Manzhong Liang

Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids

This work examines the molecular basis of heterosis by comprehensively describing the epigenetic modifications and transcriptional output, including both mRNA and small RNAs, of two rice subspecies and their reciprocal hybrids. The behavior of transcriptomes and epigenomes in hybrids of heterotic parents is of fundamental interest. Here, we report highly integrated maps of the epigenome, mRNA, and small RNA transcriptomes of two rice (Oryza sativa) subspecies and their reciprocal hybrids. We found that gene activity was correlated with DNA methylation and both active and repressive histone modifications in transcribed regions. Differential epigenetic modifications correlated with changes in transcript levels among hybrids and parental lines. Distinct patterns in gene expression and epigenetic modifications in reciprocal hybrids were observed. Through analyses of single nucleotide polymorphisms from our sequence data, we observed a high correlation of allelic bias of epigenetic modifications or gene expression in reciprocal hybrids with their differences in the parental lines. The abundance of distinct small RNA size classes differed between the parents, and more small RNAs were downregulated than upregulated in the reciprocal hybrids. Together, our data reveal a comprehensive overview of transcriptional and epigenetic trends in heterotic rice crosses and provide a useful resource for the rice community.

A Genome-Wide Transcription Analysis Reveals a Close Correlation of Promoter INDEL Polymorphism and Heterotic Gene Expression in Rice Hybrids

Heterosis, or hybrid vigor, refers to the phenomenon in which hybrid progeny of two inbred varieties exhibits enhanced growth or agronomic performance. Although a century-long history of research has generated several hypotheses regarding the genetic basis of heterosis, the molecular mechanisms underlying heterosis and heterotic gene expression remain elusive. Here, we report a genome-wide gene expression analysis of two heterotic crosses in rice, taking advantage of its fully sequenced genomes. Approximately 7-9% of the genes were differentially expressed in the seedling shoots from two sets of heterotic crosses, including many transcription factor genes, and exhibited multiple modes of gene action. Comparison of the putative promoter regions of the ortholog genes between inbred parents revealed extensive sequence variation, particularly small insertions/deletions (INDELs), many of which result in the formation/disruption of putative cis-regulatory elements. Together, these results suggest that a combinatorial interplay between expression of transcription factors and polymorphic promoter cis-regulatory elements in the hybrids is one plausible molecular mechanism underlying heterotic gene action and thus heterosis in rice.

Expression Analysis of miRNAs and Highly-expressed Small RNAs in Two Rice Subspecies and their Reciprocal Hybrids

Heterosis, or hybrid vigor, is the phenomenon whereby progeny of two inbred lines exhibit superior agronomic performance compared with either parent. We analyzed the expression of miRNAs and highly expressed small RNAs (defined according to Solexa sequencing results) in two rice (Oryza sativa) subspecies (japonica cv. Nipponbare and indica cv. 93-11) and their reciprocal hybrids using microarrays. We found that of all the 1141 small RNAs tested, 140 (12%, 140 of 1141) and 157 (13%, 157 of 1141) were identified being significantly differentially expressed in two reciprocal hybrids, respectively. All possible modes of action, including additive, high- and low- parent, above high- and below low-parent modes were exhibited. Both F1 hybrids showed non-additive expression patterns, with downregulation predominating. Interestingly, 15 miRNAs displayed stark opposite expression trends relative to mid-parent in reciprocal hybrids. Computational prediction of targets of differentially expressed miRNAs showed that they participated in multifaceted developmental pathways, and were not distinguishable from the targets of non-differentially expressed miRNAs. Together, our findings reveal that small RNAs play roles in heterosis and add a new layer in the understanding and exploitation of molecular mechanisms of heterosis.

Mitochondrial DNA genetic polymorphism in thirteen rice cytoplasmic male sterile lines

Key messageThirteen rice CMS lines derived from different cytoplasms were classified into eight groups by PCR amplification on mtDNA.Theorf79 gene, which causes Boro II CMS, possibly results in Dian1-CMS.AbstractThirteen rice cytoplasmic male sterile (CMS) lines derived from different cytoplasms are widely used for hybrid rice breeding. Based on 27 loci on mitochondrial DNA, including single nucleotide polymorphisms and segmental sequence variations between typical indica and japonica as well as high-polymorphism segmental sequence variations and single nucleotide polymorphisms among rice CMS lines, the 13 rice CMS lines were classified into eight groups: (I) wild-abortive CMS, Indonesian Shuitiangu CMS, K-CMS, Gang CMS, D-CMS and dwarf abortive CMS; (II) Maxie-CMS; (III) Honglian CMS; (IV) Boro II CMS; (V) Dian1-CMS; (VI) Liao-CMS; (VII) Lead CMS; and (VIII) Chinese wild rice CMS. According to their pollen abortion phenotypes, groups I and II (including 7 CMS lines) were classified as sporophytic CMS lines, the cytoplasmic genetic relationships among which were very close. They could have originated from similar, or even the same, cytoplasm donors. Groups III–VIII (including 6 CMS lines) were categorized as gametophytic CMS lines, the cytoplasms of which differed from one another, with some having relatively far genetic relationships. Dian1-CMS was found to harbor the orf79 gene, which causes Boro II CMS, whereas Liao-CMS had an orf79 structure that does not result in Lead CMS. Therefore, we speculated that orf79 is associated with Dian1-CMS but not with Liao-CMS. The atp6–orf79 structure related to sterility was also found to experience multiple evolutionary turnovers. All sporophytic CMS lines were indica-like. Except the Honglian CMS line, which was indica-like, all gametophytic CMS lines were japonica-like.

Analysis of indica - and japonica -specific markers of Oryza sativa and their applications

Asian rice, Oryza sativa L., is one of the most important crop species. Genetic analysis has established that rice consists of several genetically differentiated variety groups, with two main groups, namely, O. sativa ssp. japonica kata and ssp. indicakata. To determine the genetic diversity of indica and japonica rice, 45 rice varieties, including domesticated rice and Asia common wild rice (O. rufipogon Griff.), were analyzed using sequence-related amplified polymorphism, target region amplified polymorphism, simple sequence repeat, and intersimple sequence repeat marker systems. A total of 90 indica- and japonica-specific bands between typical indica and japonica subspecies were identified, which greatly helped in determining whether domesticated rice is of the indica or japonica type, and in analyzing the consanguinity of hybrid rice with japonica, which were bred from indica and japonica crossed offspring. These specific bands were both located in the coding and non-encoding region, and usually connected with quantitative trait loci. Utilizing the indica-japonica-specific markers, japonica consanguinity was detected in sterile hybrid rice lines. Many indica-japonica-specific bands were found in O. rufipogon. This result supports the multiple-origin model for domesticated rice. Javanica exhibited a greater number of indica-japonica-specific bands, which indicates that it is a subspecies of O. sativa L.

Identification of a specific molecular marker for the rice blast-resistant gene Pigm and molecular breeding of thermo-sensitive genic male sterile leaf-color marker lines

Rice blast is a damaging disease caused by Magnaportheoryzae. Marker-assisted selection of blast resistance genes could help develop cultivars with blast resistance. Pigm is a broad-spectrum blast-resistant gene. However, few rice resources contain Pigm. In this study, the Pigm gene donor Gumei4 (GM4) was investigated. By analyzing different regions of Pigm sequences, we found that marker G8900 was a specific molecular marker of Pigm gene in GM4. Correlation analysis between molecular marker detection and identification of rice blast disease nursery revealed that G8900 could be used in marker-assisted selection (MAS) of Pigm. Furthermore, we introduced Pigm gene into the KT27S line (a blast-susceptible yellow-green-leaf-color mutant) in G8900-assisted breeding and identified three new yellow-green-leaf-color marker lines that are resistant to blast. The agronomic and economic traits of the three new lines are similar to those of their parental lines. The identification and application of Pigm-specific molecular marker in breeding of yellow-green-leaf-color marker line could play an important role in the production of disease-resistant hybrid rice.

Exploring the genetic characteristics of 93-11 and Nipponbare recombination inbred lines based on the GoldenGate SNP assay

Understanding genetic characteristics in rice populations will facilitate exploring evolutionary mechanisms and gene cloning. Numerous molecular markers have been utilized in linkage map construction and quantitative trait locus (QTL) mappings. However, segregation-distorted markers were rarely considered, which prevented understanding genetic characteristics in many populations. In this study, we designed a 384-marker GoldenGate SNP array to genotype 283 recombination inbred lines (RILs) derived from 93-11 and Nipponbare Oryza sativa crosses. Using 294 markers that were highly polymorphic between parents, a linkage map with a total genetic distance of 1,583.2 cM was constructed, including 231 segregation-distorted markers. This linkage map was consistent with maps generated by other methods in previous studies. In total, 85 significant quantitative trait loci (QTLs) with phenotypic variation explained (PVE) values≥5% were identified. Among them, 34 QTLs were overlapped with reported genes/QTLs relevant to corresponding traits, and 17 QTLs were overlapped with reported sterility-related genes/QTLs. Our study provides evidence that segregation-distorted markers can be used in linkage map construction and QTL mapping. Moreover, genetic information resulting from this study will help us to understand recombination events and segregation distortion. Furthermore, this study will facilitate gene cloning and understanding mechanism of inter-subspecies hybrid sterility and correlations with important agronomic traits in rice.

Fertility response to photoperiod and temperature in indica photoperiod-sensitive male sterile rice

The aim of this work was to develop a photoperiod-sensitive male sterile rice with stable sterility. We developed Changguang S, an indica rice strain, by using a short critical day length. Differences in the fertility responses of Changguang S strain pollen to temperature and photoperiod under natural and controlled conditions were studied. The results showed that Changguang S strain exhibited stable sterility under long-day and low-temperature conditions (22°C, 15 days). The stability of sterility was significantly higher than that of other such rice strains, Nongken 58S and 7001S. The critical photoperiod for inducing male sterility in Changguang S was 13 h or shorter, and its duration was significantly shorter than that required for rice strains Nongken 58S and 7001S. It is suggested that Changguang S is a typical photoperiod-sensitive male sterile rice strain with a shorter critical day length and a lower critical temperature. It is promising to apply this strain to two-line hybrid rice production.