Diploid Rice Research Articles

Genomics Analyses Reveal Unique Classification, Population Structure and Novel Allele of Neo-Tetraploid Rice

BackgroundNeo-tetraploid rice (NTR) is a useful new germplasm that developed from the descendants of the autotetraploid rice (ATR) hybrids. NTR showed improved fertility and yield potential, and produced high yield heterosis when crossed with indica ATR for commercial utilization. However, their classification, population structure and genomic feature remain elusive.ResultsHere, high-depth genome resequencing data of 15 NTRs and 18 ATRs, together with 38 publicly available data of diploid rice accessions, were analyzed to conduct classification, population structure and haplotype analyses. Five subpopulations were detected and NTRs were clustered into one independent group that was adjacent to japonica subspecies, which maybe the reason for high heterosis when NTRs crossed with indica ATRs. Haplotype patterns of 717 key genes that associated with yield and other agronomic traits were revealed in these NTRs. Moreover, a novel specific SNP variation was detected in the first exon of HSP101, a known heat-inducible gene, which was conserved in all NTRs but absent in ATRs, 3KRG and RiceVarMap2 databases. The novel allele was named as HSP101–1, which was confirmed to be a heat response factor by qRT-PCR, and knockout of HSP101–1 significantly decreased the thermotolerance capacity of NTR. Interestingly, HSP101–1 was also specifically expressed in the anthers of NTR at pre-meiotic and meiosis stages under optimal environment without heat stress, and its loss-of-function mutant showed significant decrease in fertility of NTR.ConclusionThe construction of first genomic variation repository and the revelation of population structure provide invaluable information for optimizing the designs of tetraploid rice breeding. The detection of specific genomic variations offered useful genomic markers and new directions to resolve high fertility mechanism of NTR.

A route to de novo domestication of wild allotetraploid rice

Cultivated rice varieties are all diploid, and polyploidization of rice has long been desired because of its advantages in genome buffering, vigorousness, and environmental robustness. However, a workable route remains elusive. Here, we describe a practical strategy, namely de novo domestication of wild allotetraploid rice. By screening allotetraploid wild rice inventory, we identified one genotype of Oryza alta (CCDD), polyploid rice 1 (PPR1), and established two important resources for its de novo domestication: (1) an efficient tissue culture, transformation, and genome editing system and (2) a high-quality genome assembly discriminated into two subgenomes of 12 chromosomes apiece. With these resources, we show that six agronomically important traits could be rapidly improved by editing O.alta homologs of the genes controlling these traits in diploid rice. Our results demonstrate the possibility that de novo domesticated allotetraploid rice can be developed into a new staple cereal to strengthen world food security.

多倍体水稻优良回复二倍体品系的米质分析

多倍体水稻优良回复二倍体品系的米质分析

Integration of small RNA, degradome and proteome sequencing in Oryza sativa reveals a delayed senescence network in tetraploid rice seed.

Seed of rice is an important strategic resource for ensuring the security of China's staple food. Seed deterioration as a result of senescence is a major problem during seed storage, which can cause major economic losses. Screening among accessions in rice germplasm resources for traits such as slow senescence and increased seed longevity during storage is, therefore, of great significance. However, studies on delayed senescence in rice have been based mostly on diploid rice seed to date. Despite better tolerance have been verified by the artificial aging treatment for polyploid rice seed, the delayed senescence properties and delayed senescence related regulatory mechanisms of polyploid rice seed are rarely reported, due to the lack of polyploid rice materials with high seed set. High-throughput sequencing was applied to systematically investigate variations in small RNAs, the degradome, and the proteome between tetraploid and diploid rice seeds. Degradome sequencing analysis of microRNAs showed that expression of miR-164d, which regulates genes encoding antioxidant enzymes, was changed significantly, resulting in decreased miRNA-mediated cleavage of target genes in tetraploid rice. Comparisons of the expression levels of small RNAs (sRNAs) in the tetraploid and diploid libraries revealed that 12 sRNAs changed significantly, consistent with the findings from degradome sequencing. Furthermore, proteomics also showed that antioxidant enzymes were up-regulated in tetraploid rice seeds, relative to diploids.

Photosynthetic Physiology and Molecular Response Mechanisms of Indica–Japonica Intersubspecific Tetraploid Rice Seedlings to Ion Beams

Indica–japonica intersubspecific tetraploid rice is a useful germplasm that has greater biological and yield potentials than diploid rice. However, the physiological and molecular mechanisms of the stress effects of indica–japonica intersubspecific tetraploid rice in response to ion implantation are not fully understood. In this work, indica–japonica intersubspecific tetraploid rice seeds were implanted with different doses of ion beam to explore the responses of their seedlings. The investigation found that the growth and development of seedlings was inhibited, the leaf area and chlorophyll content was reduced, and photosynthesis and the expression levels of related genes were disturbed by ion beam irradiation. The decrease rate of chlorophyll content in tetraploid rice under medium-dose irradiation was lower than those of indica/japonica diploid parents may be due to the upregulated expression of HEMD, and the decrease rate of photosynthetic gas exchange parameters and chlorophyll fluorescence parameters in tetraploid rice under low-dose irradiation were lower than those of indica/japonica diploid parents may be due to the upregulated expression of PetB. The aforementioned results will be useful for further research on the physiological and molecular mechanisms of indica–japonica intersubspecific tetraploid rice to ion beam stress.

Deciphering global DNA variations and embryo sac fertility in autotetraploid rice line

Autotetraploid rice is a new germplasm resource obtained by doubling chromosomes through colchicine treatment. There have been many studies on the reproductive characteristics of autotetraploid rice, but little is known about global DNA variations and reasons for low embryo sac fertility in autotetraploid rice. Therefore, an autotetraploid rice line (T446) was used for resequencing and embryo sac fertility was observed. Whole-genome resequencing data revealed 87,229 SNPs and 11,022 InDels in the genome of T446 versus E246 (diploid rice), which had an average of 23.37 SNPs and 2.95 InDels per 100 kb. A total of 17,375 and 17,171 structural variations and 131 and 128 copy number variations were identified in the autotetraploid and its diploid counterpart, respectively. We detected 140 large-effects SNPs and InDel variants that might be related to the embryo sac fertility of autotetraploid rice, including 10 genes that may be closely associated with the development of the embryo sac. Of these, Os02g0292600 and Os06g0565200 were specifically expressed in the ovary. Mature embryo sac fertility was observed through whole-mount eosin B-staining confocal laser scanning microscopy. Many abnormalities were found in the embryo sac of T446, including embryo sac degeneration, embryo sac without female germ unit, abnormal polar nuclei, and poly-eggs, which, in turn, resulted in low seed set. However, whole-genome polymorphisms and genetic differences were high and exhibited broad prospects for genetic improvement. Genetic mutations in genes associated with embryo sac fertility in polyploid rice require further studies.

Cytological and transcriptome analysis reveal that interaction at Sb pollen sterility locus cause down-regulation of important meiosis-related genes associated with high pollen sterility in autotetraploid rice hybrids

Polyploidy could increase the interactions of pollen sterility loci and Sb locus interaction cause higher pollen abortion than other loci. Therefore, we focused on the interaction at Sb pollen sterility locus in autotetraploid rice compared to diploid rice hybrid using the near-isogenic lines in the present study. Cytological observations indicated that interaction at Sb locus cause high pollen sterility (69.9%) and abnormal chromosome behavior (37.02%) at Metaphase II in autotetraploid rice hybrid. A total of 139 meiosis-related or meiosis stage-specific genes were detected in the autotetraploid rice hybrid harboring interaction at Sb locus and 27 of these meiosis-related or specific genes displayed significant down-regulation, including four pollen fertility related genes (Rad51, XRI1, PSS1 and MIL1). These results revealed a stronger interaction at Sb pollen sterility locus than other loci, which cause down-regulation of many important meiosis-related genes that were associated with higher pollen sterility in autotetraploid rice hybrids.

The mechanism of starch content increase in grain of autotetraploid rice (Oryza sativa L.)

Net photosynthetic rate (PN), photorespiration (PR), chlorophyll (Chl) content, Chl fluorescence parameters, starch accumulation, and related key enzyme activities were determined during the grain-filling stage in two autotetraploid lines and corresponding diploid rice lines. The results showed that autotetraploid rice lines had a higher Chl content, PN, electron transport rate, maximum photochemical efficiency of PSII, actual photochemical efficiency of PSII, and lower PR in leaves than that in corresponding diploid rice lines during the grain-filling stage. It indicated that autotetraploid rice line had a high photosynthetic capacity and high light-utilization efficiency. The activities of ADP-glucose pyrophosphorylase, soluble starch synthase, and starch-branching enzyme in grains of autotetraploid rice lines were higher than those in grains of corresponding diploid rice lines during the grain-filling stage. Therefore, autotetraploid rice lines were more efficient than corresponding diploid rice lines in converting photosynthetic products into starch.

Genotyping genome-edited mutations in plants using CRISPR ribonucleoprotein complexes.

SummaryDespite the great achievements in genome editing, accurately detecting mutations induced by sequence‐specific nucleases is still a challenge in plants, especially in polyploidy plants. An efficient detection method is particularly vital when the mutation frequency is low or when a large population needs to be screened. Here, we applied purified CRISPR ribonucleoprotein complexes to cleave PCR products for genome‐edited mutation detection in hexaploid wheat and diploid rice. We show that this mutation detection method is more sensitive than Sanger sequencing and more applicable than PCR/RE method without the requirement for restriction enzyme site. We also demonstrate that this detection method is especially useful for genome editing in wheat, because target sites are often surrounded by single nucleotide polymorphisms. Using this screening method, we were also able to detect foreign DNA‐free tagw2 mutations induced by purified TALEN protein. Finally, we show that partial base editing mutations can also be detected using high‐fidelity SpCas9 variants or FnCpf1. The PCR/RNP method is low‐cost and widely applicable for rapid detection of genome‐edited mutation in plants.

Analysis of small RNAs revealed differential expressions during pollen and embryo sac development in autotetraploid rice

BackgroundPartial pollen and embryo sac sterilities are the two main reasons for low fertility in autotetraploid rice. Our previous study revealed that small RNAs changes may associate with pollen fertility in autotetraploid rice. However, knowledge on comparative analysis between the development of pollen and embryo sac by small RNAs in autotetraploid rice is still unknown. In the present study, WE-CLSM (whole-mount eosin B-staining confocal laser scanning microscopy) and high-throughput sequencing technology was employed to examine the cytological variations and to analyze small RNAs changes during pollen and embryo sac development in autotetraploid rice compared with its diploid counterpart.ResultsA total of 321 and 368 differentially expressed miRNAs (DEM) were detected during pollen and embryo sac development in autotetraploid rice, respectively. Gene Ontology enrichment analysis on the targets of DEM associated with embryo sac and pollen development revealed 30 prominent functional gene classes, such as cell differentiation and signal transduction during embryo sac development, while only 7 prominent functional gene classes, such as flower development and transcription factor activity, were detected during pollen development in autotetraploid rice. The expression levels of 39 DEM, which revealed interaction with meiosis-related genes, showed opposite expression patterns during pollen and embryo sac development. Of these DEM, osa-miR1436_L + 3_1ss5CT and osa-miR167h-3p were associated with the female meiosis, while osa-miR159a.1 and osa-MIR159a-p5 were related with the male meiosis. 21 nt-phasiRNAs were detected during both pollen and embryo sac development, while 24 nt-phasiRNAs were found only in pollen development, which displayed down-regulation in autotetraploid compared to diploid rice and their spatial-temporal expression patterns were similar to osa-miR2275d. 24 nt TEs-siRNAs were found to be up-regulated in embryo sac but down-regulated in pollen development.ConclusionThe above results not only provide the small RNAs changes during four landmark stages of pollen and embryo sac development in autotetraploid rice but also have identified specifically expressed miRNAs, especially meiosis-related miRNAs, pollen-specific-24 nt-phasiRNAs and TEs-siRNAs in autotetraploid rice. Together, these findings provide a foundation for understanding the effect of polyploidy on small RNAs expression patterns during pollen and embryo sac development that may lead to different abnormalities in autotetraploid rice.

Effects of genome doubling on expression of genes regulating grain size in rice.

Rice is one of the most important staple crops. It has been the major focus in breeding program to improve grain yield. A unique feature of tetraploid rice is the increased grain size and weight compared to diploid. Therefore, investigating the effects of genome doubling on expression of genes regulating grain size is important for yield improvement in rice breeding program. In this study, we analyzed differential expression of six genes regulating grain size in young panicles of various developmental stages between diploid and tetraploid rice. Transgenic approaches were employed to explore the dosage effects on gene expression and grain size. The results showed that genome duplications did not influence the developmental patterns of rice growth, but enhanced plant height, leaf width and grain size. The grain length and width in Indica tetraploid increased significantly, but the grain length showed more obvious change than width in Japonica tetraploid. The expression levels were affected not only by the developmental stages, but also by genetic background. Upon genome doubling, the positive regulation gene GS5 and HGW expression levels were generally higher in tetraploid than the corresponding diploid. Negative regulation gene GS3 in Indica tetraploid tended to be down-regulated or silenced, but increased in Japonica tetraploid. Another negative regulation GW2 was up-regulated in Indica tetraploid and silenced in Japonica tetraploid. The extra copies of GW2 in diploid transgenic lines exerted a gene dosage effect that resulted in the higher expression level than that of wild type diploid and tetraploid, which causes small grain formation in transgenic lines. Our results will help to understand the function of genes regulating the grain size in the diploid and tetraploid, and provide a theoretical basis for yield improvement.

Global Methylation Patterns and Their Relationship with Gene Expression and Small RNA in Rice Lines with Different Ploidy.

Whole genome duplication (WGD) is a major force in angiosperm evolution. Whether WGD is accompanied by the evolution of epigenetic regulators remains to be explored. Here we investigate whole genome methylation, gene expression, and miRNA regulation among monoploid, diploid, and triploid rice plants isolated from a twin-seedling population. The DNA methylation patterns in the three different ploidy plants were highly similar, with DNA methylation primarily enriched in the promoters. We examined the methylation of single genes and detected around 25,500 methylated genes, of which 22,751 were methylated in all three lines. Significantly divergent DNA methylation patterns between each pair of three lines were only detected in 64 genes, though more genes were found to exhibit differential expression. Analysis of DNA methylation and expression patterns showed that higher DNA methylation levels upstream of the transcription start sites are correlated with higher levels of expression of related genes; whereas higher DNA methylation levels in gene body regions are correlated with lower levels of expression. We also carried out high-throughput sequencing of small RNA libraries and identified 36 new miRNAs. These miRNAs have different expression levels depending on the ploidy.

Polyploidy Enhances F1 Pollen Sterility Loci Interactions That Increase Meiosis Abnormalities and Pollen Sterility in Autotetraploid Rice.

Intersubspecific autotetraploid rice (Oryza sativa ssp. indica × japonica) hybrids have greater biological and yield potentials than diploid rice. However, the low fertility of intersubspecific autotetraploid hybrids, which is largely caused by high pollen abortion rates, limits their commercial utility. To decipher the cytological and molecular mechanisms underlying allelic interactions in autotetraploid rice, we developed an autotetraploid rice hybrid that was heterozygous (S(i)S(j)) at F1 pollen sterility loci (Sa, Sb, and Sc) using near-isogenic lines. Cytological studies showed that the autotetraploid had higher percentages (>30%) of abnormal chromosome behavior and aberrant meiocytes (>50%) during meiosis than did the diploid rice hybrid control. Analysis of gene expression profiles revealed 1,888 genes that were differentially expressed between the autotetraploid and diploid hybrid lines at the meiotic stage, among which 889 and 999 were up- and down-regulated, respectively. Of the 999 down-regulated genes, 940 were associated with the combined effect of polyploidy and pollen sterility loci interactions (IPE). Gene Ontology enrichment analysis identified a prominent functional gene class consisting of seven genes related to photosystem I (Gene Ontology 0009522). Moreover, 55 meiosis-related or meiosis stage-specific genes were associated with IPE in autotetraploid rice, including Os02g0497500, which encodes a DNA repair-recombination protein, and Os02g0490000, which encodes a component of the ubiquitin-proteasome pathway. These results suggest that polyploidy enhances epistatic interactions between alleles of pollen sterility loci, thereby altering the expression profiles of important meiosis-related or meiosis stage-specific genes and resulting in high pollen sterility.

调控水稻异倍性杂交种子败育的相关基因分析

The MADS29 gene regulates the plumpness of rice seeds and affects seed development by regulating the degradation of maternal tissues and maintaining the plants hormone balance. Rice seeds produced by heteroploid crosses exhibit greater rate of sterility than that by seeds of other plants. To determine whether MADS29 and its related genes regulate seed development, we used four rice cultivars (two diploid and two tetraploid) to produce four self-crossed combinations as the control and eight hybridized combinations as reciprocal crosses. Then, pollen grain fertility, pollen germination, and seed development were observed, and the expressions of MADS29 and related genes were quantified using RT-PCR. The results showed the following: (1) heteroploid crosses showed 100% successful fertilization, with non-negligible rate of seed abortion. (2) Based on examinations of paraffin sections of seeds at 3 days after pollination (3 DAP) in a 4 n ×2 n cross, the endosperm had entered the cellularization stage, but the number of cells was lower than that in the control. However, in the endosperm of seeds of 2 n ×4 n crosses, the cell walls did not form around the nucleus. In addition, some vacuolation was noted in the endosperm, and cellularization was delayed. (3) qRT-PCR results showed that the relative expression levels of MADS29 , IAA , and programmed cell death (PCD) genes associated with maternal tissues in hybrid seeds at 6 DAP and 8 DAP were significantly higher than those of the control. On the contrary, the relative expression of starch synthesis genes in hybrid seeds was significantly lower than that of the control. This suggests that MADS29 is more highly expressed in the seeds of heteroploid crosses. In addition, it suggested that the expressions of IAA and other genes involved in the PCD of maternal tissues was upregulated in the same seeds. However, starch synthesis genes showed downregulated expression levels, leading to the abnormal development of the endosperm, followed by seed abortion. Thus, high expression of MADS29 leads to hybrid seed abortion, a novel regulatory pattern that is not observed in diploid rice seeds.

Comparative cytological and transcriptomic analysis of pollen development in autotetraploid and diploid rice

Autotetraploid rice has greater genetic variation and higher vigor than diploid rice, but low pollen fertility is one of the major reasons for low yield of autotetraploid rice. Very little is known about the molecular mechanisms of low pollen fertility of autotetraploid rice. In this study, cytological observations and microarray analysis were used to assess the genetic variation during pollen development in autotetraploid and diploid rice. Many abnormal chromosome behaviors, such as mutivalents, lagged chromosomes, asynchronous cell division, and so on, were found during meiosis in autotetraploid. Microsporogenesis and microgametogenesis in autotetraploid rice was similar to diploid rice, but many different kinds of abnormalities, including microspores degeneration, multi-aperture, and abnormal cell walls, were found in autotetraploid rice. Compared with diploid rice, a total of 1,251 genes were differentially expressed in autotetraploid rice in pollen transcriptome, among them 1,011 and 240 genes were up-regulated and down-regulated, respectively. 124 and 6 genes were co-up-regulated and co-down-regulated during three pollen development stages, respectively. These results suggest that polyploidy induced up-regulation for most of the genes during pollen development. Quantitative RT-PCR was done to validate 12 differentially expressed genes selected from functional categories based on the gene ontology analysis. These stably expressed genes not only related to the pollen development genes, but also involved in cell metabolism, cell physiology, binding, catalytic activity, molecular transducer activity, and transcription regulator activity. The present study suggests that differential expression of some key genes may lead to complex gene regulation and abnormal pollen development in autotetraploid rice.

Genome duplication improves rice root resistance to salt stress.

BackgroundSalinity is a stressful environmental factor that limits the productivity of crop plants, and roots form the major interface between plants and various abiotic stresses. Rice is a salt-sensitive crop and its polyploid shows advantages in terms of stress resistance. The objective of this study was to investigate the effects of genome duplication on rice root resistance to salt stress.ResultsBoth diploid rice (HN2026-2x and Nipponbare-2x) and their corresponding tetraploid rice (HN2026-4x and Nipponbare-4x) were cultured in half-strength Murashige and Skoog medium with 150 mM NaCl for 3 and 5 days. Accumulations of proline, soluble sugar, malondialdehyde (MDA), Na+ content, H+ (proton) flux at root tips, and the microstructure and ultrastructure in rice roots were examined. We found that tetraploid rice showed less root growth inhibition, accumulated higher proline content and lower MDA content, and exhibited a higher frequency of normal epidermal cells than diploid rice. In addition, a protective gap appeared between the cortex and pericycle cells in tetraploid rice. Next, ultrastructural analysis showed that genome duplication improved membrane, organelle, and nuclei stability. Furthermore, Na+ in tetraploid rice roots significantly decreased while root tip H+ efflux in tetraploid rice significantly increased.ConclusionsOur results suggest that genome duplication improves root resistance to salt stress, and that enhanced proton transport to the root surface may play a role in reducing Na+ entrance into the roots.

Different drought-stress responses in photosynthesis and reactive oxygen metabolism between autotetraploid and diploid rice

Photosynthetic light curve, chlorophyll (Chl) content, Chl fluorescence parameters, malondialdehyde (MDA) content, phosphoenolpyruvate carboxylase (PEPC) activity and reactive oxygen metabolism were studied under drought stress in two autotetraploid rice lines and corresponding diploid rice lines. Net photosynthetic rate decreased dramatically, especially under severe drought stress and under high photosynthetic active radiation in diploid rice, while it declined less under the same conditions in autotetraploid lines. Compared with the corresponding diploid lines, the Chl content, maximum photochemical efficiency of photosystem (PS) II, and actual photochemical efficiency of PSII were reduced less in autotetraploid lines. PEPC activities were higher in autotetraploid rice lines. PEPC could alleviate inhibition of photosynthesis caused by drought stress. The chromosome-doubling enhanced rice photoinhibition tolerance under drought stress. The lower MDA content and superoxide anion production rate was found in the autotetraploid rice indicating low peroxidation level of cell membranes. At the same time, the superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activities were higher in autotetraploid rice lines. SOD, POD, and CAT could effectively diminish the reactive oxygen species and reduced the membrane lipid peroxidation.

Studies on awns in polyploid rice (Oryza sativa L.) and preliminary cross experiments of a special awnless tetraploid rice

Awns are an important genetic character of rice (Oryza sativa L.) and almost all awnless diploid varieties will change into awned varieties after polyploidization. In order to increase the understanding of awns and promote the development of polyploid rice breeding, the effect of polyploidization on awns was investigated and the development and distribution characteristics have been summarized. Furthermore, cross experiments were made between a special awnless tetraploid rice and two awned tetraploid rice. The results showed that the awns of polyploid rice initially emerged at the pistil–stamina formation stage and there was a stable corresponding relationship between awn development and other organs or development characteristics. Polyploidization had a great effect on awns. Awn length was considerably affected when diploid rice was doubled to polyploid. However, the degree of change varied between varieties. The F1 hybrids between awnless and awned tetraploid rice in this research were all partial awn types and showed that the larger the mean, maximum awn length and the percentage of awned spikelets (PAS) of their awned parents, then the larger these of their F1 hybrids. But different cross combinations showed some variation. The F2 generations were still all partially awned and awnless type was not found. And the awn length and PAS of the plants developing from awned grains were significantly greater than that of the plants developing from awnless ones. This showed that the awn character of a grain could affect the plants developing from this grain. The results laid the foundation of further research of awn inheritance.

Analysis of Genetic Variation and DNA Methylation Alteration in Autoetraploid and Diploid Rice

DNA methylation plays an important role in regulating the process of growth and development in eukaryotes.The purpose is to investigate the genome and methylation differences between diploid and tetraploid,explore the genetic differences and genomic DNA methylation level and pattern changes.The diploid and autotetraploid rices Gang 46B,Minghui63,R725,Chenghui149,Haitian and Shixiang were analyzed by SSR and MSAP technique.The results showed that most genomes of the autotetraploid and diploid rice were the same except some sites with three pair of primers preferably polymorphic and specific bands amplified in the different ploidy rice.The consequences of MSAP suggested that the total methylation ratio in autotetraploid rice(24.0%) was significantly less than the diploid rice(28.15%);The full methylation ratio and hemimethylation ratio were different between the autotetraploid and diploid rices.The averaged full methylation rate and hemimethylation rate were 6.24% and 22.03%,respectively for diploid rice,7.44% and 16.61% for autotetraploid rice.The degree of methylation did not increase due to polyploidy,indicating that diploid and tetraploid DNA methylation of the same species of rice changed.The pattern changes of the DNA methylation in the rice of various ploidy was further analyzed,which showed that demethylation occurred in autotetraploid rice on an average of about 11.6% sites,methylations on about 24.11% sites,and the proportion of genes with methylation significantly higher than that with demethylation.The methylation of some functional genes could induce gene silencing to ease the impact of genome doubling dose effect.

Dissection of two major components of the post‐zygotic hybridization barrier in rice endosperm

A post-zygotic hybridization barrier is often observed in the endosperm of seeds produced by interspecific or interploidy crosses. In Arabidopsis thaliana, for example, hybrid endosperm from both types of cross shows altered timing of cellularization and an altered rate of nuclear divisions. Therefore, it has been proposed that interspecific and interploidy crosses share common molecular mechanisms for establishment of an effective species barrier. However, these two types of hybridization barrier may be initiated by different intrinsic cues: the interspecific cross barrier arises after hybridization of genomes with differences in DNA sequences, while the interploidy cross barrier arises after hybridization of genomes with the same DNA sequences but differences in ploidy levels. In this study, we performed interploidy crosses to identify components of the post-hybridization barrier in the endosperm of rice. We performed an intra-cultivar cross of autotetraploid (4n) × diploid (2n) rice, and found precocious cellularization and a decreased rate of nuclear division in the syncytial endosperm. By contrast, seeds from the reciprocal cross showed delayed cellularization and an increased rate of nuclear division. This differential effect on nuclear division rates contrasts with the outcome of rice interspecific crosses, which were previously shown to have altered timing of cellularization without any change in nuclear division rates. Thus, we propose that the post-zygotic hybridization barrier in rice endosperm has two separable components, namely control of the timing of cellularization and control of the nuclear division rates in the syncytial stage of endosperm development.