Rice Recombinant Inbred Lines Research Articles

Limitation of Unloading in the Developing Grains Is a Possible Cause Responsible for Low Stem Non-structural Carbohydrate Translocation and Poor Grain Yield Formation in Rice through Verification of Recombinant Inbred Lines.

Remobilisation of non-structural carbohydrates (NSC) from leaves and stems and unloading into developing grains are essential for yield formation of rice. In present study, three recombinant inbred lines of rice, R91, R156 and R201 have been tested for source-flow-sink related attributes determining the nature of NSC accumulation and translocation at two nitrogen levels in the field. Compared to R91 and R156, R201 had lower grain filling percentage, harvest index, and grain yield. Meanwhile, R201 had significantly lower stem NSC translocation during grain filling stage. Grain filling percentage, harvest index, and grain yield showed the consistent trend with stem NSC translocation among the three lines. In comparison with R91 and R156, R201 had similarity in leaf area index, specific leaf weight, stem NSC concentration at heading, biomass, panicles m-2, spikelets per panicle, remobilization capability of assimilation in stems, sink capacity, sink activity, number and cross sectional area of small vascular bundles, greater number and cross sectional area of large vascular bundles, and higher SPAD, suggesting that source, flow, and sink were not the limiting factors for low stem NSC translocation and grain filling percentage of R201. However, R201 had significant higher stem and rachis NSC concentrations at maturity, which implied that unloading in the developing grains might result in low NSC translocation in R201. The results indicate that stem NSC translocation could be beneficial for enhancement of grain yield potential, and poor unloading into caryopsis may be the possible cause of low stem NSC translocation, poor grain filling and yield formation in R201.

Low straw phosphorus concentration is beneficial for high phosphorus use efficiency for grain production in rice recombinant inbred lines

The objective of this study was to comprehensively investigate the relationship of phosphorus (P) concentration and accumulation with yield formation and P use efficiency for grain production (PUEg) using 127 rice recombinant inbred lines grown in a working field under low (LP) and high P (HP) conditions. Phosphorus concentration and accumulation, P translocation (PT) and translocation efficiency (PTE), PUEg, P harvest index (PHI), grain yield, and grain yield components were investigated. Wide ranges in grain yield, straw P concentration, total P accumulation, and PUEg were observed under LP and HP conditions. Coefficients of variance showed that the grain P concentration was considerably conserved, whereas the straw P concentration was relatively variable among inbred lines. In comparison with grain P, straw P made a larger contribution to total P accumulation (PUP) at maturity. Growth duration had no substantial effect on PUEg and positively affected P accumulation under both P conditions; however, it negatively affected the grain P concentration under the HP condition. The straw P concentration was negatively correlated with the grain filling percentage and harvest index. PUEg was negatively correlated with the grain and straw P concentrations, suggesting that low P concentrations, especially in straw, favored a high PUEg. There was no correlation between the P concentrations in grain and straw. The correlation analysis indicated that low straw P concentrations might be partly attributed to high PTE and PHI values. These results show that low straw P concentrations may simultaneously improve PUEg and grain yield by enhancing P translocation into grain, thus reducing the need for P fertilizer application.

Assessment of polymorphism at molecular level, association studies, multivariate analysis and genetic diversity among recombinant inbred lines of rice (Oryza sativa L.)

Assessment of polymorphism at molecular level, association studies, multivariate analysis and genetic diversity among recombinant inbred lines of rice (<i>Oryza sativa</i> L.)

An Integrative Genetic Study of Rice Metabolism, Growth and Stochastic Variation Reveals Potential C/N Partitioning Loci.

Studying the genetic basis of variation in plant metabolism has been greatly facilitated by genomic and metabolic profiling advances. In this study, we use metabolomics and growth measurements to map QTL in rice, a major staple crop. Previous rice metabolism studies have largely focused on identifying genes controlling major effect loci. To complement these studies, we conducted a replicated metabolomics analysis on a japonica (Lemont) by indica (Teqing) rice recombinant inbred line population and focused on the genetic variation for primary metabolism. Using independent replicated studies, we show that in contrast to other rice studies, the heritability of primary metabolism is similar to Arabidopsis. The vast majority of metabolic QTLs had small to moderate effects with significant polygenic epistasis. Two metabolomics QTL hotspots had opposing effects on carbon and nitrogen rich metabolites suggesting that they may influence carbon and nitrogen partitioning, with one locus co-localizing with SUSIBA2 (WRKY78). Comparing QTLs for metabolomic and a variety of growth related traits identified few overlaps. Interestingly, the rice population displayed fewer loci controlling stochastic variation for metabolism than was found in Arabidopsis. Thus, it is possible that domestication has differentially impacted stochastic metabolite variation more than average metabolite variation.

Fine mapping of consistent quantitative trait loci for yield under drought stress using rice (Oryza sativa) recombinant inbred lines adapted to rainfed environment

Fine mapping of consistent quantitative trait loci for yield under drought stress using rice (Oryza sativa) recombinant inbred lines adapted to rainfed environment

Fine mapping of consistent quantitative trait loci for yield under drought stress using rice (Oryza sativa) recombinant inbred lines adapted to rainfed environment

Drought stress is a serious constraint, especially in rainfed rice production, and breeding for drought tolerance by selection based on yield under stress, though effective, is slow Mapping quantitative trait loci (QTLs) for yield and its components under drought stress predominant in rainfed target populations of environment (TPE) will help overcome this limitation. In the present study, a subset of 143 F8 and F9 recombinant inbred (RI) lines derived from IR62266-42-6-2 (IR62266), a high-yielding indica ecotype and Norungan, a landrace from TPE, was used to map QTLs for yield and its components under drought predominant in TPE. A large effect yield QTL observed under drought stress in TPE was consistent across two years with a phenotypic variation of 31.3% and 37.9% and additive effect of 629.2 and 424.9 kg/ha Further, this region was fine-mapped to 94.0 kb with positive effect on grain yield under stress.

Mapping Consistent Rice (Oryza sativa L.) Yield QTLs under Drought Stress in Target Rainfed Environments.

BackgroundDrought stress is a major limitation to rainfed rice production and yield stability. Identifying yield-associated quantitative trait loci (QTLs) that are consistent under drought stress predominant in target production environments, as well as across different genetic backgrounds, will help to develop high-yielding rice cultivars suitable for water-limited environments through marker-assisted breeding (MAB). Considerable progress has been made in mapping QTLs for drought resistance traits in rice; however, few have been successfully used in MAB.ResultsRecombinant inbred lines of IR20 × Nootripathu, two indica cultivars adapted to rainfed target populations of environments (TPEs), were evaluated in one and two seasons under managed stress and in a rainfed target drought stress environment, respectively. In the managed stress environment, the severity of the stress meant that measurements could be made only on secondary traits and biomass. In the target environment, the lines experienced varying timings, durations, and intensities of drought stress. The rice recombinant inbred lines exhibited significant genotypic variation for physio-morphological, phenological, and plant production traits under drought. Nine and 24 QTLs for physio-morphological and plant production traits were identified in managed and natural drought stress conditions in the TPEs, respectively. Yield QTLs that were consistent in the target environment over seasons were identified on chromosomes 1, 4, and 6, which could stabilize the productivity in high-yielding rice lines in a water-limited rainfed ecosystem. These yield QTLs also govern highly heritable key secondary traits, such as leaf drying, canopy temperature, panicle harvest index and harvest index.ConclusionThree QTL regions on chromosome 1 (RM8085), chromosome 4 (I12S), and chromosome 6 (RM6836) harbor significant additive QTLs for various physiological and yield traits under drought stress. The similar chromosomal region on 4 and 6 were found to harbor QTLs for canopy temperature and leaf drying under drought stress conditions. Thus, the identified large effect yield QTLs could be introgressed to develop rice lines with stable yields under varying natural drought stress predominant in TPEs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-015-0053-6) contains supplementary material, which is available to authorized users.

Allelic effects on starch structure and properties of six starch biosynthetic genes in a rice recombinant inbred line population.

BackgroundThe genetic diversity of six starch biosynthetic genes (Wx, SSI, SSIIa, SBEI, SBEIIa and SBEIIb) in indica and japonica rices opens an opportunity to produce a new variety with more favourable grain starch quality. However, there is limited information about the effects of these six gene allele combinations on starch structure and properties. A recombinant inbred line population from a cross between indica and japonica varieties offers opportunities to combine specific alleles of the six genes.ResultsThe allelic (indica vs japonica) effects of six starch biosynthetic genes on starch structure, functional properties, and abundance of granule bound proteins in rice grains were investigated in a common genetic background using a recombinant inbred line population. The indica Wx (Wxi) allele played a major role while indica SSI (SSIi), japonica SSIIa (SSIIaj) and indica SBEI (SBEIi) alleles had minor roles on the increase of amylose content. SSIIaj and japonica SBEIIb (SBEIIbj) alleles had a major and a minor role on high ratio of ∑DP ≤ 10 to ∑DP ≤ 24 fractions (RCL10/24), respectively. Both major alleles (Wxi and SSIIaj) reduced peak viscosity (PV), onset, peak and end gelatinization temperatures (GTs) of amylopectin, and increased amylose-lipid complex dissociation enthalpy compared with their counterpart-alleles, respectively. SBEIIai and SBEIIbj decreased PV, whereas SSIi and SBEIIbj decreased FV. SBEIi reduced setback viscosity and gelatinization enthalpy. RCL10/24 of chain length distribution in amylopectin is negatively correlated with PV and BD of paste property and GTs of thermal properties. We also report RILs with superior starch properties combining Wxi, SSIj, SSIIaj, SBEIi and SBEIIbj alleles. Additionally, a clear relation is drawn to starch biosynthetic gene alleles, starch structure, properties, and abundance of granule bound starch biosynthetic enzymes inside starch granules.ConclusionsRice Wxi and SSIIaj alleles play major roles, while SSIi, SBEIi, SBEIIai and SBEIIbj alleles have minor roles in the determination of starch properties between indica and japonica rice through starch structural modification. The combination of these alleles is a key factor for starch quality improvement in rice breeding programs. RCL10/24 value is critical for starch structure and property determination.

WIPPER: an accurate and efficient field phenotyping platform for large-scale applications.

More accurate, rapid, and easy phenotyping tools are required to match the recent advances in high-throughput genotyping for accelerating breeding and genetic analysis. The conventional data recording in field notebooks and then inputting data to computers for further analysis is inefficient, time-consuming, laborious, and prone to human error. Here, we report WIPPER (for Wireless Plant Phenotyper), a new phenotyping platform that combines field phenotyping and data recording with the aid of Bluetooth communication, thus saving time and labor not only for field data recoding but also for inputting data to computers. Additionally, it eliminates the risk of human error associated with phenotyping and inputting data. We applied WIPPER to 100 individuals of a rice recombinant inbred line (RIL) for measuring leaf width and relative chlorophyll content (SPAD value), and were able to record an accurate data in a significantly reduced time compared with the conventional method of data collection. We are currently using WIPPER for routine management of rice germplasm including recording and documenting information on phenotypic data, seeds, and DNA for their accelerated utilization in crop breeding.

Registration of a Rice Gene Mapping Population of Lemont × Jasmine 85 Recombinant Inbred Lines

A mapping population developed from a cross of rice (Oryza sativa L.) tropical japonica cultivar Lemont and indica cultivar Jasmine 85 was developed to facilitate genetic studies for important agronomic traits. The indica- and tropical japonica-based rice recombinant inbred line (RIL) mapping population has been used to identify genomic regions associated with resistance to sheath blight (caused by Rhizoctonia solani) and rice blast (caused by Magnaporthe oryzae). The Lemont × Jasmine 85 mapping population, also referred to as SB5 (Reg. No. MP-7, NSL 506950), was developed under the Rice Coordinated Agricultural Project (RiceCAP) and released on 31 Aug. 2009 by the USDA–ARS and University of Arkansas, Division of Agriculture. The mapping population has 572 F2:8 RILs, 256 of which were used to construct a linkage map using simple sequence repeat markers to identify quantitative trait loci for sheath blight and blast resistance. This mapping population and related datasets represent a valuable resource for basic rice genomic research and applied marker-assisted breeding efforts in disease resistance and other agronomic traits.

Predicting hybrid performance in rice using genomic best linear unbiased prediction.

Genomic selection is an upgrading form of marker-assisted selection for quantitative traits, and it differs from the traditional marker-assisted selection in that markers in the entire genome are used to predict genetic values and the QTL detection step is skipped. Genomic selection holds the promise to be more efficient than the traditional marker-assisted selection for traits controlled by polygenes. Genomic selection for pure breed improvement is based on marker information and thus leads to cost-saving due to early selection before phenotypes are measured. When applied to hybrid breeding, genomic selection is anticipated to be even more efficient because genotypes of hybrids are predetermined by their inbred parents. Hybrid breeding has been an important tool to increase crop productivity. Here we proposed and applied an advanced method to predict hybrid performance, in which a subset of all potential hybrids is used as a training sample to predict trait values of all potential hybrids. The method is called genomic best linear unbiased prediction. The technology applied to hybrids is called genomic hybrid breeding. We used 278 randomly selected hybrids derived from 210 recombinant inbred lines of rice as a training sample and predicted all 21,945 potential hybrids. The average yield of top 100 selection shows a 16% increase compared with the average yield of all potential hybrids. The new strategy of marker-guided prediction of hybrid yields serves as a proof of concept for a new technology that may potentially revolutionize hybrid breeding.

Effect of Environment on Yield and Quality of Rice Recombinant Inbred Lines

Global climate change affects not only rice yield but also grain quality. A better understanding of the effect of environment factors on rice yield and quality provides information for breeding new varieties adapted to a changing world. This study uses indica-japonica recombinant inbred lines (RILs) constructed in different ecological regions of China as test materials. The objectives were to determine the effect of environment on rice yield and quality. The results revealed that: the yield of RILs in Liaoning was greater than that in the other regions, milling and appearance qualities in Sichuan and Guangdong were worse than that in Liaoning and Shanghai. High temperature and high relative humidity combined with low sunshine duration were the main reason for lower milling quality and greater chalkiness traits. The air temperature during heading stage and maturity stage seemed more important for rice milling and appearance qualities throughout the growing season.

An expression quantitative trait loci-guided co-expression analysis for constructing regulatory network using a rice recombinant inbred line population

The ability to reveal the regulatory architecture of genes at the whole-genome level by constructing a regulatory network is critical for understanding the biological processes and developmental programmes of organisms. Here, we conducted an eQTL-guided function-related co-expression analysis to identify the putative regulators and construct gene regulatory network. We performed an eQTL analysis of 210 recombinant inbred lines (RILs) derived from a cross between two indica rice lines, Zhenshan 97 and Minghui 63, the parents of an elite hybrid, using data obtained by hybridizing RNA samples of flag leaves at the heading stage with Affymetrix whole-genome arrays. Making use of an ultrahigh-density single-nucleotide polymorphism bin map constructed by population sequencing, 13 647 eQTLs for 10 725 e-traits were detected, comprising 5079 cis-eQTLs (37.2%) and 8568 trans-eQTLs (62.8%). The analysis revealed 138 trans-eQTLs hotspots, each of which apparently regulates the expression variations of many genes. Co-expression analysis of functionally related genes within the framework of regulator–target relationships outlined by the eQTLs led to the identification of putative regulators in the system. The usefulness of the strategy was demonstrated with the genes known to be involved in flowering. We also applied this strategy to the analysis of QTLs for yield traits, which also suggested likely candidate genes. eQTL-guided co-expression analysis may provide a promising solution for outlining a framework for the complex regulatory network of an organism.

Dynamics of Starch Content and the Expression Profile of the Genes Involved in Starch Metabolism in Culms of Rice Recombinant Inbred Lines after Heading

Dynamics of Starch Content and the Expression Profile of the Genes Involved in Starch Metabolism in Culms of Rice Recombinant Inbred Lines after Heading

QTL Mapping for Hull Thickness and Related Traits in Hybrid Rice Xieyou 9308

We conducted a quantitative trait locus (QTL) analysis of 165 rice recombinant inbred lines derived from a cross between Zhonghui 9308 (Z9308) and Xieqingzao B (XB) in Hainan and Hangzhou, China. Grain thickness (GT), brown rice thickness (BRT), hull thickness (HT) and milling quality were used for QTL mapping. HT was significantly and positively correlated with GT and BRT. Twenty-nine QTLs were detected with phenotypic effects ranging from 2.80% to 21.27%. Six QTLs, qGT3, qBRT3, qBRT4, qHT6.1, qHT8 and qHT11, were detected repeatedly across two environments. Inherited from XB, qHT6.1, qHT8 and qHT11 showed stable expression, explaining 9.92%, 21.27% and 10.83% of the phenotypic variances in Hainan and 9.61%, 6.40% and 6.71% in Hangzhou, respectively. Additionally, the QTL cluster between RM5944 and RM5626 on chromosome 3 was probably responsible for GT and milling quality. The cluster between RM6992 and RM6473 on chromosome 4 played an important role in grain filling. Three near isogenic lines (NILs), X345, X338 and X389, were selected because they contained homozygous fragments from Zhonghui 9308, corresponding to qHT6.1, qHT8 and qHT11, respectively. The hull of XB was thicker than those of X345, X338 and X389. In all the lines, qHT6.1, qHT8 and qHT11 that regulated rice HT were stably inherited with obvious genetic effects.

Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations

Genotyping by sequencing (GBS) is the latest application of next-generation sequencing protocols for the purposes of discovering and genotyping SNPs in a variety of crop species and populations. Unlike other high-density genotyping technologies which have mainly been applied to general interest "reference" genomes, the low cost of GBS makes it an attractive means of saturating mapping and breeding populations with a high density of SNP markers. One barrier to the widespread use of GBS has been the difficulty of the bioinformatics analysis as the approach is accompanied by a high number of erroneous SNP calls which are not easily diagnosed or corrected. In this study, we use a 384-plex GBS protocol to add 30,984 markers to an indica (IR64)×japonica (Azucena) mapping population consisting of 176 recombinant inbred lines of rice (Oryza sativa) and we release our imputation and error correction pipeline to address initial GBS data sparsity and error, and streamline the process of adding SNPs to RIL populations. Using the final imputed and corrected dataset of 30,984 markers, we were able to map recombination hot and cold spots and regions of segregation distortion across the genome with a high degree of accuracy, thus identifying regions of the genome containing putative sterility loci. We mapped QTL for leaf width and aluminum tolerance, and were able to identify additional QTL for both phenotypes when using the full set of 30,984 SNPs that were not identified using a subset of only 1,464 SNPs, including a previously unreported QTL for aluminum tolerance located directly within a recombination hotspot on chromosome 1. These results suggest that adding a high density of SNP markers to a mapping or breeding population through GBS has a great value for numerous applications in rice breeding and genetics research.

Molecular mapping of quantitative trait loci for flag leaf length and other agronomic traits in rice(Oryza sativa)

Flag leaf architecture is a very important trait which ensures the yield bearing capacity of plants by providing excellent source for photosynthesis. In this study, quantitative trait loci (QTLs) for flag leaf length and other traits were identified using rice recombinant inbred lines (RILs) derived from HP2216 × Tetep. A total of 12 QTLs were identified for the four traits located on seven different chromosomes of rice and analysis of interaction among the QTLs revealed additive effect for the leaf length and epistatic main effect for panicle length. More interestingly a QTL qLL12.1 responsible for the flag leaf length was identified on chromosome 12 within the marker interval RM247-RM6296 consistently at three climatic zones in India. Furthermore to saturate the qLL12.1 interval, additional 58 simple sequence repeat (SSR) markers were used for polymorphism survey which showed that qLL12.1 region was more conserved among parental lines. Finally, two polymorphic SSR markers were used for saturation of qLL12.1 region. Consequently, candidate gene approach was used to compliment QTL mapping. Co-localization of linkage map with physical map revealed 75 genes with evidence for expression. Functional annotation of these genes using in silico approaches and detailed literature search revealed nine candidate genes for flag leaf length. The stable QTL qLL12.1 identified in this study will provide starting point for map based cloning of leaf length related genes and tightly linked flanking markers can be used in marker assisted breeding programmes.

A Pyramid Breeding of Eight Grain-yield Related Quantitative Trait Loci Based on Marker-assistant and Phenotype Selection in Rice (Oryza sativa L.)

1000-Grain weight and spikelet number per panicle are two important components for rice grain yield. In our previous study, eight quantitative trait loci (QTLs) conferring spikelet number per panicle and 1000-grain weight were mapped through sequencing-based genotyping of 150 rice recombinant inbred lines (RILs). In this study, we validated the effects of four QTLs from Nipponbare using chromosome segment substitution lines (CSSLs), and pyramided eight grain yield related QTLs. The new lines containing the eight QTLs with positive effects showed increased panicle and spikelet size as compared with the parent variety 93-11. We further proposed a novel pyramid breeding scheme based on marker-assistant and phenotype selection (MAPS). This scheme allowed pyramiding of as many as 24 QTLs at a single hybridization without massive cross work. This study provided insights into the molecular basis of rice grain yield for direct wealth for high-yielding rice breeding.

Fragrance Analysis among Recombinant Inbred Lines of Rice

Fragrance Analysis among Recombinant Inbred Lines of Rice

Tissue culture-induced alteration in cytosine methylation in new rice recombinant inbred lines

Zizania DNA introgression could induce a large number of genetic and epigenetic changes of the new rice recombinant inbred lines genome. In this present study, we employed inter-simple sequence repeat (ISSR) to further study the genetic and epigenetic changes that are induced by tissue culture. Changes induced by tissue culture are mostly epigenetic. One kind of methylation alterations is that the unmethylated CCGG sequence was transformed into external hemimethylated cytosines. This type change, however, did not transmit to progenies of the plant. Another kind of methylation alterations is tissue culture-induced occurrence of de novo methylation at the external cytosines of the CCGG sites that are originally with hyper-methylated internal cytosines. Interestingly, many of these methylated external cytosines became demethylated again upon plant regeneration, implying that the hypomethylated state of these loci is required for successful plant regeneration. Because the changed methylation patterns are highly similar among calli subcultured for different intervals, and because apparent concordance exists between randomly selected individual regenerants, we are tempted to deduce that the DNA methylation changes did not occur randomly, rather, the methylation events likely to have hot spots, and/or occur non-randomly. Sequence analysis indicates that the loci underwent methylation alterations are predominantly genic, sharing significant homology to known-function genes or expressed sequence tag (EST) sequences. This finding implies that the epigenetic changes induced by tissue culture could potentially affect the expression of the relevant genes.