Genetic basis of 17 traits and viscosity parameters characterizing the eating and cooking quality of rice grain

Structures, gelatinization properties and enzyme hydrolyses of starches from transparent and floury grains of rices subjected to field natural extreme high temperature

Three rice varieties underwent the field natural extreme high temperature (EHT) with daily average temperature over 30 °C from 21 to 89 days after sowing, and had transparent, chalky and floury grains. The structures, gelatinization properties and enzyme hydrolyses of starches from transparent and floury grains were investigated. Compared with control transparent grains, floury grains subjected to EHT markedly decreased the contents of amylose molecules, amylopectin A chains and amylopectin B1 chains and increased the contents of amylopectin B2 and B3+ chains and the average branch-chain length of amylopectin. Both transparent and floury grains had A-type starches, but floury grain starches exhibited higher relative crystallinity, gelatinization temperature, retrogradation and pasting viscosities than transparent grain starches. Floury grain starches had lower hydrolysis rates than transparent grain starches. Native starches were more resistant to digestion but gelatinized and retrograded starches were more prone to digestion in floury grains than in transparent grains.

Improvement of Quality and Disease Resistance for a Heavy-Panicle Hybrid Restorer Line, R600, in Rice (Oryza sativa L.) by Gene Pyramiding Breeding

The utilization of heavy-panicle hybrid rice exemplifies the successful integration of architectural enhancement and heterosis, which has been widely adopted in the southwest rice-producing area of China. Iterative improvement in disease resistance and grain quality of heavy-panicle hybrid rice varieties is crucial to promote their sustainable utilization. Here, we performed a molecular design breeding strategy to introgress beneficial alleles of broad-spectrum disease resistance and grain quality into a heavy-panicle hybrid backbone restorer line Shuhui 600 (R600). We successfully developed introgression lines through marker-assisted selection to pyramid major genes (Wxb + ALKA-GC + Pigm + Xa23) derived from three parents (Huanghuazhan, I135, I488), which significantly enhance grain quality and confer resistance to rice blast and bacterial blight (BB). The improved parental R600 line (iR600) exhibited superior grain quality and elevated disease resistance while maintaining the heavy-panicle architecture and high-yield capacity of R600. Moreover, the iR600 was crossed with male sterility line 608A to obtain a new heavy-panicle hybrid rice variety with excellent eating and cooking quality (ECQ) and high yield potential. This study presents an effective breeding strategy for rice breeders to expedite the improvement of grain quality and disease resistance in heavy-panicle hybrid rice.

Characterization and structure-functionality analysis of starch in different layers of Lycoris chinensis bulb scales

According to literature, the size distribution of starch granules varies significantly in different layers of Lycoris chinensis bulb scales, however its effect on structural and physicochemical properties of starch still remains unclear. In this study, outer, middle and inner layers of bulb scales of L. chinensis were compared for starch characteristics. Also, the structure-functionality association was investigated based on correlation analysis and hierarchical cluster analysis, using 37 starch quality traits. Compared to commonly consumed starches with similar amylose content, L. chinensis starch gel had lower hardness and viscosities. Among layers, starches varied significantly in particle size, physicochemical and structural properties. As compared to middle and inner scales, the starch in outer scales had higher amylose content, hardness and viscosities, but lower gelatinization temperature, weight-average molar mass and degree of polymorphism. Correlation analysis revealed significant correlations among traits, and interestingly, gelatinization temperature (Tp) was found positively correlated to traits of molecular weight (p < 0.05). The 37 traits of starch characteristics can be divided into three subgroups, as supported by the results of Pearson correlation analysis and hierarchical cluster analysis. In general, the information presented in the current study are useful for Lycoris bulb starch utilization and insightful for a better understanding of structure-functionality association of starch.

GWAS and Transcriptomic Analysis Identify OsRING315 as a New Candidate Gene Controlling Amylose Content and Gel Consistency in Rice

Cooking quality is the main factor determining the market value of rice. Although several major genes and a certain number of QTLs controlling cooking quality have been identified, the genetic complexity and environmental susceptibility limit the further improvement for cooking quality by molecular breeding. This research conducted a genome-wide association study to elucidate the QTLs related to cooking quality including amylose content (AC), gel consistency (GC) and alkali spreading value (ASV) by using 450 rice accessions consisting of 300 indica and 150 japonica accessions in two distinct environments. A total of 54 QTLs were identified, including 25 QTLs for AC, 12 QTLs for GC and 17 QTLs for ASV. Among them, 10 QTLs were consistently observed by the same population in both environments. Six QTLs were co-localized with the reported QTLs or cloned genes. The Wx gene for AC and GC, and the ALK gene for ASV were identified in every population across the two environments. The qAC9-2 for AC and the qGC9-2 for GC were defined to the same interval. The OsRING315 gene, encoding an E3 ubiquitin ligase, was considered as the candidate gene for both qAC9-2 and qGC9-2. The higher expression of OsRING315 corresponded to the lower AC and higher GC. Three haplotypes of OsRING315 were identified. The Hap 1 mainly existed in the japonica accessions and had lower AC. The Hap 2 and Hap 3 were predominantly present in the indica accessions, associated with higher AC. Meanwhile, the GC of accessions harboring Hap 1 was higher than that of accessions harboring Hap 3. In addition, the distribution of the three haplotypes in several rice-growing regions was unbalanced. The three traits of cooking quality are controlled by both major and minor genes and susceptible to environmental factors. The expression level of OsRING315 is related to both AC and GC, and this gene can be a promising target in quality improvement by using the gene editing method. Moreover, the haplotypes of OsRING315 differentiate between indica and japonica, and reveal the differences in GC and AC between indica and japonica rice.

Deciphering the Role of Waxy Gene Mutations in Enhancing Rice Grain Quality

Amylose content (AC) stands as a pivotal determinant of rice grain quality, primarily governed by the Waxy gene (Wx). The allelic variation within this gene, particularly the presence of the Wxmp allele derived from the ancestral Wxmq allele, significantly influences AC and is prevalent among soft japonica rice varieties in southern China. Although both alleles are associated with lower AC, there remains a paucity of detailed understanding regarding the interplay between specific functional single nucleotide polymorphisms (SNPs) within these alleles and the overarching rice grain quality. To investigate this, we engineered three distinct transgenic rice lines, each harboring the Wxmp, Wxmq, or Wxb-5c alleles in the background of the glutinous rice cultivar Nip(wx). This suite of transgenic rice lines showcased varying degrees of grain transparency inversely correlated to AC, which in turn influenced other physicochemical properties of the rice grains, such as taste value of cooked rice, gel consistency, and starch pasting properties. Additionally, analyses of gene expression and enzyme activity revealed that the functional SNPs, Ex4-53G to A and Ex5-53T to C, lead to a decline in the activity of granule-bound starch synthase I (GBSSI) without altering expression levels.

Structural, Thermal, Pasting and Digestion Properties of Starches from Developing Root Tubers of Sweet Potato

Three sweet potato varieties with white-, yellow- and purple-fleshed root tubers were harvested at 100, 120, 140 and 160 days after planting (DAP). Their starch structural, thermal, pasting and digestion properties were measured to reveal the influences of harvesting dates on the physicochemical properties of sweet potato root tuber starch. Though starches from different varieties displayed some differences in physicochemical properties due to their different genetic backgrounds, they were influenced by harvesting date in similar ways. Starches isolated from root tubers at 100 and 160 DAP exhibited lower granule sizes than those at 120 and 140 DAP. The amylose content was higher in root tubers at 100 and 120 DAP than at 140 and 160 DAP. Starches from root tubers at 100 DAP exhibited CA-type X-ray diffraction patterns, and then the B-type crystallinity gradually increased at later harvesting dates. The different harvesting dates had no significant effects on the short-ranged ordered structure and lamellar thickness of starch, but the lamellar peak intensity decreased significantly at later harvesting dates. Starch had a lower gelatinization temperature and a wider gelatinization temperature range in root tubers at 140 and 160 DAP than at 100 and 120 DAP. The higher peak viscosity and lower pasting temperature were associated with the late harvesting date. The digestion of starch had slight differences among root tubers at different harvesting dates. The harvesting dates of root tubers played more important roles in starch properties than the variety. This study would be helpful for breeders, farmers and sweet potato starch users.

"Structure-function" analysis using starches isolated from Lycoris chinensis bulbs of different developmental stages

In this study, Lycoris chinensis bulbs of four developmental stages were compared for starch characteristics. Based on correlation analysis and hierarchical cluster analysis, the relationships among 36 traits were discussed. Compared to commonly consumed starches, L. chinensis starch had higher amylose content (33.4-43.2 %) and weight-average molar mass (36410-82,781 kDa), lower gelatinization temperature (61.8-68.1 °C), gel hardness (19.0-39.5 g) and viscosities. Among developmental stages, starches varied significantly in characteristics. As compared to juvenile stage (S1), mature bulbs (S4) had higher amylose content, lower gelatinization temperature, weight-average molar mass and degree of polymorphism. Correlation analysis revealed that the molecular weight-related traits had significantly positive correlations to gelatinization temperature (Tp, p < 0.05), positive but weak correlations to traits of particle size distribution, significantly negative correlations to AAC and many parameters of viscosity properties (p < 0.05). Based on the results of correlation analysis and hierarchical cluster analysis, the 36 traits of starch characteristics were proposed to be divided into three groups: particle size-related traits, molecular weight-related traits and AAC-related traits. The information presented in the current study are useful for future studies on starches of Lycoris and other bulb species, and instructive for future studies in investigating the "Structure-Function" relationship in starch.

Starch Properties and Morphology of Eight Floury Endosperm Mutants in Rice

Besides increasing grain yield, improving rice (Oryza sativa L.) quality has been paid more and more attention recently. Cooking and eating quality (CEQ) is an important indicator of rice quality. Since CEQs are quantitative traits and challenging for measurement, efforts have mainly focused on two major genes, Wx and SSIIa. Chalkiness and floury endosperm significantly affect the eating quality of rice, leading to noticeable changes in CEQ. Due to the easily observable phenotype of floury endosperm, cloning single gene mutations that cause floury endosperm and evaluating changes in CEQs indirectly facilitate the exploration of the minor genes controlling CEQ. In this study, eight mutants with different degrees of floury endosperm, generated through ethylmethane sulfonate (EMS) mutagenesis, were analyzed. These mutants exhibited wide variation in starch morphology and CEQs. Particularly, the z2 mutant showed spherical starch granules significantly increased rapid visco analyzer (RVA) indexes and urea swelling, while the z4 mutant displayed extremely sharp starch granules and significantly decreased RVA indexes and urea swelling compared to the wild type. Additionally, these mutants still maintained correlations with certain RVA profiles, suggesting that the genes PUL, which affect these indexes, may not undergo mutation. Cloning these mutated genes in the future, especially in z2 and z4, will enhance the genetic network of rice eating quality and hold significant importance for molecular marker-assisted breeding to improve rice quality.

Genome-wide association study of cooking-caused grain expansion in rice (Oryza sativa L.)

Cooking-caused rice grain expansion (CCRGE) is a critical trait for evaluating the cooking quality of rice. Previous quantitative trait locus (QTL) mapping studies on CCRGE have been limited to bi-parental populations, which restrict the exploration of natural variation and mapping resolution. To comprehensively and precisely dissect the genetic basis of CCRGE, we performed a genome-wide association study (GWAS) on three related indices: grain breadth expansion index (GBEI), grain length expansion index (GLEI), and grain length-breadth ratio expansion index (GREI), using 345 rice accessions grown in two years (environments) and 193,582 SNP markers. By analyzing each environment separately using seven different methods (3VmrMLM, mrMLM, FASTmrMLM, FASTmrEMMA, pLARmEB, pKWmEB, ISIS EM-BLASSO), we identified a total of 32, 19 and 27 reliable quantitative trait nucleotides (QTNs) associated with GBEI, GLEI and GREI, respectively. Furthermore, by jointly analyzing the two environments using 3VmrMLM, we discovered 19, 22 and 25 QTNs, as well as 9, 5 and 7 QTN-by-environment interaction (QEIs) associated with GBEI, GLEI and GREI, respectively. Notably, 12, 9 and 15 QTNs for GBEI, GLEI and GREI were found within the intervals of previously reported QTLs. In the vicinity of these QTNs or QEIs, based on analyses of mutation type, gene ontology classification, haplotype, and expression pattern, we identified five candidate genes that are related to starch synthesis and endosperm development. The five candidate genes, namely, LOC_Os04g53310 (OsSSIIIb, near QTN qGREI-4.5s), LOC_Os05g02070 (OsMT2b, near QTN qGLEI-5.1s), LOC_Os06g04200 (wx, near QEI qGBEI-6.1i and QTNs qGREI-6.1s and qGLEI-6.1t), LOC_Os06g12450 (OsSSIIa, near QTN qGLEI-6.2t), and LOC_Os08g09230 (OsSSIIIa, near QTN qGBEI-8.1t), are predicted to be involved in the process of rice grain starch synthesis and to influence grain expansion after cooking. Our findings provide valuable insights and will facilitate genetic research and improvement of CCRGE.

Structural and physicochemical properties of bracken fern (Pteridium aquilinum) starch

Introduction

Bracken fern (Pteridium aquilinum) starch is a non-mainstream, litter-researched starch, thus the starch characteristics remain largely unknown.

Methods

The structural and physicochemical properties of two bracken starches were systematically investigated, by use of various techniques that routinely applied in starch analysis.

Results and Discussion

The starches had amylose contents of 22.6 and 24.7%, respectively. The starch granules possessed C-type polymorph with D (4,3) ranging from 18.6 to 24.5 μm. During gelatinization event, the bracken starches showed lower viscosity than typical for rice starch, and lower gelatinization temperature than typical for cereal starches. After gelatinization event, bracken starches formed much softer and sticky gel than rice and potato starch. The molecular weight and branching degree (indexed by Mw, Mn and Rz values) of bracken starches were much higher than starches of many other sources. The branch chain length distributions showed that the bracken starches were structurally similar to some rice varieties (e. g. BP033, Beihan 1#), as reflected by proportions of A, B1, B2, and B3 chains. Notable differences in some starch traits between the two bracken starches were recorded, e. g. amylose content, gel hardness, gelatinization temperature and traits of structural properties. This study provides useful information on the utilization of bracken starch in both food and non-food industries.

Genetic Diversity and Association Mapping of Grain-Size Traits in Rice Landraces from the Honghe Hani Rice Terraces System in Yunnan Province

The Honghe Hani Rice Terraces System (HHRTS) of Yunnan Province is an important agricultural and cultural heritage landscape. Until now, a large number of local rice landraces have been planted. Mining excellent genes contained in these landraces provides a reference for variety improvement and new variety breeding. In this study, 96 rice landraces collected from the Hani terraces were planted in Honghe Mengzi, Yunnan Province, in 2013, 2014, 2015, and 2021, and five major grain traits were measured and analyzed. The genomic variation of 96 rice landraces was scanned by 201 simple sequence repeat (SSR) markers. The genetic diversity, population structure, and genetic relationships of the natural population were analyzed. The mixed linear model (MLM) method of the TASSEL software was used to analyze the associations between markers and traits. A total of 936 alleles were amplified by 201 pairs of SSR primers. The average number of observed alleles (Na), the effective number of alleles (Ne), Shannon's information index (I), heterozygosity (H), and the polymorphism information content (PIC) per marker were 4.66, 2.71, 1.08, 0.15, and 0.55, respectively. Ninety-six landraces were divided into two groups by population structure, clustering, and principal component analysis, and indica rice was the main group. The coefficients of variation of the five traits ranged from 6.80 to 15.24%, and their broad heritabilities were more than 70%. In addition, there were positive correlations among the same grain traits between different years. Through MLM analysis, 2, 36, 7, 7, and 4 SSR markers were significantly associated with grain length (GL), grain width (GW), grain thickness (GT), grain length-width ratio (LWR), and thousand-grain weight (TGW), respectively. The explanation rates of phenotypic variation were 16.31 (RM449, Chr. 1)-23.51% (RM316, Chr. 9), 10.84 (RM523, Chr. 3; RM161/RM305, Chr. 5)-43.01% (RM5496, Chr. 1), 11.98 (RM161/RM305, Chr. 5)-24.72% (RM275, Chr. 6), 12.68 (RM126, Chr. 8)-36.96% (RM5496, Chr. 1), and 17.65 (RM4499, Chr. 2)-26.32% (RM25, Chr. 8), respectively. The associated markers were distributed on 12 chromosomes of the genome.

Effect of storage time on chemical compositions, physiological and cooking quality characteristics of different rice types

BACKGROUND

Storage affects rice quality significantly. The aim of this study was to investigate the changes in the chemical composition and in the physiological and cooking quality characteristics of three rice types after 1 year storage at 25 °C.

RESULTS

Two japonica, two indica, and two indica-japonica hybrid rice varieties were selected. After storage, the total starch content decreased. The amylose content of japonica, indica, and indica-japonica hybrid rice increased by 9.63%-11.65%, 2.99%-4.67%, and 8.07%-8.97%, respectively, and the fat content decreased by 60.00%-65.00%, 37.21%-46.51%, and 41.67%-42.42%, respectively. The abscisic acid (ABA) and raffinose content decreased after 1 year's storage; the former decreased gradually during the storage and the latter increased by 19.35%-45.45%, 7.02%-10.77%, and 16.13%-28.13%, respectively, after 4 months' storage and then decreased to the lowest level after 1 year's storage. The activity of antioxidant enzymes deceased, which resulted in the increases in fatty acid value and malondialdehyde (MDA). The changes in chemical composition after 1 year storage led to the deterioration of rice cooking quality, which was reflected in the decrease in viscosity and increases in gelatinization temperature and cooked rice hardness.

CONCLUSION

After 1 year's storage, the rice chemical composition changed and physiological and cooking quality characteristics decreased. Compared with japonica and indica-japonica hybrid rice, indica rice was more stable during 1 year storage. This may be due to the higher content of ABA and raffinose in fresh rice. Our findings will provide information for the identification and breeding of storable rice cultivars. © 2022 Society of Chemical Industry.

Molecular bases of rice grain size and quality for optimized productivity

The accomplishment of further optimization of crop productivity in grain yield and quality is a great challenge. Grain size is one of the crucial determinants of rice yield and quality; all of these traits are typical quantitative traits controlled by multiple genes. Research advances have revealed several molecular and developmental pathways that govern these traits of agronomical importance. This review provides a comprehensive summary of these pathways, including those mediated by G-protein, the ubiquitin-proteasome system, mitogen-activated protein kinase, phytohormone, transcriptional regulators, and storage product biosynthesis and accumulation. We also generalize the excellent precedents for rice variety improvement of grain size and quality, which utilize newly developed gene editing and conventional gene pyramiding capabilities. In addition, we discuss the rational and accurate breeding strategies, with the aim of better applying molecular design to breed high-yield and superior-quality varieties.

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

Quality is a complex trait that is not only the key determinant of the market value of the rice grain, but is also a major constraint in rice breeding. It is influenced by both genetic and environmental factors. However, the combined effects of genotypes and environmental factors on rice grain quality remain unclear. In this study, we used a three-factor experimental design to examine the grain quality of different Wx genotypes grown under different nitrogen fertilization and temperature conditions during grain development. We found that the three factors contributed differently to taste, appearance, and nutritional quality. Increased Wx function and nitrogen fertilization significantly reduced eating quality, whereas high temperature (HT) had almost no effect. The main effects of temperature on appearance quality and moderate Wx function at low temperatures (LTs) contributed to better appearance, and higher nitrogen fertilization promoted appearance at HTs. With regard to nutritional quality, Wx alleles promoted amylose content (AC) as well as starch-lipids content (SLC); nitrogen fertilization increased storage protein content (PC); and higher temperature increased lipid content but decreased the PC. This study helps to broaden the understanding of the major factors that affect the quality of rice and provides constructive messages for rice quality improvement and the cultivation of high-quality rice varieties.

Genetic Control and High Temperature Effects on Starch Biosynthesis and Grain Quality in Rice

Grain quality is one of the key targets to be improved for rice breeders and covers cooking, eating, nutritional, appearance, milling, and sensory properties. Cooking and eating quality are mostly of concern to consumers and mainly determined by starch structure and composition. Although many starch synthesis enzymes have been identified and starch synthesis system has been established for a long time, novel functions of some starch synthesis genes have continually been found, and many important regulatory factors for seed development and grain quality control have recently been identified. Here, we summarize the progress in this field as comprehensively as possible and hopefully reveal some underlying molecular mechanisms controlling eating quality in rice. The regulatory network of amylose content (AC) determination is emphasized, as AC is the most important index for rice eating quality (REQ). Moreover, the regulatory mechanism of REQ, especially AC influenced by high temperature which is concerned as a most harmful environmental factor during grain filling is highlighted in this review.

Influence of starch fine structure and storage proteins on the eating quality of rice varieties with similar amylose contents

BACKGROUND

Rice eating quality largely dictates consumer preference, and the demand for new rice varieties with excellent eating quality from farmers is increasing. Identification of factors contributing to eating quality is helpful for developing high-quality rice varieties.

RESULTS

Two groups of rice with different apparent amylose content (AACs) were used in this study. One group contained four varieties with low AACs (8.8-9.4%), whereas the other contained four traditional varieties with medium AACs (17.2-17.5%). The physicochemical properties, starch fine structure and crystallinity and storage protein composition of the two groups were analyzed. We found that, in both groups, the rice varieties with high eating quality had more short-chain amylopectin, lower glutelin and prolamin content, and a higher albumin content. In addition, the low-AAC varieties produced opaque endosperms, which may result from an increased number of pores in the center of starch granules.

CONCLUSIONS

Both the fine structure of starch and the storage protein composition were closely related to rice eating quality. In both groups, short branch-chain amylopectin, short-chain amylopectin [degree of polymerization (DP) 6-12], and albumin had positive effects on eating quality. By contrast, long branch-chain amylopectin, long-chain amylopectin (DP 35-60), glutelin and prolamin had adverse effects on eating quality of rice. © 2020 Society of Chemical Industry.

Genetic diversity for starch quality and alkali spreading value in sorghum

Sorghum is an important food crop in many parts of Africa and Asia. Landraces of sorghum are known to exhibit variation in food quality traits including starch and protein content and composition. In this study, a panel of diverse sorghum breeding lines and 788 sorghum conversion (SC) lines representing the global germplasm diversity of the crop were evaluated for variation in starch quality based on alkali spreading value (ASV). A small number of genotypes with stable expression of the ASV+ phenotype across seasons were identified; mostly representing Nandyal types from India. Genetic studies showed the ASV+ phenotype was inherited as a recessive trait. Whole genome resequencing of ASV+ donor lines revealed SNPs in genes involved in starch biosynthesis. A genome wide association study (GWAS) identified a significant SNP associated with ASV near Sobic.010G273800, a starch branching enzyme I precursor, and Sobic.010G274800 and Sobic.010G275001, both annotated as glucosyltransferases. Physiochemical analyses of accessions with contrasting ASV phenotypes demonstrated an environment dependent lower starch gelatinization temperature (GT), amylose content of approximately 22%, and good gel consistency. The starch quality attributes of these lines could be valuable in food products that require good gel consistency and viscosity.

Genetic dissection of eating and cooking qualities in different subpopulations of cultivated rice (Oryza sativa L.) through association mapping

Background

Eating and cooking qualities (ECQs) of rice (Oryza sativa L.) determine consumer acceptance and the economic value of rice varieties. The starch physicochemical properties, i.e. amylose content, gel consistency, gelatinization temperature and pasting viscosity are important indices for evaluating rice ECQs. Genetic factors are required for development of rice varieties with excellent ECQs and association mapping is one of the promising approaches for discovering such associated genetic factors.

Results

A genome-wide association mapping was performed on a set of 253 non-glutinous rice accessions consisting of 83 indica and 170 japonica cultivated rice varieties through phenotyping for 11 ECQ traits in two consecutive years and genotyping with 210 polymorphic SSR and candidate-gene markers. These markers amplified 747 alleles with an average of 3.57 alleles per locus. The structure, phylogenetic relationship, and principal component analysis indicated a strong population differentiation between indica and japonica accessions and association mapping was thus undertaken within indica and japonica subpopulations. All traits showed a large phenotypic variation and highly significant phenotypic correlations were present between most of traits. A total of 33 and 30 loci were located for 11 ECQs in indica and japonica subpopulations respectively. Most of associated loci were overlapped with starch synthesis-related genes (SSRGs), and the Wx locus gathered 14 associated loci with the largest effects on amylose content, gel consistency and pasting viscosities. Eight subpopulation specific markers, RM588, Wx-(CT)_n, SSI and SBE1 for indica subpopulation and RM550, Wx^mp, SSIIa and SBE4 for japonica subpopulation, were identified, suggesting alleles of SSRGs showed the subspecific tendency. Nevertheless, allelic variation in SSIIa showed no tendency towards subspecies. One associated maker RM550 detected in japonica subpopulation for amylose content and pasting viscosity was verified a potential novel and stably expressed locus and could be selected for further fine mapping.

Conclusion

This study illustrated the potential for dissecting genetic factors of complex traits in domesticated rice subspecies and provided highly associated markers to facilitate marker-assisted selection for breeding high-quality indica or japonica rice varieties.

Breeding and biotechnological interventions for trait improvement: status and prospects

Present review describes the molecular tools and strategies deployed in the trait discovery and improvement of major crops. The prospects and challenges associated with these approaches are discussed. Crop improvement relies on modulating the genes and genomic regions underlying key traits, either directly or indirectly. Direct approaches include overexpression, RNA interference, genome editing, etc., while breeding majorly constitutes the indirect approach. With the advent of latest tools and technologies, these strategies could hasten the improvement of crop species. Next-generation sequencing, high-throughput genotyping, precision editing, use of space technology for accelerated growth, etc. had provided a new dimension to crop improvement programmes that work towards delivering better varieties to cope up with the challenges. Also, studies have widened from understanding the response of plants to single stress to combined stress, which provides insights into the molecular mechanisms regulating tolerance to more than one stress at a given point of time. Altogether, next-generation genetics and genomics had made tremendous progress in delivering improved varieties; however, the scope still exists to expand its horizon to other species that remain underutilized. In this context, the present review systematically analyses the different genomics approaches that are deployed for trait discovery and improvement in major species that could serve as a roadmap for executing similar strategies in other crop species. The application, pros, and cons, and scope for improvement of each approach have been discussed with examples, and altogether, the review provides comprehensive coverage on the advances in genomics to meet the ever-growing demands for agricultural produce.

Diversity analysis of starch physicochemical properties in 95 proso millet (Panicum miliaceum L.) accessions

In this study, 95 accessions of proso millet (Panicum miliaceum L.) were characterized for starch physicochemical properties, including apparent amylose content (AAC), gel textural properties, Rapid Visco Analyzer (RVA) pasting viscosity properties, thermal and retrogradation properties. Based on genotypic data, the genetic diversity and inter-relationship of these starch traits were analyzed. Diverse starch quality was found, for example, AAC ranged from 0 to 32.3%, gelatinization temperature (GT) varied from 71.5 to 79.0 ℃, and RVA profile showed distinct patterns among proso millet of different AAC types. Interestingly, high AAC proso millet usually had GT lower than that of low AAC proso millet, which is different from the findings in rice starch. Many starch traits were significantly correlated and most of the 18 tested traits could be classified as either AAC-related traits or GT-related traits. In summary, the information presented here will be useful for further development of proso millet products.

Genetic Analysis for Cooking and Eating Quality of Super Rice and Fine Mapping of a Novel Locus qGC10 for Gel Consistency

Rice (Oryza sativa L.) is an important cereal that provides food for more than half of the world's population. Besides grain yield, improving grain quality is also essential to rice breeders. Amylose content (AC), gelatinization temperature (GT) and gel consistency (GC) are considered to be three indicators for cooking and eating quality in rice. Using a genetic map of RILs derived from the super rice Liang-You-Pei-Jiu with high-density SNPs, we detected 3 QTLs for AC, 3 QTLs for GT, and 8 QTLs for GC on chromosomes 3, 4, 5, 6, 10, and 12. Wx locus, an important determinator for AC and GC, resided in one QTL cluster for AC and GC, qAC6 and qGC6 here. And a novel major QTL qGC10 on chromosome 10 was identified in both Lingshui and Hangzhou. With the BC₄F₂ population derived from a CSSL harboring the segment for qGC10 from 93-11 in PA64s background, it was fine mapped between two molecular markers within 181 kb region with 27 annotated genes. Quantitative real-time PCR results showed that eight genes were differentially expressed in endosperm of two parents. After DNA sequencing, only LOC_Os10g04900, which encodes a F-box domain containing protein, has 2 bp deletion in the exon of PA64s, resulting in a premature stop codon. Therefore, LOC_Os10g04900 is considered to be the most likely candidate gene for qGC10 associated with gel consistency. Identification of qGC10 provides a new genetic resource for improvement of rice quality.

Mutations in sorghum SBEIIb and SSIIa affect alkali spreading value, starch composition, thermal properties and flour viscosity

Seven novel alleles of SBEIIb and one allele of SSIIa co-segregated with the ASV phenotype and contributed to distinct starch quality traits important for food-processing applications. Sorghum is an important food crop for millions of people in Africa and Asia. Whole-genome re-sequencing of sorghum EMS mutants exhibiting an alkali spreading value (ASV) phenotype revealed candidate SNPs in Sobic.004G163700 and Sobic.010G093400. Comparative genomics identified Sobic.010G093400 as a starch synthase IIa and Sobic.004G163700 as a starch branching enzyme IIb. Segregation analyses showed that mutations in Sobic.010G093400 or Sobic.004G163700 co-segregated with the ASV phenotype. Mutants in SSIIa exhibited no change in amylose content but expressed lower final viscosity and lower starch gelatinization temperature (GT) than starches from non-mutant plants. The sbeIIb mutants exhibited significantly higher amylose levels and starch GT and lower viscosity compared to non-mutant starches and ssIIa mutants. Mutations in SBEIIb had a dosage-dependent effect on amylose content. Double mutants of sbeIIb and ssIIa resembled their sbeIIb parent in amylose content, starch thermal properties and viscosity profiles. These variants will provide opportunities to produce sorghum varieties with modified starch end-use qualities important for the beer brewing and baking industries and specialty foods for humans with diabetes.

Improving the Glossiness of Cooked Rice, an Important Component of Visual Rice Grain Quality

BACKGROUND

Rice is one of the few cereals consumed as a whole grain, and therefore the appearance of the final milled product, both before and after cooking, strongly influences the consumer's perception of product quality. Matching consumer preference for rice grain quality is a key component of rice variety development programs, as the quality drives demand, which in turn drives variety adoption, market price, and profitability. The quality of cooked rice is normally evaluated indirectly, through measurement of key elements driving quality as well as more directly by sensory evaluation, but remains a complex trait conditioned by the genetic complexity of factors driving quality, changes wrought by environment, and the complexity of consumer preferences.

RESULT

In this study, we evaluated 17 traits, including the taste value obtained by glossiness of cooked rice (TV), to explain rice eating quality by statistical methods and identified QTLs associated with TV. To explain the correlation among traits, exploratory factor analysis was performed for 2 years. The overall eating quality (OE) was correlated with TV and protein content loading at the same factor (PA1) in 2017, and there was a relationship between the OE (PA1) and the TV (PA2) in 2018 (PA1:PA2, r = 0.3). In QTL analysis using 174 RILs, three QTLs for TV derived from Wandoaengmi6 were detected on chromosomes 4, 6, and 9. The QTL qTV9 delimited within Id9007180 and 9,851,330 on chromosome 9 was detected in both years, explaining approximately 17% of the variation, on average. Through the use of fine mapping, qTV9 was delimited to an approximately 34-Kbp segment flanked by the DNA markers CTV9_9 and CTV9_13, and nine ORFs were listed in the target region as candidate genes associated with TV. In the evaluation of qTV9's effect on OE, the lines with qTV9 showed a significant increase in correlation coefficiency compared to the negative lines. These data will apply to functional analysis on the glossiness and the MAS breeding program to improve the eating quality of japonica as a donor line.

CONCLUSION

In this paper we report a number of QTL associated with changes in glossiness of cooked rice, and these may have utility in the development of MAS in breeding programs with a specific focus on cooked grain quality.

Genetic Variation of Physicochemical Properties and Digestibility of Foxtail Millet (Setaria italica) Landraces of Taiwan

Foxtail millet is considered a 'smart food' because of nutrient richness and resilience to environments. A diversity panel of 92 foxtail millet landraces preserved by Taiwan indigenous peoples containing amylose content (AC) in the range of 0.7% to 16.9% exhibited diverse physiochemical properties revealed by a rapid viscosity analyzer (RVA). AC was significantly correlated with 5 RVA parameters, and some RVA parameters were also highly correlated with one another. In comparison to rice, foxtail millet contained less starch (65.9-73.1%) and no significant difference in totals of resistant starch (RS), slowly digestible starch (SDS), hydrolysis index (HI), and expected glycemic index (eGI) according to in vitro digestibility assays of raw flour with similar AC. RS was significantly positively correlated with AC and four RVA parameters, cold paste viscosity (CPV), setback viscosity (SBV), peak time (PeT), and pasting temperature (PaT), implying that suitable food processing to alter physicochemical properties of foxtail millet might mitigate hyperglycemia. This investigation of pasting properties and digestibility of diverse foxtail millet germplasm revealed much variation and showed potential for multi-dimensional utilizations in daily staple food and food industries.

Integrating a genome-wide association study with a large-scale transcriptome analysis to predict genetic regions influencing the glycaemic index and texture in rice

Reliably generating rice varieties with low glycaemic index (GI) is an important nutritional intervention given the high rates of Type II diabetes incidences in Asia where rice is staple diet. We integrated a genome-wide association study (GWAS) with a transcriptome-wide association study (TWAS) to determine the genetic basis of the GI in rice. GWAS utilized 305 re-sequenced diverse indica panel comprising ~2.4 million single nucleotide polymorphisms (SNPs) enriched in genic regions. A novel association signal was detected at a synonymous SNP in exon 2 of LOC_Os05g03600 for intermediate-to-high GI phenotypic variation. Another major hotspot region was predicted for contributing intermediate-to-high GI variation, involves 26 genes on chromosome 6 (GI6.1). These set of genes included GBSSI, two hydrolase genes, genes involved in signalling and chromatin modification. The TWAS and methylome sequencing data revealed cis-acting functionally relevant genetic variants with differential methylation patterns in the hot spot GI6.1 region, narrowing the target to 13 genes. Conversely, the promoter region of GBSSI and its alternative splicing allele (G allele of Wxa ) explained the intermediate-to-high GI variation. A SNP (C˃T) at exon-10 was also highlighted in the preceding analyses to influence final viscosity (FV), which is independent of amylose content/GI. The low GI line with GC haplotype confirmed soft texture, while other two low GI lines with GT haplotype were characterized as hard and cohesive. The low GI lines were further confirmed through clinical in vivo studies. Gene regulatory network analysis highlighted the role of the non-starch polysaccharide pathway in lowering GI.

The qSAC3 locus from indica rice effectively increases amylose content under a variety of conditions

BACKGROUND

Amylose content (AC) is a critical factor for the quality of rice. It is determined by the biosynthesis gene Waxy (Wx) and a variety of quantitative trait loci (QTLs). Although many QTLs have been reported to affect rice AC, few of them have been investigated under varying growth conditions, especially various temperatures, which are known to greatly influence the AC.

RESULTS

We analyzed the AC at different temperatures and planting seasons in a set of chromosome segment substitution lines (CSSLs) which were derived from a cross between the indica variety 9311 and the japonica variety Nipponbare carrying the same Wx^b allele. A joint analysis detected a single locus, qSAC3, with a high logarithm of odds (LOD) score in four different conditions. The qSAC3 from indica 9311 (qSAC3^ind) substantially increased the AC in japonica Nipponbare under all tested growth conditions. Furthermore, introducing the qSAC3^ind into the soft rice variety Nangeng9108 with Wx^mq, a mutant allele of Wx^b, also moderately increased its AC and improved its appearance quality significantly by reducing the chalkiness of the polished rice.

CONCLUSIONS

Our results indicate that the qSAC3^ind could increase the AC of japonica rice in different environments as well as in the background of different Wx alleles and that qSAC3 is a valuable locus for fine-tuning the rice AC and ameliorating the dull endosperm in rice varieties with the Wx^mq allele.

QTL-seq identifies cooked grain elongation QTLs near soluble starch synthase and starch branching enzymes in rice (Oryza sativa L.)

Grain quality is one of the main targets that rice breeders focus on to improve elite rice varieties. Several characteristics are considered when determine rice grain quality, such as aroma, amylose content (AC), gelatinization temperature (GT) and, especially, lengthwise grain elongation (GE). GE is a desirable feature in premium rice of high quality, such as India and Pakistan’ Basmati. Inheritance of GE in rice has not been clearly elucidated due to its complex and inconsistent pattern. In this study, we identified QTLs for GE in rice using bulk-segregant analysis (BSA) and whole-genome sequencing based on an F₂ population segregated for GE as well as AC and GT. We identified two QTLs on chromosome 6, qGE6.1 and qGE6.2, and another QTL on chromosome 4, qGE4.1. qGE6.1 and qGE6.2 were located near starch synthase IIa (SSIIa) and starch branching enzyme III (SBEIII), respectively, and qGE4.1 was located near starch branching enzyme IIa (SBEIIa). qGE6.1 was considered to be the major QTL for GE based on this population, and SSIIa was suggested to be the best candidate gene associated with the GE trait. The results of this study may be useful for breeding rice with increased grain elongation and different starch properties.

Favorable alleles mining for gelatinization temperature, gel consistency and amylose content in Oryza sativa by association mapping

Background

Improving the gelatinization temperature (GT), gel consistency (GC) and amylose content (AC) for parental grain eating and cooking qualities (ECQs) are key factors for enhancing average grain ECQs for hybrid japonica rice.

Results

In this study, a genome-wide association mapping (GWAS) for ECQs was performed on a selected sample of 462 rice accessions in 5 environments using 262 simple sequence repeat markers. We identified 10 loci and 27 favorable alleles for GT, GC and AC, and some of these loci were overlapped with starch synthesis-related genes. Four SSR loci for the GT trait were distributed on chromosomes 3, 5, 8, and 9, of which two SSR loci were novel. Two SSR loci associated with the GC trait were distributed on chromosomes 3 and 6, although only one SSR locus was novel. Four SSR loci associated with the AC trait were distributed on chromosomes 3, 6, 10, and 11, of which three SSR loci were novel. The novel loci RM6712 and RM6327 were simultaneously identified in more than 2 environments and were potentially reliable QTLs for ECQs, with 15 parental combinations being predicted. These QTLs and parental combinations should be used in molecular breeding to improve japonica rice average ECQs.

Conclusions

Among the 10 SSR loci associated with GT, GC and AC for grain ECQs detected in 27 favorable alleles, the favorable allele RM3600-90bp on chromosome 9 could significantly reduce GT, RM5753-115bp on chromosome 6 could significantly increase GC, and RM6327-230bp on chromosome 11 could significantly reduce AC in hybrid japonica rice mixed rice samples.

Electronic supplementary material

The online version of this article (10.1186/s12863-019-0735-y) contains supplementary material, which is available to authorized users.

Detection of stable QTLs for grain protein content in rice (Oryza sativa L.) employing high throughput phenotyping and genotyping platforms

Lack of appropriate donors, non-utilization of high throughput phenotyping and genotyping platforms with high genotype × environment interaction restrained identification of robust QTLs for grain protein content (GPC) in rice. In the present investigation a  BC₃F₄ mapping population was developed using grain protein donor, ARC10075 and high-yielding cultivar Naveen and 190 lines were genotyped using 40 K Affimetrix custom SNP array with the objective to identify stable QTLs for protein content. Three of the identified QTLs, one for GPC (qGPC1.1) and the other two for single grain protein content (qSGPC2.1, qSGPC7.1) were stable over the environments explaining  13%, 14% and 7.8% of the phenotypic variances, respectively. Stability and repeatability of these additive QTLs were supported by the synergistic additive effects of multi-environmental-QTLs. One epistatic-QTL, independent of  the  main effect QTL was detected over the environment for SGPC. A few functional genes governing seed storage protein were hypothesised inside these identified QTLs. The qGPC1.1 was validated by NIR Spectroscopy-based high throughput phenotyping in BC₃F₅ population. Higher glutelin content was estimated in high-protein lines with the introgression of qGPC1.1 in telomeric region of short arm of chromosome 1. This was supported by the postulation of probable candidate gene inside this QTL region encoding glutelin family proteins.

Applications of the CRISPR/Cas9 System for Rice Grain Quality Improvement: Perspectives and Opportunities

Grain quality improvement is a key target for rice breeders, along with yield. It is a multigenic trait that is simultaneously influenced by many factors. Over the past few decades, breeding for semi-dwarf cultivars and hybrids has significantly contributed to the attainment of high yield demands but reduced grain quality, which thus needs the attention of researchers. The availability of rice genome sequences has facilitated gene discovery, targeted mutagenesis, and revealed functional aspects of rice grain quality attributes. Some success has been achieved through the application of molecular markers to understand the genetic mechanisms for better rice grain quality; however, researchers have opted for novel strategies. Genomic alteration employing genome editing technologies (GETs) like clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) for reverse genetics has opened new avenues of research in the life sciences, including for rice grain quality improvement. Currently, CRISPR/Cas9 technology is widely used by researchers for genome editing to achieve the desired biological objectives, because of its simple targeting. Over the past few years many genes that are related to various aspects of rice grain quality have been successfully edited via CRISPR/Cas9 technology. Interestingly, studies on functional genomics at larger scales have become possible because of the availability of GETs. In this review, we discuss the progress made in rice by employing the CRISPR/Cas9 editing system and its eminent applications. We also elaborate possible future avenues of research with this system, and our understanding regarding the biological mechanism of rice grain quality improvement.

Phenotypic and molecular dissection of grain quality using the USDA rice mini-core collection

Grain quality is a major breeding objective and paramount to food production. This study was aimed to phenotypically and molecularly dissect the rice grain quality, especially amylose content (AC), grain protein content (GPC) and alkali spreading value (ASV), using the USDA rice mini-core collection representing the world-wide rice germplasm lines. Grain chemical analysis combined with genome-wide association study (GWAS) was used for the study. A wide genetic variation was observed for these grain quality traits in the mini-core collection. Germplasm lines unique in AC, GPC and ASV and desirable for grain quality improvement were identified. The genetic diversity of the collection was re-analyzed using new SNPs, thus providing a more precise genotypic information about the collection. Furthermore, ten loci significantly associated with these grain quality traits were identified through GWAS using 22947 high-quality SNPs. These results, therefore, provide knowledge, resources and molecular tools for efficient rice grain quality improvement.

Effects of Wx and Its Interaction With SSIII-2 on Rice Eating and Cooking Qualities

The Wx gene encodes a granule-bound starch synthase (GBSS) and plays a key role in determining rice eating and cooking qualities (ECQs). SSIII-2 (SSIIIa), a member of the soluble starch synthases, is responsible for the synthesis of long chains of amylopectin. To investigate the effects of Wx and its interaction with SSIII-2 on grain ECQs, a population from a hybrid combination was established as a research material. The genotypes of SSIII-2 and the single nucleotide polymorphisms (SNPs) on intron1, exon6, and exon10 of Wx, and the physicochemical indicators and rapid visco analyzer (RVA) profile characteristics were analyzed. The results revealed various effects of SSIII-2 on rice quality under different backgrounds of Wx alleles. There was no obvious difference between different SSIII-2 alleles under the same background of Wx^a , whereas there was a significant diversity under the same background of Wx^b . Wx^a had a dominant epistasis to SSIII-2 because the effect of SSIII-2 was masked by the massive synthesis of GBSS under Wx^a . The apparent amylose content (AAC) was mainly controlled by the In1G/T SNP, and rice gel consistency (GC) was regulated by the Ex10C/T SNP. The combined effects of three SNPs had a significant influence on all ECQs and RVA profile parameters, except for gelatinization temperature. In1T-Ex6A-Ex10C and In1T-Ex6A-Ex10T were classified as being low AAC type. TT-AA-CC and TT-AA-TT had a low AAC and a soft GC. The combined effects of different SNPs of Wx are very important for rice quality breeding.

QTL Identification for Cooking and Eating Quality in indica Rice Using Multi-Parent Advanced Generation Intercross (MAGIC) Population

Association mapping using a multi-parent advanced generation intercross (MAGIC) population provides a promising tool in genetic dissection of rice cooking and eating quality (CEQ). In this study, QTLs were identified for ten physicochemical properties related to CEQ using 508 F₆ MAGIC lines. The whole population and eight founder lines were genotyped with 6K Illumina Infinium HD Assay. All traits had high heritability estimates and showed a large genetic variation in the MAGIC population. Highly significant phenotypic correlations were present between traits. AC was significantly positively correlated with PKT, TV, FV, SBV, PKT, and RT but significantly negatively correlated with GC and BDV. Seventeen QTLs were identified for all traits. GBSSI locus was hosted or closely to nine QTLs, qAC6, qGC6.1, qPKT6.1, qPKV6, qBDV6.1, qTV6.1, qFV6, qSBV6, and qRT6, suggesting that GBSSI impacts the overall CEQ. Another locus closed to SSIIa, located at 6.99 Mb, affects five traits, GC, PKT, BDV, SBV, and PT. The identified QTLs revealed small to modest effects where the highest percentage of phenotypic variance explained was 17.18%. These QTLs are directly relevant and useful in breeding for CEQ in indica rice. These results also confirmed that QTL mapping via association mapping using a MAGIC population is a powerful method in genetic analysis of complex traits.

Genome-wide and gene-based association mapping for rice eating and cooking characteristics and protein content

Rice eating and cooking quality and protein content (PC) are important properties affecting consumers' preferences, nutrition and health. Linkage QTL mapping and association studies are usually applied to genetically dissect related traits, which could be further facilitated by high density SNP markers and gene annotation based on reference genome to rapid identify candidate genes associated with interested traits. Here, we carried out an association study for apparent amylose content (AC), gel consistency (GC), gelatinization temperature (GT) and PC evaluated in two environments using a diverse panel of 258 accessions from 3 K Rice Genome Project. Wide phenotypic variations were observed in this panel. Genome-wide association study using 22,488 high quality SNPs identified 19 QTL affecting the four traits. Combining gene-based association study and haplotype analyses plus functional annotation allowed us to shortlist nine candidate genes for four important QTL regions affecting AC, GC and GT, including two cloned genes (Wx and ALK), and seven novels. The research suggested that GWAS and gene-based association analysis followed by haplotype analysis is an effective way to detect candidate genes. The identified genes and QTL provided valuable sources for future functional characterization and genetic improvement of rice eating and cooking quality and PC.

Identification of putative markers linked to grain plumpness in rice (Oryza sativa L.) via association mapping

BACKGROUND

Poor grain plumpness (GP) is one of the main constraints to reaching the yield potential of hybrid rice.

RESULTS

In this study, the GP of 177 rice varieties was investigated in three locations across 2 years. By combining the genotype data of 261 simple sequence repeat (SSR) markers, association mapping was conducted to identify the marker-GP association loci. Among 31 marker-GP association loci detected in two or more environments and determined using general linear model (GLM) analyses, seven association loci were also detected using mixed linear model (MLM) analyses. The seven common loci detected by the two analytical methods were located on chromosomes 2, 3 (2), 7, 8 and 12 (2) and explained 7.24~22.28% of the variance. Of these 7 association loci, five markers linked to GP were newly detected: RM5340 on Chr2, RM5480 and RM148 on Chr3, RM1235 on Chr8, and RM5479 on Chr12.

CONCLUSIONS

Five marker-GP association loci were newly detected using both the GLM and MLM analytical methods. Elite allele RM505-170 bp had the highest average phenotypic effect on increasing the GP, and the typical carrier variety was 'Maozitou'. Based on the distribution of the elite alleles among the carrier varieties, the top 10 parental combinations for improving the GP in rice via cross-breeding were predicted.

Association Analysis of Markers Derived from Starch Biosynthesis Related Genes with Starch Physicochemical Properties in the USDA Rice Mini-Core Collection

Rice eating and cooking quality is largely determined by starch physicochemical properties. The diverse accessions in the USDA rice mini-core collection (URMC) facilitate extensive association analysis of starch physicochemical properties with molecular markers specific to starch biosynthesis related genes. To identify significant trait-marker associations that can be utilized in rice breeding programs for improved starch quality, we conducted two association analyses between 26 molecular markers derived from starch biosynthesis related genes and 18 parameters measured of starch physicochemical properties in two sets of the mini-core accessions successfully grown in two environments in China. Many significant trait-marker associations (P < 0.001) were detected in both association analyses. Five markers of Waxy gene, including the (CT)n repeats, the G/T SNP of intron 1, the 23 bp sequence duplication (InDel) of exon 2, the A/C SNP of exon 6, and the C/T SNP of exon 10, were found to be primarily associated with starch traits related to apparent amylose content (AAC), and two markers targeting the 4,329-4,330 bp GC/TT SNPs and 4,198 bp G/A SNP of SSIIa gene were mainly associated with traits related to gelatinization temperature (GT). Two new haplotypes were found in the mini-core collection based on the combinations of the 23 bp InDel and three SNPs (G/T of intron 1, A/C of exon 6, and C/T of exon 10) of Waxy gene. Furthermore, our analyses indicated that the (CT)n polymorphisms of Waxy gene had a non-negligible effect on AAC related traits, as evidenced by significant variation in AAC related traits among rice accessions with the same Waxy SNPs but different (CT) n repeats. As the five Waxy markers and the two SSIIa markers showed consistent major effects on starch quality traits across studies, these markers should have priority for utilization in marker-assisted breeding.

Relationship of Rice Grain Amylose, Gelatinization Temperature and Pasting Properties for Breeding Better Eating and Cooking Quality of Rice Varieties

A total of 787 non-waxy rice lines– 116 hybrids and 671 inbreds–were used to study the apparent amylose content (AAC), gelatinization temperature (GT), and rapid visco analyzer (RVA) pasting viscosity properties of rice starch to understand their importance in breeding better rice varieties. The investigated traits showed a wide range of diversity for both hybrid (HG) and inbred (IG) groups. The combinations of the different categories of AAC and GT were random in HG but were non-random in IG. For inbred lines, the high level of AAC tended to combine with the low level of GT, the intermediate level of AAC tended to have high or intermediate GT, and the low level of AAC tended to have high or low GT. Some stable correlations of the AAC, GT, and RVA properties may be the results derived from the physicochemical relationships among these traits, which rice breeders could utilize for selection in advanced breeding generations. Through cluster analysis, IG and HG were divided into 52 and 31 sub-clusters, respectively. Identifying the cultivars having AAC, GT, and RVA properties similar to that of popular high-quality rice varieties seems to be an interesting strategy and could be directly used for adaptation trials to breed high-quality rice varieties in targeted areas in a more customized manner.

QTL Mapping of Grain Quality Traits Using Introgression Lines Carrying Oryza rufipogon Chromosome Segments in Japonica Rice

BACKGROUND

Improved eating quality is a major breeding target in japonica rice due to market demand. Consequently, quantitative trait loci (QTL) for glossiness of cooked rice and amylose content associated with eating quality have received much research focus because of their importance in rice quality.

RESULTS

In this study, QTL associated with 12 grain quality traits were identified using 96 introgression lines (IL) of rice developed from an interspecific cross between the Korean elite O. sativa japonica cultivar 'Hwaseong' and O. rufipogon over 7 years. QTL analyses indicated that QTL qDTH6 for heading date, detected on chromosome 6 is associated with variance in grain traits. Most QTLs detected in this study clustered near the qDTH6 locus on chromosome 6, suggesting the effect of qDTH6. O. rufipogon alleles negatively affected grain quality traits except for a few QTLs, including qGCR9 for glossiness of cooked rice on chromosome 9. To characterize the effect of the O. rufipogon locus harboring qGCR9, four lines with a single but different O. rufipogon segment near qGCR9 were compared to Hwaseong. Three lines (O. rufipopgon ILs) having O. rufipogon segment between RM242 and RM245 in common showed higher glossiness of cooked rice than Hwaseong and the other line (Hwaseong IL), indicating that qGCR9 is located in the 3.4-Mb region between RM242 and RM245. Higher glossiness of cooked rice conferred by the O. rufipogon allele might be associated with protein content considering that three lines had lower protein content than Hwaseong (P < 0.1). These three O. rufipogon ILs showed higher yield than Hwaseong and Hwaseong IL due to increase in spikelets per panicle and grain weight indicating the linkage of qGCR9 and yield component QTLs.

CONCLUSION

The qGCR9 locus is of particular interest because of its independence from other undesirable grain quality traits in O. rufipogon. SSR markers linked to qGCR9 can be used to develop high-quality japonica lines and offer a starting point for map-based cloning of genes underlying this trait. To our knowledge, this is the first report to map a beneficial QTL for glossiness of cooked rice from a wild rice, O. rufipogon.

A Novel FC116/BC10 Mutation Distinctively Causes Alteration in the Expression of the Genes for Cell Wall Polymer Synthesis in Rice

We report isolation and characterization of a fragile culm mutant fc116 that displays reduced mechanical strength caused by decreased cellulose content and altered cell wall structure in rice. Map-based cloning revealed that fc116 was a base substitution mutant (G to A) in a putative beta-1,6-N-acetylglucosaminyltransferase (C2GnT) gene (LOC_Os05g07790, allelic to BC10). This mutation resulted in one amino acid missing within a newly-identified protein motif "R, RXG, RA." The FC116/BC10 gene was lowly but ubiquitously expressed in the all tissues examined across the whole life cycle of rice, and slightly down-regulated during secondary growth. This mutant also exhibited a significant increase in the content of hemicelluloses and lignins, as well as the content of pentoses (xylose and arabinose). But the content of hexoses (glucose, mannose, and galactose) was decreased in both cellulosic and non-cellulosic (pectins and hemicelluloses) fractions of the mutant. Transcriptomic analysis indicated that the typical genes in the fc116 mutant were up-regulated corresponding to xylan biosynthesis, as well as lignin biosynthesis including p-hydroxyphenyl (H), syringyl (S), and guaiacyl (G). Our results indicate that FC116 has universal function in regulation of the cell wall polymers in rice.

Genome-wide association study of eating and cooking qualities in different subpopulations of rice (Oryza sativa L.)

Background

Starch and protein are two major components of polished rice, and the amylose and protein contents affect eating and cooking qualities (ECQs). In the present study, genome-wide association study with high-quality re-sequencing data was performed for 10 ECQs in a panel of 227 non-glutinous rice accessions and four derived panels.

Results

Population structure accounted for high phenotypic variation in three routine panels and had minor effects on subspecies-based panels. Using the mixed linear model method based on the P + K model, we detected 29, 24, 16, 17, and 29 loci that were significant for ECQ parameters in each of the five panels. Some of these loci were close to starch synthesis-related genes. Two quantitative trait loci (QTLs) (chr.9: 15417525 ~ 15474876; 17538294 ~ 18443016) for several starch paste viscosity properties detected in four panels were close to the isoamylase 3 gene, one QTL (chr.1: 30627943 ~ 31668474) for consistency detected in three panels was close to the starch synthase IV-1 gene. The QTL (chr.7: 1118122 ~ 1967247) for breakdown (BD), detected in the whole panel and japonica panel, and one QTL (chr.7: 25312126 ~ 26540950) for BD and setback (SB), detected in the whole panel and indica panel, may be specific gene alleles in japonica or indica panels. One previously detected QTL (chr.11: 22240707 ~ 22563596) for protein content and one new QTL (chr.5: 7756614 ~ 8042699) for many ECQ traits detected in more than two panels, may represent valuable targets for future cloning of the underlying genes.

Conclusions

This study detected minor-effect QTLs affecting ECQs, and may increase our understanding of the genetic differences regulating the formation of ECQ between indica and japonica varieties.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3000-z) contains supplementary material, which is available to authorized users.

Breeding high-yield superior quality hybrid super rice by rational design

The challenge of meeting the increasing demand for worldwide rice production has driven a sustained quest for advances in rice breeding for yield. Two breakthroughs that led to quantum leaps in productivity last century were the introduction of semidwarf varieties and of hybrid rice. Subsequent gains in yield have been incremental. The next major leap in rice breeding is now upon us through the application of rational design to create defined ideotypes. The exploitation of wide-cross compatibility and intersubspecific heterosis, combined with rapid genome sequencing and the molecular identification of genes for major yield and quality traits have now unlocked the potential for rational design.