Physicochemical characteristics of tea seed starches from twenty-five cultivars

The physicochemical features of starches separated from tea seeds of 25 cultivars were analyzed. The distinct characteristic of tea seed starches was that they had high apparent amylose content (AAC, 28.94-39.91 %) and resistant starch contents (4.64-8.24 %), suggesting that tea starch can be used for production of low glycemic index food. One cultivar (T12) had smallest breakdown (74.2 RVU) and highest gel hardness, indicating it performed stably during shear thinning, resulting in a firm texture. Another cultivar (T25) had a peak viscosity of 417.6 RVU, a large breakdown and small setback, suggesting a low tendency for retrogradation. There was a range of 61.6 °C to 77.5 °C for the peak gelatinization temperature and 0.163 to 0.390 for the flow behavior index values. These parameters could serve for selecting suitable starches with minor differences in physicochemical properties for food use. Correlation analysis indicated that AAC is a key factor determining starch retrogradation properties. The broad genetic diversity in the tea seed starch physicochemical features provided potentially versatile applications in the food industry. The results gained from the present study contribute to a better understanding of tea seed starch quality, and encourage its application in many value-added food products.

Improving rice eating and cooking quality by enhancing endogenous expression of a nitrogen-dependent floral regulator

Improving rice eating and cooking quality (ECQ) is one of the primary tasks in rice production to meet the rising demands of consumers. However, improving grain ECQ without compromising yield faces a great challenge under varied nitrogen (N) supplies. Here, we report the approach to upgrade rice ECQ by native promoter-controlled high expression of a key N-dependent floral and circadian clock regulator Nhd1. The amplification of endogenous Nhd1 abundance alters rice heading date but does not affect the entire length of growth duration, N use efficiency and grain yield under both low and sufficient N conditions. Enhanced expression of Nhd1 reduces amylose content, pasting temperature and protein content while increasing gel consistence in grains. Metabolome and transcriptome analyses revealed that increased expression of Nhd1 mainly regulates the metabolism of carbohydrates and amino acids in the grain filling stage. Moreover, expression level of Nhd1 shows a positive relationship with grain ECQ in some local main cultivars. Thus, intensifying endogenous abundance of Nhd1 is a promising strategy to upgrade grain ECQ in rice production.

Understanding the Relationship between the Molecular Structure and Physicochemical Properties of Soft Rice Starch

The relationship between the molecular structure and physicochemical properties of soft rice starch (SRS) has been investigated in this research. The amylose content of SRS ranged from 10.76% to 11.85%, classified as the very low amylose type. Compared to waxy and japonica rice starch, the largest amount of small starch granules and the highest viscosity were shown in the SRS. The results of X-ray diffraction and Fourier transform infrared proved that the SRS depicted a typical A-type pattern with a low short-range ordered structure. Additionally, SRS had a great deal of A and B1 chains. Molecular weights and density of starch from soft rice were lower than those from waxy rice but higher than those from japonica rice. Furthermore, SRS possessed a higher amount of resistant starch. Correlation analysis indicated that the amylose content and the chain-length distributions of amylopectin play a major role in influencing the molecular structure and physicochemical properties of rice starch. In conclusion, the low amylose content, highest viscosity, and other excellent properties of soft rice starch make it have bright application prospects in instant rice and rice cakes.

Differences in grain protein content and regional distribution of 706 rice accessions

BACKGROUND

Improving rice quality is one of the main goals of global rice breeding programs, and rice protein content is one of the most important factors affecting rice eating quality. The protein content of rice is mainly determined by genetic factors and also affected by environmental factors. However, the differences and regional distribution of protein content during the evolution of different rice varieties are still unclear.

RESULTS

The purpose of this study was to understand the differences in grain protein content of 706 rice accessions in different regions and different rice subtypes. The influencing factors of grain protein content differences were analyzed from the perspectives of genetic characteristics, environment, rice subtypes, and breeding process. The results showed that the grain protein content of indica rice in most countries and regions was higher than that of japonica rice. From the perspective of the rice breeding process, the protein content of modern varieties in japonica was lower than that of landrace varieties. In most countries, modern varieties of indica rice had higher protein content than landrace varieties did.

CONCLUSION

The environment and genetic characteristics caused the change in the protein content of rice. This study has improved our understanding of the differences in protein content of rice from different rice varieties. © 2022 Society of Chemical Industry.

Combined Effects of BEIIb and SSIIa Alleles on Amylose Contents, Starch Fine Structures and Physicochemical Properties of Indica Rice

Starch branching enzyme IIb (BEIIb) and soluble starch synthase IIa (SSIIa) play important roles in starch biosynthesis in cereals. Deficiency in the BEIIb gene produces the amylose extender (ae) mutant rice strain with increased amylose content (AC) and changes in the amylopectin structure. The SSIIa gene is responsible for the genetic control of gelatinization temperature (GT). The combined effects of BEIIb and SSIIa alleles on the AC, fine structures, and physicochemical properties of starches from 12 rice accessions including 10 recombinant inbred lines (RIL) and their two parents were examined in this study. Under the active BEIIb background, starches with the SSIIa-GC allele showed a higher GT than those with the SSIIa-TT allele, resulting from a lower proportion of A chain and a larger proportion of B1 chains in the amylopectin of SSIIa-GC. However, starch with the BEIIb mutant allele (be2b) in combination with any SSIIa genotype displayed more amylose long chains, higher amylose content, B2 and B3 chains, and molecular order, but smaller relative crystallinity and proportion of amylopectin A and B1 chains than those with BEIIb, leading to a higher GT and lower paste viscosities. These results suggest that BEIIb is more important in determining the structural and physicochemical properties than SSIIa. These results provide additional insights into the structure-function relationship in indica rice rather than that in japonica rice and are useful for breeding rice with high amylose content and high resistant starch.

Combined Effects of Different Alleles of FLO2, Wx and SSIIa on the Cooking and Eating Quality of Rice

The improvement of the cooking and eating quality (CEQ) of rice is one of the major objectives of current rice-breeding programs. A few major genes such as Waxy (Wx) and starch synthase IIa (SSIIa) have been successfully applied in molecular breeding. However, their interactive effects on CEQ have not been fully understood. In this study, a recombinant inbred line (RIL) population was constructed by crossing the white-core mutant GM645 with the transparent phenotype of the japonica rice variety Tainung 67 (TN67). GM645 and TN67 contain different alleles of FLOURY ENDOSPERM2 (FLO2), Wx, and SSIIa. The effects of different allele combinations of FLO2, Wx, and SSIIa on the CEQ of rice were investigated. The inbred lines with the mutation allele flo2 had a significantly lower apparent amylose content (AAC), viscosity characteristics except for setback (SB), and gel texture properties compared to those lines with the FLO2 allele. The allelic combination of FLO2 and Wx significantly affected the AAC, breakdown (BD), and gel textural properties, which could explain most of the variations in those rice quality traits that were correlated with AAC. The allelic combination of FLO2 and SSIIa significantly affected the hot paste viscosity (HPV) and pasting temperature (PT). The Wx × SSIIa interaction had a significant effect on the PT. The interaction of FLO2, Wx and SSIIa significantly affected the AAC, cold paste viscosity (CPV), PT, and consistency viscosity (CS). These results highlight the important roles of these quality-related genes in regulating the CEQ of rice and provide new clues for rice-quality improvement by marker-assisted selection.

Combined Effect of Nitrogen Fertilizer Application and High Temperature on Grain Quality Properties of Cooked Rice

Ambient temperature and nitrogen (N) fertilizer are two of the most important factors that affect rice grain quality. However, less information has been available on the interactive effect of N fertilizer and ambient temperature on grain quality under stressful high temperature (HT). In this article, the effects of panicle N fertilizer, ambient temperature, and their interaction on starch composition, particle size distribution of starch granules, starch physicochemical properties, and storage protein accumulation in milled grains were investigated to clarify the potential role of panicle N fertilizer topdressing in regulating rice grain quality under stressful HT by using a two-factor experiment of three N levels in combination with two temperature regimes. Results showed that appropriate application of panicle N fertilizer could attenuate the adverse effect of HT during grain filling on milling quality and chalky occurrence to some extent, particularly for the effective alleviation of HT-induced decrease in milling quality. However, the topdressing of panicle N fertilizer tended to enhance starch gelatinization enthalpy (ΔH) and its setback viscosity in HT-ripening grains, with the simultaneous decrements in the number and surface area proportions of smaller starch granules under the higher N fertilizer in combination with HT exposure. The effects of higher nitrogen fertilizer and HT exposure on total protein content and gluten composition of grains were additively increased. Hence, the topdressing of panicle N fertilizer exacerbated HT-induced deterioration in cooking and eating quality, rather than alleviating the negative impact of HT exposure on the palatability of cooked rice.

Mapping combined with principal component analysis identifies excellent lines with increased rice quality

Quality-related traits are some of the most important traits in rice, and screening and breeding rice lines with excellent quality are common ways for breeders to improve the quality of rice. In this study, we used 151 recombinant inbred lines (RILs) obtained by crossing the northern cultivated japonica rice variety ShenNong265 (SN265) with the southern indica rice variety LuHui99 (LH99) and simplified 18 common rice quality-related traits into 8 independent principal components (PCs) by principal component analysis (PCA). These PCs included peak and hot paste viscosity, chalky grain percentage and chalkiness degree, brown and milled rice recovery, width length rate, cooked taste score, head rice recovery, milled rice width, and cooked comprehensive score factors. Based on the weight ratio of each PC score, the RILs were classified into five types from excellent to poor, and five excellent lines were identified. Compared with SN265, these 5 lines showed better performance regarding the chalky grain percentage and chalkiness degree factor. Moreover, we performed QTL localization on the RIL population and identified 94 QTLs for quality-related traits that formed 6 QTL clusters. In future research, by combining these QTL mapping results, we will be using backcrossing to aggregate excellent traits and achieve quality improvement of SN265.

Kam Sweet Rice (Oryza sativa L.) Is a Special Ecotypic Rice in Southeast Guizhou, China as Revealed by Genetic Diversity Analysis

Kam Sweet Rice (KSR) is a special kind of rice landrace that has been domesticated for thousands of years by the local Dong people in southeast Guizhou province, China. KSR has many distinguishing characteristics including strong fragrance; high resistance to diseases, pests, and adverse abiotic conditions; difficulty of threshing; and glutinous texture. There is a lack of systematic research on its genetic diversity. In this study, we analyzed the levels and patterns of genetic diversity and nucleotide variation in 1,481 rice germplasm using simple sequence repeat (SSR) markers and single nucleotide polymorphism (SNP) haplotype analysis of six unlinked nuclear loci. The accessions included 315 KSR resources from southeast Guizhou, 578 rice landraces from six rice-growing ecological zones in Guizhou, 546 rice landraces from nine provinces around Guizhou, and 42 wild rice sources. Genetic diversity and heterozygosity of KSR were both low, and thus KSR might be close to a pure rice line. Population structure analysis showed that KSR was isolated into a single type of rice, which had a large genetic distance and a unique genetic background compared to the local varieties in Guizhou province, indicating that KSR is a special rice ecotype. Haplotype analysis of the target genes showed that the population of KSR was rich in haplotypes for resistance to bacterial blight (Xa23) and rice blast (Pid3), and identified unique haplotypes that were different from those of the six rice ecotypes in Guizhou. This study shows that KSR is an excellent rice germplasm resource, provides important information for the improvement and utilization of rice landraces, and serves as a reference for formulating effective rice conservation measures.

Haplotype Variations and Evolutionary Analysis of the Granule-Bound Starch Synthase I Gene in the Korean World Rice Collection

Granule-bound starch synthase I (GBSSI) is responsible for Waxy gene encoding the, which is involved in the amylose synthesis step of starch biosynthesis. We investigated the genotypic and haplotypic variations of GBSSI (Os06g0133000) gene, including its evolutionary relatedness in the nucleotide sequence level using single-nucleotide polymorphisms (SNPs), indels, and structural variations (SVs) from 475 Korean World Rice Collection (KRICE_CORE), which comprised 54 wild rice and 421 cultivated represented by 6 ecotypes (temperate japonica, indica, tropical japonica, aus, aromatic, and admixture) or in another way by 3 varietal types (landrace, weedy, and bred). The results revealed that 27 of 59 haplotypes indicated a total of 12 functional SNPs (fSNPs), identifying 9 novel fSNPs. According to the identified novel fSNPs, we classified the entire rice collection into three groups: cultivated, wild, and mixed (cultivated and wild) rice. Five novel fSNPs were localized in wild rice: four G/A fSNPs in exons 2, 9, and 12 and one T/C fSNP in exon 13. We also identified the three previously reported fSNPs, namely, a G/A fSNP (exon 4), an A/C fSNP (exon 6), and a C/T fSNP (exon 10), which were observed only in cultivated rice, whereas an A/G fSNP (exon 4) was observed exclusively in wild rice. All-against-all comparison of four varietal types or six ecotypes of cultivated rice with wild rice showed that the GBSSI diversity was higher only in wild rice (π = 0.0056). The diversity reduction in cultivated rice can be useful to encompass the origin of this gene GBSSI during its evolution. Significant deviations of positive (wild and indica under balancing selection) and negative (temperate and tropical japonica under purifying selection) Tajima's D values from a neutral model can be informative about the selective sweeps of GBSSI genome insights. Despite the estimation of the differences in population structure and principal component analysis (PCA) between wild and subdivided cultivated subgroups, an inbreeding effect was quantified by F _ST statistic, signifying the genetic relatedness of GBSSI. Our findings of a novel wild fSNPS can be applicable for future breeding of waxy rice varieties. Furthermore, the signatures of selective sweep can also be of informative into further deeper insights during domestication.

Dissecting the meteorological and genetic factors affecting rice grain quality in Northeast China

Background

The Northeast Plain of China, which is an important region for the production of high grain quality rice in China. However, the grain quality of the rice produced varies across this region, even for the same cultivar.

Objective

In order to explore the meteorological factors that have the greatest influence on quality and the transcriptional level differences between different cultivars and different locations at grain filling stage.

Methods

We grew eight rice cultivars in three locations in Northeast China during two growing seasons (2017 and 2018). We recorded meteorological conditions, including air temperature, air temperature range, and photosynthetically active radiation (PAR) during the grain-filling stage of each cultivar, and analyzed the grain quality of those eight cultivars.

Results

Across all eight cultivars, meteorological factors had a stronger effect on eating quality than genotype, while genotype had a stronger effect on milling quality. Of the three environmental factors assessed, PAR was significantly correlated with the most grain quality traits. Using RNA-sequencing analysis, we identified 573 environment-specific DEGs (Differentially Expressed Genes), and 119 genotype-specific DEGs; 11 DEGs were responsive to genotype × environment interactions. These DEGs were involved in many key metabolic processes.

Conclusion

Our results indicated that interactions among environmental factors, especially PAR, affected rice quality in Northeast China. Further analyses of the DEGs identified herein may provide useful information for future breeding programs aiming to develop high grain quality rice varieties suitable for cultivation across Northeast China.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13258-021-01121-z.

Grain quality evaluation of japonica rice effected by cultivars, environment, and their interactions based on appearance and processing characteristics

Appearance and processing characteristics of 45 japonica rice samples, collected from different regions in Jiangsu province, were investigated and evaluated in this study. Specifically, the chalkiness degree had been presented significant differences among different cultivars and regions. The average chalkiness degree varied from 6.81% to 15.34% for different regions and from 1.93% to 28.31% for different cultivars. The minimum head rice rate of cultivars from four regions, NJ9108 (HA), was 80.5%. The AC of CNG10, HD5, and PJ surpassed 13.68% and lower than 11.33% for the others. The protein content ranged from 6.1% to 11%, and the taste value was significantly different among cultivars. In addition, the RVA curves of the samples were similar, but the peak viscosities of NG8 and NJ5055 were higher than others, and there were significant differences in RVA traits among regions. Cultivars were the main reasons for the difference in appearance and processing quality of japonica rice, while environmental factors had leaded to the change of rice composition, texture, and gelatinization.

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.

Three Major Nucleotide Polymorphisms in the Waxy Gene Correlated with the Amounts of Extra-long Chains of Amylopectin in Rice Cultivars with S or L-type Amylopectin

Extra-long chains (ELC) of amylopectin in rice endosperm are synthesized by granule-bound starch synthase I encoded by the Waxy (Wx) gene, which primarily synthesizes amylose. Previous studies showed that single nucleotide polymorphisms (SNP) in intron 1 and exon 6 of the Wx gene influences ELC amount. However, whether these SNPs are conserved among rice cultivars and if any other SNPs are present in the Wx gene remained unknown. Here, we sequenced the Wx gene from 17 rice cultivars with S or L-type amylopectin, including those with known ELC content and those originating in China with unique starch properties, as well as typical japonica and indica cultivars. In addition to the two SNPs described above, an additional SNP correlating with ELC content was found in exon 10. Low ELC cultivars (<3.0 %) had thymine at the splicing donor site of intron 1, Tyr224 in exon 6, and Pro415 in exon 10. Cultivars with moderate ELC content (4.1–6.9 %) had guanine at the splicing donor site of intron 1, Ser224 in exon 6, and Pro415 in exon 10. Cultivars with high ELC content (7.7–13.9 %) had guanine at the splicing donor site of intron 1, Tyr224 in exon 6, and Ser415 in exon 10. The chain length distribution pattern of amylopectin was correlated with the amounts of SSIIa found in starch granules and gelatinization temperature, but not with ELC content. The combinations of SNPs in the Wx gene found in this study may provide useful information for screening specific cultivars with different ELC content.

Effects of Cultivar, Nitrogen Rate, and Planting Density on Rice-Grain Quality

To achieve superior rice-grain quality, more emphasis has been placed on the genetic diversity of breeding programs, although this improvement could be seriously restricted in the absence of comparable agricultural management practices. Nitrogen (N) application and planting density are two important agronomic practices influencing rice growth, yield, and grain quality. This study investigated the four main aspects of rice-grain quality, namely, milling (brown-rice, milled-rice, and head-rice percentage), appearance (length/width ratio, chalky-kernel percentage, and chalkiness), nutrition (protein content), and cooking and eating quality (apparent amylose content, gel consistency, and pasting viscosities) of two rice cultivars (Shendao 47 and Jingyou 586) under four N rates (0, 140, 180, and 220 kg ha−1), and three planting densities (25 × 104, 16.7 × 104, and 12.5 × 104 hills ha−1) in a field trial from 2015 to 2016. The four main aspects of rice-grain quality were significantly influenced by cultivar. Several aspects were affected by the interactions of N rate and cultivar. No significant interaction between N rate and plating density was detected for all grain-quality parameters. A higher N rate increased the percentages of brown rice and head rice, chalky-kernel percentage, and setback and peak time values, but reduced the length/width ratio, chalkiness, apparent amylose content, gel consistency, and peak-, trough-, and final-viscosity values. These results indicate that the N rate has a beneficial effect on milling and nutritional quality, but a detrimental effect on appearance and cooking and eating quality. Jingyou 586 and Shendao 47 had different responses to planting density in terms of grain quality. Our study indicates that low planting density for Jingyou 586, but a medium one for Shendao 47, is favorable for grain quality.

Comparative Phosphoproteomic Analysis of the Developing Seeds in Two Indica Rice ( Oryza sativa L.) Cultivars with Different Starch Quality

Protein phosphorylation plays important roles in regulation of various molecular events such as plant growth and seed development. However, its involvement in starch biosynthesis is less understood. Here, a comparative phosphoproteomic analysis of two indica rice cultivars during grain development was performed. A total of 2079 and 2434 phosphopeptides from 1273 and 1442 phosphoproteins were identified, covering 2441 and 2808 phosphosites in indica rice 9311 and Guangluai4 (GLA4), respectively. Comparative analysis identified 303 differentially phosphorylated peptides, and 120 and 258 specifically phosphorylated peptides in 9311 and GLA4, respectively. Phosphopeptides in starch biosynthesis related enzymes such as AGPase, SSIIa, SSIIIa, BEI, BEIIb, PUL, and Pho1were identified. GLA4 and 9311 had different amylose content, pasting viscosities, and gelatinization temperature, suggesting subtle difference in starch biosynthesis and regulation between GLA4 and 9311. Our study will give added impetus to further understanding the regulatory mechanism of starch biosynthesis at the phosphorylation level.

Analysis of Lysophospholipid Content in Low Phytate Rice Mutants

As a fundamental component of nucleic acids, phospholipids, and adenosine triphosphate, phosphorus (P) is critical to all life forms, however, the molecular mechanism of P translocation and distribution in rice grains are still not understood. Here, with the use of five different low phytic acid (lpa) rice mutants, the redistribution in the main P-containing compounds in rice grain, phytic acid (PA), lysophospholipid (LPL), and inorganic P (Pi), was investigated. The lpa mutants showed a significant decrease in PA and phytate-phosphorus (PA-P) concentration with a concomitant increase in Pi concentration. Moreover, defects in the OsST and OsMIK genes result in a great reduction of specific LPL components and LPL-phosphorus (LPL-P) contents in rice grain. In contrast, defective OsMRP5 and Os2-PGK genes led to a significant increase in individual LPL components. The effect of the Os2-PGK gene on the LPL accumulation was validated using breeding lines derived from a cross between KBNT-lpa (Os2-PGK mutation) and Jiahe218. This study demonstrates that these rice lpa mutants lead to the redistribution of Pi in endosperm and modify LPL biosynthesis. Increase LPLs in the endosperm in the lpa mutants may have practical applications in rice breeding to produce "healthier" rice.

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.

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.

Underlying Mechanisms of Zymographic Diversity in Starch Synthase I and Pullulanase in Rice-Developing Endosperm

Amylopectin is synthesized by the coordinated actions of many (iso)enzymes, including ADP-glucose pyrophosphorylase (AGPase), starch synthases (SSs), branching enzymes (BEs), and debranching enzymes (DBEs). Here, two polymorphic forms of starch synthase I (SSI) and pullulanase (PUL) in rice-developing seeds, designated as SSI-1/SSI-2 and PUL-1/PUL-2, were discovered for the first time by zymographic analysis. The SSI and PUL polymorphisms were strongly associated with the SSI microsatellite marker (p = 3.6 × 10(-37)) and PUL insertion/deletion (InDel) markers (p < 3.6 × 10(-51)). Western blotting and mass spectrometric analysis confirmed that the polymorphic bands were truly the SSI and PUL enzymes. Only one non-synonymous variation in SSI DNA sequence (the SNP A/G) causing the change of the amino acid K438 to E438 was observed, which coincided well with the polymorphic forms of SSI. Nine non-synonymous variations were found between PUL-1 and PUL-2. Two non-synonymous variations of PUL (F316L and D770E) were identified by mass spectrometric analysis, but all of the variations did not change the structure of PUL. The co-immunoprecipitation results revealed the differences in protein-protein interaction patterns, i.e., strong or weaker signals of SSI-BEI and SSI-BEIIb, between the two forms of SSI. The results will enhance our understanding of SSI and PUL properties and provide helpful information to understand their functions in starch biosynthesis in rice endosperm.

Relationships among Genetic, Structural, and Functional Properties of Rice Starch

We determined the relationships among the structural properties, in vitro digestibility, and genetic factors in starches of 14 rice cultivars. Weight-based chain-length distributions in amylopectin ranged from 18.07% to 24.71% (fa, DP 6-12), 45.01% to 55.67% (fb1, DP 13-24), 12.72% to 14.05% (fb2, DP 25-36), and 10.80 to 20.72% (fb3, DP > 36), respectively. The contents of rapidly digestible starch (RDS), slowly digestible starch (SDS), and resistant starch (RS) ranged from 78.5% to 87.5%, 1.2% to 6.0%, and 10.1% to 18.0%, respectively. AAC was negatively correlated with RDS content but positively correlated with RS content in rice starch. The proportion of short chains in amylopectin, i.e. the amount of fraction IIa (FrIIa) fractionated by gel permeation chromatography (GPC), was positively correlated with RDS. Starch synthase IIa (SSIIa) gene controlled the degree of crystallinity, the amount of fa chains of amylopectin. SSIIIa gene controlled the amount of fb1 chains. Wx gene controlled the FrI, FrIIa, RDS, and RS. Starch debranching enzyme isoamylase II (ISA2) gene also controlled the RDS, which may suggest that RDS was also affected by amylopectin structure, although no correlation between them was found. This study indicated that genetics (i.e., starch biosynthesis related genes) controlled the structural properties of starch, and both amylose content and amylopectin fine structure determined functional properties of rice starch (i.e., the digestion), each in a different way. Understanding the "genetics-structure-function" relationships in rice starches will assist plant breeders and food processors in developing new rice varieties and functional foods.

Genotypic variation in lysophospholipids of milled rice

Phospholipids (PLs) play a prominent role in both grain cellular structure and nutritional function of cereal crops. Their lyso forms (lysophospholipids, LPLs) often combine with cereal starch to form an amylose-lipid complex (ALC), which may influence starch properties. In this study, 20 rice accessions were grown over two seasons at the same location to explore diversity in LPLs of milled rice. Levels of specific LPLs differed significantly among rice genotypes, demonstrating there is a wide diversity in LPLs in rice grain. The main LPL components were lysophosphatidylcholine (LPC) 16:0 (ranging from 3009.7 to 4697.8 μg/g), LPC18:2 (836.6-2182.3 μg/g), lysophosphatidylethanolamine (LPE) 16:0 (625.7-1139.8 μg/g), and LPE18:2 (170.6-481.6 μg/g). Total LPC, total LPE, and total LPL ranged from 4727.1 to 7685.2 μg/g, from 882.8 to 1809.5 μg/g, and from 5609.8 to 9401.1 μg/g, respectively. Although significant (P < 0.001) environment and genotype × environment (G × E) interactions were detected by analysis of variance (ANOVA), these effects accounted for only 0.7-38.9 and 1.8-6.6% of the total variance, respectively. Correlation analysis between LPL components provided insight into the possible LPL biosynthesis pathway in plants. Hierarchical cluster analysis suggested that the 20 rice accessions could be classified into three groups, whereas principal component analysis also identified three groups, with the first two components explaining 57.7 and 16.2% of the total variance. Further genetic studies are needed to identify genes or quantitative trait loci (QTLs) underlying the genetic control of LPLs in rice grain.

Genetic diversity of amylose content and RVA pasting parameters in 20 rice accessions grown in Hainan, China

Starch physicochemical properties determine the eating and cooking quality of rice. The genetic diversity in the apparent amylose content (AAC) and pasting viscosity parameters of 20 geographically diverse rice accessions were investigated. It was found that AAC and pasting viscosities differed widely among different accessions, but each accession performed relatively stably across two environments. Analysis of variance (ANOVA) indicated that all traits were predominantly controlled by genotypic variance, but the genotype×environment interaction effects were also significant except for AAC and PT. Significant correlations were found for each parameter between 2years (P<0.001). Association mapping identified a total of 22 main-effect quantitative trait loci (QTLs) responsible for all traits except for CPV. This study showed that starch physicochemical properties of rice were highly stable and mainly controlled by genetic factors, and gave insight into the molecular improvement of eating quality using marker assisted breeding with the identified QTLs/genes.

Association mapping of starch physicochemical properties with starch biosynthesizing genes in waxy rice (Oryza sativa L.)

Waxy (glutinous) rice is widely used in traditional foods, and understanding the genetic bases of its diverse physicochemical properties will contribute to breeding of new waxy rice with unique qualities. The objective of this study was to investigate the genetic relationship between the starch biosynthesis related genes and the physicochemical properties of waxy rice using association mapping. A total of 36 molecular markers representing 18 genes were used to genotype 50 waxy rice accessions for which starch properties were previously available. Most of the starch properties differed between high and low gelatinization temperature (GT) groups, whereas most traits were similar between the low-GT indica rice and low-GT japonica rice, suggesting GT was the main determinant of the starch quality of waxy rice. Association mapping indicated that the starch properties of waxy rice were mainly controlled by starch synthase IIa (SSIIa or SSII-3, a major gene responsible for the gelatinization temperature) and SSI. It was found that gene-gene interactions were also important for the genetic control of starch properties of waxy rice. This study suggests that application of the functional SNPs of SSIIa in molecular breeding may facilitate quality improvement of waxy rice.