The three important traits for cooking and eating quality of rice grains are controlled by a single locus in an elite rice hybrid, Shanyou 63

Identification of introgressed alien chromosome segments associated with grain quality in Oryza rufipogon x MR219 advanced breeding lines using SSR markers

A limited backcross procedure was utilized to introgress genes associated with grain quality traits from Oryza rufipogon (Accession No. IRGC 105491), a wild rice from Malaysia, to the cultivated rice O. sativa cv. MR219, a popular high yielding Malaysian rice cultivar. A set of 10 BC(2)F(7) progenies were selected based on the field performance and phenotypic appearance in BC(2)F(5) and BC(2)F(6) generations, which initially started with 266 progenies in the BC(2)F(2) generation. These 10 advanced breeding lines are similar to each other but differ in several important grain quality traits, which can be traced to O. rufipogon introgressions. Phenotyping and genotyping of BC(2)F(7) variants were considered for QTL analysis. The introgressed lines did not show any significant changes compared to the recurrent parent MR219 for the traits grain density and milled rice percentage. All 10 progenies showed significantly higher head rice percentages (70-88%) than the recurrent parent MR219. Variants G13 and G15 had higher amylose contents than MR219. All variants were analyzed using polymorphic SSR markers. Of the 34 SSR markers, only 18 showed introgression from O. rufipogon for chromosomes 1, 2, 3, 5, 6, 8, 10, and 11. Graphical genotypes were prepared for each variant, and association between the introgression regions and the traits that increased grain quality was visualized. Based on marker trait association, some of the QTLs are stable across environments and genetic backgrounds and could be used universally.

Different isoforms of starch-synthesizing enzymes controlling amylose and amylopectin content in rice (Oryza sativa L.)

Starch, composed of amylose and amylopectin, greatly influences rice cooking and textural quality, which in turn is controlled by various isoforms of several enzymes. Activity of one or more isoforms of starch-synthesizing enzymes results in various forms of starch structure based on the amylopectin chain length and average external, internal and core chain length distribution and hence results in varying physicochemical and cooking quality. Since the synthesis of starch is highly complex, it is crucial but essential to understand its biosynthetic pathway, starch structure and effects on the physicochemical properties that control eating and cooking quality, and alongside conduct research on gene/QTL mapping for use in marker-assisted selection (MAS) with a view to improve and select cultivars with most desirable range and class of rice starch properties. This article presents the updates on current understanding of the coordination among various enzymes/isoforms towards rice starch synthesis in endosperm and their effect on rice grain physicochemical, cooking and eating qualities. The efforts in identifying regions responsible for these enzymes by mapping the gene/QTLs have provided a glimpse on their association with physicochemical and cooking properties of rice and, hence, improvement is possible by modifying the allelic pattern, resulting in down or nil regulation of a particular enzyme. The clear understanding of the tissue specific coordination between enzyme isoforms and their subsequent effect in controlling eating and cooking properties will enhance the chances to manipulate them for getting desired range of amylose content (AC) and gelatinization temperature (GT) in improved cultivars through combining desired alleles through MAS.

QTL analysis for grain quality traits in 2 BC2F2 populations derived from crosses between Oryza sativa cv Swarna and 2 accessions of O. nivara

The appearance and cooking quality of rice determine its acceptability and price to a large extent. Quantitative trait loci (QTLs) for 12 grain quality traits were mapped in 2 mapping populations derived from Oryza sativa cv Swarna × O. nivara. The BC(2)F(2) population of the cross Swarna × O. nivara IRGC81848 (population 1) was evaluated during 2005 and that from Swarna × O. nivara IRGC81832 (population 2) was evaluated during 2006. Linkage maps were constructed using 100 simple sequence repeat (SSR) markers in population 1 and 75 SSR markers in population 2. In all, 21 QTLs were identified in population 1 (43% from O. nivara) and 37 in population 2 (38% QTLs from O. nivara). The location of O. nivara-derived QTLs mp1.2 for milling percent, kw6.1 for kernel width, and klac12.1 for kernel length after cooking coincided in the 2 populations and appear to be useful for Marker Assisted Selection (MAS). Four QTLs for milling percent, 1 QTL each for amylose content, water uptake, elongation ratio, 2 QTLs for kernel width, and 3 QTLs for gel consistency, each explained more than 20% phenotypic variance. Three QTL clusters for grain quality traits were close to the genes/QTLs for shattering and seed dormancy. QTLs for 4 quality traits were associated with 5 of the 7 major yield QTLs reported in the same 2 mapping populations. Useful introgression lines have been developed for several agronomic traits. It emerges that 40% O. nivara alleles were trait enhancing in both populations, and QTLs for grain quality overlapped with yield meta-QTLs and QTLs for dormancy and seed shattering.

Fine mapping of stable QTLs related to eating quality in rice (Oryza sativa L.) by CSSLs harboring small target chromosomal segments

Amylose content (AC) and viscosity profile are primary indices for evaluating eating and cooking qualities of rice grain. Using chromosome segment substitution lines (CSSLs), previous studies identified a QTL cluster of genes for rice eating and cooking quality in the interval R727-G1149 on chromosome 8. In this study we report two QTLs for viscosity parameters, respectively controlling setback viscosity (SBV) and consistency viscosity (CSV), located in the same interval using rapid viscosity analyzer (RVA) profile as an indicator of eating quality. Previously reported QTL for AC was dissected into two components with opposite genetic effects. Of four QTLs, qCSV-8 and qAC-8-2 had stable genetic effects across three and four environments, respectively. qSBV-8, qCSV-8 and qAC-8-1 partly overlapped, but were separated from qAC-8-2. Based on data from an Affymetrix rice GeneChip, two genes related to starch biosynthesis at the qAC-8-2 locus were chosen for further quantitative expression analysis. Both genes showed enhanced expression in sub-CSSLs carrying the target qAC-8-2 allele, but not in sub-CSSLs without the target qAC-8-2 allele, indicating their possible role in rice quality determination. Molecular markers closely linked to the two stable QTL provide the opportunity for marker-assisted selection (MAS) in breeding high quality rice.

The WRKY transcription factor OsWRKY78 regulates stem elongation and seed development in rice

WRKY proteins are a large super family of transcriptional regulators primarily involved in various plant physiological programs. In present study, the expression profile and putative function of the WRKY transcriptional factor, WRKY78, in rice were identified. Real-time RT-PCR analysis showed that OsWRKY78 transcript was most abundant in elongating stems though its expression was detected in all the tested organs. The expression profiles were further confirmed by using promoter-GUS analysis in transgenic rice. OsWRKY78::GFP fusion gene transient expression analysis demonstrated that OsWRKY78 targeted to the nuclei of onion epidermal cell. Furthermore, OsWRKY78 RNAi and overexpression transgenic rice lines were generated. Transgenic plants with OsWRKY78 overexpression exhibited a phenotype identical to the wild type, whereas inhibition of OsWRKY78 expression resulted in a semi-dwarf and small kernel phenotype due to reduced cell length in transgenic plants. In addition, a T-DNA insertion mutant line oswrky78 was identified and a phenotype similar to that of RNAi plants was also observed. Grain quality analysis data showed no significant differences, with the exception of minor changes in endosperm starch crystal structure in RNAi plants. Taken together, these results suggest that OsWRKY78 may acts as a stem elongation and seed development regulator in rice.

Map-based cloning proves qGC-6, a major QTL for gel consistency of japonica/indica cross, responds by Waxy in rice (Oryza sativa L.)

In this study, one major QTL affecting gel consistency (GC) of japonica/indica cross was identified on chromosome 6 using a DH population. To understand the molecular mechanism that regulates GC in rice grains, the major QTL (qGC-6) was isolated through a map-based cloning approach utilizing chromosome segment substitution lines (CSSLs). Using 64 plants with extremely soft GC that were selected on recombinant break points between two SSR markers, RM540 and RM8200 in a BC4F2 population, qGC-6 was mapped to a 60-kb DNA region between two STS markers, S26 and S27. These two markers were then used to further identify recombination break points. Finally, qGC-6 was delimited in an interval of a 11-kb region. Gene prediction analysis of the 11-kb DNA sequence containing qGC-6 identified only one putative ORF, which encodes granule-bound starch synthesis protein (Wx protein). Results of sequencing analysis and complementation experiment confirmed that this candidate ORF is responsible for rice GC. Genetic evidences revealed that Wx might contribute equally to the grain amylose content-controlling gene as well as gel consistency. This new information is important to breed rice varieties with improved grain quality.

Identification of quantitative trait loci associated with germination using chromosome segment substitution lines of rice (Oryza sativa L.)

Rapid and uniform seed germination under diverse environmental conditions is a desirable characteristic for most crop plants, such as rice, wheat, and maize. However, the genetic base of the variations in the rate of germination is not well understood. In this study, quantitative trait loci (QTL) for germination rate were mapped with a set of 143 chromosome segment substitution lines (CSSL) each contains a small genomic fragment from a japonica variety Nipponbare in the uniform genetic background of an indica variety Zhenshan97. Nine CSSL showed significantly lower germination rate than that in Zhenshan97. Four germination-related QTL were identified located on chromosomes 2, 5, 6 and 10, at which all japonica alleles decreased germination rate. By using the CSSL-derived F2 population, a major QTL (qGR2) on chromosome 2 was confirmed, and delimited to a 10.4 kb interval containing three putative candidate genes, of which OsMADS29 was only expressed preferentially in the seed. These results would facilitate cloning of the major gene that affects germination rate, and provide an insight into the genetic basis of germination.

Identification of quantitative trait loci associated with rice eating quality traits using a population of recombinant inbred lines derived from a cross between two temperate japonica cultivars

Improved eating quality is a major breeding target in japonica rice due to market demand. In this study, we performed genetic analysis to identify quantitative trait loci (QTLs) that control rice eating quality traits using 192 recombinant inbred lines (RILs) derived from a cross between two japonica cultivars, 'Suweon365' and 'Chucheongbyeo'. We evaluated the stickiness (ST) and overall evaluation (OE) of cooked rice using a sensory test, the glossiness of cooked rice (GCR) using a Toyo-taste meter, and measured the amylose content (AC), protein content (PC), alkali digestion value (ADV), and days to heading (DH) of the RILs in the years 2006 and 2007. Our analysis revealed 21 QTLs on chromosomes 1, 4, 6, 7, 8, and 11. QTLs on chromosomes 6, 7, and 8 were detected for three traits related to eating quality in both years. QTLs for ST and OE were identified by a sensory test in the same region of the QTLs for AC, PC, ADV, GCR and DH on chromosome 8. QTL effects on the GCR were verified using QTL-NILs (near-isogenic lines) of BC(3)F(4-6) in the Suweon365 background, a low eating quality variety, and some BC(1)F(3) lines. Chucheongbyeo alleles at QTLs on chromosomes 7 and 8 increased the GCR in the NILs and backcrossed lines. The QTLs identified by our analysis will be applicable to future marker-assisted selection (MAS) strategies for improving the eating quality of japonica rice.

Deep sequencing reveals the complex and coordinated transcriptional regulation of genes related to grain quality in rice cultivars

Background

Milling yield and eating quality are two important grain quality traits in rice. To identify the genes involved in these two traits, we performed a deep transcriptional analysis of developing seeds using both massively parallel signature sequencing (MPSS) and sequencing-by-synthesis (SBS). Five MPSS and five SBS libraries were constructed from 6-day-old developing seeds of Cypress (high milling yield), LaGrue (low milling yield), Ilpumbyeo (high eating quality), YR15965 (low eating quality), and Nipponbare (control).

Results

The transcriptomes revealed by MPSS and SBS had a high correlation co-efficient (0.81 to 0.90), and about 70% of the transcripts were commonly identified in both types of the libraries. SBS, however, identified 30% more transcripts than MPSS. Among the highly expressed genes in Cypress and Ilpumbyeo, over 100 conserved cis regulatory elements were identified. Numerous specifically expressed transcription factor (TF) genes were identified in Cypress (282), LaGrue (312), Ilpumbyeo (363), YR15965 (260), and Nipponbare (357). Many key grain quality-related genes (i.e., genes involved in starch metabolism, aspartate amino acid metabolism, storage and allergenic protein synthesis, and seed maturation) that were expressed at high levels underwent alternative splicing and produced antisense transcripts either in Cypress or Ilpumbyeo. Further, a time course RT-PCR analysis confirmed a higher expression level of genes involved in starch metabolism such as those encoding ADP glucose pyrophosphorylase (AGPase) and granule bound starch synthase I (GBSS I) in Cypress than that in LaGrue during early seed development.

Conclusion

This study represents the most comprehensive analysis of the developing seed transcriptome of rice available to date. Using two high throughput sequencing methods, we identified many differentially expressed genes that may affect milling yield or eating quality in rice. Many of the identified genes are involved in the biosynthesis of starch, aspartate family amino acids, and storage proteins. Some of the differentially expressed genes could be useful for the development of molecular markers if they are located in a known QTL region for milling yield or eating quality in the rice genome. Therefore, our comprehensive and deep survey of the developing seed transcriptome in five rice cultivars has provided a rich genomic resource for further elucidating the molecular basis of grain quality in rice.

Dissecting the genetic basis for the effect of rice chalkiness, amylose content, protein content, and rapid viscosity analyzer profile characteristics on the eating quality of cooked rice using the chromosome segment substitution line population across eight environments

Quantitative trait locus (QTL) mapping and stability analysis were carried out for 16 rice (Oryza sativa L.) quality traits across eight environments, by using a set of chromosome segment substitution lines with 'Asominori' as genetic background. The 16 quality traits include percentage of grain with chalkiness (PGWC), area of chalky endosperm (ACE), amylose content (AC), protein content (PC), peak viscosity, hot paste viscosity, cool paste viscosity, breakdown viscosity (BDV), setback viscosity (SBV), consistency viscosity, cooked-rice luster (LT), scent, tenderness (TD), viscosity, elasticity, and the integrated values of organleptic evaluation (IVOE). A total of 132 additive effect QTLs are detected for the 16 quality straits in the eight environments. Among these QTLs, 56 loci were detected repeatedly in at least three environments. Interestingly, several QTL clusters were observed for multiple quality traits. Especially, one QTL cluster near the G1149 marker on chromosome 8 includes nine QTLs: qPGWC-8, qACE-8, qAC-8, qPC-8a, qBDV-8a, qSBV-8b, qLT-8a, qTD-8a, and qIVOE-8a, which control PGWC, ACE, AC, PC, BDV, SBV, LT, TD, and IVOE, respectively. Moreover, this QTL cluster shows high stability and repeatability in all eight environments. In addition, one QTL cluster was located near the C2340 marker on chromosome 1 and another was detected near the XNpb67 marker on chromosome 2; each cluster contained five loci. Near the C563 marker on chromosome 3, one QTL cluster with four loci was found. Also, there were nine QTL clusters that each had two or three loci; however, their repeatability in different environments was relatively lower, and the genetic contribution rate was relatively smaller. Considering the correlations among all of the 16 quality traits with QTL cluster distributions, we can conclude that the stable and major QTL cluster on chromosome 8 is the main genetic basis for the effect of rice chalkiness, AC, PC, and rapid viscosity analyzer profile characteristics on the eating quality of cooked rice. Consequently, this QTL cluster is a novel gene resource for controlling rice high-quality traits and should be of great significance for research on formation mechanism and molecule improvement of rice quality.

Introgression of qPE9-1 allele, conferring the panicle erectness, leads to the decrease of grain yield per plant in japonica rice (Oryza sativa L.)

Panicle architecture is closely related to yield formation. The qPE9-1 gene has been proved to be widely used in high-yield rice cultivar developments, conferring erect panicle character in japonica rice. Recently, qPE9-1 has been successfully cloned; however, the genetic effect on grain yield per plant of the erect panicle allele qPE9-1 is controversial yet. In the present study, a drooping panicle parent Nongken 57, carrying qpe9-1 allele, was used as recurrent parent to successively backcross to a typical erect panicle line from the double haploid (DH) population (Wuyunjing 8/Nongken 57), which was previously shown to carry qPE9-1 allele. Thus a pair of near-isogenic lines (NILs) was developed. The comparison of agronomic traits between the NILs showed that, when qpe9-1 was replaced by qPE9-1, the panicle architecture was changed from drooping to erect; moreover, the panicle length, plant height, 1000-grain weight and the tillers were significantly decreased, consequently resulting in the dramatic decrease of grain yield per plant by 30%. Therefore, we concluded that the qPE9-1 was a major factor controlling panicle architecture, and qPE9-1 had pleiotropic nature, with negative effects on grain yield per plant. This result strongly suggests that the erect panicle allele qPE9-1 should be used together with other favorable genes in the high-yield breeding practice. In addition, the effect of qPE9-1 on eating and cooking quality was also discussed in the present study.

Genetic control of a transition from black to straw-white seed hull in rice domestication

The genetic mechanism involved in a transition from the black-colored seed hull of the ancestral wild rice (Oryza rufipogon and Oryza nivara) to the straw-white seed hull of cultivated rice (Oryza sativa) during grain ripening remains unknown. We report that the black hull of O. rufipogon was controlled by the Black hull4 (Bh4) gene, which was fine-mapped to an 8.8-kb region on rice chromosome 4 using a cross between O. rufipogon W1943 (black hull) and O. sativa indica cv Guangluai 4 (straw-white hull). Bh4 encodes an amino acid transporter. A 22-bp deletion within exon 3 of the bh4 variant disrupted the Bh4 function, leading to the straw-white hull in cultivated rice. Transgenic study indicated that Bh4 could restore the black pigment on hulls in cv Guangluai 4 and Kasalath. Bh4 sequence alignment of all taxa with the outgroup Oryza barthii showed that the wild rice maintained comparable levels of nucleotide diversity that were about 70 times higher than those in the cultivated rice. The results from the maximum likelihood Hudson-Kreitman-Aguade test suggested that the significant reduction in nucleotide diversity in rice cultivars could be caused by artificial selection. We propose that the straw-white hull was selected as an important visual phenotype of nonshattered grains during rice domestication.

Genetic analysis of starch paste viscosity parameters in glutinous rice (Oryza sativa L.)

Starch paste viscosity plays an important role in estimating the cooking, eating, and processing quality of rice. The inheritance of starch paste viscosity in glutinous rice remains undefined. In the present study, 118 glutinous rice accessions were collected, and the genotypes of 17 starch synthesis-related genes (SSRG) were analyzed by using 43 gene-specific molecular markers. Association analysis indicated that 10 of 17 SSRGs were involved in controlling the rapid visco analyzer (RVA) profile parameters. Among these, the PUL gene was identified to play an important role in control of peak viscosity (PKV), hot paste viscosity (HPV), cool paste viscosity (CPV), breakdown viscosity (BDV), peak time (PeT), and paste temperature (PaT) in glutinous rice. Other SSRGs involved only a few RVA profile parameters. Furthermore, interactions between SSRGs were found being responsible for PeT, PaT, and BDV. Some of the RVA parameters, including PKV, HPV, CPV, CSV, and PaT, were mainly governed by single SSRG, whereas other parameters, such as BDV, SBV, and PeT, were controlled by a few SSRGs, functioning cooperatively. Further, three near-isogenic lines (NIL) of a japonica glutinous cv. Suyunuo as genetic background, with PUL, SSIII-1, and SSIII-2 alleles replaced with those of indica cv. Guichao 2, were employed to verify the genetic effects of the various genes, and the results were consistent with those obtained from the association analysis. These findings indicated that starch paste viscosity in glutinous rice had a complex genetic system, and the PUL gene played an important role in determining the RVA profile parameters in glutinous rice. These results provide important information for potentially improving the quality of glutinous rice.

Association mapping for yield and grain quality traits in rice (Oryza sativa L.)

Association analysis was applied to a panel of accessions of Embrapa Rice Core Collection (ERiCC) with 86 SSR and field data from two experiments. A clear subdivision between lowland and upland accessions was apparent, thereby indicating the presence of population structure. Thirty-two accessions with admixed ancestry were identified through structure analysis, these being discarded from association analysis, thus leaving 210 accessions subdivided into two panels. The association of yield and grain-quality traits with SSR was undertaken with a mixed linear model, with markers and subpopulation as fixed factors, and kinship matrix as a random factor. Eight markers from the two appraised panels showed significant association with four different traits, although only one (RM190) maintained the marker-trait association across years and cultivation. The significant association detected between amylose content and RM190 was in agreement with previous QTL analyses in the literature. Herein, the feasibility of undertaking association analysis in conjunction with germplasm characterization was demonstrated, even when considering low marker density. The high linkage disequilibrium expected in rice lines and cultivars facilitates the detection of marker-trait associations for implementing marker assisted selection, and the mining of alleles related to important traits in germplasm.

A global analysis of QTLs for expression variations in rice shoots at the early seedling stage

Analyses of quantitative trait loci (QTLs) for expression levels (eQTLs) of genes reveal a genetic relationship between expression variation and the regulator, thus unlocking information for identifying the regulatory network. Oligo-nucleotide expression microarrays hybridized with RNA can simultaneously provide data for molecular markers and transcript abundance. In this study, we used an Affymetrix GeneChip Rice Genome Array to analyze eQTLs in rice shoots at 72 h after germination from 110 recombinant inbred lines (RILs) derived from a cross between Zhenshan 97 and Minghui 63. In total, 1632 single-feature polymorphisms (SFPs) plus 23 PCR markers were identified and placed into 601 recombinant bins, spanning 1459 cM in length, which were used as markers to genotype the RILs. We obtained 16,372 expression traits (e-traits) each with at least one eQTL, resulting in 26,051 eQTLs in total, including both cis- and trans-eQTLs. We also identified 171 eQTL hot spots in the rice genome, each of which controls transcript variations of many e-traits. Gene ontology analysis revealed an enrichment of certain functional categories of genes in some of the eQTL hot spots. In particular, eQTLs for e-traits involving the DNA metabolic process was significantly enriched in several eQTL hot spots on chromosomes 3, 5 and 10. Several e-traits co-localizing with cis-eQTLs showed significant correlations with hundreds of e-traits, indicating possible co-regulation. We also detected correlations between QTLs for shoot dry weight and eQTLs, revealing possible candidate genes for the trait. These results provided clues for the identification and characterization of the regulatory network in the whole genome at the transcriptional level.

Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualities

More than half of the world's population uses rice as a source of carbon intake every day. Improving grain quality is thus essential to rice consumers. The three main properties that determine rice eating and cooking quality--amylose content, gel consistency, and gelatinization temperature--correlate with one another, but the underlying mechanism of these properties remains unclear. Through an association analysis approach, we found that genes related to starch synthesis cooperate with each other to form a fine regulating network that controls the eating and cooking quality and defines the correlation among these three properties. Genetic transformation results verified the association findings and also suggested the possibility of developing elite cultivars through modification with selected major and/or minor starch synthesis-related genes.

Association analysis of the amino acid contents in rice

The main objective of the present study was to identify simple sequence repeat (SSR) markers associated with the amino acid content of rice (Oryza sativa L.). SSR markers were selected by prescreening for the relationship to amino acid content. Eighty-four rice landrace accessions from Korea were evaluated for 16 kinds of amino acids in brown rice and genotyped with 25 SSR markers. Analysis of population structure revealed four subgroups in the population. Linkage disequilibrium (LD) patterns and distributions are of fundamental importance for genome-wide mapping associations. The mean r(2) value for all intrachromosomal loci pairs was 0.033. LD between linked markers decreased with distance. Marker-trait associations were investigated using the unified mixed-model approach, considering both population structure (Q) and kinship (K). A total of 42 marker-trait associations with amino acids (P < 0.05) were identified using 15 different SSR markers covering three chromosomes and explaining more than 40% of the total variation. These results suggest that association analysis in rice is a viable alternative to quantitative trait loci mapping and should help rice breeders develop strategies for improving rice quality.

Genetic dissection of complex endosperm traits

The endosperm of plants is a major source of food, feed and industrial raw materials. The genetic analysis of endosperm traits poses numerous challenges due to the endosperm's complex genetic composition and unique physical and developmental properties. Modern molecular techniques and statistical methods have greatly improved the mapping of quantitative trait loci underlying endosperm traits and have led to revolutionary insights regarding epistatic and epigenetic effects. This article describes the current state of the methodologies used in the genetic dissection of endosperm traits and highlights practical issues and statistical concepts and procedures.

Identification of quantitative trait loci for rice quality in a population of chromosome segment substitution lines

The demand for high quality rice represents a major issue in rice production. The primary components of rice grain quality include appearance, eating, cooking, physico-chemical, milling and nutritional qualities. Most of these traits are complex and controlled by quantitative trait loci (QTLs), so the genetic characterization of these traits is more difficult than that of traits controlled by a single gene. The detection and genetic identification of QTLs can provide insights into the genetic mechanisms underlying quality traits. Chromosome segment substitution lines (CSSLs) are effective tools used in mapping QTLs. In this study, we constructed 154 CSSLs from backcross progeny (BC(3)F(2)) derived from a cross between 'Koshihikari' (an Oryza sativa L. ssp. japonica variety) as the recurrent parent and 'Nona Bokra' (an O. sativa L. ssp. indica variety) as the donor parent. In this process, we carried out marker-assisted selection by using 102 cleaved amplified polymorphic sequence and simple sequence repeat markers covering most of the rice genome. Finally, this set of CSSLs was used to identify QTLs for rice quality traits. Ten QTLs for rice appearance quality traits were detected and eight QTLs concerned physico-chemical traits. These results supply the foundation for further genetic studies and breeding for the improvement of grain quality.

QTL mapping and QxE interactions of grain cooking and nutrient qualities in rice under upland and lowland environments

Grain cooking and nutrient qualities are the most important components of rice (Oryza sativa L.) quality. A doubled haploid (DH) population from a cross between two japonica cultivars was used to examine the phenotypic values and potential QTLs for the quality traits. The cooking and nutrient quality traits, including the amylose content (AC), the gel consistency (GC), the gelatinization temperature (GT), and the protein content (PC), in rice grown under upland and lowland environments were evaluated. Significant differences for AC, GC, GT, and PC between upland and lowland environments were detected. The phenotypic values of all four traits were higher under upland environment than lowland environment. The value of PC under upland environment was significantly higher (by 37.9%) than that under lowland environment. This suggests that upland cultivation had large effect on both cooking and nutrient qualities. A total of seven QTLs and twelve pairs of QTLs were detected to have significant additive and epistatic effects for the four traits. Significant Q x E interaction effects of two QTLs and two pairs of QTLs were also discovered. The general contribution of additive QTLs ranged from 1.91% to 19.77%. The Q x E interactions of QTLs QGt3 and QAc6 accounted for 8.99% and 47.86% of the phenotypic variation, respectively, whereas those of the 2 pairs of epistatic QTLs, QAc6-QAc11b and QAc8-QAc9, accounted for 32.54% and 11.82%, respectively. Five QTLs QGt6b, QGt8, QGt11, QGc1, and QPc2, which had relatively high general contribution and no Q x E interactions, were selected to facilitate the upland rice grain quality breeding.

Mapping epistatic quantitative trait loci underlying endosperm traits using all markers on the entire genome in a random hybridization design

Triploid endosperm is of great economic importance owing to its nutritious quality. Mapping endosperm trait loci (ETL) can provide an efficient way to genetically improve grain quality. However, most triploid ETL mapping methods do not produce unbiased estimates of the two dominant effects of ETL. A random hybridization design is an alternative method that may be used to overcome this problem. However, epistasis has an important role in the dissection of genetic architecture for complex traits. In this study, therefore, an attempt was made to map epistatic ETL (eETL) under a triploid genetic model of endosperm traits in a random hybridization design. The endosperm trait means of random hybrid lines, together with known marker genotype information from their corresponding parental F(2) plants, were used to estimate, efficiently and without bias, the positions and all of the effects of eETL using a penalized maximum likelihood method. The method proposed in this article was verified by a series of Monte Carlo simulation experiments. Results from the simulated studies show that the proposed method provides accurate estimates of eETL parameters with a low false-positive rate and a relatively short running time. This new method enables us to map triploid eETL in the same way as diploid quantitative traits.

Starch physicochemical properties and their associations with microsatellite alleles of starch-synthesizing genes in a rice RIL population

The physicochemical properties of starch, such as apparent amylose content, gelatinization temperature, and pasting viscosities, determine the eating, cooking, and processing qualities of various products of rice. A recombinant inbred line (RIL) population derived from the reciprocal cross of Lemont (a premium high-quality tropical japonica rice) and Jiayu 293 (a high-yield but low-quality indica rice) was used to test the association of microsatellite markers of starch-synthesizing genes with starch quality parameters. The results confirmed the association of Wx and starch synthase I (SSI) alleles with various starch properties measured in rice flour. However, the starch properties were not associated with the starch branching enzyme 1 (SBE 1) gene alleles.

The QTL analysis on maternal and endosperm genome and their environmental interactions for characters of cooking quality in rice (Oryza sativa L.)

Investigations to identify quantitative trait loci (QTLs) governing cooking quality traits including amylose content, gel consistency and gelatinization temperature (expressed by the alkali spread value) were conducted using a set of 241 RIL populations derived from an elite hybrid cross of "Zhenshan 97"x"Minghui 63" and their reciprocal backcrosses BC1F1 and BC2F1 populations in two environments. QTLs and QTLxenvironment interactions were analyzed by using the genetic model with endosperm and maternal effects and environmental interaction effects on quantitative traits of seed in cereal crops. The results suggested that a total of seven QTLs were associated with cooking quality of rice, which were subsequently mapped to chromosomes 1, 4 and 6. Six of these QTLs were also found to have environmental interaction effects.

Du1, encoding a novel Prp1 protein, regulates starch biosynthesis through affecting the splicing of Wxb pre-mRNAs in rice (Oryza sativa L.)

Starch is the major component of cereal grains. In rice, starch properties determine the eating and cooking quality. The dull endosperm of rice grains is a classical morphological and agronomical trait that has long been exploited for breeding and genetics study. To understand the molecular mechanism that regulates the starch biosynthesis in rice grains, we characterized a classic rice mutant dull endosperm1 (du1) and isolated Du1 through a map-based cloning approach. Du1, encoding a member of pre-mRNA processing (Prp1) family, is expressed mainly in panicles. Du1 specifically affects the splicing efficiency of Wx(b) and regulates starch biosynthesis by mediating the expression of starch biosynthesis genes. Analysis of du1wx shows that Du1 acts upstream of Wx(b). These results strongly suggest that Du1 may function as a regulator of the starch biosynthesis by affecting the splicing of Wx(b) and the expression of other genes involved in the rice starch biosynthetic pathways.

Strategies for developing Green Super Rice

From a global viewpoint, a number of challenges need to be met for sustainable rice production: (i) increasingly severe occurrence of insects and diseases and indiscriminate pesticide applications; (ii) high pressure for yield increase and overuse of fertilizers; (iii) water shortage and increasingly frequent occurrence of drought; and (iv) extensive cultivation in marginal lands. A combination of approaches based on the recent advances in genomic research has been formulated to address these challenges, with the long-term goal to develop rice cultivars referred to as Green Super Rice. On the premise of continued yield increase and quality improvement, Green Super Rice should possess resistances to multiple insects and diseases, high nutrient efficiency, and drought resistance, promising to greatly reduce the consumption of pesticides, chemical fertilizers, and water. Large efforts have been focused on identifying germplasms and discovering genes for resistance to diseases and insects, N- and P-use efficiency, drought resistance, grain quality, and yield. The approaches adopted include screening of germplasm collections and mutant libraries, gene discovery and identification, microarray analysis of differentially regulated genes under stressed conditions, and functional test of candidate genes by transgenic analysis. Genes for almost all of the traits have now been isolated in a global perspective and are gradually incorporated into genetic backgrounds of elite cultivars by molecular marker-assisted selection or transformation. It is anticipated that such strategies and efforts would eventually lead to the development of Green Super Rice.

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

A recombinant inbred line population derived from a cross between Zhenshan 97 and Delong 208 was used to analyze the genetic basis of the cooking and eating quality of rice as reflected by 17 traits (or parameters). These traits include amylose content (AC), gel consistency (GC), alkali spreading value (ASV), cooked rice elongation (CRE), and 13 parameters from the viscosity profile. All the traits, except peak paste viscosity (PKV), time needed from gelatinization to peak (BAtime), and CRE, can be divided into two classes according to their interrelationship. The first class consists of AC, GC, and most of the paste viscosity parameters that form a major determinant of eating quality. The second class includes ASV, pasting temperature (Atemp) and pasting time (Atime), which characterize cooking process. We identified 26 QTL (quantitative trait locus or loci) in 2 years; nine QTL clusters emerged. The two major clusters, which correspond to the Wx and Alk loci, control the traits in the first and second classes, respectively. Some QTL are co-located for the traits belonging to the same class and also for the traits to a different class. The Wx locus also affects on ASV while the Alk locus also makes minor contributions to GC and some paste viscosity parameters. The QTL clusters on other chromosomes are similar to the Wx locus or Alk locus, although the variations they explained are relatively minor. QTL for CRE and PKV are dispersed and independent of the Wx locus. Low paste viscosity corresponds to low AC and soft gel, which represents good eating quality for most Chinese consumers; high ASV and low Atemp, together with reduced time to gelatinization and PKV, indicate preferred cooking quality. The genetic basis of Atemp, Atime, BAtime, peak temperature, peak time, paste viscosity at 95 degrees C, and final paste viscosity is newly examined to reveal a complete and dynamic viscosity profile.

A mixture model approach to the mapping of QTL controlling endosperm traits with bulked samples

Endosperm traits are of triploid inheritance and have become a focus of breeding effort for their close relations with the grain quality. Current methods for mapping quantitative trait loci (QTL) underlying endosperm traits are restricted to the use of the phenotypes of single grain samples as input data set, which are often not available in practice due to the small size of the cereal seeds. This paper proposed a statistical model for one specially tailored mapping strategy, where the marker genotypes are obtained from the maternal plants in the segregation population and the phenotypic responses are replaced by the trait means of composite endosperm samples pooled from each plant. It should therefore be more practical and have wide applicability in mapping endosperm traits. The method was implemented by fitting the phenotypic means of endosperms into a Gaussian mixture model. Both the exact and approximate Expectation-Maximization algorithms were proposed to estimate the model parameters. The presence of the QTL was determined by likelihood ratio test statistics. Statistical power and other properties of the new method were investigated and compared to the current single-seed method under a variety of scenarios through simulation studies. The simulations suggest a reasonable sample size should be used to ensure reliable results. The proposed method was also applied to a simulated genome data for further evaluation. As an illustration, a real data of maize was analyzed to find the loci responsible for the popping expansion volume.

Nucleotide diversity in starch synthase IIa and validation of single nucleotide polymorphisms in relation to starch gelatinization temperature and other physicochemical properties in rice (Oryza sativa L.)

The characteristics of starch, such as gelatinization temperature (GT), apparent amylose content (AAC), pasting temperature (PT) and other physicochemical properties, determine the quality of various products of rice, e.g., eating, cooking and processing qualities. The GT of rice flour is controlled by the alk locus, which has been co-mapped to the starch synthase IIa (SSIIa) locus. In this study, we sequenced a 2,051 bp DNA fragment spanning part of intron 6, exon 7, intron 7, exon 8 and part of 3' untranslated region of SSIIa for 30 rice varieties with diverse geographical distribution and variation in starch physicochemical properties. A total of 24 single nucleotide polymorphisms (SNPs) and one insertion/deletion (InDel) were identified, which could be classified into nine haplotypes. The mean pairwise nucleotide diversity pi was 0.00292, and Watterson's estimator theta was 0.00296 in this collection of rice germplasm. Tajima's D test for selection showed no significant deviation from the neutral expectation (D = - 0.04612, P > 0.10). However, significant associations were found between seven of the SNPs and peak GT (T (p)) at P < 0.05, of which two contiguous SNPs (GC/TT) showed a very strong association with T (p) (P < 0.0001). With some rare exception, this GC/TT polymorphism alone can differentiate rice varieties with high or intermediate GT (possessing the GC allele) from those with low GT (possessing the TT allele). In contrast, none of these SNPs or InDel was significantly associated with amylose content. A further 509 rice varieties with known physicochemical properties (e.g., AAC and PT) and known alleles of other starch synthesizing genes were genotyped for the SSIIa GC/TT alleles. Association analysis indicated that 82% of the total variation of AAC in these samples could be explained by a (CT)n simple sequence repeat (SSR) and a G/T SNP of Waxy gene (Wx), and 62.4% of the total variation of PT could be explained by the GC/TT polymorphism. An additional association analysis was performed between these molecular markers and the thermal and retrogradation properties for a subset of 245 samples from the 509 rice varieties. The SSIIa GC/TT polymorphism explained more than 60% of the total variation in thermal properties, whereas the SSR and SNP of Wx gene explained as much as the SSIIa GC/TT of the total variation in retrogradation properties. Our study provides further support for the utilization of the GC/TT polymorphism in SSIIa. As shown in our study of 509 rice varieties, the GC/TT SNP could differentiate rice with high or intermediate GT from those with low GT in about 90% of cases. Using four primers in a single PCR reaction, the GC/TT polymorphism can be surveyed on a large scale. Thus, this SNP polymorphism can be very useful in marker-assisted selection for the improvement of GT and other physicochemical properties of rice.

QTLs for low nitrogen tolerance at seedling stage identified using a recombinant inbred line population derived from an elite rice hybrid

Tolerance to low nitrogen conditions is a highly desired characteristic for sustainable crop production. In this study, we analyzed the genetic components associated with low N tolerance in rice at seedling stage, including main effects, epistatic effects of the quantitative trait locus (QTLs), and QTL by environment interactions (QEs), using a population of 239 recombinant inbred lines (RILs) from a cross between Zhenshan 97 and Minghui 63, the parents of an elite hybrid. A genetic linkage map with 253 DNA maker loci was constructed. Seedlings of RILs were cultivated in low N and normal N solutions. Root, shoot and plant weight in the two N treatments were measured and the relative weight of the two treatments for each trait was considered as measurements for low N tolerance. Four to eight QTLs with main effects were detected for each of the nine traits. Very few QTLs were detected in both low and normal N conditions, and most QTLs for the relative measurements were different from those for traits under the two N treatments, indicating very little commonality in the genetic basis of the traits and their relative performance under low and normal N conditions. A total of 103 digenic interactions were detected for the nine traits. While the epistatic effects collectively accounted for large proportions of the variation for several traits, the effects of QEs appeared to be trivial. It was concluded that low N tolerance of rice seedling had complex genetic basis that requires extensive studies for full characterization.

Features of the expressed sequences revealed by a large-scale analysis of ESTs from a normalized cDNA library of the elite indica rice cultivar Minghui 63

The indica subspecies of cultivated rice occupies the largest area of rice production in the world. However, a systematic analysis of cDNA sequences from the indica subspecies has not been performed. The aim of the present study was to collect and analyze the expressed sequence tags (ESTs) of indica rice on a large scale. A total of 39 208 raw sequences were generated from a normalized cDNA library prepared by use of 15 different tissues of the indica cultivar Minghui 63. After trimming, processing and analysis, 17 835 unique sequences were obtained, each of which presumably represents a unique gene. Of these sequences, 2663 were novel, and at least 70 were indica specific. Comparison of the Minghui 63 sequences with the ESTs/full-length cDNAs in GenBank revealed a large number of deletion/insertion/substitution (DIS) at both the inter- and intra-subspecific levels. The overall number of polymorphisms in the expressed sequences was higher in the inter-subspecific comparisons than in the intra-subspecific comparisons. However, the extent of DIS-based polymorphism was highly variable among different rice varieties. In total, 15 726 unique sequences, including 697 novel sequences, were assigned to regions where large numbers of quantitative trait loci (QTLs) for agronomic traits had been detected previously. These results may be useful for developing new molecular markers for genetic mapping, detecting allelic polymorphisms associated with phenotypic variations between rice varieties, and facilitating QTL cloning by providing the starting points for candidate-gene identification.

The main effects, epistatic effects and environmental interactions of QTLs on the cooking and eating quality of rice in a doubled-haploid line population

Amylose content (AC), gel consistency (GC) and gelatinazation temperature (GT) are three important traits that influence the cooking and eating quality of rice. The objective of this study was to characterize the genetic components, including main-effect quantitative trait loci (QTLs), epistatic QTLs and QTL-by-environment interactions (QEs), that are involved in the control of these three traits. A population of doubled haploid (DH) lines derived from a cross between two indica varieties Zhenshan 97 and H94 was used, and data were collected from a field experiment conducted in two different environments. A genetic linkage map consisting of 218 simple sequence repeat (SSR) loci was constructed, and QTL analysis performed using QTLMAPPER 1.6: resolved the genetic components into main-effect QTLs, epistatic QTLs and QEs. The analysis detected a total of 12 main-effect QTLs for the three traits, with a QTL corresponding to the Wx locus showing a major effect on AC and GC, and a QTL corresponding to the Alk locus having a major effect on GT. Ten digenic interactions involving 19 loci were detected for the three traits, and six main-effect QTLs and two pairs of epistatic QTLs were involved in QEs. While the main-effect QTLs, especially the ones corresponding to known major loci, apparently played predominant roles in the genetic basis of the traits, under certain conditions epistatic effects and QEs also played important roles in controlling the traits. The implications of the findings for rice quality improvement are discussed.

Multiple-interval mapping for quantitative trait loci controlling endosperm traits

Endosperm traits are trisomic inheritant and are of great economic importance because they are usually directly related to grain quality. Mapping for quantitative trait loci (QTL) underlying endosperm traits can provide an efficient way to genetically improve grain quality. As the traditional QTL mapping methods (diploid methods) are usually designed for traits under diploid control, they are not the ideal approaches to map endosperm traits because they ignore the triploid nature of endosperm. In this article, a statistical method considering the triploid nature of endosperm (triploid method) is developed on the basis of multiple-interval mapping (MIM) to map for the underlying QTL. The proposed triploid MIM method is derived to broadly use the marker information either from only the maternal plants or from both the maternal plants and their embryos in the backcross and F2 populations for mapping endosperm traits. Due to the use of multiple intervals simultaneously to take multiple QTL into account, the triploid MIM method can provide better detection power and estimation precision, and as shown in this article it is capable of analyzing and searching for epistatic QTL directly as compared to the traditional diploid methods and current triploid methods using only one (or two) interval(s). Several important issues in endosperm trait mapping, such as the relation and differences between the diploid and triploid methods, variance components of genetic variation, and the problems if effects are present and ignored, are also addressed. Simulations are performed to further explore these issues, to investigate the relative efficiency of different experimental designs, and to evaluate the performance of the proposed and current methods in mapping endosperm traits. The MIM-based triploid method can provide a powerful tool to estimate the genetic architecture of endosperm traits and to assist the marker-assisted selection for the improvement of grain quality in crop science. The triploid MIM FORTRAN program for mapping endosperm traits is available on the worldwide web (http://www.stat.sinica.edu.tw/chkao/).

Mapping genome-genome epistasis: a high-dimensional model

MOTIVATION

The proper development of any organ or tissue requires the coordinated expression of its underlying genes that can be located on different genomes present in an organism. For instance, each step in the development of seed for a higher plant is the consequence of gene interactions from the maternal, embryo and endosperm genomes.

RESULTS

We present a multivariate statistical model for mapping quantitative trait loci (QTL) by incorporating two important aspects of seed development in plants-QTL interactions derived from different genomes, the maternal, embryo and endosperm, and genetic correlations among phenotypic traits expressed in different genome-specific tissues. This model, which has a high dimensionality, is constructed within the maximum-likelihood context based on a finite mixture model. The implementation of the expectation-maximization algorithm allows for the efficient estimation of QTL positions, their action and interaction effects and pleiotropic effects. The application of this high-dimensional model to a real rice dataset has validated its usefulness.

CONCLUSIONS

Our model was derived for self-pollinated plants, but it can be extended to cross-pollinated plants and to animals. With the burgeoning of genetic and genomic data, this high-dimensional model will have many implications for agricultural and evolutionary genetic research.

AVAILABILITY

A package of software will be provided from the corresponding author upon request.

QTL detection for eating quality of cooked rice in a population of chromosome segment substitution lines

The genetic mechanism underlying six palatability properties of cooked rice and three physico-chemical traits was dissected in 66 BC(3)F(2) chromosome segment substitution lines (CSSLs), using a complete linkage map in three successive years. The CSSLs showed transgressive segregation for all traits studied. Significant correlation was detected among most palatability traits. A total of 25 QTLs for the nine traits were identified on nine chromosomes, and many QTLs affecting different quality traits were mapped in the same regions. Six QTLs--qLT-8 for luster, qTD-6 and qTD-8 for tenderness, qIVOE-6 and qIVOE-8 for integrated value of organoleptic evaluation, and qAC-8 for amylose content--were repeatedly detected across the 3 years. Phenotypic values were significantly different between the recurrent parent, cultivar Asominori, and the CSSLs harboring any of the six QTL alleles across the three environments, indicating that these six QTLs were non-environment-specific and could be used for marker-assisted selection in rice quality improvement.

QTL mapping of grain quality traits from the interspecific cross Oryza sativa x O. glaberrima

International rice export markets are increasing demands for rapid improvements in grain quality characteristics. The African rice Oryza glaberrima is a new potential source of genes that will enhance the eating, cooking, and milling properties of the rice grain. The objective of this research was to identify and characterize quantitative trait loci (QTLs) among 312 doubled haploid lines derived from the BC3F1 of an interspecific cross of O. sativa x O. glaberrima. Genetic material was planted in replicated plots and evaluated for ten grain quality traits in 2001 in Colombia. A linkage map was constructed with 100 polymorphic microsatellite markers using the mapdisto software program to adjust for segregation distortion. Transgressive segregation was observed for all traits. Interval and composite interval analyses identified 27 QTLs for nine characters located on 11/12 chromosomes. The chromosomal positions of QTLs for percentage amylose, alkali-spreading score, and percentage protein were in agreement with data reported by others, whereas QTL markers for percentage head rice, percentage milled rice, percentage protein, and percentage brown rice were different in our mapping population. Five major QTLs were found to be associated with improved percentage rice bran, percentage amylose, and alkali-spreading score. Seven QTLs for improved percentage rice bran, percentage milled rice, alkali-spreading score, percentage protein, and grain length/width ratio were derived from the O. glaberrima accession. Three new QTLs for percentage rice bran are reported here for the first time. Results from this study suggest that the African rice might be a valuable new source for introgression and improvement of several traits that affect quality traits demanded by the different rice export markets.