Effects of Wx Genotype, Nitrogen Fertilization, and Temperature on Rice Grain Quality

Haplotype Analysis of the GL7/GW7/SLG7 Gene and Its Application in Improving the Grain Quality of Three-Line Hybrid Rice

Improving grain quality is second only to enhancing grain yield in breeding hybrid rice. Yet, rice grain quality, especially milling and appearance quality, is facing increasing threats from global warming due to climate change, leading to a relatively slow progress in high-quality rice breeding. Identifying additional grain quality genes is an effective way to combat against the threats on rice grain quality. In the present study, we used the germplasm from 3,000 Rice Genomes Project for genome-wide association study, and identified GL7/GW7/SLG7 as a major QTL besides GS3 and GW5 for grain shape. Among nine haplotypes of GL7 (H1-9), H1-H4, which harbored an 11-bp deletion, were designated as the functional GL7 allele and were primarily present in Geng/Japonica (GJ) rice. We developed KASP markers for GL7 major haplotypes (H1 and H2), and established a breeding system assisted by the markers to effectively improve Xian/Indica (XI) hybrids for grain quality. Yuehesimiao (YHSM) and Yixiang 1 A (YX1A) are widely applicated XI restorer line and sterile line in three-line hybrids. The improved hybrid YX1AGL7/YHSMGL7 exhibited longer grain, higher ratio of grain length-to-width and larger rate of head rice, but lower chalkiness rate and degree than that of any other hybrids and both parents. Furthermore, the improved hybrid with GL7 had statistically same yield of grains with all other hybrids, indicating no penalty of grain yield while improving grain quality. The GL7 haplotype along with its marker KASP-S2 and breeding strategy resulted from this study could be valuable sources for developing XI hybrids with high quality and high yield of grains in rice.

Enhancing quality traits in staple crops: current advances and future perspectives

Staple crops such as rice, wheat and maize are crucial for global food security; however, improving their quality remains a significant challenge. This review summarizes recent advances in enhancing crop quality, focusing on key areas such as the molecular mechanisms underlying endosperm filling initiation, starch granule synthesis, protein body formation, and the interactions between carbon and nitrogen metabolism. It also highlights ten unresolved questions related to starch-protein spatial distribution, epigenetic regulation, and the environmental impacts on quality traits. The integration of multi-omics approaches, and rational design strategies presents opportunities to develop high-yield "super-crop" varieties with enhanced nutritional value, better processing characteristics, and attributes preferred by consumers. Addressing these challenges is crucial to promote sustainable agriculture and achieve the dual objectives of food security and environmental conservation.

Exploring the impact of key physicochemical properties of rice on taste quality and instant rice processing

Taste quality is one of the most important indicators for assessing the quality of rice. However, there has been a lack of systematic studies investigating the impact factors of taste quality. In this study, chromosomal segment substitution lines (CSSLs) with notable differences in physicochemical properties were obtained by screening the CSSL population. A correlation analysis between the physicochemical properties and the taste qualities of rice revealed that amylose and protein content are significantly negatively correlated with the taste value of both freshly cooked and rehydrated instant rice. The alkali spreading value (ASV) had limited impact on the taste value of rice, but low-ASV rice is more resistant to cooking. Grain chalkiness played a critical role in maintaining the integrity of freshly cooked rice and instant rice grains after rehydration. In summary, our study provides crucial insights and guidance for rice breeding, with the goal of developing excellent quality and enhancing the processing of instant rice.

OsG6PGH1 affects various grain quality traits and participates in the salt stress response of rice

Cytoplasmic 6-phosphogluconate dehydrogenase (G6PGH) is a key enzyme in the pentose phosphate pathway that is involved in regulating various biological processes such as material metabolism, and growth and development in plants. However, it was unclear if OsG6PGH1 affected rice grain quality traits. We perform yeast one-hybrid experiments and reveal that OsG6PGH1 may interact with OsAAP6. Subsequently, yeast in vivo point-to-point experiments and local surface plasmon resonance experiments verified that OsG6PGH1 can bind to OsAAP6. OsG6PGH1 in rice is a constitutive expressed gene that may be localized in the cytoplasm. OsAAP6 and protein-synthesis metabolism-related genes are significantly upregulated in OsG6PGH1 overexpressing transgenic positive endosperm, corresponding to a significant increase in the number of protein bodies II, promoting accumulation of related storage proteins, a significant increase in grain protein content (GPC), and improved rice nutritional quality. OsG6PGH1 positively regulates amylose content, negatively regulates chalkiness rate and taste value, significantly affects grain quality traits such as appearance, cooking, and eating qualities of rice, and is involved in regulating the expression of salt stress related genes, thereby enhancing the salt-stress tolerance of rice. Therefore, OsG6PGH1 represents an important genetic resource to assist in the design of high-quality and multi-resistant rice varieties.

OsAAP8 mutation leads to significant improvement in the nutritional quality and appearance of rice grains

Members of the permease gene family are responsible for important biological functions in the growth and development of rice. Here, we show that OsAAP8 is a constitutive expression gene, and its translated protein is localized on the cell membrane. Mutation of the OsAAP8 can promote the expression of genes related to protein and amylopectin synthesis, and also promote the enlargement of protein bodies in its endosperm, leading to an increase in the protein, amylopectin, and total amino acid content of grains in OsAAP8 mutants. Seeds produced by the OsAAP8 mutant were larger, and the chalkiness traits of the OsAAP8 mutants were significantly reduced, thereby improving the nutritional quality and appearance of rice grains. The OsAAP8 protein is involved in the transport of various amino acids; OsAAP8 mutation significantly enhanced the root absorption of a range of amino acids and might affect the distribution of various amino acids. Therefore, OsAAP8 is an important quality trait gene with multiple biological functions, which provides important clues for the molecular design of breeding strategies for developing new high-quality varieties of rice.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01473-w.

A Novel Allele in the Promoter of Wx Decreases Gene Expression and Confers Lower Apparent Amylose Contents in Japonica Rice (Oryza sativa L.)

Wx is the key gene that controls amylose content (AC), and various alleles have been found in rice populations. Wxb is the major allele in japonica and produces moderate AC (15~18%). It was recently found that editing the promoter of Wx could produce a series of alleles that have different Wx activities. Although some studies have edited the promoter, few studies have focused on the natural variations in Wx. Here, we used the Rice3K database to investigate variations in the Wx promoter and found that the allele Wx1764178 (A/G) has a higher LD (linkage disequilibrium) with the two key SNPs (1765751, T/G; 1768006, A/C), which could produce different Wx alleles and influence AC, as reported previously. Further study showed that the Wx1764178 allele (A/G) is functional and influences the expression of Wx positively. Editing the A allele using CRISPR‒Cas9 produced 36 and 3 bp deletions and caused a decrease in the expression of Wx. The apparent amylose content (AAC) in the edited lines was decreased by 7.09% and 11.50% compared with that of the wild type, which was the japonica variety Nipponbare with Wxb and the A allele at 1764178, while a complementary line with the G allele showed a lower AAC than the A allele with no effect on other agronomic traits. The AAC of the edited lines showed a higher increase than that of the wild type (Nipponbare, Wxb) in low-nitrogen conditions relative to high-nitrogen conditions. We also developed a dCAPS marker to identify the allele and found that the G allele has widely been used (82.95%) in japonica-bred varieties from Jiangsu Province, China. Overall, we found a functional allele (Wx1764178, A/G) in the Wx promoter that could affect AAC in japonica cultivars and be developed as markers for quality improvement in rice breeding programs.

Orchestrating seed storage protein and starch accumulation toward overcoming yield-quality trade-off in cereal crops

Achieving high yield and good quality in crops is essential for human food security and health. However, there is usually disharmony between yield and quality. Seed storage protein (SSP) and starch, the predominant components in cereal grains, determine yield and quality, and their coupled synthesis causes a yield-quality trade-off. Therefore, dissection of the underlying regulatory mechanism facilitates simultaneous improvement of yield and quality. Here, we summarize current findings about the synergistic molecular machinery underpinning SSP and starch synthesis in the leading staple cereal crops, including maize, rice and wheat. We further evaluate the functional conservation and differentiation of key regulators and specify feasible research approaches to identify additional regulators and expand insights. We also present major strategies to leverage resultant information for simultaneous improvement of yield and quality by molecular breeding. Finally, future perspectives on major challenges are proposed.

OsNAC74 affects grain protein content and various biological traits by regulating OsAAP6 expression in rice

The grain protein content is an important quality trait in cereals, and the expression level of the OsAAP6 can significantly affect the grain protein content in rice. Through site-directed mutagenesis, we found that the position from -7 to -12 bp upstream of the transcription start site of the OsAAP6 was the functional variation site. By using the yeast single hybrid test, point-to-point in yeast, and the local surface plasmon resonance test, the OsNAC74 was screened and verified to be a regulator upstream of OsAAP6. The OsNAC74 is a constitutively expressed gene whose product is located on the cell membrane. The OsAAP6 and the genes related to the seed storage in the Osnac74 mutants were downregulated, and grain protein content was significantly reduced. In addition, OsNAC74 had a significant impact on quality traits such as grain chalkiness and gel consistency in rice. Although the Osnac74 mutant seeds were relatively small, the individual plant yield was not decreased. Therefore, OsNAC74 is an important regulatory factor with multiple biological functions. This study provides important information for the later use of OsNAC74 gene for molecular design and breeding in rice.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01433-w.

Combined effects of SSII-2RNAi and different Wx alleles on rice grain transparency and physicochemical properties

Near-isogenic lines Nip(Wx^b/SSII-2), Nip(Wx^b/ss2-2), Nip(Wx^mw/SSII-2), Nip(Wx^mw/ss2-2), Nip(Wx^mp/SSII-2) and Nip(Wx^mp/ss2-2) in the Nipponbare (Nip) background containing the SSII-2RNAi cassette combined with different Waxy (Wx) alleles were investigated in terms of rice grain transparency and quality profiles. Rice lines carrying the SSII-2RNAi cassette displayed downregulation of SSII-2, SSII-3 and Wx genes. Introduction of the SSII-2RNAi cassette decreased apparent amylose content (AAC) in all transgenic lines, but grain transparency differed between low AAC rice lines. Grains from Nip(Wx^b/SSII-2) and Nip(Wx^b/ss2-2) were transparent, while those of rice were increasingly translucent with decreasing moisture due to cavities within starch granules. Rice grain transparency was positively correlated with grain moisture and AAC, but negatively correlated with cavity area within starch granules. Starch fine structure analysis revealed a marked increase in short amylopectin chains with DP 6-12, but a decrease in intermediate chains with DP 13-24, resulting in decreased gelatinisation temperature. Starch crystalline structure analysis showed that the transgenic rice starches have lower crystallinity and lamellar repeat distance than controls due to differences in starch fine structure. The results highlight the molecular basis underpinning rice grain transparency, and provide strategies for improving rice grain transparency.

CRISPR/Cas9-mediated editing of Wx and BADH2 genes created glutinous and aromatic two-line hybrid rice

Amylose content (AC) is one of the physicochemical indexes of rice quality, which is largely determined by the Waxy (Wx) gene. Fragrance in rice is favored because it adds good flavor and a faint scent. Loss of function of the BADH2 (FGR) gene promotes the biosynthesis of 2-acetyl-1-pyrroline (2AP), which is the main compound responsible for aroma in rice. Here, we used a CRISPR/Cas9 system to simultaneously knock out Wx and FGR genes in 1892S and M858, which are the parents of an indica two-line hybrid rice, Huiliangyou 858 (HLY858). Four T-DNA-free homozygous mutants (1892Swxfgr-1, 1892Swxfgr-2, M858wxfgr-1, and M858wxfgr-2) were obtained. The 1892Swxfgr and M858wxfgr were crossed to generate double mutant hybrid lines HLY858wxfgr-1 and HLY858wxfgr-2. Size-exclusion chromatography (SEC) data indicated that true AC of the wx mutant starches ranged from 0.22 to 1.63%, much lower than those of the wild types (12.93 to 13.76%). However, the gelatinization temperature (GT) of the wx mutants in backgrounds of 1892S, M858, and HLY858 were still high, and showed no significant differences with the wild type controls. The aroma compounds 2AP content in grains of HLY858wxfgr-1 and HLY858wxfgr-2 were 153.0 μg/kg and 151.0 μg/kg, respectively. In contrast, 2AP was not detected in grains of HLY858. There were no significant differences in major agronomic traits between the mutants and HLY858. This study provides guidelines for cultivation of ideal glutinous and aromatic hybrid rice by gene editing.

Fine mapping of the grain chalkiness quantitative trait locus qCGP6 reveals the involvement of Wx in grain chalkiness formation

Grain chalkiness is an important index of rice appearance quality and is negatively associated with rice processing and eating qualities. However, the genetic mechanism underlying chalkiness formation is largely unknown. To identify the genetic basis of chalkiness, 410 recombinant inbred lines (RILs) derived from two representative indica rice varieties, Shuhui498 (R498) and Yihui3551 (R3551), were used to discover quantitative trait loci (QTL). The two parental lines and RILs were grown in three locations in China under three controlled fertilizer application level. Analyses indicated that chalkiness was significantly affected by genotype, the environment, and the interaction between the two, and that heritability was high. Several QTLs were isolated, including the two stable QTLs, i.e., qCGP6 and qCGP8. Fine mapping and candidate gene verification of qCGP6 showed that Wx may play a key role in chalkiness formation. Chromosomal segment substitution lines (CSSLs) and near-isogenic lines (NILs) carrying the Wxa or Wxin allele produced more chalky grain than the R498 parent. A similar result was also observed in the 3611 background. Notably, the effect of the Wx genotype on rice chalkiness was shown to be dependent on environmental conditions and Wx alleles exhibited different sensitivities to shading treatment. Using CRISPR/Cas9, the Wxa promoter region was successfully edited, down-regulating Wx alleviates chalkiness formation in NILR498-Wxa. This study developed a new strategy for synergistic improvement of eating and appearance qualities in rice, and created a novel Wx allele with great potential in breeding applications.