Inter-subspecific Hybrid Rice Research Articles

Genome-wide chromatin accessibility reveals transcriptional regulation of heterosis in inter-subspecific hybrid rice.

The utilization of rice heterosis is essential for ensuring global food security; however, its molecular mechanism remains unclear. In this study, comprehensive analyses of accessible chromatin regions (ACRs), DNA methylation, and gene expression in inter-subspecific hybrid and its parents were performed to determine the potential role of chromatin accessibility in rice heterosis. The hybrid exhibited abundant ACRs, in which the gene ACRs and proximal ACRs were directly related to transcriptional activation rather than the distal ACRs. Regarding the dynamic accessibility contribution of the parents, paternal ZHF1015 transmitted a greater number of ACRs to the hybrid. Accessible genotype-specific target genes were enriched with overrepresented transcription factors, indicating a unique regulatory network of genes in the hybrid. Compared with its parents, the differentially accessible chromatin regions with upregulated chromatin accessibility were much greater than those with downregulated chromatin accessibility, reflecting a stronger regulation in the hybrid. Furthermore, DNA methylation levels were negatively correlated with ACR intensity, and genes were strongly affected by CHH methylation in the hybrid. Chromatin accessibility positively regulated the overall expression level of each genotype. ACR-related genes with maternal Z04A-bias allele-specific expression tended to be enriched during carotenoid biosynthesis, whereas paternal ZHF1015-bias genes were more active in carbohydrate metabolism. Our findings provide a new perspective on the mechanism of heterosis based on chromatin accessibility in inter-subspecific hybrid rice.

A minimal genome design to maximally guarantee fertile inter-subspecific hybrid rice

Hybrid rice has made considerable contributions to achieve the ambitious goal of food security for the world’s population. Hybrid rice from indica/xian and japonica/geng subspecies shows much higher heterosis and is thereby an important innovation in promoting rice production in the next decade. However, such inter-subspecific hybrid rice has long suffered from serious hybrid sterility, which is a major challenge that needs to be addressed. In this study, we performed a genome design strategy to produce fertile inter-subspecific hybrid by creation of wide compatibility varieties that are able to overcome hybrid sterility. Based on combined genetic analyses in two indica-japonica crosses, we determined that four hybrid sterility loci, S5, f5, pf12 and Sc, are the major QTLs controlling inter-subspecific hybrid sterility and thus the minimal targets that can be manipulated for breeding sub-specific hybrid rice. We then cloned the pf12 locus, one of the most effective loci for hybrid male sterility, by map-based cloning, and showed that artificial disruption of pf12A gene at this locus could successfully rescue hybrid fertility. We further dissected the genetic basis of wide compatibility using three pairwise crosses from a wide-compatibility variety Dular and representative indica and japonica varieties. On this basis, we constructed and assembled different combinations of naturally compatible alleles of four loci, S5, Sc, pf12, and f5, and found that the improved lines could fully recover pollen and embryo sac fertility in test-crossed F1s, thereby completely fulfilling the demands of inter-subspecific hybrid spikelet fertility in agricultural production. This breeding scheme would facilitate redesign of future inter-subspecific hybrid rice with a higher yield potential.

Comparative Transcriptome Analysis of the Heterosis of Salt Tolerance in Inter-Subspecific Hybrid Rice.

Soil salinity is one of the major abiotic stresses limiting rice growth. Hybrids outperform their parents in salt tolerance in rice, while its mechanism is not completely understood. In this study, a higher seedling survival was observed after salt treatment in an inter-subspecific hybrid rice, Zhegengyou1578 (ZGY1578), compared with its maternal japonica Zhegeng7A (ZG7A) and paternal indica Zhehui1578 (ZH1578). A total of 2584 and 3061 differentially expressed genes (DEGs) with at least twofold changes were identified between ZGY1578 and ZG7A and between ZGY1578 and ZH1578, respectively, in roots under salt stress using the RNA sequencing (RNA-Seq) approach. The expressions of a larger number of DEGs in hybrid were lower or higher than those of both parents. The DEGs associated with transcription factors, hormones, and reactive oxygen species (ROS)-related genes might be involved in the heterosis of salt tolerance. The expressions of the majority of transcription factors and ethylene-, auxin-, and gibberellin-related genes, as well as peroxidase genes, were significantly higher in the hybrid ZGY1578 compared with those of both parents. The identified genes provide valuable clues to elucidate the heterosis of salt tolerance in inter-subspecific hybrid rice.

Synthetic apomixis with normal hybrid rice seed production

Synthetic apomixis with normal hybrid rice seed production

Non-coding RNA expression analysis revealed the molecular mechanism of flag leaf heterosis in inter-subspecific hybrid rice.

Heterosis has been used widespread in agriculture, but its molecular mechanism is inadequately understood. Plants have a large number of non-coding RNAs (ncRNAs), among them, functional ncRNAs that have been studied widely containing long non-coding RNA (lncRNA) and circular RNA (circRNA) that play a role in varied biological processes, as well as microRNA (miRNA), which can not only regulate the post-transcriptional expression of target genes, but also target lncRNA and circRNA then participate the competing endogenous RNA (ceRNA) regulatory network. However, the influence of these three ncRNAs and their regulatory relationships on heterosis is unknown in rice. In this study, the expression profile of ncRNAs and the ncRNA regulatory network related to heterosis were comprehensively analyzed in inter-subspecific hybrid rice. A total of 867 miRNAs, 3,278 lncRNAs and 2,521 circRNAs were identified in the hybrid and its parents. Analysis of the global profiles of these three types of ncRNAs indicated that significant differences existed in the distribution and sequence characteristics of the corresponding genes. The numbers of miRNA and lncRNA in hybrid were higher than those in its parents. A total of 784 ncRNAs (169 miRNAs, 573 lncRNAs and 42 circRNAs) showed differentially expressed in the hybrid, and their target/host genes were vital in stress tolerance, growth and development in rice. These discoveries suggested that the expression plasticity of ncRNA has an important role of inter-subspecific hybrid rice heterosis. It is worth mentioning that miRNAs exhibited substantially more variations between hybrid and parents compared with observed variation for lncRNA and circRNA. Non-additive expression ncRNAs and allele-specific expression genes-related ncRNAs in hybrid were provided in this study, and multiple sets of ncRNA regulatory networks closely related to heterosis were obtained. Meanwhile, heterosis-related regulatory networks of ceRNA (lncRNA and circRNA) and miRNA were also demonstrated.

Fixation of hybrid sterility genes and favorable alleles of key yield-related genes with dominance contribute to the high yield of the Yongyou series of intersubspecific hybrid rice

In rice, the Yongyou series of Xian-Geng intersubspecific hybrids have excellent production performance, as shown by their extremely high yield. However, the mechanisms underlying the success of these rice hybrids are unclear. In this study, three F2 populations are generated from three Yongyou hybrids to determine the genetic basis of the extremely high yield of intersubspecific hybrids. Genome constitution analysis reveals that the female and male parental lines belong to the Geng and Xian subspecies, respectively, although introgression of 20% of the Xian ancestry and 14% of the Geng ancestry are observed. Twenty-five percent of the hybrid genomes carries homozygous Xian or Geng fragments, which harbors hybrid sterility genes such as Sd, Sc, f5, and qS12 and favorable alleles of key yield-related genes, including NAL1, Ghd7, and Ghd8. None of the parents carries the S5+ killer of the S5 killer-protector system. Compatible allele combinations of hybrid sterility genes ensure the fertility of these intersubspecific hybrids and overcome the bottleneck in applying intersubspecific hybrids. Additive effects of favorable alleles of yield-related genes fixed in both parents enhances midparent values. Many QTLs for yield and its key component spikelets per panicle shows dominance and the net positive dominant effects lead to heterosis. These factors result in an extremely high yield of the hybrids. These findings will aid in the development of new intersubspecific rice hybrids with diverse genetic backgrounds.

Transcriptome and DNA methylome analyses provide insight into the heterosis in flag leaf of inter-subspecific hybrid rice.

Flag leaf heterosis of inter-subspecific hybrid rice is suggested to be related to leaf area, gene expression pattern and allele-specific expression, putatively related to DNA methylation differences between the hybrid and its parents. Inter-subspecific hybrid rice combinations of indica × japonica have great potential to broaden genetic diversity and enhance the heterosis. The genetic and epigenetic molecular mechanism of its heterosis is not completely understood. Here, the dissection of gene expression and epigenetic regulation of an elite inter-subspecific hybrid rice were reported. In the hybrid, plant height, flag leaf area and Pn showed significant heterosis at the heading stage. Chloroplast-related differentially expressed genes (DEGs) and 530 allele-specific expression genes in hybrid were identified. Analysis of the genome-wide distribution of DNA methylation (5-methylcytosine, 5mC) and its association with transcription showed that there were variant DNA methylation maps and that the regulation of gene expression levels was negatively regulated by DNA methylation in the inter-subspecific hybrid rice. Differentially methylated DEGs were significantly enriched in photosynthetic functions. Moreover, distinct 5mC sequence contexts and distinct functional elements (promoter/gene body) may have different influences on heterosis related genes. The data identified heterosis related molecular mechanisms in inter-subspecific hybrid rice and suggested that epigenetic changes could extensively influence the flag leaf gene expression and heterosis.

Genetic Analysis of S5-Interacting Genes Regulating Hybrid Sterility in Rice

BackgroundAsian cultivated rice (Oryza sativa L.) comprises two subspecies, O. sativa subsp. indica and subsp. japonica, and the hybrids between them display strong heterosis. However, hybrid sterility (HS) limits practical use of the heterosis between these two subspecies. S5 is a major-effect locus controlling the HS of female gametes in rice, consisting of three closely-linked genes ORF3, ORF4 and ORF5 that act as a killer-protector system. The HS effects of S5 are inconsistent for different genetic backgrounds, indicating the existence of interacting genes within the genome.ResultsIn the present study, the S5-interacting genes (SIG) and their effects on HS were analyzed by studying the hybrid progeny between an indica rice, Dular (DL) and a japonica rice, BalillaORF5+ (BLORF5+), with a transgenic ORF5+ allele. Four interacting quantitative trait loci (QTL): qSIG3.1, qSIG3.2, qSIG6.1, and qSIG12.1, were genetically mapped. To analyze the effect of each interacting locus, four near-isogenic lines (NILs) were developed. The effect of each specific locus was investigated while the other three loci were kept DL homozygous (DL/DL). Of the four loci, qSIG3.1 was the SIG with the greatest effects in which the DL allele was completely dominant. Furthermore, the DL allele displayed incomplete dominance at qSIG3.2, qSIG6.1, and qSIG12.1. qSIG3.1 will be the first choice for further fine-mapping.ConclusionsFour S5-interacting QTL were identified by genetic mapping and the effect of each locus was analyzed using advanced backcrossed NILs. The present study will facilitate elucidation of the molecular mechanism of rice HS caused by S5. Additionally, it would provide the basis to explore the origin and differentiation of cultivated rice, having practical significance for inter-subspecific hybrid rice breeding programs.

Verification of Glyphosate Resistance, Lepidopteran Resistance and Wide Compatibility of Male Sterile Line E1C4008S in Rice

Weeds and insect pests are two important biotic stresses resulting in yield loss in rice, and wide compatibility is the essential characteristic of breeding inter-subspecific hybrid rice. This study focused on glyphosate resistance, lepidopteran resistance and wide compatibility as well as identification of molecular and some agronomic characteristics of transgenic male sterile line E1C4008S. The results indicated that glyphosate resistance gene Epsps# and lepidopteran resistance gene Cry1ca# were transferred into japonica wide compatibility male sterile line 4008S by Agrobacterium-mediated method, and four independent transformation events named E1C4008S-1, E1C4008S-2, E1C4008S-3 and E1C4008S-4 were obtained, in which E1C4008S-3 and E1C4008S-4 were of single copy insertion. The EPSPS protein contents of E1C4008S-3 and E1C4008S-4 in different organs were significantly different both in descending order of leaf>stem>root, and ranged from 300.58 to 1410.69μg/g at the tillering stage. The glyphosate tolerable concentration (dosage) of E1C4008S-3 and E1C4008S-4 reached at least 16g/L (54.42kg/hm2), and the seeds of E1C4008S-4 can germinate normally on the medium containing 1g/L glyphosate. The CRY1C protein contents of E1C4008S-3 and E1C4008S-4 in different organs were significantly different both in descending order of leaf>stem>root, and ranged from 0.62 to 2.43μg/g at the tillering stage. The larvae mortalities of rice leaf rollers fed on leaves of E1C4008S-3 and E1C4008S-4 for 5 d were 95.35% and 97.77%, respectively, while the average mortalities of silkworms fed with protein extracts from leaves of E1C4008S-3 and E1C4008S-4 reached 94.55% and 83.64%, respectively. The results suggested that wide compatibility and evaluated agronomic traits of E1C4008S-4 were not significantly changed by insertion of the exogenous genes. Overall, a novel male sterile germplasm with glyphosate resistance, lepidopteran resistance and wide compatibility was verified to be developed in rice.

Molecular mechanisms of hybrid sterility in rice.

Hybrid sterility presents a major bottleneck in hybrid crop breeding and causes postzygotic reproductive isolation in speciation. Here, we summarize the current understanding of the genetics of rice hybrid sterility and highlight new advances in deciphering the molecular basis of the major genetic loci for hybrid sterility in rice. We also discuss practical strategies for overcoming reproductive barriers to utilize hybrid vigor in inter-specific and inter-subspecific hybrid rice breeding.

Comparison of agronomic performance between inter-sub-specific hybrid and inbred japonica rice under different mechanical transplanting methods

Mechanical transplanting has been applied to rice cultivation to save labor costs and ease labor shortages in Asian countries, especially in China. However, little information is available related to the characteristics of agronomic performance when comparing inter-sub-specific hybrid rice (IHR) and inbred japonica rice (IJR) under mechanical transplanting method. In 2013 and 2014, field experiments were conducted using IHR (Yongyou 2640) and IJR (Wuyunjing 24) under two cultivation patterns, that is, pot seedlings mechanically transplanted (PS) and carpet seedlings mechanically transplanted (CS). Grain yield, yield components, leaf area index (LAI), leaf area duration (LAD), aboveground biomass, crop growth rate (CGR), nitrogen (N) uptake, and N accumulation were investigated. When compared with CS, PS displayed significantly increased grain yield for both varieties because the larger sink size allowed higher N accumulation from panicle initiation to maturity. Moreover, total aboveground biomass under PS increased significantly compared with that under CS; that is, higher photosynthetic productivity resulted from a greater LAI and higher LAD during the grain filling stage. Higher N absorption capacity in the middle and late growth periods resulted in significantly enhanced total N uptake under PS. When compared with IJR for both treatments, IHR generated 75.2% more grain yield. However, the characteristics creating high yield of IHR were different from those of IJR. Greater aboveground biomass production as well as higher N uptake and accumulation created higher grain yield in IHR than in IJR. These results suggest higher yield could be achieved using PS with IHR, attributing to exploit both yield superiority and productive potential.

Hybrid Sterility in Rice (Oryza sativa L.) Involves the Tetratricopeptide Repeat Domain Containing Protein.

Intersubspecific hybrid sterility is a common form of reproductive isolation in rice (Oryza sativa L.), which significantly hampers the utilization of heterosis between indica and japonica varieties. Here, we elucidated the mechanism of S7, which specially causes Aus-japonica/indica hybrid female sterility, through cytological and genetic analysis, map-based cloning, and transformation experiments. Abnormal positioning of polar nuclei and smaller embryo sac were observed in F1 compared with male and female parents. Female gametes carrying S7(cp) and S7(i) were aborted in S7(ai)/S7(cp) and S7(ai)/S7(i), respectively, whereas they were normal in both N22 and Dular possessing a neutral allele, S7(n) S7 was fine mapped to a 139-kb region in the centromere region on chromosome 7, where the recombination was remarkably suppressed due to aggregation of retrotransposons. Among 16 putative open reading frames (ORFs) localized in the mapping region, ORF3 encoding a tetratricopeptide repeat domain containing protein was highly expressed in the pistil. Transformation experiments demonstrated that ORF3 is the candidate gene: downregulated expression of ORF3 restored spikelet fertility and eliminated absolutely preferential transmission of S7(ai) in heterozygote S7(ai)/S7(cp); sterility occurred in the transformants Cpslo17-S7(ai) Our results may provide implications for overcoming hybrid embryo sac sterility in intersubspecific hybrid rice and utilization of hybrid heterosis for cultivated rice improvement.

Balance between a Higher Degree of Heterosis and Increased Reproductive Isolation: A Strategic Design for Breeding Inter-Subspecific Hybrid Rice

The application of heterosis (hybrid vigor) has brought great success to plant breeding, particularly of hybrid rice, achieving significant yield increases. Attempts to explore the heterosis of inter-subspecific hybrids between indica and japonica rice, which result in even greater yield increases, have greatly increased in the past decades. However, because of the reduced seed setting rate in F1 hybrids as a result of increased reproductive isolation, the application of inter-subspecific hybrids in rice has slowed. Understanding the balance between heterosis and the reproductive isolation of inter-subspecific hybrids will facilitate the strategic design of inter-subspecific hybrid breeding. In this study, five indica and seven japonica rice varieties were chosen as the parental lines of a complete diallel mating design. Data from six group traits from all of the hybrids and inbred lines were collected. We found that the grain weight per plant, grain number per panicle, tiller per plant, thousand grain weight and plant height, which reflected increased heterosis, were associated with the genetic divergence index (GDI) of the parents. Meanwhile, owing to the reduced seed setting rate, which was also associated with the parents' GDI, the grain production of the hybrids was negatively affected. After analyzing the relationships between the GDI of indica-japonica parents and the grain weight per plant of the F1 hybrids, an ideal GDI value (0.37) for the two indica-japonica parents that could provide an optimal balance between the inter-subspecific heterosis and reproductive isolation was proposed. Our findings will help in the strategic design of an inter-subspecific hybrid rice breeding program by identifying the ideal indica and japonica parents for a hybrid combination to achieve hybrid rice with an optimal yield. This strategic design of an inter-subspecific hybrid rice breeding program will be time saving and cost effective.

Effects of temperature on fertility and seed set in intersubspecific hybrid rice

Since intersubspecific hybrid rice showed strong heterosis in the past 12 years, many such hybrids were released for commercialization. However, some of them exhibited unstable seed set and limited grain yield under lower temperature. To use the strong heterosis in intersubspecific hybrids, it is necessary to study the reasons for their instability. In this study, 11 intersubspecific hybrids, 1 indica hybrid, and 7 indica, japonica, or javanica inbred cultivars were used to investigate the effects of temperature on fertility and seed set, observe the variation in activity of male and female gametes, and look into suitable and safe temperatures (daily average) for the flowering stage.

Analysis of Indica-Japonica Differentiation in Rice Parents and Derived Lines Using ILP Markers

Revealing the indica-japonica differentiation in parents of hybridization between indica and japonica rice and their derived lines can provide theoretical and practical bases for the breeding of practical inter-subspecific hybrid rice. Using subspecies-specific molecular markers ILP (intron length polymorphism) and Cheng's index, the indica-japonica differentiation was analyzed with special materials including 18 indica-japonica hybrid parents and 39 derived lines, which accumulated different wide compatibility and restoring genes by convergent cross method in 21 years spanning four breeding phases. The indica-japonica differentiation was detected on all tested loci in 57 materials. Among the 18 parental lines, 4 were japonica type, 5 japonicaclinous type, 8 indicaclinous type and one indica type. The japonica proportion indexes in indica restorer lines Minghui 63 and 9308 were 12.50 and 33.33%, respectively, while that in japonica restorer line C418 was only 31.25%. Among the 39 derived lines from indica-japonica hybridization, one was japonica type, 11 japonicaclinous type, 20 indicaclinous type and 7 indica type. The japonica proportion index in Minghui 502 was only 10.42%. The results of indica and japonica classification by ILP molecular markers and Cheng's index were relatively consistent. The correlation coefficient between the japonica proportion index and morphology index was 0.794 **, while that between the indica proportion index and morphology index was −0.7662 **. ILP markers could be used to accurately detect the proportion of indica/japonica content in the genome of a rice variety. The results of indica-japonica differentiation analysis could make reasonable explanation for that the hybrids obtained from indica-japonica type restorer lines had obvious heterosis. This conclusion would provide important guidance in efficient use of beneficial genes of inter-subspecific hybrid rice.

Impact of elevated CO 2 concentration on inter-subspecific hybrid rice cultivar Liangyoupeijiu under fully open-air field conditions

Hybrid rice cultivar plays an important role in rice production system due to its high yield potential and resistance to environmental stress. Quantification of its responses to rising CO 2 concentration ([CO 2]) will reduce our uncertainty in predicting future food security and assist in development of adaptation strategies. Using free air CO 2 enrichment (FACE), we measured seasonal changes in growth and nitrogen (N) uptake of an inter-subspecific hybrid rice cultivar Liangyoupeijiu grown under two levels of [CO 2] (ambient and elevated by 200 μmol mol −1) and two levels of N fertilization in 2005–2006. Average across the 2 years, FACE increased crop growth rate similarly by 22%, 24% and 23% in the periods from transplanting to panicle initiation (PI), PI to heading and heading to maturity, which was mainly attributed to an increase in green leaf area index rather than the greater net assimilation rate. Grain yield increased greatly under FACE as a result of similar contributions by panicle number per unit area, grain number per panicle and individual grain yield. Final aboveground N acquisition showed a 10.4% increase under FACE, which resulted from enhanced N uptake at both vegetative and reproductive growth stages. Compared with previous FACE studies on final productivity of two inbred japonica cultivars, inter-subspecific hybrid cultivar appears to profit more from elevated [CO 2], which mainly resulted from its greater enhancement in photosynthetic production during reproductive growth due to a lack of N limitations late in the season.

Hybrid male sterility in rice controlled by interaction between divergent alleles of two adjacent genes

Sterility is common in hybrids between divergent populations, such as the indica and japonica subspecies of Asian cultivated rice (Oryza sativa). Although multiple loci for plant hybrid sterility have been identified, it remains unknown how alleles of the loci interact at the molecular level. Here we show that a locus for indica-japonica hybrid male sterility, Sa, comprises two adjacent genes, SaM and SaF, encoding a small ubiquitin-like modifier E3 ligase-like protein and an F-box protein, respectively. Most indica cultivars contain a haplotype SaM(+)SaF(+), whereas all japonica cultivars have SaM(-)SaF(-) that diverged by nucleotide variations in wild rice. Male semi-sterility in this heterozygous complex locus is caused by abortion of pollen carrying SaM(-). This allele-specific gamete elimination results from a selective interaction of SaF(+) with SaM(-), a truncated protein, but not with SaM(+) because of the presence of an inhibitory domain, although SaM(+) is required for this male sterility. Lack of any one of the three alleles in recombinant plants does not produce male sterility. We propose a two-gene/three-component interaction model for this hybrid male sterility system. The findings have implications for overcoming male sterility in inter-subspecific hybrid rice breeding.

Yield formation of CO 2-enriched inter-subspecific hybrid rice cultivar Liangyoupeijiu under fully open-air field condition in a warm sub-tropical climate

Hybrid rice ( Oryza sativa L.) cultivars play an important role in rice production due to its heterosis, resistance to environmental stress and high yield potential. However, no attention has been given to its yield responses to rising atmospheric CO 2 concentration ([CO 2]). To address this need, we conducted a Free Air CO 2 Enrichment (FACE) experiment at Yangzhou, Jiangsu, China, in 2004–2006. A two-line inter-subspecific hybrid rice variety Liangyoupeijiu, recently bred in China, was grown at ambient or elevated (c. 570 μmol mol −1) [CO 2] under two levels of nitrogen (N) application (12.5 and 25 g N m −2). Elevated [CO 2] slightly accelerated phenological development (1–2 days), and substantially enhanced grain yield (+30%). The magnitude of yield response to [CO 2] was independent of N fertilization, but greatly varied among years. On average, elevated [CO 2] increased panicle number per unit land area by 8%, due to an increase in maximum tiller number under FACE, while productive tiller ratio remained unaffected. Spikelet number per panicle showed an average increase of 10% due to elevated [CO 2], which was also supported by increased plant height and dry weight per stem. Meanwhile, Elevated [CO 2] caused a significant enhancement in both filled spikelet percentage (+5%) and individual grain mass (+4%). Compared with previous rice FACE studies, this hybrid cultivar appears to profit much more from elevated [CO 2] than inbred japonica cultivars (c. +13%), not only due to its stronger sink generation, but also enhanced capacity to utilize the carbon sources in a high [CO 2] environment. As sufficient intraspecific variation in yield response exists under field conditions, there is a pressing need to identify genotypes which would produce maximum grain yield under projected future [CO 2] levels.

Correlation and Regressive Model Between Spikelet Fertilized Rate and Temperature in Inter-Subspecific Hybrid Rice

To study the sensitivity of inter-subspecific hybrid rice to climatic conditions, the spikelet fertilized rate (SFR) of four types of rice including indica-japonica hybrid, intermediate hybrid, indica and japonica were analyzed during 2000–2004. The inter-subspecific hybrids showed lower SFR, and much higher fluctuation under various climatic conditions than indica and japonica rice, showing the inter-subspecific hybrids were sensitive to ecological conditions. Among 12 climatic factors, the key factor affecting rice SFR was temperature, with the most significant factor being the average temperature of the seven days around panicle flowering ( T 7). A regressive equation of SFR-temperature by T 7, and a comprehensive synthetic model by four important temperature indices were put forward. The optimum temperature for inter-subspecific hybrids was estimated to be 26.1–26.6°C, and lower limit of safe temperature to be 22.5–23.3°C for panicle flowering, showing higher by averagely 0.5°C and 1.7°C, respectively, to be compared with indica and japonica rice. This suggested that inter-subspecific hybrids require proper climatic conditions. During panicle flowering, the suitable daily average temperature was 23.3–29.0°C, with the fittest one at 26.1–26.6°C. For an application example, optimum heading season for inter-subspecific hybrids in key rice growing areas in China was as same as common pure lines, while inferior limit for safe date of heading was about a ten-day period earlier than those of common pure lines.

Mapping QTLs for defective female gametophyte development in an inter-subspecific cross in Oryza sativa L.

The embryo-sac is an essential structure for angiosperm reproduction. The cytological and genetic characterization of embryo-sac sterility was examined in a cross between Oryza sativa ssp. indica cv. ZYQ8 and ssp. japonica cultivar, JX17. The arrest of embryo-sac development was manifested following meiosis in the F1 hybrid. When the megaspore carried the lethal genotype, the nucleus either failed to divide or divided only once, and the immature embryo-sac degenerated. Abortion of the embryo-sac in the indica-japonica hybrid background was not observed in their original parents, and an effect of cytoplasmic gene(s) on embryo-sac sterility in the reciprocal F1 hybrids was not detected. Using a rice molecular linkage map based on a doubled haploid (DH) population from the cross of ZYQ8 /JX17, we mapped quantitative trait loci (QTLs) for the defective development of the female gametophyte in backcross progenies from the DH lines. The result demonstrated that a polygenic system is involved in both megagametogenesis and postzygotic isolation in inter-subspecific hybrid rice.