High-yielding Rice Cultivars Research Articles

水稲多収品種「北陸193号」とその後代系統の温暖地における収量性

水稲多収品種「北陸193号」とその後代系統の温暖地における収量性

Haplotype-based allele mining in the Japan-MAGIC rice population

Multi-parent advanced generation inter-cross (MAGIC) lines have broader genetic variation than bi-parental recombinant inbred lines. Genome-wide association study (GWAS) using high number of DNA polymorphisms such as single-nucleotide polymorphisms (SNPs) is a popular tool for allele mining in MAGIC populations, in which the associations of phenotypes with SNPs are investigated; however, the effects of haplotypes from multiple founders on phenotypes are not considered. Here, we describe an improved method of allele mining using the newly developed Japan-MAGIC (JAM) population, which is derived from eight high-yielding rice cultivars in Japan. To obtain information on the haplotypes in the JAM lines, we predicted the haplotype blocks in the whole chromosomes using 16,345 SNPs identified via genotyping-by-sequencing analysis. Using haplotype-based GWAS, we clearly detected the loci controlling the glutinous endosperm and culm length traits. Information on the alleles of the eight founders, which was based on the effects of mutations revealed by the analysis of next-generation sequencing data, was used to narrow down the candidate genes and reveal the associations between alleles and phenotypes. The haplotype-based allele mining (HAM) proposed in this study is a promising approach to the detection of allelic variation in genes controlling agronomic traits in MAGIC populations.

Characterization of high-yielding rice cultivars with different grain-filling properties to clarify limiting factors for improving grain yield

Recently developed high-yielding rice varieties with extra-large sink capacity often have unstable grain filling. Therefore, understanding the factors that limit grain filling is essential for further improvement of rice grain yield. Because grain-filling is determined by the complex sink–source balance, grain-filling ability is very difficult to evaluate. In this study, we compared grain-filling-related traits of three high-yielding cultivars with high sink capacity. We found that the translocation of non-structural carbohydrates (NSC) from stem to panicle during early ripening and grain filling was significantly lower in Momiroman than in Hokuriku 193 and Teqing, whereas dry matter accumulation of the whole plant did not differ among the cultivars throughout ripening. The NSC-components, sucrose and starch were both remained higher in stems of Momiroman than other cultivars. ADP-glucose pyrophosphorylase (AGPase; EC 2.7.7.27) activity was not enhanced and α-Amylase (EC 3.2.1.1) and β-Amylase (EC 3.2.1.2) activities were not impeded in the stems. These data suggested lower sucrose translocation is responsible for lower NSC translocation in Momiroman, rather than too high starch synthesis and too low starch degradation activities. At early ripening, grain growth of the superior spikelets was slow in Momiroman even if carbon supply was increased by spikelet-thinning treatments. These results raise the possibility that low sink strength determines low grain filling in Momiroman, which delays grain growth and decreases sucking force of NSC from the stem.

A novel QTL associated with rice canopy temperature difference affects stomatal conductance and leaf photosynthesis.

Canopy temperature can be a good indicator of stomatal conductance. To understand the genetic basis of phenotypic differences in stomatal conductance between average and high-yielding rice (Oryza sativa L.) cultivars, we conducted a quantitative trait locus (QTL) analysis of canopy temperature. We developed reciprocal series of backcross inbred lines (BC1F6) derived from a cross between the average-yielding japonica cultivar ‘Koshihikari’ and the high-yielding indica cultivar ‘Takanari’. A stable QTL, qCTd11 (QTL for canopy temperature difference on chromosome 11) on the short arm of chromosome 11, accounted for 10.4 and 19.8% of the total phenotypic variance in the two lines; the ‘Takanari’ allele decreased the canopy temperature difference value. A chromosome segment substitution line carrying the Takanari qCTd11 showed a greater reduction in canopy temperature than ‘Koshihikari’, and had higher stomatal conductance and photosynthetic rate. These results suggest that qCTd11 is not only involved in canopy temperature, but is also involved in both stomatal conductance and photosynthetic rate.

RICE LODGING RESISTANCE

The main direction of breeding grain crops is to increase yield and improve grain quality. For maximum crop yield, it is necessary to develop cultivars with high productivity and quality potential, resistant to biotic and abiotic environmental factors. One of the main characteristics is lodging. Resistance to lodging is determined by well-defined morphological traits: plant height, diameter of the lower internode, panicle length, angle of leaf plate, etc. Short plants are more resistant to lodging than tall ones. Short straw trait can be used when evaluating cultivars for lodging resistance. The ratio of plant height to the diameter of the lower internode is an objectively reliable indicator of rice lodging resistance. The value of this ratio in non-lodging cultivars is less in comparison with lodging ones. The article presents the results of studying morphological traits of different rice cultivars, determining resistance of rice plant to lodging. In the experiment, cultivars differing in height was grouped into three groups (I - tall; II - medium and III - short). Short stem forms were established to be more resistant to lodging. Accents in breeding high-yielding rice cultivars with the lowest risk of yield loss resulting from lodging were identified. The correlation analysis revealed a positive relationship (r = 0.877; 0.945 and 0.500, respectively, in groups) between grain mass per plant and diameter of the lower internode. This indicates a close genetic relationship of the traits studied.

Identification of A Major Quantitative Trait Locus for Grain Weight In Rice Using Microsatellite Marker

Rice is one of the major staple foods in the world, especially in Asia. Improving yield potential of superior cultivars is important to meeting the demand for rice production, which is increasing due to human population increase, climate change, and degradation of agricultural resources, such as land and water. In this study, a BC 3 F 2 population developed from an intraspecific cross between Ciherang and a new plant type line (B11143D) was used in a quantitative trait locus (QTL) analysis. Ciherang is a high yielding rice cultivar with good grain quality which has been planted in 37% of the irrigated rice area in Indonesia. The objective of this study was to identify QTL(s) for yield components on chromosome 12, which can be used to improve the elite cultivar Ciherang or other popular cultivars through marker-assisted breeding. A total of two hundred BC 3 F 2 lines were evaluated in the greenhouse during this study. The population was observed for eight agronomic traits including days to heading (dth), plant height (ph), flag leaf length (fll), panicles per plant (ppl), panicle length (pl), grains per panicle (gpp), 1000-grain weight (gw), and yield (yld). Four simple sequence repeats (SSR) markers (RM3472, RM28048, RM28195, and RM1986) were used for targeted mapping on chromosome 12. Linkage analysis identified a QTL for 1000-grain weight located on chromosome 12 at position 53.5 cM–73 cM.

Increasing canopy photosynthesis in rice can be achieved without a large increase in water use-A model based on free-air CO2 enrichment.

Achieving higher canopy photosynthesis rates is one of the keys to increasing future crop production; however, this typically requires additional water inputs because of increased water loss through the stomata. Lowland rice canopies presently consume a large amount of water, and any further increase in water usage may significantly impact local water resources. This situation is further complicated by changing the environmental conditions such as rising atmospheric CO2 concentration ([CO2 ]). Here, we modeled and compared evapotranspiration of fully developed rice canopies of a high-yielding rice cultivar (Oryza sativa L. cv. Takanari) with a common cultivar (cv. Koshihikari) under ambient and elevated [CO2 ] (A-CO2 and E-CO2 , respectively) via leaf ecophysiological parameters derived from a free-air CO2 enrichment (FACE) experiment. Takanari had 4%-5% higher evapotranspiration than Koshihikari under both A-CO2 and E-CO2 , and E-CO2 decreased evapotranspiration of both varieties by 4%-6%. Therefore, if Takanari was cultivated under future [CO2 ] conditions, the cost for water could be maintained at the same level as for cultivating Koshihikari at current [CO2 ] with an increase in canopy photosynthesis by 36%. Sensitivity analyses determined that stomatal conductance was a significant physiological factor responsible for the greater canopy photosynthesis in Takanari over Koshihikari. Takanari had 30%-40% higher stomatal conductance than Koshihikari; however, the presence of high aerodynamic resistance in the natural field and lower canopy temperature of Takanari than Koshihikari resulted in the small difference in evapotranspiration. Despite the small difference in evapotranspiration between varieties, the model simulations showed that Takanari clearly decreased canopy and air temperatures within the planetary boundary layer compared to Koshihikari. Our results indicate that lowland rice varieties characterized by high-stomatal conductance can play a key role in enhancing productivity and moderating heat-induced damage to grain quality in the coming decades, without significantly increasing crop water use.

3 「エアーアシスト条播機」を用いて湛水直播した多収性水稲品種タカナリの乾物生産特性(日本作物学会関東支部第100回講演会)

3 「エアーアシスト条播機」を用いて湛水直播した多収性水稲品種タカナリの乾物生産特性(日本作物学会関東支部第100回講演会)

Evaluation and application of the ORYZA rice model under different crop managements with high-yielding rice cultivars in central China

ORYZA version 3, as the successor to ORYZA2000, is an ecophysiological model that can simulate rice growth and development for targeted yield with different nitrogen (N) fertilizer rates and planting densities in a given rice production system. Currently, there is little published information on the application of ORYZA (v3) and ORYZA2000 in simulating high-yielding rice cultivars under different N rates and planting density schemes in central China. This paper combines field experimentation with ORYZA (v3) to calibrate the crop growth characteristics of widely grown high-yielding inbred and hybrid rice cultivars. The calibrated model was applied to simulate yields under different N rates, planting densities, and seedlings per hill, using historical weather data from 1986 to 2015. ORYZA (v3) reliably simulated the dynamics of crop biomass and leaf area index, and seasonal yield, with relatively small normalized root mean square error (RMSEn) and high adjusted linear correlation coefficient (R2), but slightly over-estimated leaf N concentration. Scenario analyses indicated that the maximum differences in simulated yields were 72.1kgha−1 due to planting density, 112.8kgha−1 due to seedlings per hill, and 3266.2kgha−1 due to N rates. The simulations demonstrated that further field experiments are crucial in investigating the effects of rice genotype, N management and their interactions on yield for optimal crop management.

Putting Plant Genetic Diversity and Variability at Work for Breeding: Hybrid Rice Suitability in West Africa

Rice is a staple food in West Africa, where its demand keeps increasing due to population growth. Hence, there is an urgent need to identify high yielding rice cultivars that fulfill this demand locally. Rice hybrids are already known to significantly increase productivity. This study evaluated the potential of Asian hybrids with good adaptability to irrigated and rainfed lowland rice areas in Mali, Nigeria, and Senegal. There were 169 hybrids from China included in trials at target sites during 2009 and 2010. The genotype × environment interaction was highly significant (p < 0.0001) for grain yield indicating that the hybrids’ and their respective cultivar checks’ performance differed across locations. Two hybrids had the highest grain yield during 2010 in Mali, while in Nigeria, four hybrids in 2009 and one hybrid in 2010 had higher grain yield and matured earlier than the best local cultivar. The milling recovery, grain shape and cooking features of most hybrids had the quality preferred by West African consumers. Most of the hybrids were, however, susceptible to African rice gall midge (AfRGM) and Rice Yellow Mottle Virus (RMYV) isolate Ng40. About 60% of these hybrids were resistant to blast. Hybrids need to incorporate host plant resistant for AfRGM and RYMV to be grown in West Africa.

Higher yields and lower methane emissions with new rice cultivars.

Breeding high-yielding rice cultivars through increasing biomass is a key strategy to meet rising global food demands. Yet, increasing rice growth can stimulate methane (CH4 ) emissions, exacerbating global climate change, as rice cultivation is a major source of this powerful greenhouse gas. Here, we show in a series of experiments that high-yielding rice cultivars actually reduce CH4 emissions from typical paddy soils. Averaged across 33 rice cultivars, a biomass increase of 10% resulted in a 10.3% decrease in CH4 emissions in a soil with a high carbon (C) content. Compared to a low-yielding cultivar, a high-yielding cultivar significantly increased root porosity and the abundance of methane-consuming microorganisms, suggesting that the larger and more porous root systems of high-yielding cultivars facilitated CH4 oxidation by promoting O2 transport to soils. Our results were further supported by a meta-analysis, showing that high-yielding rice cultivars strongly decrease CH4 emissions from paddy soils with high organic C contents. Based on our results, increasing rice biomass by 10% could reduce annual CH4 emissions from Chinese rice agriculture by 7.1%. Our findings suggest that modern rice breeding strategies for high-yielding cultivars can substantially mitigate paddy CH4 emission in China and other rice growing regions.

Effect of Temperature Pretreatment and Culture Media on Callus Induction and Regeneration in Composite Crosses between High Yielding Rice Cultivars and Ghaem line

Effect of Temperature Pretreatment and Culture Media on Callus Induction and Regeneration in Composite Crosses between High Yielding Rice Cultivars and Ghaem line

Identification and validation of QTLs for seedling salinity tolerance in introgression lines of a salt tolerant rice landrace 'Pokkali'.

Salinity is a major threat to rice production worldwide. Several studies have been conducted to elucidate the molecular basis of salinity tolerance in rice. However, the genetic information such as quantitative trait loci (QTLs) and molecular markers, emanating from these studies, were rarely exploited for marker-assisted breeding. To better understand salinity tolerance and to validate previously reported QTLs at seedling stage, a set of introgression lines (ILs) of a salt tolerant donor line ‘Pokkali’ developed in a susceptible high yielding rice cultivar ‘Bengal’ background was evaluated for several morphological and physiological traits under salt stress. Both SSR and genotyping-by-sequencing (GBS) derived SNP markers were utilized to characterize the ILs and identify QTLs for traits related to salinity tolerance. A total of eighteen and thirty-two QTLs were detected using SSR and SNP markers, respectively. At least fourteen QTLs detected in the RIL population developed from the same cross were validated in IL population. Analysis of phenotypic responses, genomic composition, and QTLs present in the tolerant ILs suggested that the mechanisms of tolerance could be Na+ dilution in leaves, vacuolar Na+ compartmentation, and possibly synthesis of compatible solutes. Our results emphasize the use of salt injury score (SIS) QTLs in marker-assisted breeding to improve salinity tolerance. The tolerant lines identified in this study will serve as improved breeding materials for transferring salinity tolerance without the undesirable traits of Pokkali. Additionally, the lines will be useful for fine mapping and map-based cloning of genes responsible for salinity tolerance.

Genotypic and Environmental Variations in Grain Cadmium and Arsenic Concentrations Among a Panel of High Yielding Rice Cultivars

BackgroundRice is a major dietary source of cadmium (Cd) and arsenic (As) for populations consuming rice as the staple food. Excessive Cd and As accumulation in rice grain is of great concern worldwide, especially in South China where soil contamination with heavy metals and metalloids is widespread. It is important to reduce Cd and As accumulation in rice grain through selection and breeding of cultivars accumulating low levels of Cd or As.ResultsTo assess the genetic and environmental variations in the concentrations of Cd and As in rice grains, 471 locally adapted high-yielding rice cultivars were grown at three moderately contaminated sites in South China for two years. Cadmium and As concentrations in brown rice varied by 10 – 32 and 2.5 – 4 fold, respectively. Genotype (G), environment (E) and G x E interactions were highly significant factors explaining the variations. Brown rice Cd concentration was found to correlate positively with the heading date among different cultivars, whereas As concentration and heading date correlated negatively. There was a significant and negative correlation between grain Cd and As concentrations.ConclusionsEight and 6 rice cultivars were identified as stable low accumulators of Cd and As, respectively, based on the multiple site and season trials. These cultivars are likely to be compliant with the grain Cd or As limits of the Chinese Food Safety Standards when grown in moderately contaminated paddy soils in South China.

Identification of Heading Date Six (Hd6) Gene Derived from Rice Mutant Varieties

<p>Genes which were associated with flowering time to indicate the early maturity is known as heading date (<em>Hd</em>). Heading date six (<em>Hd6)</em> gene<em> </em>was identified from rice mutant varieties were Atomita 2, Atomita 3, Atomita 4, Bestari, Cilosari, Diah Suci, Sidenuk, Kahayan, Mayang, Meraoke, Mira-1, Pandan Putri, Superwin, Suluttan Unsrat 1, Suluttan Unsrat 2, Winongo, Woyla, Yuwono, while the rice var. Nipponbare was used as a positive control. All of rice mutant varieties derived from mutation induction by the dose of 0.2 kGy. The aim of this experiment was to find out the data base of mutant varieties which could be used as parent material with earlier maturity trait genetically. To obtain the DNA of plants, young leaves of each variety were extracted by liquid nitrogen, and then lysis and extracted by Kit Plant Genomic DNA. The amplification of DNA with 7 primers of <em>Hd6</em> conducted of 40 cycles by PCR and were continues to separated by 1 % agarose. The results were shown that the rice Mira-1 and Bestari varieties obtained from mutation of Cisantana highly different from one to another on 7 primers of <em>Hd6</em> used. Mayang variety from mutation of cross breeding between Cilosari and IR64, Pandan putri from Pandan wangi and Woyla from mutation of cross breeding from Atomita 2 and IR64 were highly different with those of their parents. Identification of <em>Hd6</em> gene on Sidenuk variety was shown the same bands pattern with Nipponbare as control positive toward all primers used, this variety would be better for earlier maturity parent material compared to others. The information could be useful for breeding programs aiming to develop early maturing widely adaptive and high yielding rice cultivars.</p>

Effects of common Echinochloa varieties on grain yield and grain quality of rice

Barnyard grass, such as Echinochloa crus-galli var. mitis, Echinochloa crus-galli var. zelayensis and Echinochloa colonum, are the main troublesome weeds in rice (Oryza sativa) paddies. This study aimed to investigate the rice yield (quality and quantity) when grown with these common barnyard grass varieties. A 2-year field experiment was conducted using two high-yielding rice cultivars, Liangyoupeijiu (an O. sativa indica hybrid cultivar) and Nanjing 9108 (an O. sativa japonica cultivar) at different developmental stages from transplant to maturity. Treatments included a weed-free (control), rice grown with Echinochloa. crus-galli var. mitis (Ecm), rice grown with E. crus-galli. crusgali var. zelayensis (Ecz), and rice grown with E. colonum (Ec). The results showed that when barnyard grasses were grown with the same rice cultivar, the order of plant height of the three barnyard grass varieties was Ecz>Ecm>Ec, the growth duration was Ecm>Ecz>Ec and the dry matter accumulation of both Ecm and Ecz was greater than Ec. Compared with the weed-free control, there was no significance difference in rice tiller numbers among the treatments within the same rice cultivar. The Ecm and Ecz treatments for both rice cultivars and the Ec treatment of Nanjing 9108 had significantly lower leaf photosynthetic rate, root biomass, root oxidation activity, and dry matter accumulation at both the heading and maturity stages. Lower rice yield loss was detected for all rice grown with barnyard grass, but the loss in yield differed by treatments. Losses in grain yield of rice were 12.7–42.6% in the Ecm treatment, 22.3–55.2% in the Ecz treatment, and 1.5–12.1% in the Ec treatment. For both rice cultivars, Ecm and Ecz treatments had significantly lower grain yield compared with the control. The Ec treatment for Nanjing 9108 had significantly lower grain yield compared to the control, but there was not a significant difference between Ec and the control for Liangyoupeijiu. In general, the japonica cultivar had a greater loss in grain yield compared with the indicia hybrid cultivar under the same treatment. The degree of yield loss by barnyard grass cultivar was Ecz>Ecm>Ec. Grain quality in head rice, chalky kernel, chalky size, and gel consistency was significantly lower for both rice cultivars in the Ecm and Ecz treatments and also for Nanjing 9108 but not for Liangyoupeijiu in the Ec treatment. We conclude that the reduction in leaf photosynthetic rate, root biomass, root oxidation activity at the grain filling stage, and dry matter accumulation at maturity was caused by interference in canopy light transmission caused by barnyard grass and that these factors resulted in losses in grain yield and quality.

Engineering the lodging resistance mechanism of post-Green Revolution rice to meet future demands.

Traditional breeding for high-yielding rice has been dependent on the widespread cultivation of gibberellin (GA)-deficient semi-dwarf varieties. Dwarfism lowers the “center of gravity” of the plant body, which increases resistance against lodging and enables plants to support high grain yield. Although this approach was successful in latter half of the 20th century in rice and wheat breeding, this may no longer be enough to sustain rice with even higher yields. This is because relying solely on the semi-dwarf trait is subject to certain limitations, making it necessary to use other important traits to reinforce it. In this review, we present an alternative approach to increase lodging resistance by improving the quality of the culm by identifying genes related to culm quality and introducing these genes into high-yielding rice cultivars through molecular breeding technique.

Induction of useful variability for pericarp colour and bacterial blight resistance in rice (Oryza sativa L.) cv. PAU 201 through EMS based mutagenesis

PAU 201, a high yielding variety of rice released by Punjab Agricultural University in 2007, was withdrawn from cultivation in the year 2010 mainly due to its red coloured pericarp. It also became susceptible to a new pathotype (PbXo-8) of bacterial blight (BB) pathogen. To improve these specific defects, PAU 201 was mutagenized with ethyl methane sulphonate in different concentrations of 0.6, 0.8 and 1.0% in water (v/v). A total of 841 M1 single panicles were harvested and advanced to M4 generation following selfing and selection for white pericarp colour in each generation. A set of promising 68 M4 progenies was also screened for BB resistance and one putative mutant possessing white pericarp colour as well as BB resistance (designated as RYT 3207) was identified. On further evaluation, RYT 3207 was found to be resistant to all the ten pathotypes of BB pathogen prevalent in the Punjab state and it yielded at par with the PAU 201 in multi-location trials during 2011 to 2013. Molecular marker analysis showed presence of xa13 locus in RYT 3207. The acquired resistance to all the ten pathotypes in RYT 3207, compared to nine pathotypes in PAU 201, could be due to modified function of xa13 gene. The new genotype RYT 3207 is a mutagenized version of the high yielding rice cultivar PAU 201 possessing white pericarp and enhanced resistance to bacterial blight.

NARROW AND ROLLED LEAF 2 regulates leaf shape, male fertility, and seed size in rice.

Grain yield in rice (Oryza sativa L.) is closely related to leaf and flower development. Coordinative regulation of leaf, pollen, and seed development in rice as a critical biological and agricultural question should be addressed. Here we identified two allelic rice mutants with narrow and semi-rolled leaves, named narrow and rolled leaf 2-1 (nrl2-1) and nrl2-2. Map-based molecular cloning revealed that NRL2 encodes a novel protein with unknown biochemical function. The mutation of NRL2 caused pleiotropic effects, including a reduction in the number of longitudinal veins, defective abaxial sclerenchymatous cell differentiation, abnormal tapetum degeneration and microspore development, and the formation of more slender seeds compared with the wild type (WT). The NRL2 protein interacted with Rolling-leaf (RL14), causing the leaves of the nrl2 mutants to have a higher cellulose content and lower lignin content than the WT, which may have been related to sclerenchymatous cell differentiation and tapetum degeneration. Thus, this gene is an essential developmental regulator controlling fundamental cellular and developmental processes, serving as a potential breeding target for high-yielding rice cultivars.

水稲多収性品種「モミロマン」の基肥を省略した少肥栽培における収量性

水稲多収性品種「モミロマン」の基肥を省略した少肥栽培における収量性