The Origin and Spread of Early-Ripening Champa Rice: It’s Impact on Song Dynasty China

Often overlooked is the importance of early-maturing rice varieties with their ability to escape droughts, avoid floods, and in some localities, open up the opportunity for double cropping. Most varieties grown in the tropics until the last half century matured in 150 to 180 days or longer and were photoperiod sensitive. However, non-photoperiod sensitive one-hundred-day varieties were grown in the Champa Kingdom in what is now Central Vietnam centuries ago. How these varieties moved into Song Dynasty China and the impact of the early-ripening rice on population growth in South China is well documented. However, the origin of the Champa varieties is less clear. According to a recent DNA test (see below), the Champa varieties belong to the aus sub-population. The aus have the characteristics of both indica and japonica and originated in the hill areas of what are now Eastern India, Bangladesh, and Myanmar. Because the Champa Kingdom adopted the Indian language and religion, at least in the higher courts, it seems logical that the Champa rice must have been disseminated from the hilly areas in the Indian sub-continent to Central Vietnam and eventually to China—first Fujian and later to the Yangtze region during the Song Dynasty in the eleventh century.     

Identification of New Resistance Loci Against Sheath Blight Disease in Rice Through Genome-Wide Association Study

Sheath blight (SB) caused by the soil borne pathogen Rhizoctonia solani is one of the most serious global rice diseases. Breeding resistant cultivar is the most economical and effective strategy to control the disease. However, no rice varieties are completely resistant to SB, and only a few reliable quantitative trait loci (QTLs) linked with SB resistance have been identified to date. In this study, we conducted a genome-wide association study (GWAS) of SB resistance using 299 varieties from the rice diversity panel 1 (RDP1) that were genotyped using 44 000 high-density single nucleotide polymorphism (SNP) markers. Through artificial inoculation, we found that only 36.5% of the tested varieties displayed resistance or moderate resistance to SB. In particular, the aromatic and aus sub-populations displayed higher SB resistance than the tropical japonica (TRJ), indica and temperate japonica sub-populations. Seven varieties showed similar resistance levels to the resistant control YSBR1. GWAS identified at least 11 SNP loci significantly associated with SB resistance in the three independent trials, leading to the identification of two reliable QTLs, qSB-3 and qSB-6, on chromosomes 3 and 6. Using favorable alleles or haplotypes of significantly associated SNP loci, we estimated that both QTLs had obvious effects on reducing SB disease severity and can be used for enhancing SB resistance, especially in improving SB resistance of TRJ sub-population rice varieties. These results provided important information and genetic materials for developing SB resistant varieties through breeding.     

Identification of novel glutelin subunits and a comparison of glutelin composition between japonica and indica rice (Oryza sativa L.)

Glutelin, a major protein in rice grains, is encoded by a multigene family. However, its protein composition is not well characterised. Here, we identified and characterised two novel glutelin subunits, GluBX and GluC. The individual glutelin subunits of japonica cv. Nipponbare and indica cv. 93-11 rice were analysed using 2-dimensional gel electrophoresis, LC–MS/MS, and Western blotting. Comparison of the glutelin profiles between three japonica and three indica cultivars indicated two distinct subunits (GluA-1 and GluA-3 isomers) and a distinction in the subunit composition (notably GluA-3 and Lys-rich GluB-1 components) of these two subspecies. Sequence alignment revealed different nutritional (Lys residues) and functional (Cys residues) characteristics between the type-A and type-B glutelin subfamilies. We also analysed amino acid and total protein contents of the grains in thirty-five cultivars, and we demonstrated that the Lys-rich glutelin composition of indica cultivars is superior to that of japonica cultivars. The Lys-rich and Cys-poor GluBX subunit is a native protein and is a high nutritional protein in grains. Our combined approaches for the identification of glutelin subunits have revealed the nutritional characteristics of individual subunits in rice, and this knowledge will provide new insights for improving grain quality during rice breeding.     

Metabolite profiling of colored rice (Oryza sativa L.) grains

HPLC analysis of dehulled red, black and non-colored indica and japonica rice subspecies revealed significant differences in the contents of the anthocyanins cyanidin-3-glucoside and peonidin-3-glucoside. The rice materials were subjected to a comparative capillary gas chromatography-based metabolite profiling approach. The employed extraction and fractionation protocol enables the analysis of a broad spectrum of lipophilic and hydrophilic low molecular weight constituents from different chemical classes. The method covers not only primary metabolites (e.g. sugars, fatty acids) but also nutritionally relevant constituents (e.g. α-tocopherol, γ-aminobutyric acid). Statistical assessment of the data via principal component analysis and agglomerative hierarchical clustering revealed a distinct grouping of the different colored rice subspecies on the basis of their metabolite profiles. Compared to non-colored and red rice, black rice exhibited, in particular, higher levels of fatty acid methyl esters, free fatty acids, organic acids and amino acids.     

Genetic Diversity of Isolated Populations of Indonesian Landraces of Rice (Oryza sativa L.) Collected in East Kalimantan on the Island of Borneo

Although the genetic diversity of rice germplasm has been well characterized globally, few studies have taken an in-depth view of a large number of rice landraces on a local scale. To better understand the relationships between rice genetic diversity and associated geographic and cultural factors, we collected and characterized 183 rice landraces from 18 villages along the Bahau and Kayan rivers in the Indonesian province of East Kalimantan on the island of Borneo. A genetic diversity analysis using 30 microsatellite markers detected a clear distinction between the indica and japonica varietal groups (F _st?=?0.59), with 80% of the landraces identified as tropical japonica and 20% indica, which largely correlated with the field-level ecotypes: upland japonica and lowland indica. Indigenous knowledge from local farmers was gathered about the names, origins, and uses of the landraces, which provides a rich background to compare with the genetic relationships of these traditional varieties.     

Genome-wide association study and candidate gene analysis of rice cadmium accumulation in grain in a diverse rice collection

Background

Cadmium (Cd) accumulation in rice followed by transfer to the food chain causes severe health problems in humans. Breeding of low Cd accumulation varieties is one of the most economical ways to solve the problem. However, information on the identity of rice germplasm with low Cd accumulation is limited, particularly in indica, and the genetic basis of Cd accumulation in rice is not well understood.

Results

Screening of 312 diverse rice accessions revealed that the grain Cd concentrations of these rice accessions ranged from 0.12 to 1.23?mg/kg, with 24 accessions less than 0.20?mg/kg. Three of the 24 accessions belong to indica. Japonica accumulated significantly less Cd than indica (p < 0.001), while tropical japonica accumulated significantly less Cd than temperate japonica (p < 0.01). GWAS in all accessions identified 14 QTLs for Cd accumulation, with 7 identified in indica and 7 identified in japonica subpopulations. No common QTL was identified between indica and japonica. The previously identified genes (OsHMA3, OsNRAMP1, and OsNRAMP5) from japonica were colocalized with QTLs identified in japonica instead of indica. Expression analysis of OsNRAMP2, the candidate gene of the novel QTL (qCd3–2) identified in the present study, demonstrated that OsNRAMP2 was mainly induced in the shoots of high Cd accumulation accessions after Cd treatment. Four amino acid differences were found in the open reading frame of OsNRAMP2 between high and low Cd accumulation accessions. The allele from low Cd accumulation accessions significantly increased the Cd sensitivity and accumulation in yeast. Subcellular localization analysis demonstrated OsNRAMP2 expressed in the tonoplast of rice protoplast.

Conclusion

The results suggest that grain Cd concentrations are significantly different among subgroups, with Cd concentrations decreasing from indica to temperate japonica to tropical japonica. However, considerable variations exist within subgroups. The fact that no common QTL was identified between indica and japonica implies that there is a different genetic basis for determining Cd accumulation between indica and japonica, or that some QTLs for Cd accumulation in rice are subspecies-specific. Through further integrated analysis, it is speculated that OsNRAMP2 could be a novel functional gene associated with Cd accumulation in rice.

     

Developing rice cultivars for high-fertility upland systems in the Asian tropics

Traditionally, upland rice is grown in Asia in low-input, subsistence systems. More productive upland systems, using more fertilizer and improved varieties, are emerging in China and Philippines, and could contribute to productivity increases in rainfed environments in other countries. Here, we evaluate, on-station and on-farm, the yield under upland management of improved indica upland cultivars selected for yield under high-fertility conditions. These cultivars are compared with traditional and improved tropical japonica upland varieties, and with elite indica high-yielding varieties (HYV) developed for irrigated lowland production, to characterize the features of varieties that produce high yields in favorable upland environments. Forty-four improved and traditional varieties and experimental lines were evaluated in irrigated lowland, non-stressed upland, moderately stressed upland, severely water-stressed upland, and low-fertility upland environments in southern Luzon, Philippines. Correlations between yields in non-stress and mild-stress environments were low but positive. Some cultivars, like IR55423-01, were among the highest yielding under both conditions, indicating that high yield and moderate water-stress tolerance can be combined. Upland-selected indica varieties yielded 3.56 t ha⁻¹ in favorable upland environments on-station in southern Luzon, outperforming improved tropical japonica and irrigated varieties by 23 and 69%, respectively. They were also the highest-yielding class in infertile, acid soils. The improved upland indica cultivars are about 110 cm tall under favorable upland conditions and maintain a harvest index of nearly 0.4, or about one-third higher than other cultivar types. The best upland-adapted rice varieties produced average yields on-farm of 3.3 and 4.1 t ha⁻¹ in southern Luzon and Yunnan, respectively, outyielding traditional checks by 30–50% with moderate N application. Screening under both high-fertility, non-stress conditions and moderate reproductive-stage stress appears to be needed to develop cultivars combining high-yield potential with drought tolerance. Upland-adapted indica cultivars offer a new approach to increasing productivity and reducing risk in Asian rainfed rice systems.     

Molecular and Evolutionary Analysis of the Hd6 Photoperiod Sensitivity Gene Within Genus Oryza

Heading date determines rice’s adaptation to its area and cropping season. We analyzed the molecular evolution of the Hd6 quantitative trait locus for photoperiod sensitivity in a total of 20 cultivated varieties and wild rice species and found 74 polymorphic sites within its coding region (1,002 bp), of which five were nonsynonymous substitutions. Thus, natural mutations and modifications of the coding region of Hd6 within the genus Oryza have been suppressed during its evolution; this is supported by low Ka (≤0.003) and Ka/Ks (≤0.576) values between species, indicating purifying selection for a protein-coding gene. A nonsynonymous substitution detected in the japonica variety “Nipponbare” (a premature stop codon and nonfunctional allele) was found within only some local Japanese japonica varieties, which suggests that this point mutation happened recently, probably after the introduction of Chinese rice to Japan, and is likely involved in rice adaptation to high latitudes. Phylogenetic analysis and genome divergence using the entire Hd6 genomic region confirmed the current taxonomic sections of Oryza and supported the hypothesis of independent domestication of indica and japonica rice.     

The Endosperm Morphology of Rice and its Wild Relatives as Observed by Scanning Electron Microscopy

While cultivated rice, Oryza sativa, is arguably the world’s most important cereal crop, there is little comparative morphological information available for the grain of rice wild relatives. In this study, the endosperm of 16 rice wild relatives were compared to O. sativa subspecies indica and O. sativa subspecies japonica using scanning electron microscopy. Although the aleurone, starch granules, protein bodies and endosperm cell shapes of the cultivated and non-cultivated species were similar, several differences were observed. The starch granules of some wild species had internal channels that have not been reported in cultivated rice. Oryza longiglumis, Microlaena stipoides and Potamophila parviflora, had an aleurone that was only one-cell thick in contrast to the multiple cell layers observed in the aleurone of the remaining Oryza species. The similarity of the endosperm morphology of undomesticated species with cultivated rice suggests that some wild species may have similar functional properties. Obtaining a better understanding of the wild rice species grain ultrastructure will assist in identifying potential opportunities for development of these wild species as new cultivated crops or for their inclusion in plant improvement programmes.     

Characterization of physicochemical qualities and starch structures of two indica rice varieties tolerant to high temperature during grain filling

An extreme high temperature during grain filling is an important environmental factor that reduce the yield and quality of rice. In this study, we compared the grain appearance, composition and starch structure of four rice varieties response to high temperature during grain filling. The results obviously revealed that two indica AUS varieties Halwa and Jamir showed more tolerance to high temperature during grain filling than either the japonica Nipponbare or another AUS rice DJ24. The data showed that Halwa and Jamir presented less chalkiness, less grain weight loss, less change of endosperm components as well as starch structure than Nipponbare and DJ24 under high temperature treatment. Hence, the results implied that Halwa and Jamir might be useful targets to further identify genetic mechanism response to high temperature, at least during grain filling and endosperm development. Moreover, these AUS varieties have potential application value in further breeding of rice with good quality and heat tolerance.     

Breeding Novel Short Grain Rice for Tropical Region to Combine Important Agronomical Traits,Biotic Stress Resistance and Cooking Quality in Koshihikari Background

Breeding program strategies to develop novel short grain white rice varieties such as japonica (short grain) that introgress biotic stress resistance and high grain quality have been developed using indica rice (Pin Kaset + 4 and Riceberry) for applications in japonica rice (Koshihikari) improvement. Four breeding lines showing promising agronomic performance with short grain and low amylose content (< 20%) were obtained. In addition, sensory testing of these breeding lines showed high scores that similar to Koshihikari. Two promising lines, KP48-1-5 and KP48-1-9, which possessed a combination of four genes resistance to different biotic stresses (Bph3 + TPS + Xa21 + Pi-ta) and four genes for grain quality (GS3 + SSIIa + wx^b + badh2), were developed using marker-assisted selection (MAS) with the pedigree method. The current study clearly illustrated the successful use of MAS in combining resistance to multiple biotic stresses while maintaining a high yield potential and preferred grain quality. Moreover, the results indicated that this breeding program, which includes crossing temperate japonica with indica, can create novel short grain rice varieties adapted to a tropical environment, like the japonica type.     

Molecular genetic mapping of quantitative trait loci for milling quality in rice (Oryza sativa L.)

Identification and mapping of genomic regions controlling quantitative trait loci (QTLs) was undertaken to determine the genomic regions associated with milling traits in rice to facilitate breeding of new rice varieties with high milling quality. The recombinant inbred (RI) population used was derived from cross of a japonica variety, ‘Asominori’, with an indica variety, ‘IR24’ through 289 RFLP markers. Three milling traits, namely, brown rice percentage (BRP), milled rice percentage (MRP), and milled head rice percentage (MHP), which are the main indicators of milling quality in rice, were estimated for each RI line and their parental varieties. Continuous distributions and transgressive segregations of three milling traits were observed in the RI population, showing that the three traits were quantitatively inherited. Two QTLs (qBRP-9 and qBRP-10) for BRP were identified and mapped to chromosomes 9 and 10, and explained 7.2 and 21.3% of the total phenotype variation, respectively. Two QTLs (qMRP-11 and qMRP-12) governing MRP were detected and mapped to chromosomes 11 and 12, accounted for 12.2 and 7.7% of total phenotype variation, respectively. In addition, three QTLs (qMHP-1, qMHP-3 and qMHP-5) controlling MHP were observed and mapped to chromosomes 1, 3 and 5, and explained 16.0, 22.1 and 8.7% of the total phenotype variation, respectively. Among them, five QTLs (qBRP-9, qBRP-10, qMRP-11, qMHP-3 and qMHP-5) from japonica parent, Asominori, and two QTLs (qMRP-12, qMHP-1) from indica IR24 can improve milling quality in rice. The results and the tightly linked molecular markers that flank the QTL will be useful in breeding for improvement of milling quality in rice.     

Research Progress on Heat Stress of Rice at Flowering Stage

Global warming has caused frequent occurrence of heat stress at the flowering stage of single-season rice in the Yangtze River region of China, which results in declines of spikelet fertility and yield in rice. Rice flowering stage is the most sensitive period to high temperatures, and therefore, the key for heat stress happening is the flowering stage coinciding with high temperature, which causes spikelet fertility decreasing in heat-sensitive varieties, and is the major factor for heat injury differences among various rice planting regions. With the development of rice breeding, temperature indexes for heat stress has been converted from daily maximum temperature of 35 °C to 38 °C with the stress duration of more than 3 d. During the flowering stage, anther dehiscence inhibition and low pollen shedding onto the stigma are two main reasons for spikelet fertility reduction under high temperatures. At panicle initiation stage, high temperatures aggravate spikelet degeneration, and destroy floral organ development. Various types of rice varieties coexist in production, and indica-japonica hybrid rice demonstrates the highest heat resistance in general, followed by indica and japonica rice varieties. In production, avoiding high temperature is the main strategy of preventing heat stress, and planting suitable cultivars and adjustment of sowing date are the most effective measures. Irrigation is an effective real-time cultivation measure to decline the canopy temperature during the rice flowering stage. We suggested that further study should be focused on exploring heat injury differences among different rice variety types, and innovating rice-planting methods according to planting system changes in rice planting regions with extreme heat stress. Meanwhile, high temperature monitor and warning systems should be improved to achieve optimal heat stress management efficiencies.     

Quantitative trait loci responsible for the difference in γ-oryzanol content in brown rice between japonica-type and indica-type rice cultivars

γ-Oryzanol is a main oleophilic component in rice bran oil and has been well recognized as a good dietary supplement for human health, as well as having uses in industrial materials. japonica-type rice cultivars generally showed significantly higher contents of total γ-oryzanol in brown rice compared with indica-type cultivars, although within-group variation was significant. The objective of this study was to explore quantitative trait loci (QTLs) responsible for the difference in the γ-oryzanol content between japonica-type and indica-type rice cultivars, using recombinant inbred lines (RILs), backcross inbred lines (BILs), and corresponding chromosome segment substitution lines (CSSLs) derived from crosses between japonica-type and indica-type. Results from RILs and BILs showed that eight QTLs were detected with R² from .09 to .16. Nine candidate regions for QTL were also suggested from corresponding CSSLs. These QTLs from RILs and BILs and the candidate regions from CSSLs were not overlapped, although one QTLs was mapped near the boundaries of the respective candidate region. At four QTLs and three candidate regions, alleles or segments from japonica-type caused higher contents than those from indica-type. On the other hand, at the other four QTLs and six candidate regions, alleles or segments from indica-type caused higher contents than those from japonica-type, which is a reverse result to the parental differences. This result strongly suggested that alleles with increasing effects on γ-oryzanol content could be accumulated not only from japonica-type but also from indica-type, leading to a potential for increase in γ-oryzanol content in future breeding programs.     

Rice root morphological traits are related to isozyme group and adaptation

Rice accessions from the International Rice Research Institute (IRRI) germplasm bank were evaluated for root traits of 40-day-old plants grown in soil in the greenhouse. The 136 accessions represented six groups defined on the basis of isozyme classification, with isozyme group six further subdivided on the basis of origin and morphology. An additional 28 rice cultivars were evaluated for seminal root xylem vessel diameter when grown in pots in a growth chamber. Rice groups differed in root thickness, root xylem vessel diameter, root:shoot ratio, and patterns of root distribution. Isozyme group 1, which corresponds generally to the indica subspecies, had thin, superficial roots with narrow vessels and a low root:shoot ratio. The other major isozyme group, group 6, comprising japonica types, was characterized by thick roots with wider vessels, a greater proportion of the root weight below 15 cm, and a larger root:shoot ratio. On an average, the bulu and temperate group 6 accessions were similar to the non-bulu types except that their root:shoot ratios and proportion of root weight above 15 cm were more similar to group 1. Group 2, with aus types from South Asia, was characterized by intermediate root thickness, but vertical root distribution and root:shoot ratio were more similar to group 6. The minor isozyme groups 3–5 were represented by few accessions, and in general, they had root thickness and root distribution profiles more similar to group 1 than to group 6. While significant differences were observed among isozyme groups for all the traits under study, there was significant variation within groups and groups overlapped for all traits measured. This study highlights the wide range of variability for constitutive root traits in rice. For example, root thickness ranged from 0.68 to 1.04 mm, seminal root xylem vessel diameters from 30 to 58 μm, root:shoot ratios from 0.05 to 0.21, and accessions had from 44 to 73% of the total root weight concentrated in the surface 15 cm of soil. For the 28 cultivars evaluated, root xylem vessel diameter was highly correlated with reported values of leaf epicuticular wax content (r=0.89). These values indicate the range of genetic variation within the rice genome for root morphological traits.     

Diversity of Sodium Transporter HKT1;5 in Genus Oryza

Asian cultivated rice shows allelic variation in sodium transporter, OsHKT1;5, correlating with shoot sodium exclusion (salinity tolerance). These changes map to intra/extracellularly-oriented loops that occur between four transmembrane-P loop-transmembrane (MPM) motifs in OsHKT1;5. HKT1;5 sequences from more recently evolved Oryza species (O. sativa/O. officinalis complex species) contain two expansions that involve two intracellularly oriented loops/helical regions between MPM domains, potentially governing transport characteristics, while more ancestral HKT1;5 sequences have shorter intracellular loops. We compared homology models for homoeologous OcHKT1;5-K and OcHKT1;5-L from halophytic O. coarctata to identify complementary amino acid residues in OcHKT1;5-L that potentially enhance affinity for Na⁺. Using haplotyping, we showed that Asian cultivated rice accessions only have a fraction of HKT1;5 diversity available in progenitor wild rice species (O. nivara and O. rufipogon). Progenitor HKT1;5 haplotypes can thus be used as novel potential donors for enhancing cultivated rice salinity tolerance. Within Asian rice accessions, 10 non-synonymous HKT1;5 haplotypic groups occur. More HKT1;5 haplotypic diversities occur in cultivated indica gene pool compared to japonica. Predominant Haplotypes 2 and 10 occur in mutually exclusive japonica and indica groups, corresponding to haplotypes in O. sativa salt-sensitive and salt-tolerant landraces, respectively. This distinct haplotype partitioning may have originated in separate ancestral gene pools of indica and japonica, or from different haplotypes selected during domestication. Predominance of specific HKT1;5 haplotypes within the 3 000 rice dataset may relate to eco-physiological fitness in specific geo-climatic and/or edaphic contexts.     

Progress in varietal improvement for increasing upland rice productivity in the tropics

Enhancing rice yield in upland rice systems through genetic improvement remains a major challenge in the tropics. This review aims to provide the trends on upland rice cultivation over the last 30 years and recent distribution of upland rice in the tropics, and to report progress in studies on genetic improvement for enhancing productivity in Africa, Asia, and Latin America. While upland rice cultivation area has reduced in Asia and Latin America over the last 30 years, the area in Africa has increased. The current share of upland rice area in total rice area is related to rainfall and gross national income per capita, especially in Africa, and higher share is associated with lower rice self-sufficiency at national level. Breeding programs in Asia and Latin America have developed high-yielding varieties using indica materials as parents. In Africa, New Rice for Africa (NERICA) varieties were developed from crosses between improved tropical japonica and Oryza glaberrima. However, recent studies report that there is scope for improving existing NERICA using upland indica materials from Asia. In highlands of Africa, there are ongoing breeding programs using japonica varieties, such as the Nepalese Chhomrong Dhan. Key important plant traits used in the breeding programs are not largely different across regions, especially intermediate plant height and tillering capacity (which may be related to weed-suppressive ability), and high harvest index. In conclusion, we propose an international network for breeding upland rice with accelerating seed exchange across regions that could enhance upland rice productivity through genetic improvement.     

Genetic Characterization of Indigenous Rice Varieties in Eastern Himalayan Region of Northeast India

The eastern Himalayan region of Northeast （NE） India is home to a large number of indigenous rice varieties, which are traditionally classified as Oryza sativa subspecies indica, japonica or intermediate types. The classification based on traditional Cheng’s index is often inconclusive due to phenotypic plasticity of morphological characters, which are influenced by environmental conditions. We used molecular markers specific for indica and japonica subspecies to assess the degree of genetic relatedness of indigenous rice varieties in NE India. The results revealed that majority of upland （jum） and glutinous rice varieties, traditionally considered as japonica, were genetically close to the subspecies indica. All varieties of boro ecotype were found to be indica type, and only a few varieties cultivated in lowland and upland areas were japonica type. Some of the lowland varieties of the sali ecotype were intermediate between indica and japonica, and they showed a closer genetic affinity to O. rufipogon.     

Mapping quantitative trait loci (QTLs) for seedling-vigor using recombinant inbred lines of rice (Oryza sativa L.)

Seedling-vigor is important for optimum stand establishment and increasing weed competitive ability in rice cropping systems. In the current study, three seedling-vigor-related traits, seed germination rate, seedling shoot length and dry matter weight, were investigated by the paper-roll tests with rice recombinant inbred lines derived from a cross between Lemont (japonica) and Teqing (indica). The phenotype data, together with a linkage map consisting of 198 marker loci, was used to conduct composite interval mapping by QTLMapper 1.0 to simultaneously map both main-effect and epistatic QTLs for seedling-vigor in rice. Totally, 13 putative main-effect QTLs and 19 pairs of epistatic loci with R² ≥ 5% were identified. Almost all of these QTLs or interactions individually explained only around 5–10% of the phenotypic variation. The majority (68%) of these main-effect and epistatic loci were clustered in seven chromosome regions, each spanning 12–28 cM (centi-Morgan) and containing three or more detectable loci. When detectable for the multiple seedling-vigor-related traits, either the main-effect QTLs or the epistatic interactions sharing the same map location had their additive or epistatic effects in the same direction, which agreed well with the positive correlations among the traits. The results demonstrated that seedling-vigor in rice could be controlled by many loci, most of which had small effects, but, relatively, epistasis as a genetic factor was much more important than main-effects of QTLs. Along with the results reported previously, this study revealed the extensive genetic diversity for seedling-vigor in rice. In addition, the QTL q^SV-7 on chromosome 7 was found to have the largest main-effects on multiple seedling-vigor-related traits and therefore could be used as a potential target to be genetically manipulated by marker-assisted selection in rice seedling-vigor breeding programs.     

Testing of Rice Stocks for Their Survival of Winter Cold

Rice cultivation is considered to be initiated by vegetative propagation of sprout from wild perennial stocks. To test whether any presently cultivated rice cultivar can survive the winter cold or not, rice stocks of several cultivars including indica and japonica types were placed in a shallow pool from October to April in 2015–2016 and 2016–2017. During the coldest period of the winter, the bases of the stocks were placed 5–6 cm below the surface of water, where temperatures ranged from 3 ℃ to 5 ℃, while the surface was frozen for two or three times and covered with snow for a day. Only one cultivar, Nipponbare, a japonica type, survived the winter cold and regenerated sprouts in the end of April or early May. A possibility to develop perennial cultivation of rice or perennial hybrid rice is discussed.