Natural variation of OsML1, a mitochondrial transcription termination factor, contributes to mesocotyl length variation in rice.

Mesocotyl length (ML) is a crucial factor in determining the establishment and yield of rice planted through dry direct seeding, a practice that is increasingly popular in rice production worldwide. ML is determined by the endogenous and external environments, and inherits as a complex trait. To date, only a few genes have been cloned, and the mechanisms underlying mesocotyl elongation remain largely unknown. Here, through a genome-wide association study using sequenced germplasm, we reveal that natural allelic variations in a mitochondrial transcription termination factor, OsML1, predominantly determined the natural variation of ML in rice. Natural variants in the coding regions of OsML1 resulted in five major haplotypes with a clear differentiation between subspecies and subpopulations in cultivated rice. The much-reduced genetic diversity of cultivated rice compared to the common wild rice suggested that OsML1 underwent selection during domestication. Transgenic experiments and molecular analysis demonstrated that OsML1 contributes to ML by influencing cell elongation primarily determined by H2 O2 homeostasis. Overexpression of OsML1 promoted mesocotyl elongation and thus improved the emergence rate under deep direct seeding. Taken together, our results suggested that OsML1 is a key positive regulator of ML, and is useful in developing varieties for deep direct seeding by conventional and transgenic approaches.

Upland rice genomic signatures of adaptation to drought resistance and navigation to molecular design breeding.

Upland rice is a distinctive drought-aerobic ecotype of cultivated rice highly resistant to drought stress. However, the genetic and genomic basis for the drought-aerobic adaptation of upland rice remains largely unclear due to the lack of genomic resources. In this study, we identified 25 typical upland rice accessions and assembled a high-quality genome of one of the typical upland rice varieties, IRAT109, comprising 384 Mb with a contig N50 of 19.6 Mb. Phylogenetic analysis revealed upland and lowland rice have distinct ecotype differentiation within the japonica subgroup. Comparative genomic analyses revealed that adaptive differentiation of lowland and upland rice is likely attributable to the natural variation of many genes in promoter regions, formation of specific genes in upland rice, and expansion of gene families. We revealed differentiated gene expression patterns in the leaves and roots of the two ecotypes and found that lignin synthesis mediated by the phenylpropane pathway plays an important role in the adaptive differentiation of upland and lowland rice. We identified 28 selective sweeps that occurred during domestication and validated that the qRT9 gene in selective regions can positively regulate drought resistance in rice. Eighty key genes closely associated with drought resistance were appraised for their appreciable potential in drought resistance breeding. Our study enhances the understanding of the adaptation of upland rice and provides a genome navigation map of drought resistance breeding, which will facilitate the breeding of drought-resistant rice and the "blue revolution" in agriculture.

Lost genome segments associate with trait diversity during rice domestication.

BACKGROUND: DNA mutations of diverse types provide the raw material required for phenotypic variation and evolution. In the case of crop species, previous research aimed to elucidate the changing patterns of repetitive sequences, single-nucleotide polymorphisms (SNPs), and small InDels during domestication to explain morphological evolution and adaptation to different environments. Additionally, structural variations (SVs) encompassing larger stretches of DNA are more likely to alter gene expression levels leading to phenotypic variation affecting plant phenotypes and stress resistance. Previous studies on SVs in rice were hampered by reliance on short-read sequencing limiting the quantity and quality of SV identification, while SV data are currently only available for cultivated rice, with wild rice largely uncharacterized. Here, we generated two genome assemblies for O. rufipogon using long-read sequencing and provide insights on the evolutionary pattern and effect of SVs on morphological traits during rice domestication. RESULTS: In this study, we identified 318,589 SVs in cultivated and wild rice populations through a comprehensive analysis of 13 high-quality rice genomes and found that wild rice genomes contain 49% of unique SVs and an average of 1.76% of genes were lost during rice domestication. These SVs were further genotyped for 649 rice accessions, their evolutionary pattern during rice domestication and potential association with the diversity of important agronomic traits were examined. Genome-wide association studies between these SVs and nine agronomic traits identified 413 candidate causal variants, which together affect 361 genes. An 824-bp deletion in japonica rice, which encodes a serine carboxypeptidase family protein, is shown to be associated with grain length. CONCLUSIONS: We provide relatively accurate and complete SV datasets for cultivated and wild rice accessions, especially in TE-rich regions, by comparing long-read sequencing data for 13 representative varieties. The integrated rice SV map and the identified candidate genes and variants represent valuable resources for future genomic research and breeding in rice.

Genome-Wide Association Study for Seed Dormancy Using Re-Sequenced Germplasm under Multiple Conditions in Rice.

Seed dormancy is a key factor used to determine seed germination in rice production. So far, only a few genes controlling seed dormancy have been reported, and the genetic mechanism of rice seed dormancy is still elusive. In this study, a population of 195 diverse re-sequenced accessions from 40 countries was evaluated for the seed germination rate (GR) without dormancy breaking (WDB) as a control and under dry heating (DH) and gibberellic acid (GA) treatments, as dormancy breaking agents to identify QTLs for seed dormancy. Phenotypic assessment revealed that these accessions had abundant variations in seed dormancy. GWAS using 1,120,223 high-quality single nucleotide polymorphisms (SNPs) and a mixed linear model (MLM) incorporating both principal components (PCs) and kinship (K) identified 30 QTLs on 10 chromosomes, accounting for 7.3-20.4% of the phenotypic variance in GR. Ten of the QTLs were located in the regions of previously reported QTLs, while the rest were novel ones. Thirteen high-confidence candidate genes were predicted for the four QTLs detected in two or three conditions (qGR4-4, qGR4-5, qGR8 and qGR11-4) and one QTL with a large effect (qGR3). These genes were highly expressed during seed development and were significantly regulated by various hormone treatments. This study provides new insights into the genetic and molecular basis of rice seed dormancy/germination. The accessions with moderate and strong dormancy and markers for the QTLs and candidate genes are useful for attaining a proper level of seed dormancy.

OsNAC15 Regulates Tolerance to Zinc Deficiency and Cadmium by Binding to OsZIP7 and OsZIP10 in Rice.

Zinc (Zn) deficiency and cadmium (Cd) stress are severe threats to the growth and development of plants. Increasing Zn content and/or decreasing Cd content in grain are also important objectives of rice breeding. However, the molecular mechanisms of Zn deficiency tolerance (ZDT) and Cd stress tolerance (CDT) are largely unknown in rice. Here, we report that a NAM/CUC2-like transcription factor, OsNAC15, contributes to ZDT and CDT in rice. Knockout of OsNAC15 reduced ZDT and CDT at the vegetative stage. OsNAC15 expresses in all tissues of different developmental stages, and is repressed by Zn deficiency and induced by Cd stress. OsNAC15 is a functional transcription factor with transactivation and DNA binding activities. Expression analysis of rice ZIP family genes suggested that the knockout of OsNAC15 activates or inhibits their transcriptions under Zn deficiency or Cd stress conditions. The yeast one-hybrid assay, transient transcriptional activity assay using the dual-luciferase reporter system and electrophoretic mobility shift assay demonstrated that OsNAC15 directly binds to the zinc deficiency-responsive element motifs in the promoters of OsZIP7 and OsZIP10 to repress their transcriptions. The OsNAC15-OsZIP7/10 module is an essential foundation for further study on the regulatory mechanisms of ZDT and CDT in rice.

Loci and natural alleles underlying robust roots and adaptive domestication of upland ecotype rice in aerobic conditions.

A robust (long and thick) root system is characteristic of upland japonica rice adapted to drought conditions. Using deep sequencing and large scale phenotyping data of 795 rice accessions and an integrated strategy combining results from high resolution mapping by GWAS and linkage mapping, comprehensive analyses of genomic, transcriptomic and haplotype data, we identified large numbers of QTLs affecting rice root length and thickness (RL and RT) and shortlisted relatively few candidate genes for many of the identified small-effect QTLs. Forty four and 97 QTL candidate genes for RL and RT were identified, and five of the RL QTL candidates were validated by T-DNA insertional mutation; all have diverse functions and are involved in root development. This work demonstrated a powerful strategy for highly efficient cloning of moderate- and small-effect QTLs that is difficult using the classical map-based cloning approach. Population analyses of the 795 accessions, 202 additional upland landraces, and 446 wild rice accessions based on random SNPs and SNPs within robust loci suggested that there could be much less diversity in robust-root candidate genes among upland japonica accessions than in other ecotypes. Further analysis of nucleotide diversity and allele frequency in the robust loci among different ecotypes and wild rice accessions showed that almost all alleles could be detected in wild rice, and pyramiding of robust-root alleles could be an important genetic characteristic of upland japonica. Given that geographical distribution of upland landraces, we suggest that during domestication of upland japonica, the strongest pyramiding of robust-root alleles makes it a unique ecotype adapted to aerobic conditions.

The Rice Cation/H+ Exchanger Family Involved in Cd Tolerance and Transport.

Cadmium (Cd), a heavy metal toxic to humans, easily accumulates in rice grains. Rice with unacceptable Cd content has become a serious food safety problem in many rice production regions due to contaminations by industrialization and inappropriate waste management. The development of rice varieties with low grain Cd content is seen as an economic and long-term solution of this problem. The cation/H+ exchanger (CAX) family has been shown to play important roles in Cd uptake, transport and accumulation in plants. Here, we report the characterization of the rice CAX family. The six rice CAX genes all have homologous genes in Arabidopsis thaliana. Phylogenetic analysis identified two subfamilies with three rice and three Arabidopsis thaliana genes in both of them. All rice CAX genes have trans-member structures. OsCAX1a and OsCAX1c were localized in the vacuolar while OsCAX4 were localized in the plasma membrane in rice cell. The consequences of qRT-PCR analysis showed that all the six genes strongly expressed in the leaves under the different Cd treatments. Their expression in roots increased in a Cd dose-dependent manner. GUS staining assay showed that all the six rice CAX genes strongly expressed in roots, whereas OsCAX1c and OsCAX4 also strongly expressed in rice leaves. The yeast (Saccharomyces cerevisiae) cells expressing OsCAX1a, OsCAX1c and OsCAX4 grew better than those expressing the vector control on SD-Gal medium containing CdCl2. OsCAX1a and OsCAX1c enhanced while OsCAX4 reduced Cd accumulation in yeast. No auto-inhibition was found for all the rice CAX genes. Therefore, OsCAX1a, OsCAX1c and OsCAX4 are likely to involve in Cd uptake and translocation in rice, which need to be further validated.

Advances in Sensing, Response and Regulation Mechanism of Salt Tolerance in Rice.

Soil salinity is a serious menace in rice production threatening global food security. Rice responses to salt stress involve a series of biological processes, including antioxidation, osmoregulation or osmoprotection, and ion homeostasis, which are regulated by different genes. Understanding these adaptive mechanisms and the key genes involved are crucial in developing highly salt-tolerant cultivars. In this review, we discuss the molecular mechanisms of salt tolerance in rice-from sensing to transcriptional regulation of key genes-based on the current knowledge. Furthermore, we highlight the functionally validated salt-responsive genes in rice.

Using Heading date 1 preponderant alleles from indica cultivars to breed high-yield, high-quality japonica rice varieties for cultivation in south China.

Heading date 1 (Hd1) is an important gene for the regulation of flowering in rice, but its variation in major cultivated rice varieties, and the effect of this variation on yield and quality, remains unknown. In this study, we selected 123 major rice varieties cultivated in China from 1936 to 2009 to analyse the relationship between the Hd1 alleles and yield-related traits. Among these varieties, 19 haplotypes were detected in Hd1, including two major haplotypes (H8 and H13) in the japonica group and three major haplotypes (H14, H15 and H16) in the indica group. Analysis of allele frequencies showed that the secondary branch number was the major aimed for Chinese indica breeding. In the five major haplotypes, SNP316 (C-T) was the only difference between the two major japonica haplotypes, and SNP495 (C-G) and SNP614 (G-A) are the major SNPs in the three indica haplotypes. Association analysis showed that H16 is the most preponderant allele in modern cultivated Chinese indica varieties. Backcrossing this allele into the japonica variety Chunjiang06 improved yield without decreasing grain quality. Therefore, our analysis offers a new strategy for utilizing these preponderant alleles to improve yield and quality of japonica varieties for cultivation in the southern areas of China.

Mesocotyl elongation, an essential trait for dry-seeded rice (Oryza sativa L.): a review of physiological and genetic basis.

MAIN CONCLUSIONS: (1) Mesocotyl elongation is responsive to abiotic stresses, such as deep sowing drought, submergence, chilling, and salinity. (2) Humus soil culture with a burial depth of 6 cm and at the temperature of 30 °C could be the optimum method for mesocotyl length phenotyping, The frequently colocalized quantitative trait loci (QTL) controlling mesocotyl elongation were located on chromosome (3) 1 (RM562-RG146), chromosome 2 (RZ288-RM145), and chromosome 3 (RM426-RM520). Dry direct-seeding is becoming a popular rice cultivation technology in many countries, which reduces water use and labor costs enormously. Meanwhile, direct-seeding rice is also facing the problems of low seedling emergence rate, poor seedling establishment, weed infestation, and high crop lodging rate. To take the full advantages of direct-seeding, both agronomic and genetic solutions are needed. Varieties with optimum mesocotyl length are desired for improving rice seedling emergence rate, particularly under deep sowing and submergence, which is adopted to reduce lodging and increase tolerance to abiotic stresses. In this review, we summarized the physiological and genetic mechanisms of mesocotyl elongation in rice. The elongation of mesocotyl is affected by light, temperature, and water, and, as a result, is responsive to sowing depth, water content, and soil salinity. Plant hormones such as abscisic acid (ABA), brassinosteroid (BR), strigolactones (SLs), cytokinin (CTK), ethylene (ETH), jasmonic acid (JA), gibberellin (GA), and indole-3-acetic acid (IAA) play important roles in regulating mesocotyl elongation. A humus soil culture protocol developed by our team was shown to be a better high-throughput method for measuring mesocotyl length in large scale. Sixty-seven QTL controlling mesocotyl length were reported, which are distributed on all the 12 chromosomes. Twelve chromosomal regions were repeatedly found to have QTL using various mapping populations and methods. These regions should be targeted in future studies to isolate genes and develop markers for molecular breeding. Two genes with very different molecular functions have been cloned, highlighting the genetic complexity of mesocotyl elongation.

Complete Genome Sequence of Pseudomonas Parafulva PRS09-11288, a Biocontrol Strain Produces the Antibiotic Phenazine-1-carboxylic Acid.

Rhizoctonia solani is a plant pathogenic fungus, which can infect a wide range of economic crops including rice. In this case, biological control of this pathogen is one of the fundmental way to effectively control this pathogen. The Pseudomonas parafulva strain PRS09-11288 was isolated from rice rhizosphere and shows biocontrol ability against R. solani. Here, we analyzed the P. parafulva genome, which is ~ 4.7 Mb, with 4310 coding sequences, 76 tRNAs, and 7 rRNAs. Genome analysis identified a phenazine biosynthetic pathway, which can produce antibiotic phenazine-1-carboxylic acid (PCA). This compound is responsible for biocontrol ability against R. solani Kühn, which is one of the most serious fungus disease on rice. Analysis of the phenazine biosynthesis gene mutant, ΔphzF, which is very important in this pathway, confirmed the relationship between the pathway and PCA production using LC-MS profiles. The annotated full genome sequence of this strain sheds light on the role of P. parafulva PRS09-11288 as a biocontrol bacterium.

Advances in the Uptake and Transport Mechanisms and QTLs Mapping of Cadmium in Rice.

Cadmium (Cd), as a heavy metal, presents substantial biological toxicity and has harmful effects on human health. To lower the ingress levels of human Cd, it is necessary for Cd content in food crops to be reduced, which is of considerable significance for ensuring food safety. This review will summarize the genetic traits of Cd accumulation in rice and examine the mechanism of Cd uptake and translocation in rice. The status of genes related to Cd stress and Cd accumulation in rice in recent years will be summarized, and the genes related to Cd accumulation in rice will be classified according to their functions. In addition, an overview of quantitative trait loci (QTLs) mapping populations in rice will be introduced, aiming to provide a theoretical reference for the breeding of rice varieties with low Cd accumulation. Finally, existing problems and prospects will be put forward.

Genetic Dissection of Leaf Senescence in Rice.

Leaf senescence, the final stage of leaf development, is a complex and highly regulated process that involves a series of coordinated actions at the cellular, tissue, organ, and organism levels under the control of a highly regulated genetic program. In the last decade, the use of mutants with different levels of leaf senescence phenotypes has led to the cloning and functional characterizations of a few genes, which has greatly improved the understanding of genetic mechanisms underlying leaf senescence. In this review, we summarize the recent achievements in the genetic mechanisms in rice leaf senescence.

Validation of genes affecting rice mesocotyl length through candidate association analysis and identification of the superior haplotypes.

Mesocotyl is an essential organ of rice for pushing buds out of soil and plays a crucial role in seeding emergence and development in direct-seeding. Thus, identify the loci associated with mesocotyl length (ML) could accelerate breeding progresses for direct-seeding cultivation. Mesocotyl elongation was mainly regulated by plant hormones. Although several regions and candidate genes governing ML have been reported, the effects of them in diverse breeding populations were still indistinct. In this study, 281 genes related to plant hormones at the genomic regions associated with ML were selected and evaluated by single-locus mixed linear model (SL-MLM) and multi-locus random-SNP-effect mixed linear model (mr-MLM) in two breeding panels (Trop and Indx) originated from the 3K re-sequence project. Furthermore, superior haplotypes with longer mesocotyl were also identified for marker assisted selection (MAS) breeding. Totally, LOC_Os02g17680 (explained 7.1-8.9% phenotypic variations), LOC_Os04g56950 (8.0%), LOC_Os07g24190 (9.3%) and LOC_Os12g12720 (5.6-8.0%) were identified significantly associated with ML in Trop panel, whereas LOC_Os02g17680 (6.5-7.4%), LOC_Os04g56950 (5.5%), LOC_Os06g24850 (4.8%) and LOC_Os07g40240 (4.8-7.1%) were detected in Indx panel. Among these, LOC_Os02g17680 and LOC_Os04g56950 were identified in both panels. Haplotype analysis for the six significant genes indicated that haplotype distribution of the same gene varies at Trop and Indx panels. Totally, 8 (LOC_Os02g17680-Hap1 and Hap2, LOC_Os04g56950-Hap1, Hap2 and Hap8, LOC_Os07g24190-Hap3, LOC_Os12g12720-Hap3 and Hap6) and six superior haplotypes (LOC_Os02g17680-Hap2, Hap5 and Hap7, LOC_Os04g56950-Hap4, LOC_Os06g24850-Hap2 and LOC_Os07g40240-Hap3) with higher ML were identified in Trop and Indx panels, respectively. In addition, significant additive effects for ML with more superior haplotypes were identified in both panels. Overall, the 6 significantly associated genes and their superior haplotypes could be used to enhancing ML through MAS breeding and further promote direct-seedling cultivation.

Sparse Phenotyping and Haplotype-Based Models for Genomic Prediction in Rice.

The multi-environment genomic selection enables plant breeders to select varieties resilient to diverse environments or particularly adapted to specific environments, which holds a great potential to be used in rice breeding. To realize the multi-environment genomic selection, a robust training set with multi-environment phenotypic data is of necessity. Considering the huge potential of genomic prediction enhanced sparse phenotyping on the cost saving of multi-environment trials (MET), the establishment of a multi-environment training set could also benefit from it. Optimizing the genomic prediction methods is also crucial to enhance the multi-environment genomic selection. Using haplotype-based genomic prediction models is able to capture local epistatic effects which could be conserved and accumulated across generations much like additive effects thereby benefitting breeding. However, previous studies often used fixed length haplotypes composed by a few adjacent molecular markers disregarding the linkage disequilibrium (LD) which is of essential role in determining the haplotype length. In our study, based on three rice populations with different sizes and compositions, we investigated the usefulness and effectiveness of multi-environment training sets with varying phenotyping intensities and different haplotype-based genomic prediction models based on LD-derived haplotype blocks for two agronomic traits, i.e., days to heading (DTH) and plant height (PH). Results showed that phenotyping merely 30% records in multi-environment training set is able to provide a comparable prediction accuracy to high phenotyping intensities; the local epistatic effects are much likely existent in DTH; dividing the LD-derived haplotype blocks into small segments with two or three single nucleotide polymorphisms (SNPs) helps to maintain the predictive ability of haplotype-based models in large populations; modelling the covariances between environments improves genomic prediction accuracy. Our study provides means to improve the efficiency of multi-environment genomic selection in rice.

Genomic prediction of rice mesocotyl length indicative of directing seeding suitability using a half-sib hybrid population.

Direct seeding has been widely adopted as an economical and labor-saving technique in rice production, though problems such as low seedling emergence rate, emergence irregularity and poor lodging resistance are existing. These problems are currently partially overcome by increasing seeding rate, however it is not acceptable for hybrid rice due to the high seed cost. Improving direct seeding by breeding is seen as the ultimate solution to these problems. For hybrid breeding, identifying superior hybrids among a massive number of hybrids from crossings between male and female parental populations by phenotypic evaluation is tedious and costly. Contrastingly, genomic selection/prediction (GS/GP) could efficiently detect the superior hybrids capitalizing on genomic data, which holds a great potential in plant hybrids breeding. In this study, we utilized 402 rice inbred varieties and 401 hybrids to investigate the effectiveness of GS on rice mesocotyl length, a representative indicative trait of direct seeding suitability. Several GP methods and training set designs were studied to seek the optimal scenario of hybrid prediction. It was shown that using half-sib hybrids as training set with the phenotypes of all parental lines being fitted as a covariate could optimally predict mesocotyl length. Partitioning the molecular markers into trait-associated and -unassociated groups based on genome-wide association study using all parental lines and hybrids could further improve the prediction accuracy. This study indicates that GS could be an effective and efficient method for hybrid breeding for rice direct seeding.

Mapping QTLs and gene validation studies for Mg2+ uptake and translocation using a MAGIC population in rice.

Magnesium (Mg) is an essential element for plant growth and development. Rice is an important food crop in the world, but there are few studies on the uptake and translocation of Mg2+ in rice. We used a multi-parent advanced generation inter-cross (MAGIC) population constructed using four parental lines and genotyped by a 55 K rice SNP array for association analysis to locate QTLs related to Mg2+ uptake and translocation in rice at the seedling stage. Four QTLs (qRMg1, qRMg2, qRMg7 and qRMg8) were detected for the root Mg2+ concentration, which explained 11.45-13.08% of the phenotypic variation. The Mg2+ transporter gene, OsMGT1, was within the region of qRMg1. Three QTLs (qSMg3, qSMg7 and qSMg10) were detected for the shoot Mg2+ concentration, which explained 4.30-5.46% of the phenotypic variation. Two QTLs (qTrMg3 and qTrMg8) were found to affect the translocation of Mg2+ from the roots to the shoots, and explained 10.91% and 9.63% of phenotypic variation. qSMg3 and qTrMg3 might be the same, since they are very close to each other on chromosome 3. Analysis of candidate genes in the region of qSMg3 and qTrMg3 through qRT-PCR, complementation assay in the yeast Mg2+ transport-defective mutant CM66, and sequence analysis of the parental lines suggested that LOC_Os03g04360 may play important roles in Mg2+ uptake, translocation and accumulation in rice. Overexpression of LOC_Os03g04360 can significantly increase the Mg2+ concentration in rice seedlings, especially under the condition of low Mg2+ supply.

Dynamic analysis of QTLs on tiller number in rice (Oryza sativa L.) with single segment substitution lines.

Twelve single segment substitution lines (SSSLs) in rice, which contain quantitative trait loci (QTLs) for tiller number detected previously, were used to study dynamic expression of the QTLs in this study. These SSSLs and their recipient, Hua-Jing-Xian 74 (HJX74), were used to produce 78 crossing combinations first, and then these combinations and their parents were grown in two planting seasons with three cropping densities. Tiller number was measured at seven developmental stages. QTL effects including main effects (additive, dominance and epistasis), QTL × season and QTL × density interaction effects were analyzed at each measured stage. The additive, dominant and epistatic effects of the 12 QTLs as well as their interaction effects with the seasons and with the densities all display dynamic changes with the development. Eight QTLs are detected with significant additive effects and/or additive × season and/or additive × density interaction effects at least at one developmental stage, and all QTLs have significant dominant and epistatic effects and/or interaction effects involved in. For most of the QTLs dominant effects are much bigger than additive effects, showing overdominance. Each QTL interacts at least with eight other QTLs. Additive and dominant effects of these QTLs are mostly positive while epistatic effects are negative and minor. Most of the QTLs show significant interactions with planting seasons and cropping densities, but the additive effects of QTLs Tn3-1 and Tn3-2, the dominant effects of QTL Tn7 and Tn8, and the epistatic effects of 14 pairs of QTLs are stable across seasons and the dominant effect of QTL Tn3-3 and the epistatic effects of QTL pairs Tn2-1/Tn6-2, Tn2-1/Tn9 and Tn3-3/Tn6-3 are nearly consistent across cropping densities. This paper is the first report of dynamics on dominances and epistasis of QTLs for tiller number in rice and provides abundant information, which is useful to improve rice tiller number via heterosis and/or QTL pyramiding.

Identification of stably expressed QTL for heading date using reciprocal introgression line and recombinant inbred line populations in rice.

Two sets of reciprocal introgression lines (ILs) and a population of recombinant inbred lines (RILs) derived from the cross between japonica cultivar Xiushui09 and indica breeding line IR2061-520-6-9 (abbreviated as IR2061) were used to identify QTL for heading date (HD). Phenotyping was conducted in Hainan Island for two winter seasons (2007 and 2009). Nine QTLs were detected in the ILs with Xiushui09 background (XS-ILs), and four of which were repeatedly mapped across 2 years. Five QTLs were identified in the ILs with IR2061 background (IR-ILs), and three of which were commonly detected in 2 years. All commonly detected QTL had the same direction of gene effect. Seven QTL for HD were identified in the RILs in 2009. Only three (25%) QTLs were commonly detected using all the three populations (XS-ILs, IR-ILs and RILs). The number of commonly identified QTLs among populations was related to degree of similarity of their genetic backgrounds, suggesting that the genetic background effect is important for detecting HD QTL. QHd7 and QHd10b stably expressed in different populations and across years thus would be exploited in rice breeding programme. Moreover, lines with both of QHd7 and QHd10b resulted in at least 3 days earlier than lines with only one of them QTL, showing evident pyramiding effect.