Search

How to overcome yield stagnation is a big challenge to rice breeders. An effective method for quickly developing new cultivars is to further improve an outstanding cultivar. In this study, three advanced backcross populations under yield selection that consist of 123 BC2F2:4 introgression lines (ILs) were developed by crossing Minghui 86 (recurrent parent, RP) with three high-yielding varieties (donors), namely, ZDZ057, Fuhui 838, and Teqing, respectively. The progeny testing allowed the identification of 12 promising ILs that had significantly higher mean grain yields than Minghui 86 in two environments. A total of 55 QTLs that affect grain yield and its related traits were identified, which included 50 QTLs that were detected using the likelihood ratio test based on stepwise regression (RSTEP-LRT) method, and eight grain yield per plant (GY) QTLs were detected using chi-squared (c2) test. Among these QTLs, five QTLs were simultaneously detected in different populations and 22 QTLs were detected in both environments. The beneficial donor alleles for increased GY and its related traits were identified in 63.6% (35 out of 55) of the QTLs. These promising ILs and QTLs identified will provide the elite breeding materials and genetic information for further improvement of the grain yield for Minghui 86 through pyramiding breeding.

All members of the SnRK2 protein kinase gene family encoded by the rice (Oryza sativa L.) genome are activated by hyperosmotic stress, and have been designated as stress-activated protein kinases (SAPKs). In this study, gene structures, phylogeny, and conserved motifs for the entire OsSAPK gene family in rice have been analyzed. Moreover, expression patterns of OsSAPK in response to infection with Xanthomonas oryzae pv. oryzicola (Xoc) were investigated. A total of ten OsSAPK genes in the japonica rice cultivar 9804 were identified and classified into four groups. All genes had similar exon–intron structures and organization of putative motifs/domains, and shared the same four motifs (motifs 1–4). Group I (OsSAPK1 and OsSAPK2) shared another two motifs (motif 5 and motif 10), while group III (OsSAPK8, OsSAPK9 and OsSAPK10) had seven motifs in common (motifs 1–7). Moreover, we found that four OsSAPKs, including OsSAPK3, OsSAPK5, OsSAPK7 and OsSAPK9, were significantly upregulated in response to infection by Xoc in rice plants carrying the nonhost resistance gene Rxo1. Four of the OsSAPK genes in which expression was upregulated were localized to both the cytoplasm and nucleus, but clustered in different groups, suggesting that they are involved in different resistance signal transduction pathways. These results will provide useful information for the future functional dissection of this gene family.

Three populations with a total of 125 BC2F3:4 introgression lines (ILs) selected for high yields from three BC2F2 populations were used for genetic dissection of rice yield and its related traits. The progeny testing in replicated phenotyping across two environments and genotyping with 140 polymorphic simple sequence repeat markers allowed the identification of 21 promising ILs that had significantly higher yields than the recurrent parent Shuhui527 (SH527). A total of 94 quantitative trait loci (QTL) were identified using the selective introgression method based on Chi-squared (χ2) and multi-locus probability tests and the RSTEP-LRT method based on stepwise regression. These QTL were mostly mapped to 12 clusters on seven rice chromosomes. Several important properties of the QTL affecting grain yield (GY) and its related traits were revealed. The first one was the presence of strong and frequent non-random associations between or among QTL that affect low-heritability traits (GY and spikelet number per panicle, SN) in the ILs with high trait values. Second, beneficial alleles at 88.9 % GY and 75 % SN QTL for increased productivity were from the donors, suggesting that direct phenotypic selection for high yield in our introgression breeding program was a powerful way to transfer beneficial alleles at many loci from the donors into SH527. Third, most QTL were in clusters with large effects on multiple traits, which should be the focal points in further investigations and marker-assisted selection in rice. The majority of the QTL identified were expressed only in one of the environments, suggesting that differential expression of QTL in different environments is the primary genetic basis of genotype × environment interaction. Finally, a large variation in both the direction and magnitude of QTL effects was detected for different donor alleles at seven QTL in the same genetic background and environments. This finding suggests the possible presence of functional diversity among the donor alleles at these loci. The promising ILs and QTL identified provide valuable materials and genetic information for further improving the yield potential of SH527, which is a backbone restorer of hybrid rice in China.

A set of 240 introgression lines derived from the advanced backcross population of a cross between a japonica cultivar, Xiushui 09, and an indica breeding line, IR2061, was developed to dissect QTLs affecting cold tolerance (CT) at seedling stage and heat tolerance (HT) at anthesis. Survival rate of seedlings (SRS) and spikelet fertility (SF), the index traits of CT and HT, showed significant differences between the two parents under stresses. A total of four QTLs (qSRS1, qSRS7, qSRS11a and qSRS11b) for CT were identified on chromosomes 1, 7, 11, and the Xiushui 09 alleles increased SRS at all loci except qSRS7. Four QTLs for SF were identified on chromosomes 4, 5, 6, and 11. These QTLs could be classified into two major types based on their behaviors under normal and stress conditions. The first was QTL expressed only under normal condition; and the second QTL was apparently stress induced and only expressed under stress. Among them, two QTLs (qSF4 and qSF6) which reduced the trait difference between heat stress and normal conditions must have contributed to HT because of their obvious contribution to trait stability, and the IR2061 allele at the qSF6 and the Xiushui 09 allele at the qSF4 improved HT, respectively. No similar QTL was found between CT at seedling stage and HT at anthesis. Therefore, it is possible to breed a new variety with CT and HT by pyramiding the favorable CT- and HT-improved alleles at above loci from Xiushui 09 and IR2061, respectively, through marker-assisted selection (MAS).

The genetic components responsible for the qualitative and quantitative resistance of rice to three Chinese races (C2, C4, and C5) of Xanthomonas oryzae pv. oryzae (Xoo) were investigated at the seedling and adult stages in two successive years in set of Lemont/Teqing cross introgression lines (ILs) in a Teqing background, to create a complete linkage map using 160 well-distributed SSR markers. Teqing was resistant to C2 and C4, but moderately susceptible to C5, whereas Lemont was susceptible to all three races. Highly significant correlations were detected among the resistance to different races at different developmental stages. A major gene (Xa4), 14 main-effect QTLs (M-QTLs), and 18 epistatic QTLs were identified in the two developmental stages over 2 years, and were largely responsible for the segregation of resistance in the ILs. In 2007, the Lemont alleles at all loci in the seedling stage, except QBbr10 to C4, increased lesion length (LL) or decreased resistance. The Teqing allele at the Xa4 locus acted as a resistance gene against C2 and C4, but acted as a M-QTL when its resistance was overcome by the virulent race C5. M-QTLs showed a degree of race specificity and had a cumulative effect on resistance. Most M-QTLs (94%) consistently expressed resistance to the same race at the seedling and adult stages, indicating that a high degree of genetic overlap exists between Xoo resistance at both developmental stages in rice. Among the digenic interactions, most co-introgressed Lemont alleles at the two epistatic loci lead to significantly smaller LL with all three races, compared to other types of interacting alleles at both development stages. The results indicate that a high level of resistance may be achieved by the cumulative effect of multiple M-QTLs, including the residual effects of “defeated” major resistance genes and the epistatic effects of co-introgression from diverse susceptible varieties.

Rice black-streaked dwarf virus (RBSDV) and stripe virus (RSV) are the two chronic viral diseases causing great damage to rice (Oryza sativa L.) production in China, and both are transmitted by the small brown planthopper (SBPH, Laodelphaxstriatellus Fallen). Quantitative trait loci (QTL) affecting field resistance to these two viral diseases were identified using QTL mapping software in a set of reciprocal introgression lines derived from the cross between Lemont and Teqing. A panel of 119 landraces was used for marker confirmation and allele mining. A total of 17 quantitative resistance loci (QRL) for the infection incidences of RBSDV and RSV were discovered and belong to 16 regions on all chromosomes except chromosome 12. Among them, 12 QRL were confirmed by association mapping, and many novel alleles at these loci were mined from the set of landraces. Only one region was found to be responsible for the genetic overlap between the field resistance against RBSDV and RSV, which was reported to be associated with SBPH resistance. The favorable alleles at the above novel and/or overlapping loci should be effective for marker-assisted selection breeding for resistance against the two diseases and the insect. Different strategies of varietal development and effective deployment against the two viral diseases are also discussed.

Perenniality is one of the important topics in rice breeding which is generally accompanied by complex physiobiochemical processes. To understand the metabolic characteristics of perennial rice, in the present study, gas chromatography–mass spectrometry and enzyme-linked immunosorbent assays were used to profile the distribution patterns of 33 primary metabolites and hormones [indole-3-acetic acid (IAA) and zeatin riboside (ZR)] of annual (RD23) and perennial (Oryza longistaminata and the line AA with RD23 genetic background) rice genotypes. Results showed that both metabolites and hormones have distinct genotype and organ distribution patterns, and considerable variations were observed between the metabolites in stem bases of perennial and annual rice. Most of the metabolites, including sugars, organic acids, and amino acids, significantly accumulated in the stem bases of perennial rice by decreasing the level in roots and leaves. Fifteen metabolites consistently accumulated significantly in the stem bases of both perennial genotypes. Additionally, the organ-level IAA content and IAA/ZR ratio in the two perennials were considerably higher than those in RD23. The present study indicated that the significant accumulation of the metabolites at stem base and the higher IAA/ZR ratio are involved in the regulatory metabolism for rhizome development.

The present study was carried out to illustrate high-efficient detection of quantitative trait loci (QTLs) with selected introgression lines (ILs) and the existence of ‘hidden genes’ conferring drought tolerance (DT). 52 selected DT ILs, derived from BC 2 F 2 population developed by crossing and backcrossing the susceptible recurrent parent (RP) IR64 with the susceptible donor Khazar were planted under irrigation and drought condition. Four important agronomic traits, e.g., grain yield (GY), heading date (HD), panicle numbers per plant (PN), and plant height (PH) were evaluated and 83 SSR polymorphic molecular markers were used for genotypic analysis. Chi-square test based on genetic hitch-hiking and one-way analysis of variances (ANOVA) were used to detect drought-related loci. Nine and 36 loci were detected by chi-square test and one-way ANOVA, respectively. Five common loci were observed by comparing the results of the two methods, among which two QTLs linked with RM7, and RM241 were detected under irrigation condition, both of the favorable alleles were from RP and explained 13% phenotypic variation (PV) for GY and 28% PV for PH, respectively. The other three QTLs linked with RM163, RM18, and RM270 were detected under drought condition, the favorable alleles were all from the donor and explained 10, 24, and 19% PV for HD, PH, and PH, respectively. Five common loci were observed by comparing the results of chi-square test and one-way ANOVA including two QTLs (one for GY and one for PH) under irrigation condition and three QTLs (one for HD and two for PH) under drought condition. By combining phenotypic and genotypic analysis, drought escape could be inferred as the main mechanism for drought tolerance in the present study. The results in present study suggested that the selected ILs population analyzed by chi-square test and one-way ANOVA was quite effective for DT QTL detection with low inputs and could also produce useful materials for breeding with wide genetic diversity for drought tolerance.

Iron is an important micro-nutrient to human health. Malnutrition of iron is a serious problem associated with resource poor population in many developing countries. Development and consumption of iron-rich rice (Oryza sativa L.) varieties are considered one of the ways to solve this problem. To facilitate large-scale screening of breeding materials for iron concentration in the rice iron-biofortified breeding program of China, a new method “surging and grind-milling of orthophenanthroline colorimetry testing (SGOC)” was developed. Based on the testing results of 3 sets of 84 diverse rice genotypes that differ greatly in grain iron concentration, the correlation coefficient was as high as 0.87 between the SGOC method and the standard ICP-MS testing method. The per sample cost of the SGOC method was about 0.1 US dollar or 50 times less the ICP-MS method, indicating that the SGOC method is robust, fast, and cost-effective, particularly useful for preliminary screening of the iron concentration of large numbers of early generation breeding materials. The iron concentration of processed rice that tended to be significantly increased when milling and polishing with iron-made equipment was also eliminated in the SGOC method. Based on the analysis of iron concentration in 59 backcross progenies, the introgression of genes/quantitative trait loci for high iron concentration from high iron rice germplasm into elite local rice varieties is an efficient way to develop high yielding rice varieties with significantly improved rice iron concentration in future rice biofortified breeding.

The objectives of this study were to gain insight into the temporal and spatial expression patterns of two-component system (TCS) genes in rice (Oryza sativa L.) under drought stress and to understand the relationship between TCS gene expression and drought resistance. Using a whole rice genome microarray, the expression profiles of TCS genes of rice lines with different drought resistance were analyzed at various growth stages. The TCS genes showed greatly difference of expression pattern in various organs but in similar patterns in the same tissues at different stages. Genes for type-A response regulator (RR), a negative regulator of cytokinin (CK) signaling, were mostly repressed by drought stress, whereas, genes for type-B RR with an opposite role to type-A RR were mostly induced by drought stress. These changes were supposed to be related to the enhancement of CK signaling under drought stress. This supposition was confirmed by the down regulation of ethylene receptor genes and the cross-talk of hormones under drought condition. The His kinase genes (HK5 and HK3) that are homologous to CK receptor genes (AHK2, AHK3, and CRE1) in Arabidopsis were induced by drought stress. However, HK6 homologous to AHK5 (CK-independent 2, CKI2) was repressed when exposed to drought stress. These results provided further confirmations of the above supposition. In drought resistant introgression lines and IR64, no significant differences of TCS gene expression profiles were observed under drought stress. This result indicates that the TCS genes are probably in relation to drought responsiveness.

Expression of quantitative trait locus (QTL) is affected by genetic background (GB) and environment. The GB effect on QTL mapping and QTL by environment interaction for heading date (HD) and plant height (PH) were studied in Beijing and Hainan environments using a large set of reciprocal introgression lines (ILs) derived from a japonica rice (Oryza sativa L.) variety Lemont and an indica variety Teqing. In both environments, the 2 IL populations showed transgressive segregation for HD and PH traits. A total of 16 and 17 main-effect QTLs (M-QTLs) were identified for HD and PH, respectively. Among them, only 5 M-QTLs were detected under the 2 GBs, indicating that the expressions of most M-QTLs are specific to GB. Under both GBs, significant interactions between QTLs and environment responsible for HD were observed at 3 M-QTLs, of which QHd8a antedated heading for 2–3 d in Hainan but delayed heading for 2–3 d in Beijing. Therefore, QHd8a could be considered as an important M-QTL for HD. By comparing with the previous results on QTL mapping using another 7 populations derived from the same parents, a few M-QTLs were found to express stably under different GBs in various environments, such as QHd3, QHd8a, QPh3, and QPh4. These QTLs show applicable potential in marker-assisted breeding for HD and PH in rice.

Rice bacterial leaf blight (BB) caused by Xanthomonasoryzae pv. oryzae and bacterial leaf streak (BLS) caused by X. oryzae pv. oryzicola (Xoc) are two important diseases of rice that often outbreak simultaneously and constrain rice production in much of Asia and parts of Africa. Developing resistant cultivars has been the most effective approach to control BB, however, most single resistance genes have limited value in breeding programs because of their narrow-spectrum of resistance to the races of the pathogen. By contrast, there is little progress in breeding varieties resistant to Xoc since BLS resistance in rice was a quantitative trait and so far only a few quantitative resistance loci have been identified. We reported here the development of a high yield elite line, Lu-You-Zhan highly resistant to both BB and BLS by pyramiding Xa23 with a wide-spectrum resistance to BB derived from wild rice and a non-host maize resistance gene, Rxo1, using both marker assisted selection (MAS) and genetic engineering. Our study has provided strong evidence that non-host R genes could be a valuable source of resistance in combating those plant diseases where no single R gene controlling high level of resistance exists and demonstrated that MAS combined with transgenic technologies are an effective strategy to achieve high level of resistance against multiple plant diseases.

To detect quantitative trait loci (QTLs) for resistance to rice sheath blight (SB) that expressed stably in different genetic backgrounds and environments, the reciprocal introgression line populations derived from the cross of Lemont and Teqing (LT-ILs and TQ-ILs) were planted in the field in 2006–2007 and inoculated with isolate RH-9 of Rhizoctonia solani . Lemont was highly susceptible, whereas Teqing was moderately resistant to RH-9. The relative lesion height (a ratio of lesion height to plant height) of TQ-ILs was normally distributed, whereas that of LT-ILs was apparently inclined to the susceptible parent Lemont. A total of 10 main-effect QTLs (M-QTLs) and 13 epistatic QTLs (E-QTLs) conferring sheath blight resistance (SBR) were mapped using data obtained from different years and genetic backgrounds. Among them, 6 M-QTLs detected in 2006 were verified in 2007, suggesting that these M-QTLs had reliable performance across years. QRlh4 was the only M-QTL expressed under the reciprocal backgrounds. On chromosome 10, QRlh10a between RM216 and RM311 detected in TQ-ILs and QRlh10b between RM222 and RM216 detected in LT-ILs were regarded as different genes because their directions of additive effect were opposite. Most QTLs identified in TQ-ILs were not expressed in LT-ILs, indicating the presence of a significant effect of genetic background. By comparative mapping, 8 M-QTLs detected in this study were located in the same or near regions that were associated with SBR identified in the previous studies. These M-QTLs have great potential to be applied in rice breeding for SBR by marker-assisted selection (MAS), and M-QTLs expressed stably in different backgrounds are favorable for gene pyramiding in SBR improvement in rice.

Plant photosynthetic traits such as net photosynthetic rate (Pn), stomata conductance (gs), transpiration rate (Tr), and intercellular CO2 concentration (Ci), are known to relate to drought tolerance in plants, but the genetic basis of these traits remains largely uncharacterized because of the difficulty in phenotyping physiological traits in a large mapping population. In this study, a set of 55 overlapping introgression lines (ILs) in the Teqing (indica) background were used to genetically dissect several morph-physiological traits and their relationship with grain yield under water stress and non-stress conditions. These traits included specific leaf weight (SLW), chlorophyll content (CC), leaf stomata frequency (SF), Pn, gs, Tr, and Ci. A total of 40 QTLs affecting the measured traits were identified and mapped to 21 genomic regions in the rice genome. Clustered QTLs affecting Pn, gs, Tr, and Ci in the same genomic regions suggest common genetic bases for the physiological traits. Low or no phenotypic correlations between leaf morphological traits and photosynthetic traits and between morph-physiological traits and grain yield (GY) appeared to be due to inconsistence in QTL effect for clustered QTLs, unlinked QTLs affecting different traits, and to possible epistasis that could not be adequately addressed in this study. Our results indicate that improving drought tolerant (DT) of rice by selecting any single secondary traits is not expected to be effective and the identified QTLs for GY and related morph-physiological traits should be carefully confirmed before to be used for improving DT in rice by MAS.

Cell death in the roots of two rice ecotypes under PEG-induced osmotic and NaCl stresses were assayed by TUNEL and DAPI techniques. Although both ecotypes exhibited cell death in response to the osmotic and salt stresses, they appeared to adapt to the two types of stresses through different timing and tissue specificity of cell death. Under the stresses, the occurrence of cell death was always delayed in IRAT109, a drought tolerant upland line, than in IR20, a drought sensitive lowland line. Under the salt stress, cell death progressed successively in a well regulated manner, starting from the outer layer cells in the epidermis and exodermis of roots and subsequently to the endodermis and stele, suggesting a possible function of the dead cells in preventing the influx of excess Na+ ions into the inner parts of roots and into shoots, leading to salt exclusion. In contrast, cell death induced by PEG-induced osmotic stress occurred randomly in roots, allowing a better ability to recover after stress. Thus, the coincidence of the difference in drought tolerance between the two rice ecotypes and their differences in the osmotic/salt induced cell death indicate that cell death may have played an important role contributing to rice tolerances to different abiotic stresses.

Tremendous efforts have been taken worldwide to develop genome-wide genetic stocks for rice functional genomic (FG) research since the rice genome was completely sequenced. To facilitate FG research of complex polygenic phenotypes in rice, we report the development of over 20,000 introgression lines (ILs) in three elite rice genetic backgrounds for a wide range of complex traits, including resistances/tolerances to many biotic and abiotic stresses, morpho-agronomic traits, physiological traits, etc., by selective introgression. ILs within each genetic background are phenotypically similar to their recurrent parent but each carries one or a few traits introgressed from a known donor. Together, these ILs contain a significant portion of loci affecting the selected complex phenotypes at which allelic diversity exists in the primary gene pool of rice. A forward genetics strategy was proposed and demonstrated with examples on how to use these ILs for large-scale FG research. Complementary to the genome-wide insertional mutants, these ILs opens a new way for highly efficient discovery, candidate gene identification and cloning of important QTLs for specific phenotypes based on convergent evidence from QTL position, expression profiling, functional and molecular diversity analyses of candidate genes, highlights the importance of genetic networks underlying complex phenotypes in rice that may ultimately lead to more complete understanding of the genetic and molecular bases of quantitative trait variation in rice.

Transcriptomic data for Sorghum propinquum, the wild-type sorghum, are limited in public databases. S. propinquum has a subterranean rhizome and transcriptome data will help in understanding the molecular mechanisms underlying rhizome formation. We sequenced the transcriptome of S. propinquum aerial-shoot and rhizome using an Illumina platform. More than 70 % of the genes in the S. propinquum genome were expressed in aerial-shoot and rhizome. The expression patterns of 1963 and 599 genes, including transcription factors, were specific or enriched in aerial-shoot and rhizome respectively, indicating their possible roles in physiological processes in these tissues. Comparative analysis revealed several cis-elements, ACGT box, GCCAC, GATC and TGACG box, which showed significantly higher abundance in aerial-shoot-specific genes. In rhizome-specific genes MYB and ROOTMOTIFTAPOX1 motifs, and 10 promoter and cytokinin-responsive elements were highly enriched. Of the S. propinquum genes, 27.9 % were identified as alternatively spliced and about 60 % of the alternative splicing (AS) events were tissue-specific, suggesting that AS played a crucial role in determining tissue-specific cellular function. The transcriptome data, especially the co-localized rhizome-enriched expressed transcripts that mapped to the publicly available rhizome-related quantitative trait loci, will contribute to gene discovery in S. propinquum and to functional studies of the sorghum genome. Deep transcriptome sequencing revealed a clear difference in the expression patterns of genes between aerial-shoot and rhizome in S. propinquum. This data set provides essential information for future studies into the molecular genetic mechanisms involved in rhizome formation.

Sorghum (Sorghum bicolor) is one of the world's most important cereal crops. S. propinquum is a perennial wild relative of S. bicolor with well-developed rhizomes. Functional genomics analysis of S. propinquum, especially with respect to molecular mechanisms related to rhizome growth and development, can contribute to the development of more sustainable grain, forage, and bioenergy cropping systems. In this study, we used a whole rice genome oligonucleotide microarray to obtain tissue-specific gene expression profiles of S. propinquum with special emphasis on rhizome development. A total of 548 tissue-enriched genes were detected, including 31 and 114 unique genes that were expressed predominantly in the rhizome tips (RT) and internodes (RI), respectively. Further GO analysis indicated that the functions of these tissue-enriched genes corresponded to their characteristic biological processes. A few distinct cis-elements, including ABA-responsive RY repeat CATGCA, sugar-repressive TTATCC, and GA-responsive TAACAA, were found to be prevalent in RT-enriched genes, implying an important role in rhizome growth and development. Comprehensive comparative analysis of these rhizome-enriched genes and rhizome-specific genes previously identified in Oryza longistaminata and S. propinquum indicated that phytohormones, including ABA, GA, and SA, are key regulators of gene expression during rhizome development. Co-localization of rhizome-enriched genes with rhizome-related QTLs in rice and sorghum generated functional candidates for future cloning of genes associated with rhizome growth and development.

Rice is sensitive to chilling stress, especially at the seedling stage. To elucidate the molecular genetic mechanisms of chilling tolerance in rice, comprehensive gene expressions of two rice genotypes (chilling-tolerant LTH and chilling-sensitive IR29) with contrasting responses to chilling stress were comparatively analyzed. Results revealed a differential constitutive gene expression prior to stress and distinct global transcription reprogramming between the two rice genotypes under time-series chilling stress and subsequent recovery conditions. A set of genes with higher basal expression were identified in chilling-tolerant LTH compared with chilling-sensitive IR29, indicating their possible role in intrinsic tolerance to chilling stress. Under chilling stress, the major effect on gene expression was up-regulation in the chilling- tolerant genotype and strong repression in chilling-sensitive genotype. Early responses to chilling stress in both genotypes featured commonly up-regulated genes related to transcription regulation and signal transduction, while functional categories for late phase chilling regulated genes were diverse with a wide range of functional adaptations to continuous stress. Following the cessation of chilling treatments, there was quick and efficient reversion of gene expression in the chilling-tolerant genotype, while the chilling-sensitive genotype displayed considerably slower recovering capacity at the transcriptional level. In addition, the detection of differentially-regulated TF genes and enriched cis-elements demonstrated that multiple regulatory pathways, including CBF and MYBS3 regulons, were involved in chilling stress tolerance. A number of the chilling-regulated genes identified in this study were co-localized onto previously fine-mapped cold-tolerance-related QTLs, providing candidates for gene cloning and elucidation of molecular mechanisms responsible for chilling tolerance in rice.

An indica pyramiding line, DK151, and its recurrent parent, IR64, were evaluated under drought stress and non-stress conditions for three consecutive seasons. DK151 showed significantly improved tolerance to drought. The DNA methylation changes in DK151 and IR64 under drought stress and subsequent recovery were assessed using methylation-sensitive amplified polymorphism analysis. Our results indicate that drought-induced genome-wide DNA methylation changes accounted for ∼12.1% of the total site-specific methylation differences in the rice genome. This drought-induced DNA methylation pattern showed three interesting properties. The most important one was its genotypic specificity reflected by large differences in the detected DNA methylation/demethylation sites between DK151 and IR64, which result from introgressed genomic fragments in DK151. Second, most drought-induced methylation/demethylation sites were of two major types distinguished by their reversibility, including 70% of the sites at which drought-induced epigenetic changes were reversed to their original status after recovery, and 29% of sites at which the drought-induced DNA demethylation/methylation changes remain even after recovery. Third, the drought-induced DNA methylation alteration showed a significant level of developmental and tissue specificity. Together, these properties are expected to have contributed greatly to rice response and adaptation to drought stress. Thus, induced epigenetic changes in rice genome can be considered as a very important regulatory mechanism for rice plants to adapt to drought and possibly other environmental stresses.

Background Rhizomatousness is a key component of perenniality of many grasses that contribute to competitiveness and invasiveness of many noxious grass weeds, but can potentially be used to develop perennial cereal crops for sustainable farmers in hilly areas of tropical Asia. Oryza longistaminata, a perennial wild rice with strong rhizomes, has been used as the model species for genetic and molecular dissection of rhizome development and in breeding efforts to transfer rhizome-related traits into annual rice species. In this study, an effort was taken to get insights into the genes and molecular mechanisms underlying the rhizomatous trait in O. longistaminata by comparative analysis of the genome-wide tissue-specific gene expression patterns of five different tissues of O. longistaminata using the Affymetrix GeneChip Rice Genome Array. Results A total of 2,566 tissue-specific genes were identified in five different tissues of O. longistaminata, including 58 and 61 unique genes that were specifically expressed in the rhizome tips (RT) and internodes (RI), respectively. In addition, 162 genes were up-regulated and 261 genes were down-regulated in RT compared to the shoot tips. Six distinct cis-regulatory elements (CGACG, GCCGCC, GAGAC, AACGG, CATGCA, and TAAAG) were found to be significantly more abundant in the promoter regions of genes differentially expressed in RT than in the promoter regions of genes uniformly expressed in all other tissues. Many of the RT and/or RI specifically or differentially expressed genes were located in the QTL regions associated with rhizome expression, rhizome abundance and rhizome growth-related traits in O. longistaminata and thus are good candidate genes for these QTLs. Conclusion The initiation and development of the rhizomatous trait in O. longistaminata are controlled by very complex gene networks involving several plant hormones and regulatory genes, different members of gene families showing tissue specificity and their regulated pathways. Auxin/IAA appears to act as a negative regulator in rhizome development, while GA acts as the activator in rhizome development. Co-localization of the genes specifically expressed in rhizome tips and rhizome internodes with the QTLs for rhizome traits identified a large set of candidate genes for rhizome initiation and development in rice for further confirmation.