NADH dehydrogenase-like complex L subunit improves salt tolerance by enhancing photosynthetic electron transport.

Cyclic electron transport (CET) around photosystem I (PSI) mediated by the NADH dehydrogenase-like (NDH) complex is closely related to plant salt tolerance. However, whether overexpression of a core subunit of the NDH complex affects the photosynthetic electron transport under salt stress is currently unclear. Here, we expressed the NDH complex L subunit (Ndhl) genes ZmNdhl1 and ZmNdhl2 from C4 plant maize (Zea mays) or OsNdhl from C3 plant rice (Oryza sativa) using a constitutive promoter in rice. Transgenic rice lines expressing ZmNdhl1, ZmNdhl2, or OsNdhl displayed enhanced salt tolerance, as indicated by greater plant height, dry weight, and leaf relative water content, as well as lower malondialdehyde content compared to wild-type plants under salt stress. Fluorescence parameters such as post-illumination rise (PIR), the prompt chlorophyll a fluorescence transient (OJIP), modulated 820-nm reflection (MR), and delayed chlorophyll a fluorescence (DF) remained relatively normal in transgenic plants during salt stress. These results indicate that expression of ZmNdhl1, ZmNdhl2, or OsNdhl increases cyclic electron transport activity, slows down damage to linear electron transport, alleviates oxidative damage to the PSI reaction center and plastocyanin, and reduces damage to electron transport on the receptor side of PSI in rice leaves under salt stress. Thus, expression of Ndhl genes from maize or rice improves salt tolerance by enhancing photosynthetic electron transport in rice. Maize and rice Ndhl genes played a similar role in enhancing salinity tolerance and avoiding photosynthetic damage.

Isolation and Identification of the Causal Agent of Top Rot and the Genetic Architecture of Resistance in Maize.

In maize (Zea mays), the disease known as "top rot" causes necrosis of the upper plant, disrupts tassel formation and pollen dispersal, and decreases yield. However, the causal agent, mode of pathogen infestation, and genetic architecture of resistance in maize remain to be explored. Here, to identify the causal agent, we isolated 41 fungal strains from maize plants infected with top rot. We classified these strains into six groups based on their morphological and molecular characteristics. Four species of Fusarium (F. fujikuroi, F. equiseti, F. proliferatum, and F. verticillioides) were able to cause top rot, with F. fujikuroi and F. equiseti being the main causal agents. Microscopic observations of a F. fujikuroi strain labeled with enhanced green fluorescent protein revealed that this pathogen first colonizes the stomata of leaves and then spreads through intercellular spaces, creating an expanding lesion. To dissect the genetic basis of maize resistance to top rot, we performed quantitative trait locus (QTL) mapping using a recombinant inbred line population constructed from the resistant parent LDC-1 and the susceptible parent YS501. Under natural conditions in Yangzhou and Hainan, we detected three and five QTLs, respectively, with qRtr7-1, located on chromosome 7, detected in both environments. Using inoculated seedlings, we detected three QTLs for resistance on chromosomes 1, 5, and 8. These results improve our understanding of maize top rot and provide a theoretical basis for its control.

Effects of OsRCA Overexpression on Rubisco Activation State and Photosynthesis in Maize.

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the rate-limiting enzyme for photosynthesis. Rubisco activase (RCA) can regulate the Rubisco activation state, influencing Rubisco activity and photosynthetic rate. We obtained transgenic maize plants that overproduced rice RCA (OsRCAOE) and evaluated photosynthesis in these plants by measuring gas exchange, energy conversion efficiencies in photosystem (PS) I and PSII, and Rubisco activity and activation state. The OsRCAOE lines showed significantly higher initial Rubisco activity and activation state, net photosynthetic rate, and PSII photochemical quantum yield than wild-type plants. These results suggest that OsRCA overexpression can promote maize photosynthesis by increasing the Rubisco activation state.

Genetic Architecture of Maize Stalk Diameter and Rind Penetrometer Resistance in a Recombinant Inbred Line Population.

Stalk lodging presents a major constraint on maize (Zea mays L.) quantity and quality and hampers mechanized grain harvesting. Stalk diameter (SD) and rind penetrometer resistance (RPR) are crucial indicators of stalk lodging. To dissect the genetic architecture of these indicators, we constructed a recombinant inbred line (RIL) population derived from a cross between maize inbred lines LDC-1 and YS501 to identify quantitative trait loci (QTLs) controlling SD and RPR. Corresponding phenotypes of basal second, third, and fourth internodes in four environments were determined. By integrating QTL mapping results based on individual environments and best linear unbiased prediction (BLUP) values, we identified 12, 12, and 13 QTLs associated with SD and 17, 14, and 17 associated with RPR. Each QTL accounted for 3.83-21.72% of phenotypic variation. For SD-related QTLs, 30 of 37 were enriched in 12 QTL clusters; similarly, RPR-related QTLs had 38 of 48 enriched in 12 QTL clusters. The stable QTL qSD9-2 for SD on chromosome 9 was validated and delimited within a physical region of 9.97 Mb. Confidence intervals of RPR-related QTLs contained 169 genes involved in lignin and polysaccharide biosynthesis, with 12 of these less than 500 kb from the peak of the corresponding QTL. Our results deepen our understanding of the genetic mechanism of maize stalk strength and provide a basis for breeding lodging resistance.

Comparative transcriptome profiling and co-expression network analysis uncover the key genes associated withearly-stage resistance to Aspergillus flavus in maize.

BACKGROUND: The fungus Aspergillus flavus (A. flavus) is a serious threat to maize (Zea mays) production worldwide. It causes considerable yield and economic losses, and poses a health risk to humans and livestock due to the high toxicity of aflatoxin. However, key genes and regulatory networks conferring maize resistance to A. flavus are not clear, especially at the early stage of infection. Here, we performed a comprehensive transcriptome analysis of two maize inbred lines with contrasting resistance to A. flavus infection. RESULTS: The pairwise comparisons between mock and infected kernels in each line during the first 6 h post inoculation (hpi) showed that maize resistance to A. flavus infection was specific to the genotype and infection stage, and defense pathways were strengthened in the resistant line. Further comparison of the two maize lines revealed that the infection-induced up-regulated differentially expressed genes (DEGs) in the resistant line might underlie the enhanced resistance. Gene co-expression network analysis by WGCNA (weighted gene co-expression network analysis) identified 7 modules that were significantly associated with different infection stages, and 110 hub genes of these modules. These key regulators mainly participate in the biosynthesis of fatty acid and antibiotics. In addition, 90 candidate genes for maize resistance to A. flavus infection and/or aflatoxin contamination obtained in previous studies were confirmed to be differentially expressed between the resistant and susceptible lines within the first 6 hpi. CONCLUSION: This work unveiled more A. flavus resistance genes and provided a detailed regulatory network of early-stage resistance to A. flavus in maize.

Effects of Different Planting Densities on Photosynthesis in Maize Determined via Prompt Fluorescence, Delayed Fluorescence and P700 Signals.

The mutual shading among individual field-grown maize plants resulting from high planting density inevitably reduces leaf photosynthesis, while regulating the photosynthetic transport chain has a strong impact on photosynthesis. However, the effect of high planting density on the photosynthetic electron transport chain in maize currently remains unclear. In this study, we simultaneously measured prompt chlorophyll a fluorescence (PF), modulated 820 nm reflection (MR) and delayed chlorophyll a fluorescence (DF) in order to investigate the effect of high planting density on the photosynthetic electron transport chain in two maize hybrids widely grown in China. PF transients demonstrated a gradual reduction in their signal amplitude with increasing planting density. In addition, high planting density induced positive J-step and G-bands of the PF transients, reduced the values of PF parameters PIABS, RC/CSO, TRO/ABS, ETO/TRO and REO/ETO, and enhanced ABS/RC and N. MR kinetics showed an increase of their lowest point with increasing high planting density, and thus the values of MR parameters VPSI and VPSII-PSI were reduced. The shapes of DF induction and decay curves were changed by high planting density. In addition, high planting density reduced the values of DF parameters I1, I2, L1 and L2, and enhanced I2/I1. These results suggested that high planting density caused harm on multiple components of maize photosynthetic electron transport chain, including an inactivation of PSII RCs, a blocked electron transfer between QA and QB, a reduction in PSI oxidation and re-reduction activities, and an impaired PSI acceptor side. Moreover, a comparison between PSII and PSI activities demonstrated the greater effect of plant density on the former.

Genetic determinants controlling maize rubisco activase gene expression and a comparison with rice counterparts.

BACKGROUND: Rubisco activase (RCA) regulates the activity of Rubisco and is a key enzyme of photosynthesis. RCA expression was widely reported to affect plant photosynthesis and crop yield, but the molecular basis of natural variation in RCA expression in a wide range of maize materials has not been fully elucidated. RESULTS: In this study, correlation analysis in approximately 200 maize inbred lines revealed a significantly positive correlation between the expression of maize RCA gene ZmRCAß and grain yield. A genome-wide association study revealed both cis-expression quantitative trait loci (cis-eQTLs) and trans-eQTLs underlying the expression of ZmRCAß, with the latter playing a more important role. Further allele mining and genetic transformation analysis showed that a 2-bp insertion and a 14-bp insertion in the promoter of ZmRCAß conferred increased gene expression. Because rice is reported to have higher RCA gene expression than does maize, we subsequently compared the genetic factors underlying RCA gene expression between maize and rice. The promoter activity of the rice RCA gene was shown to be stronger than that of the maize RCA gene, suggesting that replacing the maize RCA gene promoter with that of the rice RCA gene would improve the expression of RCA in maize. CONCLUSION: Our results revealed two DNA polymorphisms regulating maize RCA gene ZmRCAß expression, and the RCA gene promoter activity of rice was stronger than that of maize. This work increased understanding of the genetic mechanism that underlies RCA gene expression and identify new targets for both genetic engineering and selection for maize yield improvement.

Physicochemical properties of starches from vitreous and floury endosperms from the same maize kernels.

Starches were isolated from vitreous and floury endosperms from the same kernels, and their physicochemical properties were investigated to reveal their differences. Starch from vitreous endosperm had more surface indentations, larger granule size, and higher contents of protein, amylose and damaged starch than that from floury endosperm. Both starches from vitreous and floury endosperms exhibited A-type crystalline structure, but starch from vitreous endosperm had lower relative crystallinity and lamellar peak intensity than that from floury endosperm. Starch from floury endosperm had higher gelatinization temperature and enthalpy but lower gelatinization temperature range and percentage of retrogradation than that from vitreous endosperm. Native starch from floury endosperm was more resistant to enzyme hydrolysis than that from vitreous endosperm. Gelatinized and retrograded starches had similar digestion properties between starches from vitreous and floury endosperms. Principal component analysis indicated that starches from vitreous and floury endosperms had significant differences in their physicochemical properties.

Spatiotemporal accumulation and characteristics of starch in developing maize caryopses.

The accumulation and morphology of starch in the pericarp, embryo and endosperm of normal and waxy maize were investigated using whole sections of complete caryopses. Pericarp starch took the form of compound granules, was distributed in the bottom of caryopses, and degraded from the top to the bottom. Embryo starch mostly took the form of simple granules and accumulated in the scutellum beginning approximately 10 DAP. In the endosperm, starch accumulated longitudinally from the top to the bottom and transversely from the centre to the periphery with caryopsis development. The peripheral endosperm cells synthesized starch faster than did the inner ones. Simple and compound starches were both observed, but the compound starch granules were distributed in the central region of the endosperm. At a late stage of development, compound starch was only observed in the bottom central portion of the endosperm. The pericarp starch of normal maize showed higher amylose content than did the embryo and endosperm starch. The waxy maize pericarp and embryo starches had similar amylose contents, but amylose was hardly detected in the endosperm due to the granule-bound starch synthase I gene mutation. The starches from the endosperm, embryo and pericarp of normal and waxy maize all had A-type crystallinity.

Genetic Mapping of the Leaf Number above the Primary Ear and Its Relationship with Plant Height and Flowering Time in Maize.

The leaf number above the primary ear (LA) is a major contributing factor to plant architecture in maize. The yield of leafy maize, which has extra LA compared to normal maize, is higher than normal maize in some regions. One major concern is that increasing LA may be accompanied by increased plant height and/or flowering time. Using an F2:3 population comprising 192 families derived from a leafy maize line and a normal maize line, an association population comprising 437 inbred maize lines, and a pair of near-isogenic maize lines, we mapped the quantitative trait loci (QTL) associated with LA and assessed its genetic relationship with flowering time and plant height. Ten QTL with an additive and dominant effect, 18 pairs of interacting QTL in the F2:3 population and seventeen significant SNPs in the association population were detected for LA. Two major QTL, qLA3-4 and qLA7-1, were repeatedly detected and explained a large proportion of the phenotypic variation. The qLA3-4 was centered on lfy1, which is a dominant gene underlying extra leaves above the ear in leafy maize. Four LA QTL were found to overlap with flowering time and/or plant height, which suggested that these QTL might have a pleiotropic effect. The pleiotropy of the lfy1 locus on LA, flowering time and plant height were validated by near-isogenic line analysis. These results enhance our understanding of the genetic architecture affecting maize LA and the development of maize hybrids with increased LA.

Ability to Remove Na+ and Retain K+ Correlates with Salt Tolerance in Two Maize Inbred Lines Seedlings.

Maize is moderately sensitive to salt stress; therefore, soil salinity is a serious threat to its production worldwide. Here, excellent salt-tolerant maize inbred line TL1317 and extremely salt-sensitive maize inbred line SL1303 were screened to understand the maize response to salt stress and its tolerance mechanisms. Relative water content, membrane stability index, stomatal conductance, chlorophyll content, maximum photochemical efficiency, photochemical efficiency, shoot and root fresh/dry weight, and proline and water soluble sugar content analyses were used to identify that the physiological effects of osmotic stress of salt stress were obvious and manifested at about 3 days after salt stress in maize. Moreover, the ion concentration of two maize inbred lines revealed that the salt-tolerant maize inbred line could maintain low Na+ concentration by accumulating Na+ in old leaves and gradually shedding them to exclude excessive Na+. Furthermore, the K+ uptake and retention abilities of roots were important in maintaining K+ homeostasis for salt tolerance in maize. RNA-seq and qPCR results revealed some Na+/H+ antiporter genes and Ca2+ transport genes were up-regulated faster and higher in TL1317 than those in SL1303. Some K+ transport genes were down-regulated in SL1303 but up-regulated in TL1317. RNA-seq results, along with the phenotype and physiological results, suggested that the salt-tolerant maize inbred line TL1317 possesses more rapidly and effectively responses to remove toxic Na+ ions and maintain K+ under salt stress than the salt-sensitive maize inbred line SL1303. This response should facilitate cell homoeostasis under salt stress and result in salt tolerance in TL1317.

Confirmation and Fine Mapping of a Major QTL for Aflatoxin Resistance in Maize Using a Combination of Linkage and Association Mapping.

Maize grain contamination with aflatoxin from Aspergillus flavus (A. flavus) is a serious health hazard to animals and humans. To map the quantitative trait loci (QTLs) associated with resistance to A. flavus, we employed a powerful approach that differs from previous methods in one important way: it combines the advantages of the genome-wide association analysis (GWAS) and traditional linkage mapping analysis. Linkage mapping was performed using 228 recombinant inbred lines (RILs), and a highly significant QTL that affected aflatoxin accumulation, qAA8, was mapped. This QTL spanned approximately 7 centi-Morgan (cM) on chromosome 8. The confidence interval was too large for positional cloning of the causal gene. To refine this QTL, GWAS was performed with 558,629 single nucleotide polymorphisms (SNPs) in an association population comprising 437 maize inbred lines. Twenty-five significantly associated SNPs were identified, most of which co-localised with qAA8 and explained 6.7% to 26.8% of the phenotypic variation observed. Based on the rapid linkage disequilibrium (LD) and the high density of SNPs in the association population, qAA8 was further localised to a smaller genomic region of approximately 1500 bp. A high-resolution map of the qAA8 region will be useful towards a marker-assisted selection (MAS) of A. flavus resistance and a characterisation of the causal gene.

Identification of Two bZIP Transcription Factors Interacting with the Promoter of Soybean Rubisco Activase Gene (GmRCAα).

Rubisco activase (RCA), a key photosynthetic protein, catalyses the activation of Rubisco and thus plays an important role in photosynthesis. Although the RCA gene has been characterized in a variety of species, the molecular mechanism regulating its transcription remains unclear. Our previous studies on RCA gene expression in soybean suggested that expression of this gene is regulated by trans-acting factors. In the present study, we verified activity of the GmRCAα promoter in both soybean and Arabidopsis and used a yeast one-hybrid (Y1H) system for screening a leaf cDNA expression library to identify transcription factors (TFs) interacting with the GmRCAα promoter. Four basic leucine zipper (bZIP) TFs, GmbZIP04g, GmbZIP07g, GmbZIP1, and GmbZIP71, were isolated, and GmbZIP04g and GmbZIP07g were confirmed as able to bind to a 21-nt G-box-containing sequence. Additionally, the expression patterns of GmbZIP04g, GmbZIp07g, and GmRCAα were analyzed in response to abiotic stresses and during a 24-h period. Our study will help to advance elucidation of the network regulating GmRCAα transcription.

A comprehensive meta-analysis of plant morphology, yield, stay-green, and virus disease resistance QTL in maize (Zea mays L.).

MAIN CONCLUSION: The meta-QTL and candidate genes will facilitate the elucidation of molecular bases underlying agriculturally important traits and open new avenues for functional markers development and elite alleles introgression in maize breeding program. A large number of QTLs attributed to grain productivity and other agriculturally important traits have been identified and deposited in public repositories. The integration of fruitful QTL becomes a major issue in current plant genomics. To this end, we first collected QTL for six agriculturally important traits in maize, including yield, plant height, ear height, leaf angle, stay-green, and maize rough dwarf disease resistance. The meta-analysis method was then employed to retrieve 113 meta-QTL. Additionally, we also isolated candidate genes for target traits by the bioinformatic technique. Several candidates, including some well-characterized genes, GA3ox2 for plant height, lg1 and lg4 for leaf angle, zfl1 and zfl2 for flowering time, were co-localized with established meta-QTL intervals. Intriguingly, in a relatively narrow meta-QTL region, the maize ortholog of rice yield-related gene GW8/OsSPL16 was believed to be a candidate for yield. Leveraging results presented in this study will provide further insights into the genetic architecture of maize agronomic traits. Moreover, the meta-QTL and candidate genes reported here could be harnessed for the enhancement of stress tolerance and yield performance in maize and translation to other crops.

Characterization of Rubisco activase genes in maize: an α-isoform gene functions alongside a ß-isoform gene.

Rubisco activase (RCA) catalyzes the activation of Rubisco in vivo and plays a crucial role in regulating plant growth. In maize (Zea mays), only ß-form RCA genes have been cloned and characterized. In this study, a genome-wide survey revealed the presence of an α-form RCA gene and a ß-form RCA gene in the maize genome, herein referred to as ZmRCAα and ZmRCAß, respectively. An analysis of genomic DNA and complementary DNA sequences suggested that alternative splicing of the ZmRCAß precursor mRNA (premRNA) at its 3' untranslated region could produce two distinctive ZmRCAß transcripts. Analyses by electrophoresis and matrix-assisted laser desorption/ionization-tandem time-of-flight mass spectrometry showed that ZmRCAα and ZmRCAß encode larger and smaller polypeptides of approximately 46 and 43 kD, respectively. Transcriptional analyses demonstrated that the expression levels of both ZmRCAα and ZmRCAß were higher in leaves and during grain filling and that expression followed a specific cyclic day/night pattern. In 123 maize inbred lines with extensive genetic diversity, the transcript abundance and protein expression levels of these two RCA genes were positively correlated with grain yield. Additionally, both genes demonstrated a similar correlation with grain yield compared with three C4 photosynthesis genes. Our data suggest that, in addition to the ß-form RCA-encoding gene, the α-form RCA-encoding gene also contributes to the synthesis of RCA in maize and support the hypothesis that RCA genes may play an important role in determining maize productivity.

Functional properties and expression quantitative trait loci for phosphate transporter GmPT1 in soybean.

Phosphate (Pi) remobilization within a plant is critical for plant survival under Pi-limiting conditions. In this paper, a soybean Pi transporter gene, GmPT1, was characterized. A marked induction of GmPT1 transcript was observed in young leaves, mature leaves and lateral roots during long-term Pi starvation. Transgenic tobacco plants containing the GmPT1 gene were obtained using an Agrobacterium-mediated transformation system. Compared with wild-type plants, transgenic plants showed significant increases in phosphorus-use efficiency (PUE), photosystem II (PSII) function, total dry weight and seed weight under Pi-deficient conditions. GmPT1 expression levels and PUE were determined in a soybean recombinant inbred line population during a pot experiment that was conducted to measure chlorophyll fluorescence parameters, photosynthetic rate (PN ) and seed yield. Correlation analysis revealed that GmPT1 expression levels had significantly positive correlations with seed yield, PUE, PN and the quantum yield of PSII primary photochemistry (ΦPSII ). Expression quantitative trait loci (eQTL) mapping for GmPT1 revealed two eQTLs, one of which coincided with both the physical location of GmPT1 and a QTL associated with seed yield. These results suggest that GmPT1 plays a role in Pi remobilization, and it may be possible to improve soybean seed yields under Pi-limiting conditions by modulating GmPT1 expression levels.

Variation in Rubisco activase (RCAß) gene promoters and expression in soybean [Glycine max (L.) Merr].

Understanding the genetic basis of Rubisco activase (RCA) gene regulation and altering its expression levels to optimize Rubisco activation may provide an approach to enhance plant productivity. However, the genetic mechanisms and the effect of RCA expression on phenotype are still unknown in soybean. This work analysed the expression of RCA genes and demonstrated that two RCA isoforms presented different expression patterns. Compared with GmRCAα, GmRCAß was expressed at higher mRNA and protein levels. In addition, GmRCAα and GmRCAß were positively correlated with chlorophyll fluorescence parameters and seed yield, suggesting that changes in expression of RCA has a potential applicability in breeding for enhanced soybean productivity. To identify the genetic factors that cause expression level variation of GmRCAß, expression quantitative trait loci (eQTL) mapping was combined with allele mining in a natural population including 219 landraces. The eQTL mapping showed that a combination of both cis- and trans-acting eQTLs might control GmRCAß expression. As promoters can affect both cis- and trans-acting eQTLs by altering cis-acting regulatory elements or transcription factor binding sites, this work subsequently focused on the promoter region of GmRCAß. Single-nucleotide polymorphisms in the GmRCAß promoter were identified and shown to correlate with expression level diversity. These SNPs were classified into two groups, A and B. Further transient expression showed that GUS expression driven by the group A promoter was stronger than that by the group B promoter, suggesting that promoter sequence types could influence gene expression levels. These results would improve understanding how variation within promoters affects gene expression and, ultimately, phenotypic diversity in natural populations.

Gibberellin biosynthetic deficiency is responsible for maize dominant Dwarf11 (D11) mutant phenotype: physiological and transcriptomic evidence.

Dwarf stature is introduced to improve lodging resistance and harvest index in crop production. In many crops including maize, mining and application of novel dwarf genes are urgent to overcome genetic bottleneck and vulnerability during breeding improvement. Here we report the characterization and expression profiling analysis of a newly identified maize dwarf mutant Dwarf11 (D11). The D11 displays severely developmental abnormalities and is controlled by a dominant Mendelian factor. The D11 seedlings responds to both GA3 and paclobutrazol (PAC) application, suggesting that dwarf phenotype of D11 is caused by GA biosynthesis instead of GA signaling deficiency. In contrast, two well-characterized maize dominant dwarf plants D8 and D9 are all insensitive to exogenous GA3 stimulation. Additionally, sequence variation of D8 and D9 genes was not identified in the D11 mutant. Microarray and qRT-PCR analysis results demonstrated that transcripts encoding GA biosynthetic and catabolic enzymes ent-kaurenoic acid oxidase (KAO), GA 20-oxidase (GA20ox), and GA 2-oxidase (GA2ox) are up-regulated in D11. Our results lay a foundation for the following D11 gene cloning and functional characterization. Moreover, results presented here may aid in crops molecular improvement and breeding, especially breeding of crops with plant height ideotypes.

Characterization of an Abc1 kinase family gene OsABC1-2 conferring enhanced tolerance to dark-induced stress in rice.

Leaf senescence is a complex and highly organized process resulting in numerous changes of gene expression and metabolic procedures. However, the exact mechanisms underlying these changes are not well understood. In this study, we reported a rice (Oryza sativa) T-DNA insertion mutant impaired in an Abc1 kinase family gene with a dwarf and pale-green phenotype. The mutant showed reduced pigment content and photosynthetic efficiency and increased superoxide dismutase activity in leaves. The mutated gene, designated OsABC1-2, is expressed primarily in green tissues and/or organs and encodes a protein localized in chloroplast envelope. Expression of the gene was drastically suppressed by dark treatment. Overexpression of the gene in rice enhanced tolerance to prolonged dark-induced stress. Phylogenetic analysis revealed that the plant Abc1 proteins could be divided into three subgroups and OsAbc1-2 resides in a subgroup with potential chloroplast origin. Our results suggest that divergence has occurred among plant Abc1 family and chloroplast Abc1 kinases play potential roles in regulating dark-induced senescence of plants.

Systematic analysis of plant-specific B3 domain-containing proteins based on the genome resources of 11 sequenced species.

B3 domain-containing proteins constitute a large transcription factor superfamily. The plant-specific B3 superfamily consists of four family members, i.e., LAV (LEC2 [LEAFY COTYLEDON 2]/ABI3 [ABSCISIC ACID INSENSITIVE 3] − VAL [VP1/ABI3-LIKE]), RAV (RELATED to ABI3/VP1), ARF (AUXIN RESPONSE FACTOR) and REM (REPRODUCTIVE MERISTEM) families. The B3 superfamily plays a central role in plant life, from embryogenesis to seed maturation and dormancy. In previous research, we have characterized ARF family, member of the B3 superfamily in silico (Wang et al., Mol Biol Rep, 2011, doi:10.1007/s11033-011-0991-z). In this study, we systematically analyzed the diversity, phylogeny and evolution of B3 domain-containing proteins based on genomic resources of 11 sequenced species. A total of 865 B3 domain-containing genes were identified from 11 sequenced species through an iterative strategy. The number of B3 domain-containing genes varies not only between species but between gene families. B3 domain-containing genes are unevenly distributed in chromosomes and tend to cluster in the genome. Numerous combinations of B3 domains and their partner domains contribute to the sequences and structural diversification of the B3 superfamiy. Phylogenetic results showed that moss VAL proteins are related to LEC2/ABI3 instead of VAL proteins from higher plants. Lineage-specific expansion of ARF and REM proteins was observed. The REM family is the most diversified member among the B3 superfamily and experiences a rapid divergence during selective sweep. Based on structural and phylogenetic analysis results, two possible evolutional modes of the B3 superfamily were presented. Results presented here provide a resource for further characterization of the B3 superfamily.