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Heterosis contributes greatly to crop production, but the genetic basis of heterosis is not fully understood. To identify heterotic loci (HLs) for grain yield, 12 yield traits were evaluated in four rice (Oryza sativa L.) mapping populations: one parental population of chromosome segment substitution lines derived from a cross between the japonica cultivar Nipponbare and indica cultivar 9311 and three connected test populations in either a homozygous 9311 genetic background or a heterozygous background. A total of 390 HLs were detected for the measured traits in two environments. The genetic bases of heterosis differed between the backcross and testcross populations. At least 10 HLs were confirmed in F1 hybrids between 9311 and near-isogenic lines, each of which carried a heterotic locus of interest in the same 9311 background. All 10 showed overdominant or dominant effects on grain yield and yield components. Among them, three were verified as being associated with yield heterosis and colocalized in the same regions as those containing previously reported heterosis-associated genes. Five HLs were identified to be promising candidate loci that could be used to achieve more than 15% yield heterosis in several commercial rice hybrids. These findings suggest the potential of indica or japonica introgression for increasing yield in hybrid rice breeding programs.

Rice grain oil is a valuable nutrient source. However, the genetic basis of oil biosynthesis in rice grains remains unclear. In this study, we performed a genome-wide association study on oil composition and oil concentration in a diverse panel of 533 cultivated rice accessions. High variation for 11 oil-related traits was observed, and the oil composition of rice grains showed differentiation among the subpopulations. We identified 46 loci that are significantly associated with grain oil concentration or composition, 16 of which were detected in three recombinant inbred line populations. Twenty-six candidate genes encoding enzymes involved in oil metabolism were identified from these 46 loci, four of which (PAL6, LIN6, MYR2, and ARA6) were found to contribute to natural variation in oil composition and to show differentiation among the subpopulations. Interestingly, population genetic analyses revealed that specific haplotypes of PAL6 and LIN6 have been selected in japonica rice. Based on these results, we propose a possible oil biosynthetic pathway in rice grains. Collectively, our results provide new insights into the genetic basis of oil biosynthesis in rice grains and can facilitate marker-based breeding of rice varieties with enhanced oil and grain quality.

Stigma exsertion, a key determinant of the rice mating system, greatly contributes to the application of heterosis in rice. Although a few quantitative trait loci associated with stigma exsertion have been fine mapped or cloned, the underlying genetic architecture remains unclear. We performed a genome-wide association study on stigma exsertion and related floral traits using 6.5 million SNPs characterized in 533 diverse accessions of Oryza sativa. We identified 23 genomic loci that are significantly associated with stigma exsertion and related traits, three of which are co-localized with three major grain size genes GS3, GW5, and GW2. Further analyses indicated that these three genes affected the stigma exsertion by controlling the size and shape of the spikelet and stigma. Combinations of GS3 and GW5 largely defined the levels of stigma exsertion and related traits. Selections of these two genes resulted in specific distributions of floral traits among subpopulations of O. sativa. The low stigma exsertion combination gw5GS3 existed in half of the cultivated rice varieties; therefore, introducing the GW5gs3 combination into male sterile lines is of high potential for improving the seed production of hybrid rice.

Liquid chromatography-mass spectrometry (LC-MS)-based metabolomics has been facilitated by the construction of MS(2) spectral tag (MS2T) library from the total scan ESI MS/MS data, and the development of widely targeted metabolomics method using MS/MS data gathered from authentic standards. In this report, a novel strategy called stepwise multiple ion monitoring-enhanced product ions (stepwise MIM-EPI) was developed to construct the MS2T library, in which stepwise MIM was used as survey scans to trigger the acquisition of EPI. A total number of 698 (almost) non-redundant metabolites with MS(2) spectra were obtained, of which 135 metabolites were identified/annotated. Integrating the data gathered from our MS2T library and other available multiple reaction monitoring (MRM) information, a widely targeted metabolomics method was developed to quantify 277 metabolites, including some phytohormones. Evaluation of the dehydration responses and natural variations of these metabolites in rice leaf not only suggested the coordinated regulation of abscisic acid (ABA) with metabolites such as serotonin derivative(s), polyamine conjugates under drought stress, but also revealed some C-glycosylated flavones as the potential markers for the discrimination of indica and japonica rice subspecies. The new MS2T library construction and widely targeted metabolomics strategy could be used as a tool for rice functional genomics.

Rice yield and heading date are two distinct traits controlled by quantitative trait loci (QTLs). The dissection of molecular mechanisms underlying rice yield traits is important for developing high-yielding rice varieties. Here, we report the cloning and characterization of Ghd8, a major QTL with pleiotropic effects on grain yield, heading date, and plant height. Two sets of near isogenic line populations were developed for the cloning of Ghd8. Ghd8 was narrowed down to a 20-kb region containing two putative genes, of which one encodes the OsHAP3 subunit of a CCAAT-box binding pro- tein (HAP complex); this gene was regarded as the Ghd8 candidate. A complementary test confirmed the identity and pleiotropic effects of the gene; interestingly, the genetic effect of Ghd8 was dependent on its genetic background. By regulating Ehd1, RFT1, and Hd3a, Ghd8 delayed flowering under long-day conditions, but promoted flowering under short-day conditions. Ghd8 up-regulated MOC1, a key gene controlling tillering and branching; this increased the number of tillers, primary and secondary branches, thus producing 50% more grains per plant. The ectopic expression of Ghd8 in Arabidopsis caused early flowering by 10 d—a situation similar to the one observed by its homolog AtHAP3b, when com- pared to wild-type under long-day conditions; these findings indicate the conserved function of Ghd8 and AtHAP3b in flowering in Arabidopsis. Our results demonstrated the important roles of Ghd8 in rice yield formation and flowering, as well as its opposite functions in flowering between rice and Arabidopsis under long-day conditions.

Traits related to plant development and lodging resistance in 292 rice recombinant inbred lines (RILs) were investigated by dissecting QTLs affecting four basal internodal traits of the main stem, lengths of five elongated internodes contributing to plant height (PH), and three traits related to heading date (HD). The RILs showed tremendous transgressive segregation for all the traits and a total of 41 genomic regions associated with one or more measured traits were detected. These included 17 QTL regions affecting one or more basal internodal traits, 21 associated with one or more PH and related traits, and 12 for HD and/or its component traits. Of the 21 genomic regions associated with PH traits, two QTL clusters on chromosomes 6 and 10 were expressed consecutively during rice development, and the remaining 19 QTLs appeared to be expressed at one or more specific developmental stages, revealing an important aspect of the relationship between PH and its component traits. The transition from the vegetative growth to the reproductive stage in rice appeared to have a large effect on QTL expression, reflected by the different behaviors of most QTLs affecting panicle length from other PH QTLs. The 17QTL regions associated with one or more basal internodal traits plus nine QTLs affecting two lower elongated internodes were expected to contribute to lodging resistance (LR) of rice. The large allelic differences at these QTLs between japonica and indica parents imply that improved LR in rice can be readily achieved by combining large numbers of QTL alleles affecting stem length, strength, and thickness in indica/japonica crosses. Specific expression patterns of the identified QTLs and their contributions to morphological traits related to plant development and LR are expected to provide important information for marker-assisted improvement of the target traits in rice and cloning genes underlying QTL of interest.

Low and unstable rice productivity in many areas of Asia is associated with many abiotic and biotic stresses such as drought, salinity, anaerobic conditions during germination, submergence, phosphorus and zinc deficiency, etc. To develop rice varieties with tolerance to these stresses, we undertook a large backcross (BC) breeding effort for the last 6 years, using three recurrent elite rice lines and 203 diverse donors, which represent a significant portion of the genetic diversity in the primary gene pool of rice. Significant progress has been made in the BC breeding program, which resulted in development of large numbers ofintrogression lines with improved tolerance to these stresses. Promising lines have been developed with excellent tolerances (extreme phenotypes) to salinity, submergence and zinc deficiency; resistance to brown plant hopper, ability to germinate under the anaerobic condition and low temperature. Our results indicated that there exist tremendous amounts of ‘hidden’ diversity for abiotic and biotic stress tolerances in the primary gene pool of rice. Furthermore, we demonstrated that despite the complex genetics and diverse physiological mechanisms underlying the abiotic stress tolerances, introgression of genes from a diverse source of donors into elitegenetic backgrounds through BC breeding and efficient selection (careful screening under severestress) is a powerful way to exploit this hidden diversity for improving abiotic stress tolerances of rice. We have developed three large sets of introgression lines, which not only provide an unique platform of breeding materials for developing new rice cultivars with superior yield and stability by trait/gene pyramiding, but also represent unique genetic stocks for a large-scale discovery of genes/alleles underlying the abiotic and biotic stress tolerances of rice using genomic tools. # 2005 Elsevier B.V. All rights reserved.

A large-scale backcross breeding project has been undertaken to improve drought tolerance in rice. Over 160 donor cultivars from 25 countries have been used in this project, representing a significant proportion of the genetic variation in cultivated rice. These cultivars were evaluated in field experiments in the Philippines to assess their responses to drought in terms of plant height, heading date, and grain yield. Drought was imposed near heading stage, in experiments that were established either in lowland (anaerobic) fields or upland (aerobic) soil. Despite the poor adaptation of some cultivars to the tropics, it was possible to identify significant variation in plant response to drought treatments, and contrasting effects on flowering delay and growth. Subsequently, 325 BC2F2 bulk populations, developed by backcrossing many of these donors to one of three elite recurrent parents, were screened under drought in lowland or upland nurseries. Stress levels were managed to eliminate almost all seed set in recurrent parents, and those progeny that produced grain were selected as being putatively drought-tolerant. The selection intensity varied across years and in selection environments with more severe stress, higher selection intensity could be imposed. The number of plants selected within a population was not associated with the per se drought response of the donors in the direct evaluation, indicating the wide presence of cryptic genetic variation for drought tolerance in the apparently drought-susceptible cultivars. The genetic background of the recurrent parent affected the number of plants selected, as did the selection environment (upland versus lowland nurseries). These drought-selected introgression lines represent a useful genetic resource to develop improved cultivars for farmers in rainfed or water-scarce rice-growing regions, and also to improve our understanding of the genetic and molecular basis of drought tolerance in rice. Genetic analysis of the selected lines, reported elsewhere, indicated specific regions of high introgression. Yield evaluations of the selected lines are now underway across a range of drought scenarios.

Seedling-vigor is important for optimum stand establishment and increasing weed competitive ability in rice cropping systems. In the current study, three seedling-vigor-related traits, seed germination rate, seedling shoot length and dry matter weight, were investigated by the paper-roll tests with rice recombinant inbred lines derived from a cross between Lemont ( japonica ) and Teqing ( indica ). The phenotype data, together with a linkage map consisting of 198 marker loci, was used to conduct composite interval mapping by QTLMapper 1.0 to simultaneously map both main-effect and epistatic QTLs for seedling-vigor in rice. Totally, 13 putative main-effect QTLs and 19 pairs of epistatic loci with R 2 ≥ 5% were identified. Almost all of these QTLs or interactions individually explained only around 5–10% of the phenotypic variation. The majority (68%) of these main-effect and epistatic loci were clustered in seven chromosome regions, each spanning 12–28 cM (centi-Morgan) and containing three or more detectable loci. When detectable for the multiple seedling-vigor-related traits, either the main-effect QTLs or the epistatic interactions sharing the same map location had their additive or epistatic effects in the same direction, which agreed well with the positive correlations among the traits. The results demonstrated that seedling-vigor in rice could be controlled by many loci, most of which had small effects, but, relatively, epistasis as a genetic factor was much more important than main-effects of QTLs. Along with the results reported previously, this study revealed the extensive genetic diversity for seedling-vigor in rice. In addition, the QTL q SV-7 on chromosome 7 was found to have the largest main-effects on multiple seedling-vigor-related traits and therefore could be used as a potential target to be genetically manipulated by marker-assisted selection in rice seedling-vigor breeding programs.