Changlan Zhu

Identification and Genetic Analysis of Fertility Restoration Ability in Dongxiang Wild Rice (Oryza rufipogon)

Two populations of Dongxiang wild rice (Oryza rufipogon), Shuitaoshu and Dongtangshang, were crossed with five male sterile rice lines with different cytoplasmic backgrounds (B06S, Zhenshan 97A, Xieqingzao A, Zhong 9A, and Yuetai A), and the seed setting rate of the F1 was used to judge the fertility restoration ability in the Dongxiang wild rice. With P1, F1, P2, and F2 populations as materials, the Akaikes Information Criterion (AIC) was used to identify the major genes affecting quantitative traits, and when the major genes existed, the genetic effects of the major gene and the polygene and their genetic variance were estimated through segregation analysis. The seed setting rates of the F1 generation varied from 45.98% to 76.57%, suggesting that the Dongxiang wild rice had the fertility restoration ability. One major gene plus polygene mixed inheritance model was the most fitted genetic model for this trait in all the F2 populations. The heritability values of the major genes varied from 56.63% to 88.29% and those of the polygenes from 2.74% to 30.97%, and the total heritability values were from 63.17% to 94.01%. The major gene inheritance of the combination Zhong 9A/Dongtangshang was controlled by the additive effect without dominant effect, and the other nine combinations were by the completely dominant inheritance.

Mapping QTL for Seed Germinability under Low Temperature Using a New High-Density Genetic Map of Rice

Mapping major quantitative trait loci (QTL) responsible for rice seed germinability under low temperature (GULT) can provide valuable genetic source for improving cold tolerance in rice breeding. In this study, 124 rice backcross recombinant inbred lines (BRILs) derived from a cross indica cv. Changhui 891 and japonica cv. 02428 were genotyped through re-sequencing technology. A bin map was generated which includes 3057 bins covering distance of 1266.5 cM with an average of 0.41 cM between markers. On the basis of newly constructed high-density genetic map, six QTL were detected ranging from 40 to 140 kb on Nipponbare genome. Among these, two QTL qCGR8 and qGRR11 alleles shared by 02428 could increase GULT and seed germination recovery rate after cold stress, respectively. However, qNGR1 and qNGR4 may be two major QTL affecting indica Changhui 891germination under normal condition. QTL qGRR1 and qGRR8 affected the seed germination recovery rate after cold stress and the alleles with increasing effects were shared by the Changhui 891 could improve seed germination rate after cold stress dramatically. These QTL could be a highly valuable genetic factors for cold tolerance improvement in rice lines. Moreover, the BRILs developed in this study will serve as an appropriate choice for mapping and studying genetic basis of rice complex traits.

QTL mapping and correlation analysis for 1000-grain weight and percentage of grains with chalkiness in rice

The study of 1000-grain weight (TGW) and percentage of grains with chalkiness (PGWC) is very important in rice. In this study, a set of introgression lines (ILs), derived from Sasanishiki/Habataki with Sasanishiki as the recurrent parent, were used to detect correlations and quantitative trait loci (QTL) on TGW and PGWC in two different environments. Phenotypic correlation analysis showed that there was no significant correlation between TGW and PGWC in both environments, which indicated that the linkage of TGW and PGWC traits could be broken via suitable population. A total of 20 QTL were detected in both environments, nine QTL for 1000-paddy-grain weight (PTGW), five QTL for 1000-brown-grain weight (BTGW) and six QTL for percentage of grains with chalkiness (PGWC). Moreover, five QTL, qPTGW3, qPTGW8.2, qPTGW11.1 for PTGW and qPGWC1.1, qPGWC1.2 for PGWC, were stably expressed in both environments. Phenotypic values were significantly different (P < 0.01) between the introgression lines carrying these five QTL alleles and the genetic background parent, Sasanishiki. The introgression lines carrying these QTL also represent a useful genetic resource in the context of rice yield and quality improvement via a design-breeding approach.

Genome-wide identification and phylogenetic analysis of the chalcone synthase gene family in rice

The enzymes of the chalcone synthase family are also known as type III polyketide synthases (PKS), and produce a series of secondary metabolites in bacteria, fungi and plants. In a number of plants, genes encoding PKS comprise a large multigene family. Currently, detailed reports on rice (Oryza sativa) PKS (OsPKS) family genes and tissue expression profiling are limited. Here, 27 candidate OsPKS genes were identified in the rice genome,and 23 gene structures were confirmed by EST and cDNA sequencing; phylogenetic analysis has indicated that these 23 OsPKS members could be clustered into three groups (I-III). Comparative analysis has shown OsPKS08 and OsPKS26 could be classified with the CHS genes of other species. Two members OsPKS10 and OsPKS21 were grouped into anther specific chalcone synthase-like (ASCL) clade. Intron/exon structure analysis revealed that nearly all of the OsPKS members contained one phase-1 intron at a conserved Cys. Analysis of chromosomal localization and genome distribution showed that some of the members were distributed on a chromosome as a cluster. Expression data exhibited widespread distribution of the rice OsPKS gene family within plant tissues, suggesting functional diversification of the OsPKS genes. Our results will contribute to future study of the complexity of the OsPKS gene family in rice.

Molecular dissection of developmental behavior of tiller number and the relationship with effective panicle using indica–japonica introgression lines in rice

To analyze the developmental behavior of tiller number and the relationship with effective panicle for indica and japonica in rice, an introgression line (IL) population of indica variety Habataki in the background of japonica cultivar Sasanishiki was applied for these traits across three environments. The analysis of variance showed that tiller number was highly influenced by growing environment, and 21 and 10 quantitative trait loci (QTLs) for tiller number and effective panicle were observed, respectively. Different QTLs apparently controlled tiller number at different developmental stages, indicating that QTLs for tiller number might be differentially spatially and temporally expressed at different development stages. Seven of the 10 loci for effective panicle were located in the same intervals within the tiller number QTLs, suggesting that the traits are related and this is consistent with the correlations detected between phenotypic variables, especially the correlation at the stage around heading. The results showed that tiller number around the heading period has a strong promoting effect on the formation of effective panicle. Furthermore, two new key tiller number QTLs, qTN2.3 and qTN4.2, stably expressed at the stage around heading. The genetic effect of qTN4.2 was further verified by a secondary population. These QTLs could provide useful information for marker-assisted selection in improving effective panicle with regard to tiller number. This paper was focused on the comprehensive study of dynamic tiller number at the whole genome level using indica–japonica ILs, which will represent useful genetic resources for indica–japonica tiller number molecular breeding.

Genome-wide analysis of long non-coding RNAs affecting roots development at an early stage in the rice response to cadmium stress

BackgroundLong non-coding RNAs (lncRNAs) have been found to play a vital role in several gene regulatory networks involved in the various biological processes in plants related to stress response. However, systematic analyses of lncRNAs expressed in rice Cadmium (Cd) stress are seldom studied. Thus, we presented the characterization and expression of lncRNAs in rice root development at an early stage in response to Cd stress.ResultsThe lncRNA deep sequencing revealed differentially expressed lncRNAs among Cd stress and normal condition. In the Cd stress group, 69 lncRNAs were up-regulated and 75 lncRNAs were down-regulated. Furthermore, 386 matched lncRNA-mRNA pairs were detected for 120 differentially expressed lncRNAs and 362 differentially expressed genes in cis, and target gene-related pathway analyses exhibited significant variations in cysteine and methionine metabolism pathway-related genes. For the genes in trans, overall, 28,276 interaction relationships for 144 lncRNAs and differentially expressed protein-coding genes were detected. The pathway analyses found that secondary metabolites, such as phenylpropanoids and phenylalanine, and photosynthesis pathway-related genes were significantly altered by Cd stress. All of these results indicate that lncRNAs may regulate genes of cysteine-rich peptide metabolism in cis, as well as secondary metabolites and photosynthesis in trans, to activate various physiological and biochemical reactions to respond to excessive Cd.ConclusionThe present study could provide a valuable resource for lncRNA studies in response to Cd treatment in rice. It also expands our knowledge about lncRNA biological function and contributes to the annotation of the rice genome.

Metabolomics and proteomics analyses of grain yield reduction in rice under abrupt drought-flood alternation

Highlight Abrupt drought-flood alteration is a frequent meteorological disaster that occurs during summer in southern China and the Yangtze river basin, which often causes a large area reduction of rice yield. We previously reported abrupt drought-flood alteration effects on yield and its components, physiological characteristics, matter accumulation and translocation, rice quality of rice. However, the molecular mechanism of rice yield reduction caused by abrupt drought-flood alternation has not been reported. In this study, four treatments were provided, no drought and no floods (control), drought without floods (duration of drought 10 d), no drought with floods (duration of floods 8 d), and abrupt drought-flood alteration (duration of drought 10 d and floods 8 d). The quantitative analysis of spike metabolites was proceeded by LC-MS (liquid chromatograph-mass spectrometry) firstly. Then the Heat-map, PCA, PLS-DA, OPLS-DA and response ranking test of OPLS-DA model methods were used to analysis the function of differential metabolites (DMs) during the rice panicle differentiation stage under abrupt drought-flood alteration. In addition, relative quantitative analysis of spike total proteins under the treatment was conducted iTRAQ (isobaric tags for relative and absolute quantification) and LC-MS. In this study, 5708 proteins were identified and 4803 proteins were quantified. The identification and analysis of DEPs function suggested that abrupt drought-flood alteration treatment can promote carbohydrate metabolic, stress response, oxidation-reduction, defense response, and energy reserve metabolic process, etc, during panicle differentiation stage. In this study relative quantitative proteomics, metabolomics and physiology data (soluble protein content, superoxide dismutase activity, hydrogen peroxidase activity, peroxidase activity, malondialdehyde content, free proline content, soluble sugar content and net photosynthetic rate) analysis were applied to explicit the response mechanism of rice panicle differentiation stage under abrupt drought-flood alteration and provides a theoretical basis for the disaster prevention and mitigation. Abstract Abrupt drought-flood alternation is a meteorological disaster that frequently occurs during summer in southern China and the Yangtze river basin, often causing a significant loss of rice production. In this study, a quantitative analysis of spike metabolites was conducted via liquid chromatograph-mass spectrometry (LC-MS), and Heat-map, PCA, PLS-DA, OPLS-DA, and a response ranking test of OPLS-DA model methods were used to analyze functions of differential metabolites (DMs) during the rice panicle differentiation stage under abrupt drought-flood alternation. The results showed that 102 DMs were identified from the rice spike between T1 (abrupt drought-flood alternation) and CK0 (control) treatment, 104 DMs were identified between T1 and CK1 (drought) treatment and 116 DMs were identified between T1 and CK2 (flood) treatment. In addition, a relative quantitative analysis of spike total proteins was conducted using isobaric tags for relative and absolute quantification (iTRAQ) and LC-MS. The identification and analysis of DEPs functions indicates that abrupt drought-flood alternation treatment can promote carbohydrate metabolic, stress response, oxidation-reduction, defense response, and energy reserve metabolic process during the panicle differentiation stage. In this study, relative quantitative metabolomics and proteomics analyses were applied to explore the response mechanism of rice panicle differentiation in response to abrupt drought-flood alternation. Abbreviations CK0 no drought and no floods CK1 drought without floods CK2 no drought with floods T1 abrupt drought-flood alteration LC-MS liquid chromatograph-mass spectrometry PCA principle component analysis (O)PLS-DA (orthogonal) partial least-squares-discriminant analysis DMs differential metabolites iTRAQ isobaric tags for relative and absolute quantification DEPs differentially expressed proteins KEGG kyoto encyclopedia of genes and genomes GO gene ontology SOD superoxide dismutase CAT hydrogen peroxidase POD peroxidase MDA malondialdehyde Pn net photosynthetic rate ROS reactive oxygen species VIP variable importance in the projection FC fold change

Additional file 6: of Genome-wide analysis of long non-coding RNAs affecting roots development at an early stage in the rice response to cadmium stress

Figure S1. Scatter plot of KEGG pathway enrichment statistics. Rich Factor is the ratio of differentially expressed gene numbers annotated in this pathway term to all gene numbers annotated in this pathway term. Greater Rich Factor means greater intensiveness. q-value is corrected p-value ranging from 0~â 1, and its less value means greater intensiveness. We just display the top 20 pathway terms enriched by KEGG database. (TIFF 646 kb)

Mapping quantitative trait loci for cold tolerance at the booting stage in rice by using chromosome segment substitution lines

Abstract. Low temperature at the booting stage in rice (Oryza sativa L.) can cause male sterility, resulting in yield losses. A set of chromosome segment substitution lines derived from the varieties Sasanishiki (cold-tolerant, ssp. japonica) and Habataki (cold-susceptible, ssp. indica) was used for analysis across two natural, low-temperature environments to study the genetic basis for cold tolerance at the booting stage. Spikelet fertility was used as the evaluation index for cold tolerance identification. Eight quantitative trait loci (QTLs) for cold tolerance were detected, two of which were located on chromosomes 3 (qCTSF3.1 and qCTSF3.2), and the others on chromosomes 4 (qCTSF4), 5 (qCTSF5), 6 (qCTSF6), 7 (qCTSF7), 8 (qCTSF8) and 9 (qCTSF9). The phenotypic variation explained by each QTL ranged from 5.4% to 25.3%. Of the eight QTLs, six (qCTSF3.2, qCTSF5, qCTSF6, qCTSF7, qCTSF8, qCTSF9) were repeatedly detected in two environments. QTLs qCTSF3.1, qCTSF7 and qCTSF9 overlapped with previously reported QTLs. All tolerant alleles for all QTLs were contributed by Sasanishiki.

Molecular tagging of the male fertility restorer gene for the 501-8S cytoplasmic male sterility in rapeseed (Brassica napus L.)

The cytoplasmic male sterile (CMS) system has been successfully used to explore heterosis in rapeseed (Brassica napus L.). A newly developed male sterile line (501-8S) was characterised for its male fertility response to temperature and photoperiod, and the inheritance of fertility restoration. Segregation analysis using F1 and F2, BC1, and F3 populations of the crosses between the 501-8S and fertile lines of B. napus revealed that fertility restoration was conferred by a dominant nuclear gene (Rf). The F2 population of the cross 501-8S × Yuyou1 was used as a mapping population to map the Rf gene. A combination of bulked segregant analysis (BSA) and amplified fragment length polymorphism (AFLP) methodology was used to identify putative markers linked to the Rf gene. Twenty-nine of the 1280 primer combinations tested revealed polymorphism between the 2 extreme bulks. Further testing of these primer combinations in individual plants identified 5 AFLP markers tightly linked to the Rf gene with a map distance of less than 5.0 cM. All 5 markers were on one side of the restoration gene in the coupling phase. The closest marker, EA02MG03-260, is only 0.4 cM from the Rf gene. The EA02MG03-260 marker was converted to a dominant sequence characterised amplified region (SCAR) marker (SCARE2M3-214). Amplification using this locus-specific primer generated specific bands with male fertile plants when tested using the mapping population. Specific amplification of SCARE2M3-214 was also detected in all 3 male sterile plants and their F1 hybrids, with 5 restorer lines used for verification. Thus, SCARE2M3-214 will be very useful for the development of new restorer lines by the transfer of the Rf gene into other breeding lines. It can also be used for isolating the Rf gene by means of map-based cloning.