High yielding ability of a large-grain rice cultivar, Akita 63

Natural variation in LONELY GUY-Like 1 regulates rice grain weight under warmer night conditions

Global nighttime temperatures are rising at twice the rate of daytime temperatures and pose a challenge for rice (Oryza sativa) production. High nighttime temperature (HNT) stress affects rice yield by reducing grain weight, size, and fertility. Although the genes associated with these yield parameters have been identified and characterized under normal temperatures, the genetic basis of grain weight regulation under HNT stress remains less explored. We examined the natural variation for rice single grain weight (SGW) under HNT stress imposed during grain development. A genome-wide association analysis identified several loci associated with grain weight under HNT stress. A locus, SGW1, specific to HNT conditions resolved to LONELY GUY-Like 1 (LOGL1), which encodes a putative cytokinin-activation enzyme. We demonstrated that LOGL1 contributes to allelic variation at SGW1. Accessions with lower LOGL1 transcript abundance had higher grain weight under HNT. This was supported by the higher grain weight of logl1-mutants relative to the wild type under HNT. Compared to logl1-mutants, LOGL1 over-expressers showed increased sensitivity to HNT. We showed that LOGL1 regulates the thiamin biosynthesis pathway, which is under circadian regulation, which in turn is likely perturbed by HNT stress. These findings provide a genetic source to enhance rice adaptation to warming night temperatures and improve our mechanistic understanding of HNT stress tolerance pathways.

Selenium mitigates the loss of nutritional quality in rice grown at an elevated concentration of carbon dioxide

Atmospheric CO2 enrichment has the potential to improve rice (Oryza sativa L.) yield, but it may also reduce grain nutritional quality, by reducing mineral and protein concentrations. Selenium (Se) fertilization may improve rice grain nutritional composition, but it is not known if this response extends to plants grown in elevated carbon dioxide concentration (eCO2). We conducted experiments to identify the impacts of Se fertilization on yield and quality of rice grains in response to eCO2. The effect of the Se treatment was not significant for the grain yield within each CO2 condition. However, the reduction in macronutrients and micronutrients under eCO2 was mitigated in grains of plants fertilized with Se. Fertilization with Se increased the concentration of Se in roots, flag leaves, and grains independently of atmospheric CO2 concentrations. Elevation of the transcripts of ion transport-related genes could, at least partially, explain the positive relationship between mineral concentrations and grain mass resulting from Se fertilization under eCO2. Treatment with Se also increased the accumulation of total protein in grains under eCO2. Overall, our results revealed that Se fertilization represents a potential asset to maintain rice grain nutritional quality in a future with rising atmospheric CO2 concentration.

Agronomic potential of plant-specific Gγ proteins

The vascular plant-specific type III Gγ proteins have emerged as important targets for biotechnological applications. These proteins are exemplified by Arabidopsis AGG3, rice Grain Size 3 (GS3), Dense and Erect Panicle 1 (DEP1), and GGC2 and regulate plant stature, seed size, weight and quality, nitrogen use efficiency, and multiple stress responses. These Gγ proteins are an integral component of the plant heterotrimeric G-protein complex and differ from the canonical Gγ proteins due to the presence of a long, cysteine-rich C-terminal region. Most cereal genomes encode three or more of these proteins, which have similar N-terminal Gγ domains but varying lengths of the C-terminal domain. The C-terminal domain is hypothesized to give specificity to the protein function. Intriguingly, many accessions of cultivated cereals have natural deletion of this region in one or more proteins, but the mechanistic details of protein function remain perplexing. Distinct, sometimes contrasting, effects of deletion of the C-terminal region have been reported in different crops or under varying environmental conditions. This review summarizes the known roles of type III Gγ proteins, the possible action mechanisms, and a perspective on what is needed to comprehend their full agronomic potential.

QTL Mapping of Tiller Number in Korean Japonica Rice Varieties

Tiller number is an important trait associated with yield in rice. Tiller number in Korean japonica rice was analyzed under greenhouse conditions in 160 recombinant inbred lines (RILs) derived from a cross between the temperate japonica varieties Odae and Unbong40 to identify quantitative trait loci (QTLs). A genetic map comprising 239 kompetitive allele-specific PCR (KASP) and 57 cleaved amplified polymorphic sequence markers was constructed. qTN3, a major QTL for tiller number, was identified at 132.4 cm on chromosome 3. This QTL was also detected under field conditions in a backcross population; thus, qTN3 was stable across generations and environments. qTN3 co-located with QTLs associated with panicle number per plant and culm diameter, indicating it had pleiotropic effects. The qTN3 regions of Odae and Unbong40 differed in a known functional variant (4 bp TGTG insertion/deletion) in the 5' UTR of OsTB1, a gene underlying variation in tiller number and culm strength. Investigation of variation in genotype and tiller number revealed that varieties with the insertion genotype had lower tiller numbers than those with the reference genotype. A high-resolution melting marker was developed to enable efficient marker-assisted selection. The QTL qTN3 will therefore be useful in breeding programs developing japonica varieties with optimal tiller numbers for increased yield.

Three Starch Synthase IIa (SSIIa) Alleles Reveal the Effect of SSIIa on the Thermal and Rheological Properties, Viscoelasticity, and Eating Quality of Glutinous Rice

Glutinous rice accumulates amylose-free starch and is utilized for rice cakes and crackers, owing to the loss of the Waxy gene which encodes granule-bound starch synthase I (GBSSI). Starch synthase IIa (SSIIa) elongates amylopectin chains with a degree of polymerization (DP) of 6-12 to 13-24 and greatly influences starch properties. To elucidate the relationship between the branch length of amylopectin and the thermal and rheological properties, viscoelasticity, and eating quality of glutinous rice, three allelic near isogenic lines with high, low, or no SSIIa activity were generated (designated as SS2a wx, ss2a^L wx, and ss2a wx, respectively). Chain length distribution analyses revealed that ss2a wx exhibited the highest short chain (DP < 12) number and lowest gelatinization temperature, whereas SS2a wx showed the opposite results. Gel filtration chromatography showed that the three lines contained essentially no amylose. Viscoelasticity analyses of rice cakes stored at low temperature for different durations revealed that ss2a wx maintained softness and elasticity for up to 6 days, while SS2a wx hardened within 6 h. Sensory evaluation was consistent with mechanical evaluation. The relationship of amylopectin structure with the thermal and rheological properties, viscoelasticity, and eating quality of glutinous rice is discussed.

Enhancing photosynthesis and yield in rice with improved N use efficiency

The success of the dwarf breeding of rice, called the Green Revolution in Asia, resulted from increased source and sink capacities depending on significant inputs of N fertilizer. Although N fertilization is essential for increasing cereal production, large inputs of N application have significantly impacted the environment. Transgenic rice overproducing Rubisco has demonstrated increased yields with improved N use efficiency for increasing biomass production under high N fertilization in a paddy field. A large grain cultivar, Akita 63, had a high yield by enlarging the sink capacity without photosynthesis improvement. However, source capacity strongly limited the yield potential under high N fertilization. Enhancing photosynthesis is important for further increasing the yield of current high-yielding cultivars. Developing innovative rice plants with both high photosynthesis and large sink capacity is essential.

Effect of Heading Date on the Starch Structure and Grain Yield of Rice Lines with Low Gelatinization Temperature

Early flowering trait is essential for rice cultivars grown at high latitude since delayed flowering leads to seed development at low temperature, which decreases yield. However, early flowering at high temperature promotes the formation of chalky seeds with low apparent amylose content and high starch gelatinization temperature, thus affecting grain quality. Deletion of starch synthase IIa (SSIIa) shows inverse effects of high temperature, and the ss2a mutant shows higher apparent amylose content and lower gelatinization temperature. Heading date 1 (Hd1) is the major regulator of flowering time, and a nonfunctional hd1 allele is required for early flowering. To understand the relationship among heading date, starch properties, and yield, we generated and characterized near-isogenic rice lines with ss2a Hd1, ss2a Hd1 hd1, and ss2a hd1 genotypes. The ss2a Hd1 line showed the highest plant biomass; however, its grain yield varied by year. The ss2a Hd1 hd1 showed higher total grain weight than ss2a hd1. The ss2a hd1 line produced the lowest number of premature seeds and showed higher gelatinization temperature and lower apparent amylose content than ss2a Hd1. These results highlight Hd1 as the candidate gene for developing high-yielding rice cultivars with the desired starch structure.

The gs3 allele from a large-grain rice cultivar, Akita 63, increases yield and improves nitrogen-use efficiency

The Green Revolution allowed a large amount of nitrogen (N) fertilization to increase crop yield but has led to severe environmental pollution. Therefore, increasing the crop grain yield must be achieved without such considerable input of N fertilization. A large-grain japonica rice cultivar, Akita 63, significantly increased grain yield and improved N-use efficiency (NUE) for yield per amount of N absorbed by plants. This study found that the nonsense mutated GS3 gene, the gs3 allele of Akita 63, has a superior yield production with enlarged grain size. The gs3 allele increased the yield with improvements in harvest index and NUE for yields per plant N content by analyzing the near-isogenic line of rice plants with a large grain (LG-Notohikari), which was developed by introducing the gs3 allele of Akita 63 into normal-grain japonica cultivar, Notohikari. Thus, the gs3 allele would be promising for further yield increase without additional large input of N fertilization in non-gs3-allele rice varieties.

Improving Agricultural Traits While Maintaining High Resistant Starch Content in Rice

BACKGROUND

Resistant starch (RS) is beneficial for human health. Loss of starch branching enzyme IIb (BEIIb) increases the proportion of amylopectin long chains, which greatly elevates the RS content. Although high RS content cereals are desired, an increase in RS content is often accompanied by a decrease in seed weight. To further increase the RS content, genes encoding active-type starch synthase (SS) IIa, which elongates amylopectin branches, and high expression-type granule-bound SSI (GBSSI), which synthesizes amylose, were introduced into the be2b mutant rice. This attempt increased the RS content, but further improvement of agricultural traits was required because of a mixture of indica and japonica rice phonotype, such as different grain sizes, flowering times, and seed shattering traits. In the present study, the high RS lines were backcrossed with an elite rice cultivar, and the starch properties of the resultant high-yielding RS lines were analyzed.

RESULTS

The seed weight of high RS lines was greatly improved after backcrossing, increasing up to 190% compared with the seed weight before backcrossing. Amylopectin structure, gelatinization temperature, and RS content of high RS lines showed almost no change after backcrossing. High RS lines contained longer amylopectin branch chains than the wild type, and lines with active-type SSIIa contained a higher proportion of long amylopectin chains compared with the lines with less active-SSIIa, and thus showed higher gelatinization temperature. Although the RS content of rice varied with the cooking method, those of high RS lines remained high after backcrossing. The RS contents of cooked rice of high RS lines were high (27-35%), whereas that of the elite parental rice was considerably low (< 0.7%). The RS contents of lines with active-type SSIIa and high-level GBSSI expression in be2b or be2b ss3a background were higher than those of lines with less-active SSIIa.

CONCLUSIONS

The present study revealed that backcrossing high RS rice lines with elite rice cultivars could increase the seed weight, without compromising the RS content. It is likely that backcrossing introduced loci enhancing seed length and width as well as loci promoting early flowering for ensuring an optimum temperature during RS biosynthesis.

Effects of Various Allelic Combinations of Starch Biosynthetic Genes on the Properties of Endosperm Starch in Rice

Rice endosperm accumulates large amounts of photosynthetic products as insoluble starch within amyloplasts by properly arranging structured, highly branched, large amylopectin molecules, thus avoiding osmotic imbalance. The amount and characteristics of starch directly influence the yield and quality of rice grains, which in turn influence their application and market value. Therefore, understanding how various allelic combinations of starch biosynthetic genes, with different expression levels, affect starch properties is important for the identification of targets for breeding new rice cultivars. Research over the past few decades has revealed the spatiotemporal expression patterns and allelic variants of starch biosynthetic genes, and enhanced our understanding of the specific roles and compensatory functions of individual isozymes of starch biosynthetic enzymes through biochemical analyses of purified enzymes and characterization of japonica rice mutants lacking these enzymes. Furthermore, it has been shown that starch biosynthetic enzymes can mutually and synergistically increase their activities by forming protein complexes. This review focuses on the more recent discoveries made in the last several years. Generation of single and double mutants and/or high-level expression of specific starch synthases (SSs) allowed us to better understand how the starch granule morphology is determined; how the complete absence of SSIIa affects starch structure; why the rice endosperm stores insoluble starch rather than soluble phytoglycogen; how to elevate amylose and resistant starch (RS) content to improve health benefits; and how SS isozymes mutually complement their activities. The introduction of active-type SSIIa and/or high-expression type GBSSI into ss3a ss4b, isa1, be2b, and ss3a be2b japonica rice mutants, with unique starch properties, and analyses of their starch properties are summarized in this review. High-level accumulation of RS is often accompanied by a reduction in grain yield as a trade-off. Backcrossing rice mutants with a high-yielding elite rice cultivar enabled the improvement of agricultural traits, while maintaining high RS levels. Designing starch structures for additional values, breeding and cultivating to increase yield will enable the development of a new type of rice starch that can be used in a wide variety of applications, and that can contribute to food and agricultural industries in the near future.

Contribution of the grain size QTL GS3 to yield properties and physiological nitrogen-use efficiency in the large-grain rice cultivar 'Akita 63'

The development of crop varieties with high nitrogen-use efficiency (NUE) is thought to be important in achieving sustainable cereal crop production. The high yield large-grain rice cultivar Oryza sativa L. 'Akita 63' (temperate japonica) has high physiological NUE (PNUE) for grain yield (GY). Our previous study revealed that a large-grain allele of GS3 is present in 'Akita 63'. Here, we verified the influence of GS3 on the yield properties and PNUE for GY in 'Akita 63'. The frequency distribution of brown rice length in F₂ crosses of 'Iwate 75' and 'Akita 63' showed a continuous distribution that could be explained by GS3. A near-isogenic line was developed to substitute the GS3 segment of 'Koshihikari', which harbours a normal-sized grain allele, in the genetic background of 'Akita 63' and the line was designated as Akita63NILGS3-Koshihikari. Compared with Akita63NILGS3-Koshihikari, 'Akita 63' exhibited a significantly increased grain length, single brown grain weight and GY, although no significant differences were observed in the nitrogen content and above-ground biomass per unit of cultivated area. These results indicate that the GS3 large-grain allele is a contributing factor to high PNUE for GY in 'Akita 63'. These findings will facilitate the development of nitrogen-efficient rice varieties.

Parent-of-Origin Effects on Seed Size Modify Heterosis Responses in Arabidopsis thaliana

Parent-of-origin effects arise when a phenotype depends on whether it is inherited maternally or paternally. Parent-of-origin effects can exert a strong influence on F1 seed size in flowering plants, an important agronomic and life-history trait that can contribute to biomass heterosis. Here we investigate the natural variation in the relative contributions of the maternal and paternal genomes to F1 seed size across 71 reciprocal pairs of F1 hybrid diploids and the parental effect on F1 seed size heterosis. We demonstrate that the paternally derived genome influences F1 seed size more significantly than previously appreciated. We further demonstrate (by disruption of parental genome dosage balance in F1 triploid seeds) that hybridity acts as an enhancer of genome dosage effects on F1 seed size, beyond that observed from hybridity or genome dosage effects on their own. Our findings indicate that interactions between genetic hybridity and parental genome dosage can enhance heterosis effects in plants, opening new avenues for boosting heterosis breeding in crop plants.

Photosynthetic Enhancement, Lifespan Extension, and Leaf Area Enlargement in Flag Leaves Increased the Yield of Transgenic Rice Plants Overproducing Rubisco Under Sufficient N Fertilization

BACKGROUND

Improvement in photosynthesis is one of the most promising approaches to increase grain yields. Transgenic rice plants overproducing Rubisco by 30% (RBCS-sense rice plants) showed up to 28% increase in grain yields under sufficient nitrogen (N) fertilization using an isolated experimental paddy field (Yoon et al. in Nat Food 1:134-139, 2020). The plant N contents above-ground sections and Rubisco contents of the flag leaves were higher in the RBCS-sense plants than in the wild-type rice plants during the ripening period, which may be reasons for the increased yields. However, some imprecise points were left in the previous research, such as contributions of photosynthesis of leaves below the flag leaves to the yield, and maintenance duration of high photosynthesis of RBCS-sense rice plants during ripening periods.

RESULT

In this research, the photosynthetic capacity and canopy architecture were analyzed to explore factors for the increased yields of RBCS-sense rice plants. It was found that N had already been preferentially distributed into the flag leaves at the early ripening stage, contributing to maintaining higher Rubisco content levels in the enlarged flag leaves and extending the lifespan of the flag leaves of RBCS-sense rice plants throughout ripening periods under sufficient N fertilization. The higher amounts of Rubisco also improved the photosynthetic activity in the flag leaves throughout the ripening period. Although the enlarged flag leaves of the RBCS-sense rice plants occupied large spatial areas of the uppermost layer in the canopy, no significant prevention of light penetration to leaves below the flag leaves was observed. Additionally, since the CO2 assimilation rates of lower leaves between wild-type and RBCS-sense rice plants were the same at the early ripening stage, the lower leaves did not contribute to an increase in yields of the RBCS-sense rice plants.

CONCLUSION

We concluded that improvements in the photosynthetic capacity by higher leaf N and Rubisco contents, enlarged leaf area and extended lifespan of flag leaves led to an increase in grain yields of RBCS-sense rice plants grown under sufficient N fertilization.

Characterization of functional genes GS3 and GW2 and their effect on the grain size of various landraces of rice (Oryza sativa)

BACKGROUND

Grain size is an essential factor of grain quality and yield in rice. The genetic studies have substantially contributed to enhancing yield and maintaining a good quality of rice. The two major genes GS3 (a negative regulator of grain length) and GW2 (a negative regulator of grain width) with functional mutation play a significant role in controlling the grain size of rice. METHODS AND RESULTS: In the study, 17 different widely grown Pakistani landraces of various genetic and geographic backgrounds were evaluated for grain phenotypic traits (1000-grain weight, length, width, and thickness) and also screened for genotypic mutation in GS3 and GW2 genes. Phenotypic data revealed the range for grain weight from 16.86 g (Lateefy) to 26.91 g (PS2), grain length ranged from 7.27 mm (JP-5) to 12.18 mm (PS2), grain width ranged from 2.01 mm (Lateefy) to 3.51 mm (JP5), and grain thickness ranged from 1.79 mm to 2.19. Correlation revealed a negative and significant correlation between grain width and length. There was no significant correlation between grain length and 1000-grain weight and grain width. LSD test displayed that the means of three variables grain length, grain width, and 1000-grain weight were statistically different from one another except grain width and grain breadth. Fifteen accessions carried the domesticated allele of GS3 while JP5 and Fakhr-e-Malakand carried the dominant allele. Similarly, fifteen accessions carried the dominant allele of GW2 while JP-5 and Fakhr-e-Malakand carried the mutant allele.

CONCLUSIONS

The study shows that the mutant alleles of both genes are of significance to pyramid them in any breeding program. However, just incorporating favorable alleles is not the sole solution for improving the grain size. Therefore, further elucidation of GS3 and GW2 genes regulatory network, their interaction, trade-off, and pathways will better coordinate their marker-assisted selection in the future breeding program. Additionally, the study concluded that the selection of grain size was not dependent on 1000-grain weight in the selected germplasm.

Genetic and Molecular Factors Determining Grain Weight in Rice

Grain weight is one of the major factors determining single plant yield production of rice and other cereal crops. Research has begun to reveal the regulatory mechanisms underlying grain weight as well as grain size, highlighting the importance of this research for plant molecular biology. The developmental trait of grain weight is affected by multiple molecular and genetic aspects that lead to dynamic changes in cell division, expansion and differentiation. Additionally, several important biological pathways contribute to grain weight, such as ubiquitination, phytohormones, G-proteins, photosynthesis, epigenetic modifications and microRNAs. Our review integrates early and more recent findings, and provides future perspectives for how a more complete understanding of grain weight can optimize strategies for improving yield production. It is surprising that the acquired wealth of knowledge has not revealed more insights into the underlying molecular mechanisms. To accelerating molecular breeding of rice and other cereals is becoming an emergent and critical task for agronomists. Lastly, we highlighted the importance of leveraging gene editing technologies as well as structural studies for future rice breeding applications.