F1 Hybrid Rice Research Articles

Effects of row ratio and plant spacing for enhancing hybrid rice seed production in the tropics

The seed yield production determines the success of the development of hybrid rice. Here, an effective and efficient cultivation technology for producing hybrid rice seeds is optimized through spacing and row ratio management. This study aimed to evaluate the effects of spacing and row ratio of restorer (R) : CMS (A) on F1 hybrid rice seed production. The experiment was conducted at the Indonesian Center of Rice Research's experimental field in the dry season of 2016, using parental lines HIPA18 hybrid rice, i.e., CMS: IR79156A line and Restorer: IR53942 line. The experiment was laid out in a strip-plot design replicated three times. Two factors were studied, i.e., plant spacing between CMS lines and row ratio R by A-lines. The results indicated that the highest HIPA18 seed production was obtained from 20 cm x 20 cm spacing of CMS with row ratio 2R:14A, i.e., 3.62 tons ha-1. Plant spacing and row ratio interactions were improved tillers number per plant of restorer and F1 seed yields. Keywords: A-lines; CMS; F1 hybrid rice; R-lines

Genotype calling and haplotype inference from low coverage sequence data in heterozygous plant genome using HetMap.

This study developed a new genotyping method that can accurately infer heterozygous genotype information from the complex plant genome sequence data, which helped discover new alleles in the association studies. Many software packages and pipelines had been developed to handle the sequence data of the model species. However, Genotyping from complex heterozygous plant genome needs further improvement on the previous methods. Here we present a new pipeline available at https://github.com/Ncgrhg/HetMapv1 ) for variant calling and missing genotype imputation from low coverage sequence data for heterozygous plant genomes. To check the performance of the HetMap on the real sequence data, HetMap was applied to both the F1 hybrid rice population, which consists of 1495 samples and the wild rice population with 446 samples. The high coverage sequence data of four hybrid rice accessions and two wild rice accessions, which were also included in low coverage sequence data, were used to validate the accuracy of genotype inference. The validation results showed that HetMap archieved significant improvement in heterozygous genotype inference accuracy (13.65% for hybrid rice, 26.05% for wild rice) and total accuracy compared with similar software packages. The application of the new genotype with the genome-wide association study also showed improvement of association power in wild rice awn length phenotype. It could archive high genotype inference accuracy in low sequence coverage in a small population with both the natural and constructed recombination population. HetMap provided a powerful tool for the heterozygous plant genome sequence data analysis, which may help to discover new phenotype regions for the plant species with the complex heterozygous genome.

High-Yielding Ability of F1 Hybrid Rice Varieties “Hybrid Togo Series” in the Direct Seeding on Well-Drained Paddy Field in Temperate Regions

熟期の異なる水稲F1品種群「ハイブリッドとうごうシリーズ」は乾田直播栽培において高い苗立率を示した．収量は，晩生のハイブリッドとうごう3号で高く，特に後期重点施肥において778 kg/10 aと，移植栽培に近い収量が得られた．該品種では後期重点施肥による一穂籾数の増加が大きく，多収のためのシンク容量を確保しやすい一方で，着生枝梗別の籾数割合の変化がなく登熟歩合が低下しなかったと考えられた．また，生育後半においても高い窒素栄養状態が保持された.

Genetic variability studies in F1 rice (Oryza sativa L.) hybrids for yield and quality traits

Analysis of variance among lines, significant differences was observed for plant height, number of productive tillers per plant, panicle length, number of filled grains per panicle, single plant yield and 1000 grain weight while days to 50 per cent flowering, plant height, panicle length, single plant yield, 1000 grain weight, milling per cent, head rice recovery, grain length, L/B ratio, kernel length after cooking, kernel breadth after cooking, breadth wise elongation ratio and amylose content exhibited significant differences among testers besides in L x T interaction, all characters along with yield. The magnitude of difference between genotypic coefficient of variation (GCV) and phenotypic coefficient of variation was less for the traits indicating slight influence of environment. A wide range of PCV (4.09 – 43.43 %) and GCV (6.58 – 43.39 %) was resulted for 19 traits. The presence of higher GCV and PCV observed in number of filled grains per panicle followed by single plant yield, Alkali spreading value, gel consistency and amylose content, which signifies the additive genetic control in inheritance of that trait. The presence of high scale of GCV and PCV for observed traits suggested having better possibility for the enhancement through simple selection procedure.

Transcriptome and metabolome profiling of unheading in F1 hybrid rice

Heading date is a crucial agronomic trait. However, rice usually delays heading due to the photoperiod, temperature, hormones or age. The present research was conducted to analyze the mechanism controlling heading date in F1 hybrid rice. We constructed two test-crossing populations using two introgression lines (ILs), P20 and P21 coming from SH527/FH838 as the male parent, respectively, and male sterile line Jin23A as the female parent. Meanwhile, the F1 hybrids of H20, obtained by mating P20 with Jin23A and having no heading, and H21, from the crossing between P21 and Jin23A having normal heading, were both observed under long days. Here, we analyzed the photoperiodic response of F1 hybrids by transcriptome and metabolome profiling. The greater differences displayed in the transcriptome and the metabolome were caused by photoperiod (exogenous) instead of genes (endogenous). The coping mechanism resulted from long days (LD) in H20, leading to differences in the circadian rhythm and glutathione metabolism relative to other samples. The circadian oscillator and GSH/GSSG cycle typically regulate ROS homeostasis, and both of them are responsible for modulating ROS in H20 under LD condition. Both circadian rhythm genes and the reported genes related to heading date function via the DHD1/OsMFT1-Ehd1-RFT1-OsMADS14/OsMADS18 pathway and the glutathione metabolism pathway by regulating oxidative reduction processes. Both pathways are involved in the heading process and they interacted through the oxidative reduction process which was induced by photoperiod regulation, and all of them collectively modulated the heading process. The results of this study will be helpful for unraveling the mechanism of F1 hybrid responses to unheading under LD condition.

Divergent selection and genetic introgression shape the genome landscape of heterosis in hybrid rice

The successful application of heterosis in hybrid rice has dramatically improved rice productivity, but the genetic mechanism for heterosis in the hybrid rice remains unclear. In this study, we generated two populations of rice F1 hybrids with present-day commercial hybrid parents, genotyped the parents with 50k SNP chip and genome resequencing, and recorded the phenotype of ∼2,000 hybrids at three field trials. By integrating these data with the collected genotypes of ∼4,200 rice landraces and improved varieties that were reported previously, we found that the male and female parents have different levels of genome introgressions from other rice subpopulations, including indica, aus, and japonica, therefore shaping heterotic loci in the hybrids. Among the introgressed exogenous genome, we found that heterotic loci, including Ghd8/DTH8, Gn1a, and IPA1 existed in wild rice, but were significantly divergently selected among the rice subpopulations, suggesting these loci were subject to environmental adaptation. During modern rice hybrid breeding, heterotic loci were further selected by removing loci with negative effect and fixing loci with positive effect and pyramid breeding. Our results provide insight into the genetic basis underlying the heterosis of elite hybrid rice varieties, which could facilitate a better understanding of heterosis and rice hybrid breeding.

Effect of Various Phytochemicals for Evaluating Genetic Variability in Parental Lines for Producing F1 Hybrid Rice Seeds Using Modern CMS Breeding Technology

Effect of Various Phytochemicals for Evaluating Genetic Variability in Parental Lines for Producing F1 Hybrid Rice Seeds Using Modern CMS Breeding Technology

Breeding Hybrid Rice with Genes Resistant to Diseases and Insects Using Marker-Assisted Selection and Evaluation of Biological Assay

Developing elite hybrid rice varieties is one important objective of rice breeding programs. Several genes related to male sterilities, restores, and pollinators have been identified through map-based gene cloning within natural variations of rice. These identified genes are good targets for introducing genetic traits in molecular breeding. This study was conducted to breed elite hybrid lines with major genes related to hybrid traits and disease/insect resistance in 240 genetic resources and F1 hybrid combinations of rice. Molecular markers were reset for three major hybrid genes (S5, Rf3, Rf4) and thirteen disease/insect resistant genes (rice bacterial blight resistance genes Xa3, Xa4, xa5, Xa7, xa13, Xa21; blast resistance genes Pita, Pib, Pi5, Pii; brown planthopper resistant genes Bph18(t) and tungro virus resistance gene tsv1). Genotypes were then analyzed using molecular marker-assisted selection (MAS). Biological assay was then performed at the Red River Delta region in Vietnam using eleven F1 hybrid combinations and two control vatieties. Results showed that nine F1 hybrid combinations were highly resistant to rice bacterial blight and blast. Finally, eight F1 hybrid rice varieties with resistance to disease/insect were selected from eleven F1 hybrid combinations. Their characteristics such as agricultural traits and yields were then investigated. These F1 hybrid rice varieties developed with major genes related to hybrid traits and disease/insect resistant genes could be useful for hybrid breeding programs to achieve high yield with biotic and abiotic resistance.

Late flowering in F1 hybrid rice brought about by the complementary effect of quantitative trait loci.

Late flowering sometimes occurs in F1 hybrids between rice varieties (Oryza sativa L.), although the parental varieties show similar days-to-flowering (DTF). The genetic architecture prompting the occurrence of such late flowering is poorly understood. To clarify the genetic architecture of late flowering in F1 hybrids from a cross between rice varieties, 'Koshihikari' and 'IR64', we performed quantitative trait locus (QTL) analysis using an F2 population (selfed progeny of an F1 plant), in which heterozygous genotypes should segregate in a certain proportion in a Mendelian manner. The QTL analysis detected three significant QTLs. At one QTL (putatively Heading date 1), the 'Koshihikari' allele increased DTF, and at the other two QTLs (putatively Heading date 6 and Oryza sativa Pseudo-Response Regulator 37/Heading date 2), the 'IR64' alleles increased DTF. All alleles at these three QTLs showed partial dominance. The combination of the QTLs explained 82.2% of the total phenotypic variance of DTF in the F2 population, with contribution from epistasis between QTLs. There was no difference between DTFs of F1 hybrids and heterozygous genotypes for the three QTLs. Our results demonstrated that the complementary effects accompanied by epistasis of at least three QTLs were responsible for late flowering in F1 hybrids.

Clonal seeds from hybrid rice by simultaneous genome engineering of meiosis and fertilization genes.

Heterosis, or hybrid vigor, is exploited by breeders to produce elite high-yielding crop lines, but beneficial phenotypes are lost in subsequent generations owing to genetic segregation. Clonal propagation through seeds would enable self-propagation of F1 hybrids. Here we report a strategy to enable clonal reproduction of F1 rice hybrids through seeds. We fixed the heterozygosity of F1 hybrid rice by multiplex CRISPR-Cas9 genome editing of the REC8, PAIR1 and OSD1 meiotic genes to produce clonal diploid gametes and tetraploid seeds. Next, we demonstrated that editing the MATRILINEAL (MTL) gene (involved in fertilization) could induce formation of haploid seeds in hybrid rice. Finally, we combined fixation of heterozygosity and haploid induction by simultaneous editing of all four genes (REC8, PAIR1, OSD1 and MTL) in hybrid rice and obtained plants that could propagate clonally through seeds. Application of our method may enable self-propagation of a broad range of elite F1 hybrid crops.

Competition among wild rice, landrace, improved cultivar and F1 hybrid rice

Four genotypes, namely Oryza rufipogon, F1 of IR68888A/Chaite-6, Chaite-6 and Ratodhan were grown in crop and competition environment at Rampur, Nepal to study the effect of genotypes mixture on the characters. Univariate, multivariate and correlation methods of analysis were applied. Seven characters namely panicle length, panicle number, grain yield, harvest index, internode length and leaf width showed significantly different response in crop and competition environment. The performance of cultivar was poor in competition environment than hybrid and wild rice. Hybrid and wild rice showed longer panicle length in competition environment. Significant reduction in panicle number was found in cultivars. The pattern of tiller number over the growth period showed that the competition started after 50 days of seeding. Grain yield of cultivars was significantly reduced in competition environment. Considering the most important characters, hybrid was best competitor and local landrace (Ratodhan) was poorest competitor. Significant variations in culm characters were not found between two environments but leaf characters varied significantly. Highest increment in plant height was found in F1 grown in competition than crop environment. Relationship between characters was affected by growing environment. Among 162 pairs of characters r-value of six and 36 pairs were highly significant different from zero in crop and competition environment respectively. Multivariate analysis indicates that growing environment does not suppress the genetic characters. Competition among the tested genotypes exists even in the recommended spacing. Competition should be studied in detail planting at different spacing.

Prebreeding selection of rice with colored pericarp based on genotyping Rc and Pb genes

The research was aimed at developing prebreeding resources of Kazakhstan rice varieties with colored pericarp for breeding. During the study, hybrid analysis of inheritance of the trait “colored pericarp” in breeding material used for the work was performed. Rice genotypes with colored pericarp, as well as white rice varieties possessing important breeding traits and maturing under conditions of the republic, were selected from the collection of the Institute of Plant Biology and Biotechnology, Republic of Kazakhstan. Identification of allelic status of Rc (red pericarp) and Pb (anthocyanin pericarp) genes was performed for selected samples using the PCR method. When selecting parental forms for crossing, foreign rice varieties with colored pericarp (Rubin, Mavr, Black rice, etc.) were used as recipient forms. As donors, we used local white rice varieties of Kazakhstan breeding adapted to the soil and climate conditions of rice growing regions (Madina, Marzhan, Bakanasskiy, PakLi) as well as foreign varieties. The ability to set hybrid caryopses and the percentage of sterility were determined in obtained F1 rice hybrids. As a result, the most promising prebreeding material was selected, which will be used for breeding Kazakhstan rice varieties with colored pericarp.

一代雑種イネの苗丈・葉色・葉幅の優性表現

一代雑種イネの苗丈・葉色・葉幅の優性表現

GENETIC DIVERGENCE ANALYSIS IN HRDC RICE (Oryza sativa L.) HYBRIDS IN BANGLADESH

Genetic divergence of 48 IRRI developed F1 rice hybrids were studied through Mahalanobis D2 and principal component analysis for ten characters in Gazipur and Pabna district during dry season 2012-13. Among 48 genotypes, cluster analysis resulted in five clusters following Ward’s method. During dry season for both regions, cluster I incorporated the highest number of genotypes. Significant differences among the genotypes but non-significant differences among replications were noticed for most of the parameters under study. The inter-cluster distance was larger than intra-cluster distance suggesting wider diversity among the genotypes. In Gazipur, the maximum inter-cluster D2 value was recorded between cluster III and V (6.69) and the minimum between cluster II and IV (0.69). The intra-cluster distance was maximum in cluster IV (3.60) and minimum in cluster I (0.33). In Pabna, maximum inter-cluster distance was exhibited between cluster IV and II (16.43) but minimum between cluster II and III (3.98). Maximum intra-cluster distance (4.40) was recorded in cluster IV whereas minimum in cluster I (0.83). Based on positive value of vector 1 and vector 2, panicle number m-2, spikelet fertility (%) and 1000-grain wt. (g) had maximum contribution towards genetic divergence among the characters studied. Cluster means indicated considerable differences in the mean values of different parameters. The highest cluster means for panicle weight (g), spikelet fertility (%), 1000 grain wt. (g) and grain yield (kg ha-1) were derived from cluster IV. Therefore, more prominence should be given to the lines under cluster IV that having genetic potentiality to contribute better for yield maximization of hybrid rice.

Genetic Diversity Analysis in Exotic Hybrid Rice Genotypes Grown During Wet Season in Bangladesh

Two experiments were conducted with 43 IRRI developed F1 hybrid rice genotypes (HRDC) for ten agronomic characters in a randomized complete block design to study the genetic diversity through multivariate analysis in Gazipur and Pabna districts, respectively during wet season 2013. On the basis of D2 values, the genotypes were grouped into five different clusters. During wet season, cluster III comprised maximum number of genotypes (15). The data obtained across locations showed that there are significant differences among HRDC genotypes for all growth parameters, yield and yield components. The highest yield (5.65 t ha-1) was observed in HRDC 1341 because of produced heaviest panicle (4.28 g) and the lowest (2.48 t ha-1) in HRDC 1311 because of obtained lowest fertility (49.9 %) and 1000-grain wt. (12.9 g), respectively. The maximum inter-cluster distances were observed between cluster I and V (11.63) and the minimum between cluster III and IV (2.35). The highest intra-cluster distance (1.73) was observed in cluster III and minimum in cluster I (0.00), since it consisted with one genotype. Difference in cluster means existed for almost all the characters studied. Among the characters, growth duration, spikelet panicle-1, fertility (%) and 1000-grain wt contributed the most for divergence in the genotypes. The highest mean values for fertility percentage, panicle weight and 1000 grain wt. but early flowering and short maturing genotypes were grouped into Cluster II followed by Cluster III and IV indicating that the genotypes have genetic potentiality to contribute better for yield maximization of hybrid rice.The Agriculturists 2015; 13(2) 89-96

F1 Hybrid Rice in Eastern India: Silver Bullet or Capitalist Ploy?

This paper questions the role agricultural scientists are playing in addressing the problem of how rice production should be improved and increased, an issue that continues to be hotly debated and ...

Global epigenomic analysis indicates that Epialleles contribute to Allele-specific expression via Allele-specific histone modifications in hybrid rice

BackgroundFor heterozygous genes, alleles on the chromatin from two different parents exhibit histone modification variations known as allele-specific histone modifications (ASHMs). The regulation of allele-specific gene expression (ASE) by ASHMs has been reported in animals. However, to date, the regulation of ASE by ASHM genes remains poorly understood in higher plants.ResultsWe used chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) to investigate the global ASHM profiles of trimethylation on histone H3 lysine 27 (H3K27me3) and histone H3 lysine 36 (H3K36me3) in two rice F1 hybrids. A total of 522 to 550 allele-specific H3K27me3 genes and 428 to 494 allele-specific H3K36me3 genes were detected in GL × 93-11 and GL × TQ, accounting for 11.09% and 26.13% of the total analyzed genes, respectively. The epialleles between parents were highly related to ASHMs. Further analysis indicated that 52.48% to 70.40% of the epialleles were faithfully inherited by the F1 hybrid and contributed to 33.18% to 46.55% of the ASHM genes. Importantly, 66.67% to 82.69% of monoallelic expression genes contained the H3K36me3 modification. Further studies demonstrated a significant positive correlation of ASE with allele-specific H3K36me3 but not with H3K27me3, indicating that ASHM-H3K36me3 primarily regulates ASE in this study.ConclusionsOur results demonstrate that epialleles from parents can be inherited by the F1 to produce ASHMs in the F1 hybrid. Our findings indicate that ASHM-H3K36me3, rather than H3K27me3, mainly regulates ASE in hybrid rice.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1454-z) contains supplementary material, which is available to authorized users.

Pollen and Spikelet Analysis in F1 Rice Hybrids and their Parents

Pollen analysis can be used to discriminate between different species, identify possible interspecies hybrids, identify restorer and maintainer lines, useful to study genetics of restorer gene, interaction between chromosome and cytoplasm and relationship between parents. Pollen abortion system of male sterility is an important tool in hybrid rice production and spikelet is the major yield components. Nine improved cultivars, six landraces and three wild aborted cytoplasmic-genetic male sterile (CMS) lines were used to analyze pollen and spikelet in F1 rice hybrids and their parents. The frequency of pollen categories and its relationship to spikelet fertility were investigated. Pollen sterility of the F1s was determined by staining pollen grains in 1% potassium iodide-iodine (I-KI) solution. Spikelet fertility was determined by counting the total number of seed set in proportion to the total number of spikelets. Correlation and regression coefficients for some traits were computed. In hybrids, pollen fertility ranged from 0.5 to 82% and spikelet fertility from 0 to 87%. Pollen fertility varied from 28 to 97%, while spikelet fertility from 73 to 91% in pollen parents. The highest and the lowest percentages of pollen fertility were found in Chaite-6 and Chiunde cultivars respectively. Spikelet fertility percentage varied widely among hybrids and many hybrids had lower spikelet fertility percentage than their parents. Therefore, it is of practical importance to understand the causes of high spikelet sterility in hybrids for possible increase in spikelet fertility. Highly significant positive correlation was found between stained round fertile (SRF) pollen and spikelet fertility. The positive value of correlation and regression coefficient on SRF and spikelet fertility were found between F1 and mid parent, and F1 and male parent. High fertility of cross may be due to the presence of a wide compatibility gene or restorer genes in the cultivar. Lower pollen and spikelet fertility of the crosses was attributed to effect of the genetic background of the tester parent. Nepal Agric. Res. J. Vol. 8, 2007, pp. 120-126 DOI: http://dx.doi.org/10.3126/narj.v8i0.11605

Photosynthesis and panicle growth responses to drought stress in F_1 hybrid rice (Oryza sativa L.) from a cross between thermo–sensitive genic male sterile (TGMS) line 103S and upland rice IR17525

An F1 hybrid rice combination from a cross between a thermo-sensitive genic male sterility (TGMS) '103S' line and an upland rice 'IR17525' were investigated for physiological response traits under drought stress and recovery at the heading time by comparing with its parents. The F1 and parental plants were planted in pots in a net house at different times for synchronizing flowering. At the stage of 5-3 days before heading, water was withdrawn from the pot. When the soil water potential in the pot reached -60 kPa, pho- tosynthetic rate and dry matter accumulation were measured. Recovery traits including photosynthetic rate and dry weight of panicle were measured at 5 days interval until harvesting. The results showed that the photosynthetic rate was lower in the F1 hybrid than that in the parents during drought treatment, in contrary it was higher during recovery stage. The grain yield was maintained in the F1 hybrid under drought treatment as much as under the control condition, whereas it significantly reduced as drought treatment in the male parent. The grain yield was higher in the F1 hybrid than that in the male parent under the well- irrigated condition, and even much higher under drought treatment. It is suggested that such advantageous characters, including the shorter ripening duration, the longer panicle exertion, the higher recovery photo- synthetic rate as well as the faster of dry matter translocation into panicle at the ripening stage, contribute drought tolerance in rice. Thus, the F1 hybrid rice 103S/IR17525 would be a promising rice with high yield potential under drought stress.

Assessment of Genetic Parameters for Yield and Yield Components in Hybrid Rice and Parents

Thirty F1 rice hybrids along with complete set of 13 parents and checks were evaluated for variability, heritability and genetic advance in different yield and yield contributing traits. The data was recorded on five randomly selected plants for fifteen quantitative characters. The treatment, i.e. mean sum of squares due to genotypes showed significant differences for 14 characters studied, indicating the presence of high genetic variability among the genotypes. The estimates of GCV were lower than the respective PCV, indicating the influence of environmental factors on the expression of the traits studied. Characters like percent pollen fertility (99.9, 33.33), grain yield hill-1 (99.2, 31.13), harvest index (98.5, 30.42) and number of filled grains panicle-1 (97.8, 30.04) showed high heritability coupled with moderate genetic advance as percent of mean, suggesting that selection for the improvement of these characters may be rewarding. This also indicates greater role of non-additive gene action in their inheritance suggesting heterosis breeding could be used to improve these traits.