccharide (CE) or a combination of dextran and Lactobacillus casei ssp. casei strain JCM1134T (synbiotic; SB) feeding on growth performance, fecal condition and hormone concentrations in Holstein calves. Fifty-two female Holstein calves were randomly assigned to three treatment groups: CE feeding group (n = 16), SB feeding group (n = 18), and control group (n = 18). Body weight at 90 days of age, as well as daily body weight gain (DG) and feed efficiency after weaning to 90 days of age were greater (P

Backcross populations at advanced generations are useful in evaluating the agronomic traits from unadapted germplasms, such as wild species. In this study, we generated 159 backcross recombinant inbred lines (BRILs) at the BC2F8 generation between Oryza sativa Nipponbare (a recurrent parent) and O. rufipogon W630 (a donor parent). These BRILs were found to have nearly homozygous genome constitutions based on the marker genotypes at 180 SSR loci covering whole chromosomes. Since their selfed progenies have almost identical genotypes in each line, they were further used for QTL analysis of drought tolerance. Out of six QTLs detected, three were found to have wild alleles with favorable effects on drought tolerance. The present BRILs with known marker data can be applied to more QTL analyses of traits specific to wild species.

In the near future, global average temperature is expected to increase due to the accumulation of greenhouse gases, and increased temperatures will cause severe sterility in many crop species. In rice, since wild species show high genetic variation, they may have the potential to improve the flowering characters of cultivars. In this study, we investigated flowering characters under natural conditions by comparing an Asian wild rice accession of Oryza rufipogon W630 (originated from Myanmar) with a Japanese rice cultivar, O. sativa Japonica cv. Nipponbare. Further, QTL analysis for days to heading (DH) and spikelet opening time (SOT: the time of day when the spikelet opens) was carried out using BC(2)F(8) backcross population derived from the cross between them. Regarding DH, four QTLs were detected, and two of them were found to have wild alleles with strong effects leading to longer days to heading during the Japanese summer. These wild alleles may be used to produce late-heading cultivars that do not flower during the high summer temperatures anticipated in the future. As for SOT, two parameters of SOTb (beginning time when the first spikelet opens) and SOTm (median time when 50% of the spikelets open) were recorded and the time differences from Nipponbare were investigated. Two QTLs on chromosomes 5 and 10 and two QTLs on chromosomes 4 and 5 were detected for SOTb and SOTm, respectively. The wild alleles were responsible for early spikelet opening time at all loci. If the wild alleles detected in this study have the same effects in the genetic background of other cultivars, they will be very useful in producing early-flowering rice cultivars that complete fertilization in the morning before the temperature rises.

Domesticated timopheevi wheat (Triticum timopheevi) is an endemic crop of western Georgia in Transcaucasia. It has a distinct nuclear genome (2n = 28, AAGG) and is genetically isolated from other wheat species. To clarify the genetic diversity and the domestication of this interesting wheat, we analyzed molecular variation at 23 microsatellite loci in the chloroplast genome. Allelic diversity was evaluated using 94 accessions representing domesticated timopheevi wheat (T. timopheevi), wild timopheevi wheat (T. araraticum), and wild emmer wheat (T. dicoccoides). The average diversity index (H) in T. araraticum (0.206) was smaller than that in T. dicoccoides (0.284). No polymorphisms were detected among the six accessions of T. timopheevi, suggested a monophyletic origin of domesticated timopheevi wheat. Phylogenetic analyses of the plastotypes revealed clear differences between the chloroplast DNA of timopheevi wheat and emmer wheat, and thus supported the hypothesis that these two wheat species originated independently. None of the T. araraticum plastotypes collected in Transcaucasia were closely related to the T. timopheevi plastotype. On the other hand, the plastotypes found in northern Syria and southern Turkey showed closer relationships with T. timopheevi. These results suggested that the domestication of timopheevi wheat might have occurred in the region including southern Turkey and northern Syria.

The effects of different culture temperatures, culture media and saccharides on the anther culture efficiency in two salt tolerant rice (Oryza sativa ssp. indica) cultivars, Pokkali and Nona Bokra, were examined. Comparison of two culture temperatures (constant temperature at 25°C and alternating temperatures at 30°C/20°C) indicated that alternating temperatures showed remarkable effects not only on the callus induction but also on the plant regeneration. Among the basal media examined, higher callus productivity was observed in SK-I medium and higher shoot productivity was obtained in SK-II medium than other basal media. When alternating temperatures and revised N6 medium including maltose were used throughout anther culture, callus productivity and green shoot productivity showed the highest score in the salt tolerant two cultivars used in this study. Maltose and alternating temperatures increases the anther culture efficiency of recalcitrant indica rice cultivars. This is the first report suggesting high production of haploids or doubled haploids from anther culture of these salt tolerant indica cultivars.

AA genome species in the genus Oryza are valuable resources for improvement of cultivated rice. Oryza rufipogon and O. barthii were progenitors of two domesticated rice species, O. sativa and O. glaberrima, respectively. We used chloroplast single-nucleotide repeats (RCt1-10) to evaluate genetic diversity among AA genome species. Higher diversity was detected in the American species O. glumaepatula and the Asian species O. rufipogon. Other chloroplast sequences indicated that O. glumaepatula shares high similarity with O. longistaminata. Insertions of retrotransposable elements, however, showed a close relation between O. barthii and O. glumaepatula. To clarify phylogenetic relationships among AA genomes, whole-genome sequences obtained from different species were used to develop chloroplast INDEL markers. The INDEL patterns clearly showed multiple maternal origins of O. glumaepatula. The complicated origins have resulted in high genetic diversity in this species. In contrast, the Australian endemic species O. meridionalis tended to show narrower diversity than the other species. High variation in O. rufipogon, reconfirmed using the chloroplast INDELs, covered the variation in O. meridionalis and part of the variation in O. glumaepatula. Maternal lineages including O. barthii, O. longistaminata and the remainder of O. glumaepatula were phylogenetically close to each other and carried low genetic diversity. They were separated from independent lineages, suggesting that they had diverged from a single ancestral maternal lineage, but diverged later to keep gene flow within respective species, as SSR compositions suggested. Genetic relationships among AA genome species indicate how these species have evolved and become distributed across four continents.

Loss of seed shattering was one of the key phenotypic changes selected for in the domestication of many crop species. Asian cultivated rice, Oryza sativa L., was domesticated from its wild ancestor, O. rufipogon, and three seed-shattering loci, qSH1, sh4 and qSH3, have been reported to be involved in the loss of seed shattering in cultivated rice. Here, we analysed the seed-shattering behaviour of wild rice using introgression lines carrying the cultivated alleles from O. sativa Nipponbare in the genetic background of wild rice, O. rufipogon W630. We first carried out fine mapping of the qSH3 region and found that the qSH3 locus is localized in an 850-kb region on chromosome 3. We then analysed the effects of the Nipponbare alleles at sh4 and qSH3 on seed-shattering behaviour in wild rice, as a mutation at qSH1 was not commonly found in rice cultivars. Seed-shattering behaviour did not change in the two types of introgression line independently carrying the Nipponbare-homozygous alleles at sh4 or qSH3 in the genetic background of wild rice. However, the introgression lines having the Nipponbare-homozygous alleles at both sh4 and qSH3 showed a reduction in the degree of seed shattering. Histological and scanning electron microscopy analyses revealed that abscission layer formation was inhibited around the vascular bundles in these lines. Since the qSH3 region, as well as sh4, has been shown to be under artificial selection, the interaction of mutations at these two loci may have played a role in the initial loss of seed shattering during rice domestication.

The obligate root hemiparasite, Striga hermonthica (Del.) Benth., native to sub-Saharan Africa causes serious economic constraint to cereal production. Studies on Striga spp. interactions with rice are desirable as it is a model monocot with high density molecular linkage maps. In this study, quantitative trait locus (QTL) analysis for S. hermonthica resistance was carried out using 141 backcross recombinant inbreed lines (BRILs) derived from a cross between Oryza sativa (cv. Nipponbare) and O. rufipogon W630. The population was grown in the field at Lake Basin Development Authority, Alupe farm in 2013 and infected with S. hermonthica from Alupe, Kenya. Putative QTL for S. hermonthica resistance was assumed using single-point analysis (qGene program) at p < 0.01 significance level. As a result, a single QTL explaining 6.6% of total phenotypic variance was detected near RM242 marker locus on chromosome 9, and the Nipponbare allele was found to have S. hermonthica resistance. The QTL chromosomal region can also be further studied to promote better understanding on the nature of resistance.

The amount of long chains (LC) of amylopectin in high-amylose rice is thought to be one of the important determinants of its quality when cooked. A wide range of differences in LC content have been reported in rice varieties, which can be clearly divided into four classes based on LC and apparent amylose content: namely, amylose and LC-free, low or medium-amylose and low-LC, high-amylose and medium-LC, high-amylose and high-LC. However, genetic factors controlling LC content have not been fully understood. Here, we performed quantitative trait loci (QTL) analysis of LC content using 157 recombinant inbred lines (RILs) derived from a cross of a low-LC cultivar, Hyogokitanishiki, and a high-LC line, Hokuriku 142. By analyzing randomly selected 15 RILs, it was shown that high LC content (≥11%) was associated with high setback viscosity (≥200 RVU), and that low LC (≤ 3%) was associated with low setback viscosity (≤ 130 RVU), as measured by a Rapid Visco Analyzer. With setback viscosity as an indicator for LC content, QTL analysis was conducted using 60 DNA markers including a CAPS marker that distinguished Wx a and Wx b alleles coding for granule-bound starch synthase I (GBSSI or Wx protein), the enzyme working for amylose biosynthesis. Only one QTL with a peak log of likelihood score at the wx locus was detected, and no line showing setback viscosity corresponding to the medium-LC class appeared. The fact that wx mutants of Hokuriku 142 lacked LC in their rice starch supports the view that the functional Wx allele is indispensable for LC synthesis in addition to amylose synthesis in rice endosperm. We suggest three possible reasons why no line with medium-LC content was observed. First, the locus (loci) responsible for generation of medium-LC may be located very close to the wx locus and not able to be dissected by the population and DNA markers we used. Second, there may be special QTLs for medium-LC cultivars that do not exist in low- or high-LC cultivars. Third, medium-LC cultivars may have an as-yet unidentified Wx allele with lower capability in LC synthesis compared to the Wx allele in high-LC cultivars.

We found that several BC 2 F 4 lines had high leaf photosynthetic rates under light-saturated and ambient CO 2 conditions. These lines are progenies of BC 2 F 1 plants with high photosynthetic capacities which were generated by backcrossing between Oryza rufipogon (W630) and O. sativa cv. Nipponbare, as a recurrent parent. Some photosynthetic characteristics of the BC 2 F 4 lines were investigated to identify the factors increasing photosynthetic rates. Photosynthetic rates of these lines under light-saturated conditions at 50 to 700 ppm CO 2 concentrations were higher than those in Nipponbare. The estimated-maximum photosynthetic rates under light-saturated and CO 2 -saturated conditions in BC 2 F 4 lines were also higher than that in Nipponbare. The photosynthetic rate under light-saturated and ambient CO 2 conditions was positively correlated with the carboxylation efficiency as an indicator of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) activity in vivo rather than stomatal conductance. Initial and total Rubisco activities in vitro tended to be higher in the BC 2 F 4 lines than in Nipponbare. The content of active Rubisco calculated from the activation state of Rubisco was also higher in the BC 2 F 4 lines than in Nipponbare. These results suggest that high photosynthetic capacities of BC 2 F 1 plants can be maintained high in their progenies and high photosynthetic rates under light-saturated and ambient CO 2 conditions in the BC 2 F 4 lines are achieved mainly by the high activity of Rubisco due to the high active Rubisco content.

To study whether wild rice species have genes that may increase potential photosynthetic capacities of rice cultivars, we generated BC2 populations by reciprocally backcrossing Oryza rufipogon (W630) with O. sativa cv. Nipponbare and IR36; N-BC2 populations and IR-BC2 populations, respectively. We measured the oxygen evolution rates (OER) of single leaves under saturating light and CO2 as the maximum photosynthetic rates and the contents of ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) and Rubisco activase. Several lines in each BC2 population had significantly higher OERs than parental cultivars, and 14~25% of plants inBC2 populations had higher OERs than the highest values in parental cultivars. The highest OERs in BC2 populations were about 60% higher than average OERs in parental cultivars. The BC2 populations contained 30~40% more Rubisco than parental cultivars. The Rubisco activase contents in N-BC2 populations were 15~30% lower than that in Nipponbare. Cytoplasms derived from O. rufipogon and O. sativa had different effects on the contents of Rubisco and Rubisco activase particularly in N-BC2 populations. In several lines of each BC2 population the OERs had positive correlations with the contents of Rubisco and/or Rubisco activase. These results suggest that O. rufipogon can be used as a source of germplasm to enhance the photosynthetic capacity of O. sativa.

Rice (Oryza sativa L.) varieties used for brewing sake are commonly characterized by traits such as large grain size with white-core (an opaque structure inside the rice grain). A linkage map was constructed using doubled haploid lines derived from the cross of Reiho (a cooking variety) and Yamada-nishiki (a sake-brewing variety). Random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) marker systems were employed in QTL analysis. A total of 145 markers were identified and mapped on rice chromosomes. QTLs for plant and grain characters were detected by interval mapping and single point analysis. Several QTLs with a significant contribution were identified for important sake-brewing characters including grain size, grain shape, white-core grain rate and protein content. Several QTLs simultaneously affected the grain weight, width and thickness, while QTLs for the grain length independently affected the grain size. QTLs for the white-core grain rate did not affect the grain size, although one QTL for the white-belly grain rate simultaneously affected the grain weight, width and thickness. Several QTLs were detected for the protein content in both brown and polished rice. One QTL on chromosome 4 that was effective for the decrease of the protein content in polished rice showed a positive relation with the grain length. One QTL with the largest effect on the grain length on chromosome 11 did not contribute to the decrease of the protein content in polished rice. Therefore, it is suggested that the grain length QTL on chromosome 4 might control not only the grain shape but also the internal structure related to the milling efficiency and/or location of the storage protein.

日本, 韓国, 中国, 台湾, ブータンおよびネパールにおいて収集された在来アズキ203系統を供試材料としてDNAレベルの遺伝的変異を解析した. RAPD法により48個のプライマーを用いて解析した結果, 全部で413本の明瞭なバンドが検出され, そのうち97本のバンドで多型が認められた. これらのRAPDバンドを用いると, 供試系統のほとんどを識別することができた. そこで, 多型を示したバンドの有無について1-0データマトリクスを作成し, Simple matching coefficientを求めて非類似度を算出した. その結果, 各地域間の非類似度は, 地域内のそれよりも大きな値を示した. 特に, ブータン-ネパール地域の系統群と日本および韓国-中国-台湾地域の系統群との間において, それぞれ0.615および0.598と極めて大きな値が認められた。全系統間の非類似度をもとにUPGMA法によりクラスター分析を行ったところ, ほぼ日本, 韓国-中国-台湾地域およびブータン-ネパール地域に対応したグループに供試系統を分類することができた. これらのことから, 地域間での在来系統の交流があまりなかったことが推察された. また, 本研究では, 在来アズキ系統にはDNAレベルで大きな遺伝的変異が存在し, これらが今後の育種素材として有用であること, さらに, ブータン-ネパール地域の系統と東アジア地域の系統との雑種集団を用いることにより, 種内レベルでの分子地図作成が可能であることが示唆された.

We prevent an ultra-simple DNA extraction method for microsatellite analysis of rice. Each extraction requires only one microtube, one disposable pipette tip, TE buffer and few pieces (about 5 mm) of rice leaf tissue. This is sufficient for 200 PCR reactions. The extract can be kept in the freezer for long-term storage. Also, DNA can be extracted from 200–300 individuals in a few hours. These features enabled us to perform rapid largescale seedling genotyping required for marker-assisted selection. We have also examined the applicability of this method for other PCR-based markers: RAPDs, nuclear STS, chloroplast STS and chloroplast microsatellites.

A Sri Lankan indica rice (Oryza sativa L.) cultivar Babawee harboring a brown planthopper (BPH)(Nilaparvata lugens Stal) resistance gene bph4 was crossed as a male parent with two susceptible cultivars, either indica IR24 or japonica Tsukushibare. Segregation of the BPH resistance in the two crosses was studied by directly assaying the F2 phenotypes and by determining the F2 genotypes based on the F3 phenotypes. In both cross combinations, the segregation of the BPH resistance significantly deviated from the ratio expected for the single recessive gene model. Using bulked DNAs of homozygous resistant and susceptible F2s and the parents, seven out of 214 RFLP markers were selected as linked markers, of which six on chromosome 6 were common in the two cross combinations. Two microsatellite markers on chromosome 6 were also linked to bph4. Although the map position of bph4 could not be determined, the gene was assigned to the distal region of the short arm of rice chromosome 6 based on the bulked segregant analysis and linkage analysis.