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A20/AN1 zinc-finger domain-containing proteins are well characterized in animals, and their role in regulating the immune response is established. Recently, such A20/AN1 zinc-finger proteins have been reported from plants. These plant proteins are involved in stress response, but their exact molecular mechanism of action is yet to be deciphered. Sequence information available in public databases has been used to conduct a survey of A20/AN1 zinc-finger proteins across diverse organisms with a special emphasis on plants. Domain analysis provides some interesting insights into their biological function, the most important being that A20/AN1 zinc-finger proteins could represent common elements of stress response in plants and animals. [ABSTRACT FROM AUTHOR]

Homeobox genes play a critical role in regulating various aspects of plant growth and development. In the present study, we identified a total of 107 homeobox genes in the rice genome and grouped them into ten distinct subfamilies based upon their domain composition and phylogenetic analysis. A significantly large number of homeobox genes are located in the duplicated segments of the rice genome, which suggests that the expansion of homeobox gene family, in large part, might have occurred due to segmental duplications in rice. Furthermore, microarray analysis was performed to elucidate the expression profiles of these genes in different tissues and during various stages of vegetative and reproductive development. Several genes with predominant expression during various stages of panicle and seed development were identified. At least 37 homeobox genes were found to be differentially expressed significantly (more than two-fold; P < 0.05) under various abiotic stress conditions. The results of the study suggest a critical role of homeobox genes in reproductive development and abiotic stress signaling in rice, and will facilitate the selection of candidate genes of agronomic importance for functional validation. [ABSTRACT FROM AUTHOR]

Plants are exposed to different abiotic stresses, such as water deficit, high temperature, salinity, cold, heavy metals and mechanical wounding, under field conditions. It is estimated that such stress conditions can potentially reduce the yield of crop plants by more than 50%. Investigations of the physiological, biochemical and molecular aspects of stress tolerance have been conducted to unravel the intrinsic mechanisms developed during evolution to mitigate against stress by plants. Before the advent of the genomics era, researchers primarily used a gene-by-gene approach to decipher the function of the genes involved in the abiotic stress response. However, abiotic stress tolerance is a complex trait and, although large numbers of genes have been identified to be involved in the abiotic stress response, there remain large gaps in our understanding of the trait. The availability of the genome sequences of certain important plant species has enabled the use of strategies, such as genome-wide expression profiling, to identify the genes associated with the stress response, followed by the verification of gene function by the analysis of mutants and transgenics. Certain components of both abscisic acid-dependent and -independent cascades involved in the stress response have already been identified. Information originating from the genome-wide analysis of abiotic stress tolerance will help to provide an insight into the stress-responsive network(s), and may allow the modification of this network to reduce the loss caused by stress and to increase agricultural productivity. [ABSTRACT FROM AUTHOR]

DNA topoisomerase 6 (TOP6) belongs to a novel family of type II DNA topoisomerases present, other than in archaebacteria, only in plants. Here we report the isolation of full-length cDNAs encoding putative TOP6 subunits A and B from rice ( Oryza sativa ssp. indica), preserving all the structural domains conserved among archaebacterial TOP6 homologs and eukaryotic meiotic recombination factor SPO11. OsTOP6A1 was predominantly expressed in prepollinated flowers. The transcript abundance of OsTOP6A2, OsTOP6A3 and OsTOP6B was also higher in prepollinated flowers and callus. The expression of OsTOP6A2, OsTOP6A3 and OsTOP6B was differentially regulated by the plant hormones, auxin, cytokinin, and abscisic acid. Yeast two-hybrid analysis revealed that the full-length OsTOP6B protein interacts with both OsTOP6A2 and OsTOP6A3, but not with OsTOP6A1. The nuclear localization of OsTOP6A3 and OsTOP6B was established by the transient expression of their β-glucuronidase fusion proteins in onion epidermal cells. Overexpression of OsTOP6A3 and OsTOP6B in transgenic Arabidopsis plants conferred reduced sensitivity to the stress hormone, abscisic acid, and tolerance to high salinity and dehydration. Moreover, the stress tolerance coincided with enhanced induction of many stress-responsive genes in transgenic Arabidopsis plants. In addition, microarray analysis revealed that a large number of genes are expressed differentially in transgenic plants. Taken together, our results demonstrate that TOP6 genes play a crucial role in stress adaptation of plants by altering gene expression. [ABSTRACT FROM AUTHOR]

Abstract: Small auxin-up RNAs (SAURs) are the early auxin-responsive genes represented by a large multigene family in plants. Here, we report the identification of 58 OsSAUR gene family members from rice (Oryza sativa japonica cv Nipponbare), the model monocot plant, by a reiterative database search and manual reannotation; 2 of these are pseudogenes. The coding sequences of OsSAURs do not possess any intron. Most of the predicted OsSAUR protein sequences harbor a putative nuclear localization signal at their N-terminus. Localized gene duplications appear to be the primary genetic event responsible for SAUR gene family expansion in rice. Interestingly, the duplication of OsSAURs was found to be associated with the chromosomal block duplication as well. The phylogenetic analysis revealed that the SAUR gene family expanded in rice and Arabidopsis due to species-specific expansion of the family in monocots and dicots. The auxin-responsive elements and downstream element are conserved in the upstream and downstream sequences, respectively, of OsSAURs. In addition to the 21 OsSAURs with full-length cDNA sequences and 20 with expressed sequence tags, gene expression analyses of at least 7 OsSAURs by RT-qPCR indicated that the majority of identified OsSAURs most likely are expressed in rice. The transcript abundance of the OsSAURs examined increased within a few minutes of exogenous auxin application with varying kinetics. The present study provides basic genomic information for the rice SAUR gene family and will pave the way for deciphering the precise role of SAURs in plant growth and development. [Copyright &y& Elsevier]

Light can modulate development and differentiation of the vital photosynthetic organelle, chloroplast, by photomorphogenetic mechanisms involved in regulating transcription of various photosynthetic genes encoded by nuclear genome. The nuclear genes encode majority of proteins involved in photosynthesis. After perception, light signal is transduced via signaling intermediates, which have been identified using various approaches. These signaling components can either directly influence the binding of light regulatory trans-acting factors to cis-acting elements present in a photosynthetic gene promoter or modulate their activity by various means to facilitate transcription in response to light. Some cis-acting elements show a high degree of conservation among photo-responsive nuclear genes in plants and have been designated as light regulatory elements (LREs). The gene regulation seems to involve interplay of several cis-acting elements and regulatory factors. Additional information available about the post-transcriptional mechanisms responsible for light-regulated expression of photosynthetic genes suggests the importance of these levels in regulation biology. [ABSTRACT FROM AUTHOR]

Key message: Overexpression of rice A20/AN1 zinc-finger protein, OsSAP10, improves water-deficit stress tolerance in Arabidopsis via interaction with multiple proteins. Stress-associated proteins (SAPs) constitute a class of A20/AN1 zinc-finger domain containing proteins and their genes are induced in response to multiple abiotic stresses. The role of certain SAP genes in conferring abiotic stress tolerance is well established, but their mechanism of action is poorly understood. To improve our understanding of SAP gene functions, OsSAP10, a stress-inducible rice gene, was chosen for the functional and molecular characterization. To elucidate its role in water-deficit stress (WDS) response, we aimed to functionally characterize its roles in transgenic Arabidopsis, overexpressing OsSAP10. OsSAP10 transgenics showed improved tolerance to water-deficit stress at seed germination, seedling and mature plant stages. At physiological and biochemical levels, OsSAP10 transgenics exhibited a higher survival rate, increased relative water content, high osmolyte accumulation (proline and soluble sugar), reduced water loss, low ROS production, low MDA content and protected yield loss under WDS relative to wild type (WT). Moreover, transgenics were hypersensitive to ABA treatment with enhanced ABA signaling and stress-responsive genes expression. The protein-protein interaction studies revealed that OsSAP10 interacts with proteins involved in proteasomal pathway, such as OsRAD23, polyubiquitin and with negative and positive regulators of stress signaling, i.e., OsMBP1.2, OsDRIP2, OsSCP and OsAMTR1. The A20 domain was found to be crucial for most interactions but insufficient for all interactions tested. Overall, our investigations suggest that OsSAP10 is an important candidate for improving water-deficit stress tolerance in plants, and positively regulates ABA and WDS signaling via protein–protein interactions and modulation of endogenous genes expression in ABA-dependent manner. [ABSTRACT FROM AUTHOR]

In recent years liquid medium has been shown to he better than agar-gelled medium for production of haploids in anther culture. However, on addition of charcoal to agar medium the anther response in Datura innoxia Mill. increases dramatically and is better than in liquid medium. For anthers with pollen at the premitotic stage, the best result was observed with 1% charcoal in Difco agar and 1.5% in Normal agar. The effect is possibly due to adsorption of substances inhibitory to androgenesis and emanating from anthers, as well as to substances present in the nutrient medium and agar. [ABSTRACT FROM AUTHOR]

SUMMARY: Seed color is one of the key target traits of domestication and artificial selection in chickpeas due to its implications on consumer preference and market value. The complex seed color trait has been well dissected in several crop species; however, the genetic mechanism underlying seed color variation in chickpea remains poorly understood. Here, we employed an integrated genomics strategy involving QTL mapping, high‐density mapping, map‐based cloning, association analysis, and molecular haplotyping in an inter‐specific RIL mapping population, association panel, wild accessions, and introgression lines (ILs) of Cicer gene pool. This delineated a MATE gene, CaMATE23, encoding a Transparent Testa (TT) and its natural allele (8‐bp insertion) and haplotype underlying a major QTL governing seed color on chickpea chromosome 4. Signatures of selective sweep and a strong purifying selection reflected that CaMATE23, especially its 8‐bp insertion natural allelic variant, underwent selection during chickpea domestication. Functional investigations revealed that the 8‐bp insertion containing the third cis‐regulatory RY‐motif element in the CaMATE23 promoter is critical for enhanced binding of CaFUSCA3 transcription factor, a key regulator of seed development and flavonoid biosynthesis, thereby affecting CaMATE23 expression and proanthocyanidin (PA) accumulation in the seed coat to impart varied seed color in chickpea. Consequently, overexpression of CaMATE23 in Arabidopsis tt12 mutant partially restored the seed color phenotype to brown pigmentation, ascertaining its functional role in PA accumulation in the seed coat. These findings shed new light on the seed color regulation and evolutionary history, and highlight the transcriptional regulation of CaMATE23 by CaFUSCA3 in modulating seed color in chickpea. The functionally relevant InDel variation, natural allele, and haplotype from CaMATE23 are vital for translational genomic research, including marker‐assisted breeding, for developing chickpea cultivars with desirable seed color that appeal to consumers and meet global market demand. Significance Statement: Integrated genomic strategy provides novel insights into the transcriptional regulatory role of functional allele and haplotype delineated in a MATE gene selected during Cicer domestication, in regulating varied seed color of chickpea. [ABSTRACT FROM AUTHOR]

Significance Statement: Superior natural alleles of Mediator subunit genes have efficacy to develop desirable semi‐dwarf chickpea cultivars by modulating lignin and phenylpropanoid biosynthesis without compromising agronomic performance. [ABSTRACT FROM AUTHOR]

Pollen embryos of Datura innoxia Mill are produced in larger numbers from anthers on agar-gelled medium containing polyvinylpolypyrrolidone than on control. The best response is observed with 0.5% polyvinylpolypyrrolidone. The effect is possibly due to adsorption of substances (phenolics) emanating from cultured anthers and inhibiting the development of pollen grains into embryos. [ABSTRACT FROM AUTHOR]

Background: Rice grain size (GS) is an essential agronomic trait. Though several genes and miRNA modules influencing GS are known and seed development transcriptomes analyzed, a comprehensive compendium connecting all possible players is lacking. This study utilizes two contrasting GS indica rice genotypes (small-grained SN and large-grained LGR). Rice seed development involves five stages (S1–S5). Comparative transcriptome and miRNome atlases, substantiated with morphological and cytological studies, from S1–S5 stages and flag leaf have been analyzed to identify GS proponents. Results: Histology shows prolonged endosperm development and cell enlargement in LGR. Stand-alone and comparative RNAseq analyses manifest S3 (5–10 days after pollination) stage as crucial for GS enhancement, coherently with cell cycle, endoreduplication, and programmed cell death participating genes. Seed storage protein and carbohydrate accumulation, cytologically and by RNAseq, is shown to be delayed in LGR. Fourteen transcription factor families influence GS. Pathway genes for four phytohormones display opposite patterns of higher expression. A total of 186 genes generated from the transcriptome analyses are located within GS trait-related QTLs deciphered by a cross between SN and LGR. Fourteen miRNA families express specifically in SN or LGR seeds. Eight miRNA-target modules display contrasting expressions amongst SN and LGR, while 26 (SN) and 43 (LGR) modules are differentially expressed in all stages. Conclusions: Integration of all analyses concludes in a "Domino effect" model for GS regulation highlighting chronology and fruition of each event. This study delineates the essence of GS regulation, providing scope for future exploits. The rice grain development database (RGDD) (www.nipgr.ac.in/RGDD/index.php; https://doi.org/10.5281/zenodo.7762870) has been developed for easy access of data generated in this paper. [ABSTRACT FROM AUTHOR]

Identifying potential molecular tags for drought tolerance is essential for achieving higher crop productivity under drought stress. We employed an integrated genomics-assisted breeding and functional genomics strategy involving association mapping, fine mapping, map-based cloning, molecular haplotyping and transcript profiling in the introgression lines (ILs)- and near isogenic lines (NILs)-based association panel and mapping population of chickpea (Cicer arietinum). This combinatorial approach delineated a bHLH (basic helix-loop-helix) transcription factor, CabHLH10 (Cicer arietinum bHLH10) underlying a major QTL, along with its derived natural alleles/haplotypes governing yield traits under drought stress in chickpea. CabHLH10 binds to a cis-regulatory G-box promoter element to modulate the expression of RD22 (responsive to desiccation 22), a drought/abscisic acid (ABA)- responsive gene (via a trans-expression QTL), and two strong yield-enhancement photosynthetic efficiency (PE) genes. This, in turn, upregulates other downstream drought-responsive and ABA signaling genes, as well as yield-enhancing PE genes, thus increasing plant adaptation to drought with reduced yield penalty. We showed that a superior allele of CabHLH10 introgressed into the NILs improved root and shoot biomass and PE, thereby enhancing yield and productivity during drought without compromising agronomic performance. Furthermore, overexpression of CabHLH10 in chickpea and Arabidopsis (Arabidopsis thaliana) conferred enhanced drought tolerance by improving root and shoot agro-morphological traits. These findings facilitate translational genomics for crop improvement and the development of genetically tailored, climate-resilient, high-yielding chickpea cultivars. [ABSTRACT FROM AUTHOR]

SUMMARY: The advent of the pangenome era has unraveled previously unknown genetic variation existing within diverse crop plants, including rice. This untapped genetic variation is believed to account for a major portion of phenotypic variation existing in crop plants. However, the use of conventional single reference‐guided genotyping often fails to capture a large portion of this genetic variation leading to a reference bias. This makes it difficult to identify and utilize novel population/cultivar‐specific genes for crop improvement. Thus, we developed a Rice Pangenome Genotyping Array (RPGA) harboring probes assaying 80K single‐nucleotide polymorphisms (SNPs) and presence–absence variants spanning the entire 3K rice pangenome. This array provides a simple, user‐friendly and cost‐effective (60–80 USD per sample) solution for rapid pangenome‐based genotyping in rice. The genome‐wide association study (GWAS) conducted using RPGA‐SNP genotyping data of a rice diversity panel detected a total of 42 loci, including previously known as well as novel genomic loci regulating grain size/weight traits in rice. Eight of these identified trait‐associated loci (dispensable loci) could not be detected with conventional single reference genome‐based GWAS. A WD repeat‐containing PROTEIN 12 gene underlying one of such dispensable locus on chromosome 7 (qLWR7) along with other non‐dispensable loci were subsequently detected using high‐resolution quantitative trait loci mapping confirming authenticity of RPGA‐led GWAS. This demonstrates the potential of RPGA‐based genotyping to overcome reference bias. The application of RPGA‐based genotyping for population structure analysis, hybridity testing, ultra‐high‐density genetic map construction and chromosome‐level genome assembly, and marker‐assisted selection was also demonstrated. A web application (http://www.rpgaweb.com) was further developed to provide an easy to use platform for the imputation of RPGA‐based genotyping data using 3K rice reference panel and subsequent GWAS. Significance Statement: RPGA is a vital tool for diverse genomics‐assisted breeding applications and accelerated crop improvement in rice, as it provides an efficient pangenome‐based genotyping solution to overcome reference bias imposed by conventional single reference genome‐based genotyping strategies. [ABSTRACT FROM AUTHOR]

Stress associated protein ( SAP ) genes in plants regulate abiotic stress responses. SAP gene family consists of 18 members in rice. Although their abiotic stress responsiveness is well established, the mechanism of their action is poorly understood. OsiSAP7 was chosen to investigate the mechanism of its action based on the dual nature of its sub-cellular localization preferentially in the nucleus or sub-nuclear speckles upon transient expression in onion epidermal cells. Its expression was down-regulated in rice seedlings under abiotic stresses. OsiSAP7 was localized evenly in the nucleus under unstressed conditions and in sub-nuclear speckles on MG132 treatment. OsiSAP7 exhibits E3 ubiquitin ligase activity in vitro . Abiotic stress responses of OsiSAP7 were assessed by its overexpression in Arabidopsis under the control of a stress inducible promoter rd29A . Stress response assessment was done at seed germination and advanced stages of development. Transgenics were ABA insensitive at seed germination stage and sensitive to water-deficit stress at advanced stage as compared to wild type (WT). They were also impaired in ABA and stress-responsive gene expression. Our study suggests that OsiSAP7 acts as a negative regulator of ABA and water-deficit stress signalling by acting as an E3 ubiquitin ligase. [ABSTRACT FROM AUTHOR]

Pollen, regarded as the gold dust carrying the male germ line of flowering plants, is generated in the male reproductive organ called stamen. During the last few years, molecular biology and genetics have been integrated to enhance our knowledge regarding the structural and functional aspects of anther and pollen development. The promoters of several anther-/pollen-specific genes have been characterized to help understand the development of anther that involves the expression of a large number of genes temporally as well as spatially. The cis-acting regulatory elements of promoters necessary for interaction with transcription factors and their activity have been delineated. Many transcription factor genes having distinct anther-specific expression pattern have been identified with the help of transcriptome studies in Oryza sativa as well as Arabidopsis thaliana. The nature of complex interactions between genes and regulatory hierarchy involving developmental signal cascades have been investigated to design a working model for anther development. The immediate challenge ahead is to isolate and functionally characterize missing links and terminal ends of regulatory components for enhancing our knowledge about the male gametophyte development. The information generated on this aspect would help design suitable strategies to develop traits such as male sterility in crop plants. [ABSTRACT FROM AUTHOR]

The article explores the different types of transcription factors (TF) which are known for regulating the progression of dicot and monocot seed development. It mentions that in order to unveil the truth behind the integrated developmental process, it is essential to understand the interplay among these factors including the B3 and AP2 domains. The authors classify the stages of seed development into three, namely organ initiation, cell division and maturation.

Abstract: The real-time polymerase chain reaction (PCR) data requires normalization with an internal control gene expressed at constant levels under all the experimental conditions being analyzed for accurate and reliable gene expression results. In this study, the expression of 12 candidate internal control genes, including ACT1, EF1α, GAPDH, IF4a, TUB6, UBC, UBQ5, UBQ10, 18SrRNA, 25SrRNA, GRX and HSP90, in a diverse set of 18 tissue samples representing different organs/developmental stages and stress conditions in chickpea (Cicer arietinum L.) has been validated. Their expression levels vary considerably in various tissue samples analyzed. The expression levels of EF1α and HSP90 are most constant across various organs/developmental stages analyzed. Similarly, the expression levels of IF4a and GAPDH are most constant across various stress conditions. A set of two most stable genes is found sufficient for accurate and reliable normalization of real-time PCR data in the given set of tissue samples of chickpea. The genes with most constant expression identified in this study should be useful for normalization of gene expression data in a wide variety of tissue samples in chickpea. [Copyright &y& Elsevier]

The basic leucine (Leu) zipper (bZIP) proteins compose a family of transcriptional regulators present exclusively in eukaryotes. The bZIP proteins characteristically harbor a bZIP domain composed of two structural features: a DNA-binding basic region and the Leu zipper dimerization region. They have been shown to regulate diverse plant-specific phenomena, including seed maturation and germination, floral induction and development, and photomorphogenesis, and are also involved in stress and hormone signaling. We have identified 89 bZIP transcription factor-encoding genes in the rice (Oryza sativa) genome. Their chromosomal distribution and sequence analyses suggest that the bZIP transcription factor family has evolved via gene duplication. The phylogenetic relationship among rice bZIP domains as well as with bZIP domains from other plant bZIP factors suggests that homologous bZIP domains exist in plants. Similar intron/exon structural patterns were observed in the basic and hinge regions of their bZIP domains. Detailed sequence analysis has been done to identify additional conserved motifs outside the bZIP domain and to predict their DNA-binding site specificity as well as dimerization properties, which has helped classify them into different groups and subfamilies, respectively. Expression of bZIP transcription factor-encoding genes has been analyzed by full-length cDNA and expressed sequence tag-based expression profiling. This expression profiling was complemented by microarray analysis. The results indicate specific or coexpression patterns of rice bZIP transcription factors starting from floral transition to various stages of panicle and seed development. bZIP transcription factor-encoding genes in rice also displayed differential expression patterns in rice seedlings in response to abiotic stress and light irradiation. An effort has been made to link the structure and expression pattern of bZIP transcription factor-encoding genes in rice to their function, based on the information obtained from our analyses and earlier known results. This information will be important for functional characterization of bZIP transcription factors in rice. [ABSTRACT FROM AUTHOR]

Intronless genes, a characteristic feature of prokaryotes, constitute a significant portion of the eukaryotic genomes. Our analysis revealed the presence of 11,109 (19.9%) and 5,846 (21.7%) intronless genes in rice and Arabidopsis genomes, respectively, belonging to different cellular role and gene ontology categories. The distribution and conservation of rice and Arabidopsis intronless genes among different taxonomic groups have been analyzed. A total of 301 and 296 intronless genes from rice and Arabidopsis, respectively, are conserved among organisms representing the three major domains of life, i.e., archaea, bacteria, and eukaryotes. These evolutionarily conserved proteins are predicted to be involved in housekeeping cellular functions. Interestingly, among the 68% of rice and 77% of Arabidopsis intronless genes present only in eukaryotic genomes, approximately 51% and 57% genes have orthologs only in plants, and thus may represent the plant-specific genes. Furthermore, 831 and 144 intronless genes of rice and Arabidopsis, respectively, referred to as ORFans, do not exhibit homology to any of the genes in the database and may perform species-specific functions. These data can serve as a resource for further comparative, evolutionary, and functional analysis of intronless genes in plants and other organisms. [ABSTRACT FROM AUTHOR]

Recent advances in cereal genomics have made it possible to analyse the architecture of cereal genomes and their expressed components, leading to an increase in our knowledge of the genes that are linked to key agronomically important traits. These studies have used molecular genetic mapping of quantitative trait loci (QTL) of several complex traits that are important in breeding. The identification and molecular cloning of genes underlying QTLs offers the possibility to examine the naturally occurring allelic variation for respective complex traits. Novel alleles, identified by functional genomics or haplotype analysis, can enrich the genetic basis of cultivated crops to improve productivity. Advances made in cereal genomics research in recent years thus offer the opportunities to enhance the prediction of phenotypes from genotypes for cereal breeding. [Copyright &y& Elsevier]

For accurate and reliable gene expression results, normalization of real-time PCR data is required against a control gene, which displays highly uniform expression in living organisms during various phases of development and under different environmental conditions. We assessed the gene expression of 10 frequently used housekeeping genes, including 18S rRNA, 25S rRNA, UBC, UBQ5, UBQ10, ACT11, GAPDH, eEF-1α, eIF-4a, and β-TUB, in a diverse set of 25 rice samples. Their expression varied considerably in different tissue samples analyzed. The expression of UBQ5 and eEF-1α was most stable across all the tissue samples examined. However, 18S and 25S rRNA exhibited most stable expression in plants grown under various environmental conditions. Also, a set of two genes was found to be better as control for normalization of the data. The expression of these genes (with more uniform expression) can be used for normalization of real-time PCR results for gene expression studies in a wide variety of samples in rice. [Copyright &y& Elsevier]

Auxin regulates plant growth and development by altering the expression of diverse genes. Among these, the genes of Aux/ IAA, SAUR, and GH3 classes have been extensively studied in dicots, but little information is available on monocots. We have identified 12 members of GH3 gene family in rice using sequences of full-length cDNA clones available from KOME and analysis of the whole genome sequence of rice. The genomic organization as well as chromosomal location of all the OsGH3 genes is reported. The rice GH3 proteins can be classified in two groups (groups I and II) on the basis of their phylogenetic relationship with Arabidopsis GH3 proteins. Based upon the sequences available in the database, not a single group III GH3 protein could be identified in rice. An extensive survey of EST sequences of other monocots led to the conclusion that although GH3 gene family is highly conserved in both dicots and monocots but the group III is conspicuous by its absence in monocots. The in silico analysis has been complemented with experimental data to quantify transcript levels of all GH3 gene family members. Using real-time polymerase chain reaction, the organ-specific expression of individual OsGH3 genes in light- and dark-grown seedlings/plants has been examined. The transcript abundance of nearly all OsGH3 genes is enhanced on auxin treatment, with the effect more pronounced on OsGH3-1, -2, and -4. The functional validation of these genes in transgenics or analysis of gene-specific insertional mutants will help in elucidating their precise role in auxin signal transduction. [ABSTRACT FROM AUTHOR]

Abstract: Auxin regulates many aspects of plant growth and development by altering the expression of diverse genes. Among these, the early auxin-responsive genes of Aux/IAA class have been extensively studied in dicots but little information is available on monocots. Earlier, we reported the isolation of OsiIAA1 cDNA, first monocot member of Aux/IAA gene family from rice. Extending this work further, we have isolated the OsiIAA1 gene from rice localized on chromosome 3. The transcriptional start site was mapped to 158 bp upstream to the translational start site. The increased accumulation of OsiIAA1 transcript in auxin-treated rice coleoptiles even in the presence of a protein synthesis inhibitor, cycloheximide, suggested that OsiIAA1 is a primary auxin response gene; the expression of OsiIAA1 gene was also upregulated in the presence of cycloheximide alone. The OsiIAA1 transcript levels were down-regulated in etiolated rice coleoptiles irradiated with far-red, red and blue light, suggesting the existence of a cross-talk between auxin and light signaling. The antibodies raised against His6–OsiIAA1 recombinant protein could detect the OsiIAA1 protein in the plant extract only in the presence of a proteasome inhibitor, MG132, indicating that OsiIAA1 is rapidly degraded by proteasome complex. The degradation of the protein was enhanced by the application of exogenous auxin. Also, the proteasome inhibitor MG132 stabilized the purified His6–OsiIAA1 protein to some extent in the cell-free extracts of rice coleoptiles. The OsiIAA1 protein harbors two nuclear localization signals (NLSs), one bipartite and the other resembling SV40 type NLS. Although both the NLSs were able to target the protein to the nucleus, the bipartite NLS was more effective. These studies indicate that nuclear localization of OsiIAA1 could be a prerequisite for its role in auxin signal transduction. [Copyright &y& Elsevier]

Abstract: The 33kDa polypeptide of the oxygen-evolving complex in Arabidopsis is encoded by two paralogous genes, PSBO1 and PSBO2 (located on chromosomes 5 and 3, respectively), which show 80.35% homology at the nucleotide level, 95.18% homology at the protein level and conservation of a large number of cis-regulatory elements within −500bp from the translational start site. Mapping of the transcription start site revealed that PSBO1 has a 45bp long leader sequence. The expression of PSBO1 and PSBO2 is tissue-specific and is stimulated by light in both young and mature plants of Arabidopsis. However, the transcript for PSBO1 accumulates at higher level than PSBO2. To define the regulatory elements, four deletion constructs, designed from the upstream sequence of the PSBO1 gene and the 2.7kb promoter, fused with GUS, were mobilized in tobacco and the T0 transgenics as well as the progeny analyzed for light-inducibility and organ-specific expression. Promoter-deletion analysis revealed that the regulatory elements conferring light-responsivity reside within −165bp of the translational start site. The existence of some positive regulatory elements in the region between −165 and −570bp has also been unravelled. [Copyright &y& Elsevier]

The regulation of chloroplast gene expression by light involves multiple signaling components. In an earlier study, we demonstrated the role of calcium and phosphorylation in regulating the expression of photosynthesis-related plastid genes, psbA, psaA and rbcL, using rice as a model monocot system. This work has been extended further to examine the possible involvement of heterotrimeric GTP-binding proteins and calmodulin. Vacuum infiltration of 5-day-old etiolated rice seedlings with G-protein agonists, cholera toxin and GTPγS, increased the steady-state transcript levels of the plastid genes. The antagonists/inhibitors of calmodulin action, trifluoperazine and W7, inhibited the light-induced increase in steady-state transcript levels of these genes. The light-regulated expression of photosynthetic genes was also adversely affected by tagetitoxin, a specific inhibitor of plastid-encoded RNA polymerase. These results indicate the involvement of various signaling components in transduction of light signal that probably also recruits PEP to regulate plastid gene expression. [Copyright &y& Elsevier]

Summary: Rice grain size and weight are major determinants of grain quality and yield and so have been under rigorous selection since domestication. However, the genetic basis for contrasting grain size/weight trait among Indian germplasms and their association with domestication‐driven evolution is not well understood. In this study, two long (LGG) and two short grain (SGG) genotypes were resequenced. LGG (LGR and PB 1121) differentiated from SGG (Sonasal and Bindli) by 504 439 single nucleotide polymorphisms (SNPs) and 78 166 insertion‐and‐deletion polymorphisms. The LRK gene cluster was different and a truncation mutation in the LRK8 kinase domain was associated with LGG. Phylogeny with 3000 diverse rice accessions revealed that the four sequenced genotypes belonged to the japonica group and were at the edge of the clades indicating them to be the potential source of genetic diversity available in Indian rice germplasm. Six SNPs were significantly associated with grain size/weight and the top four of these could be validated in mapping a population, suggesting this study as a valuable resource for high‐throughput genotyping. A contiguous long low‐diversity region (LDR) of approximately 6 Mb carrying a major grain weight quantitative trait loci (harbouring OsTOR gene) was identified on Chromosome 5. This LDR was identified as an evolutionary important site with significant positive selection and multiple selection sweeps, and showed association with many domestication‐related traits, including grain size/weight. The aus population retained more allelic variations in the LDR than the japonica and indica populations, suggesting it to be one of the divergence loci. All the data and analyses can be accessed from the RiceSzWtBase database. [ABSTRACT FROM AUTHOR]

Summary: Mediator, a multisubunit co‐activator complex, regulates transcription in eukaryotes and is involved in diverse processes in Arabidopsis through its different subunits. Here, we have explored developmental aspects of one of the rice Mediator subunit gene OsMED14_1. We analyzed its expression pattern through RNA in situ hybridization and pOsMED14_1:GUS transgenics that showed its expression in roots, leaves, anthers and seeds prominently at younger stages, indicating possible involvement of this subunit in multiple aspects of rice development. To understand the developmental roles of OsMED14_1 in rice, we generated and studied RNAi‐based knockdown rice plants that showed multiple effects including less height, narrower leaves and culms with reduced vasculature, lesser lateral root branching, defective microspore development, reduced panicle branching and seed set, and smaller seeds. Histological analyses showed that slender organs were caused by reduction in both cell number and cell size in OsMED14_1 knockdown plants. Flow cytometric analyses and expression analyses of cell cycle‐related genes revealed that defective cell‐cycle progression led to these defects. Expression analyses of auxin‐related genes and indole‐3‐acetic acid (IAA) immunolocalization study indicated altered auxin level in these knockdown plants. Reduction of lateral root branching in knockdown plants was corrected by exogenous IAA supplement. OsMED14_1 physically interacts with transcription factors YABBY5, TAPETUM DEGENERATION RETARDATION (TDR) and MADS29, possibly regulating auxin homeostasis and ultimately leading to lateral organ/leaf, microspore and seed development. Significance Statement: The current study addresses the mechanism of developmental control by the Mediator subunit gene OsMED14_1 in rice, thereby enhancing the understanding of subunit specific Mediator functions in plants. Spatio‐temporal expression pattern, knockdown effects, auxin‐related gene expression/immunolocalization studies and protein level interactions unravel the involvement of OsMED14_1 in various developmental processes and provide a mechanistic view of its action in regulating these processes. [ABSTRACT FROM AUTHOR]

Developing functional molecular tags from the cis-regulatory sequence components of genes is vital for their deployment in efficient genetic dissection of complex quantitative traits in crop plants including chickpea. The current study identified 431,194 conserved non-coding SNP (CNSNP) from the cis-regulatory element regions of genes which were annotated on a chickpea genome. These genome-wide CNSNP marker resources are made publicly accessible through a user-friendly web-database (http://www.cnsnpcicarbase.com). The CNSNP-based quantitative trait loci (QTL) and expression QTL (eQTL) mapping and genome-wide association study (GWAS) were further integrated with global gene expression landscapes, molecular haplotyping, and DNA-protein interaction study in the association panel and recombinant inbred lines (RIL) mapping population to decode complex genetic architecture of one of the vital seed yield trait under drought stress, drought yield index (DYI), in chickpea. This delineated two constituted natural haplotypes and alleles from a histone H3 protein-coding gene and its transcriptional regulator NAC transcription factor (TF) harboring the major QTLs and trans-acting eQTL governing DYI in chickpea. The effect of CNSNPs in TF-binding cis-element of a histone H3 gene in altering the binding affinity and transcriptional activity of NAC TF based on chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) assay was evident. The CNSNP-led promising molecular tags scanned will essentially have functional significance to decode transcriptional gene regulatory function and thus can drive translational genomic analysis in chickpea. [ABSTRACT FROM AUTHOR]

Key message: A combinatorial genomic strategy delineated functionally relevant natural allele of a CLAVATA gene and its marker (haplotype)-assisted introgression led to development of the early-flowering chickpea cultivars with high flower number and enhanced yield/productivity. Unraveling the genetic components involved in CLAVATA (CLV) signaling is crucial for modulating important shoot apical meristem (SAM) characteristics and ultimately regulating diverse SAM-regulated agromorphological traits in crop plants. A genome-wide scan identified 142 CLV1-, 28 CLV2- and 6 CLV3-like genes, and their comprehensive genomic constitution and phylogenetic relationships were deciphered in chickpea. The QTL/fine mapping and map-based cloning integrated with high-resolution association analysis identified SNP loci from CaCLV3_01 gene within a major CaqDTF1.1/CaqFN1.1 QTL associated with DTF (days to 50% flowering) and FN (flower number) traits in chickpea, which was further ascertained by quantitative expression profiling. Molecular haplotyping of CaCLV3_01 gene, expressed specifically in SAM, constituted two major haplotypes that differentiated the early-DTF and high-FN chickpea accessions from late-DTF and low-FN. Enhanced accumulation of transcripts of superior CaCLV3_01 gene haplotype and known flowering promoting genes was observed in the corresponding haplotype-introgressed early-DTF and high-FN near-isogenic lines (NILs) with narrow SAM width. The superior haplotype-introgressed NILs exhibited early-flowering, high-FN and enhanced seed yield/productivity without compromising agronomic performance. These delineated molecular signatures can regulate DTF and FN traits through SAM proliferation and differentiation and thereby will be useful for translational genomic study to develop early-flowering cultivars with enhanced yield/productivity. [ABSTRACT FROM AUTHOR]

Summary: Plant height (PH) and plant width (PW), two of the major plant architectural traits determining the yield and productivity of a crop, are defined by diverse morphometric characteristics of the shoot apical meristem (SAM). The identification of potential molecular tags from a single gene that simultaneously modulates these plant/SAM architectural traits is therefore prerequisite to achieve enhanced yield and productivity in crop plants, including chickpea. Large‐scale multienvironment phenotyping of the association panel and mapping population have ascertained the efficacy of three vital SAM morphometric trait parameters, SAM width, SAM height and SAM area, as key indicators to unravel the genetic basis of the wide PW and PH trait variations observed in desi chickpea. This study integrated a genome‐wide association study (GWAS); quantitative trait locus (QTL)/fine‐mapping and map‐based cloning with molecular haplotyping; transcript profiling; and protein‐DNA interaction assays for the dissection of plant architectural traits in chickpea. These exertions delineated natural alleles and superior haplotypes from a CabHLH121 transcription factor (TF) gene within the major QTL governing PW, PH and SAM morphometric traits. A genome‐wide protein‐DNA interaction assay assured the direct binding of a known stem cell master regulator, CaWUS, to the WOX‐homeodomain TF binding sites of a CabHLH121 gene and its constituted haplotypes. The differential expression of CaWUS and transcriptional regulation of its target CabHLH121 gene/haplotypes were apparent, suggesting their collective role in altering SAM morphometric characteristics and plant architectural traits in the contrasting near isogenic lines (NILs). The NILs introgressed with a superior haplotype of a CabHLH121 exhibited optimal PW and desirable PH as well as enhanced yield and productivity without compromising any component of agronomic performance. These molecular signatures of the CabHLH121 TF gene have the potential to regulate both PW and PH traits through the modulation of proliferation, differentiation and maintenance of the meristematic stem cell population in the SAM; therefore, these signatures will be useful in the translational genomic study of chickpea genetic enhancement. The restructured cultivars with desirable PH (semidwarf) and PW will ensure maximal planting density in a specified cultivable field area, thereby enhancing the overall yield and productivity of chickpea. This can essentially facilitate the achievement of better remunerative outputs by farmers with rational land use, therefore ensuring global food security in the present scenario of an increasing population density and shrinking per capita land area. Significance Statement: Superior transcriptional signatures delineated from CabHLH121 enhanced yield and productivity by modulating vital plant architectural (plant width and plant height) and SAM morphometric traits without compromising any component of agronomic performance in chickpea. [ABSTRACT FROM AUTHOR]

The identification of functionally relevant molecular tags is vital for genomics-assisted crop improvement and enhancement of seed yield, quality, and productivity in chickpea (Cicer arietinum). The simultaneous improvement of yield/productivity as well as quality traits often requires pyramiding of multiple genes, which remains a major hurdle given various associated epistatic and pleotropic effects. Unfortunately, no single gene that can improve yield/productivity along with quality and other desirable agromorphological traits is known, hampering the genetic enhancement of chickpea. Using a combinatorial genomics-assisted breeding and functional genomics strategy, this study identified natural alleles and haplotypes of an ABCC3-type transporter gene that regulates seed weight, an important domestication trait, by transcriptional regulation and modulation of the transport of glutathione conjugates in seeds of desi and kabuli chickpea. The superior allele/haplotype of this gene introgressed in desi and kabuli near-isogenic lines enhances the seed weight, yield, productivity, and multiple desirable plant architecture and seed-quality traits without compromising agronomic performance. These salient findings can expedite crop improvement endeavors and the development of nutritionally enriched high-yielding cultivars in chickpea. [ABSTRACT FROM AUTHOR]

Understanding the genetic basis of photosynthetic efficiency (PE) contributing to enhanced seed yield per plant (SYP) is vital for genomics‐assisted crop improvement of chickpea. The current study employed an integrated genomic strategy involving photosynthesis pathway gene‐based association mapping, genome‐wide association study, quantitative trait loci (QTL) mapping, and expression profiling. This identified 16 potential single nucleotide polymorphism loci linked to major QTLs underlying 16 candidate genes significantly associated with PE and SYP traits in chickpea. The allelic variants were tightly linked to positively interacting QTLs regulating both enhanced PE and SYP traits as exemplified by a chlorophyll A‐B binding protein‐coding gene. The leaf tissue‐specific pronounced up‐regulated expression of 16 associated genes in germplasm accessions and homozygous individuals of mapping population was evident. Such combinatorial genomic strategy coupled with gene haplotype‐specific association and in silico protein–protein interaction study delineated natural alleles and superior haplotypes from a chlorophyll A‐B binding (CAB) protein‐coding gene and its interacting gene, Timing of CAB Expression 1 (TOC1), which appear to be most promising candidates in modulating chickpea PE and SYP traits. These functionally pertinent molecular signatures identified have efficacy to drive marker‐assisted selection for developing PE‐enriched cultivars with high seed yield in chickpea. The photosynthetic efficiency of a crop contributes immensely to its ultimate yield and productivity. The present study aimed at identification of functionally relevant genetic factors for efficient dissection of photosynthetic efficiency and seed yield traits through integrated genomics‐assisted breeding strategies in chickpea. Natural allelic variants and superior haplotypes delineated from a chlorophyll A‐B binding protein‐coding gene and its interacting gene, Timing of CAB Expression 1, come up as the most potential candidates to enhance both photosynthetic efficiency and seed yield of chickpea. The salient outcomes can essentially drive translational genomic analysis to develop photosynthetically efficient high‐yielding cultivars in chickpea. [ABSTRACT FROM AUTHOR]

The present study exploited integrated genomics-assisted breeding strategy for genetic dissection of complex branch number quantitative trait in chickpea. Candidate gene-based association analysis in a branch number association panel was performed by utilizing the genotyping data of 401 SNP allelic variants mined from 27 known cloned branch number gene orthologs of chickpea. The genome-wide association study (GWAS) integrating both genome-wide GBS- (4556 SNPs) and candidate gene-based genotyping information of 4957 SNPs in a structured population of 60 sequenced desi and kabuli accessions (with 350–400 kb LD decay), detected 11 significant genomic loci (genes) associated (41% combined PVE) with branch number in chickpea. Of these, seven branch number-associated genes were further validated successfully in two inter (ICC 4958 × ICC 17160)- and intra (ICC 12299 × ICC 8261)-specific mapping populations. The axillary meristem and shoot apical meristem-specific expression, including differential up- and down-regulation (4–5 fold) of the validated seven branch number-associated genes especially in high branch number as compared to the low branch number-containing parental accessions and homozygous individuals of two aforesaid mapping populations was apparent. Collectively, this combinatorial genomic approach delineated diverse naturally occurring novel functional SNP allelic variants in seven potential known/candidate genes [ PIN1 (PIN-FORMED protein 1), TB1 (teosinte branched 1), BA1 / LAX1 ( BARREN STALK1 / LIKE AUXIN1 ), GRAS8 (gibberellic acid insensitive/GAI, Repressor of ga13/RGA and Scarecrow8/SCR8), ERF (ethylene-responsive element-binding factor), MAX2 (more axillary growth 2) and lipase] governing chickpea branch number. The useful information generated from this study have potential to expedite marker-assisted genetic enhancement by developing high-yielding cultivars with more number of productive (pods and seeds) branches in chickpea. [ABSTRACT FROM AUTHOR]

Pollen development and its germination are obligatory for the reproductive success of flowering plants. Calcium-dependent protein kinases (CPKs, also known as CDPKs) regulate diverse signaling pathways controlling plant growth and development. Here, we report the functional characterization of a novel OsCPK29 from rice, which is mainly expressed during pollen maturation stages of the anther. OsCPK29 exclusively localizes in the nucleus, and its N-terminal variable domain is responsible for retaining it in the nucleus. OsCPK29 knockdown rice plants exhibit reduced fertility, set fewer seeds, and produce collapsed non-viable pollen grains that do not germinate. Cytological analysis of anther semi-thin sections during different developmental stages suggested that pollen abnormalities appear after the vacuolated pollen stage. Detailed microscopic study of pollen grains further revealed that they were lacking the functional intine layer although exine layer was present. Consistent with that, downregulation of known intine development-related rice genes was also observed in OsCPK29 silenced anthers. Furthermore, it has been demonstrated that OsCPK29 interacts in vitro as well as in vivo with the MADS68 transcription factor which is a known regulator of pollen development. Therefore, phenotypic observations and molecular studies suggest that OsCPK29 is an important regulator of pollen development in rice. • OsCPK29 is a nuclear-localized protein kinase expressed during late pollen development. • Silencing of OsCPK29 severely affects fertility and seed set in rice owing to the failure of pollen maturation. • OsCPK29 silenced pollen grains lack an intine layer and fail to germinate. • OsCPK29 physically interacts with MADS68 in vitro and in vivo and possibly controls the expression of its target genes. [ABSTRACT FROM AUTHOR]

Development and an integrated utilization of genome-wide conserved non-coding microsatellite (CNMS) markers in genetical genomics for quantitative dissection of seed weight in chickpea are described.Phylogenetic footprinting identified 666 genome-wide paralogous and orthologous CNMS (conserved non-coding microsatellite) markers from 5′-untranslated and regulatory regions (URRs) of 603 protein-coding chickpea genes. The (CT)n and (GA)n CNMS carrying CTRMCAMV35S and GAGA8BKN3 regulatory elements, respectively, are abundant in the chickpea genome. The mapped genic CNMS markers with robust amplification efficiencies (94.7%) detected higher intraspecific polymorphic potential (37.6%) among genotypes, implying their immense utility in chickpea breeding and genetic analyses. Seventeen differentially expressed CNMS marker-associated genes showing strong preferential and seed tissue/developmental stage-specific expression in contrasting genotypes were selected to narrow down the gene targets underlying seed weight quantitative trait loci (QTLs)/eQTLs (expression QTLs) through integrative genetical genomics. The integration of transcript profiling with seed weight QTL/eQTL mapping, molecular haplotyping, and association analyses identified potential molecular tags (GAGA8BKN3 and RAV1AAT regulatory elements and alleles/haplotypes) in the LOB-domain-containing protein- and KANADI protein-encoding transcription factor genes controlling the cis-regulated expression for seed weight in the chickpea. This emphasizes the potential of CNMS marker-based integrative genetical genomics for the quantitative genetic dissection of complex seed weight in chickpea. [ABSTRACT FROM PUBLISHER]

Background Availability of the draft nuclear genome sequences of small-seeded desi-type legume crop Cicer arietinum has provided an opportunity for investigating unique chickpea genomic features and evaluation of their biological significance. The increasing number of legume genome sequences also presents a challenge for developing reliable and information-driven bioinformatics applications suitable for comparative exploration of this important class of crop plants. Results The Chickpea Genomic Web Resource (CGWR) is an implementation of a suite of web-based applications dedicated to chickpea genome visualization and comparative analysis, based on next generation sequencing and assembly of Cicer arietinum desi-type genotype ICC4958. CGWR has been designed and configured for mapping, scanning and browsing the significant chickpea genomic features in view of the important existing and potential roles played by the various legume genome projects in mutant mapping and cloning. It also enables comparative informatics of ICC4958 DNA sequence analysis with other wild and cultivated genotypes of chickpea, various other leguminous species as well as several non-leguminous model plants, to enable investigations into evolutionary processes that shape legume genomes. Conclusions CGWR is an online database offering a comprehensive visual and functional genomic analysis of the chickpea genome, along with customized maps and gene-clustering options. It is also the only plant based web resource supporting display and analysis of nucleosome positioning patterns in the genome. The usefulness of CGWR has been demonstrated with discoveries of biological significance made using this server. The CGWR is compatible with all available operating systems and browsers, and is available freely under the open source license at http://www.nipgr.res.in/CGWR/home.php [ABSTRACT FROM AUTHOR]

Characterization of natural allelic diversity and understanding the genetic structure and linkage disequilibrium (LD) pattern in wild germplasm accessions by large-scale genotyping of informative microsatellite and single nucleotide polymorphism (SNP) markers is requisite to facilitate chickpea genetic improvement. Large-scale validation and high-throughput genotyping of genome-wide physically mapped 478 genic and genomic microsatellite markers and 380 transcription factor gene-derived SNP markers using gel-based assay, fluorescent dye-labelled automated fragment analyser and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass array have been performed. Outcome revealed their high genotyping success rate (97.5%) and existence of a high level of natural allelic diversity among 94 wild and cultivated Cicer accessions. High intra- and inter-specific polymorphic potential and wider molecular diversity (11–94%) along with a broader genetic base (13–78%) specifically in the functional genic regions of wild accessions was assayed by mapped markers. It suggested their utility in monitoring introgression and transferring target trait-specific genomic (gene) regions from wild to cultivated gene pool for the genetic enhancement. Distinct species/gene pool-wise differentiation, admixed domestication pattern, and differential genome-wide recombination and LD estimates/decay observed in a six structured population of wild and cultivated accessions using mapped markers further signifies their usefulness in chickpea genetics, genomics and breeding. [ABSTRACT FROM AUTHOR]

Eukaryotic A20/AN1 zinc-finger proteins (ZFPs) play an important role in the regulation of immune and stress response. After elucidation of the role of first such protein, OsSAP1, in abiotic stress tolerance, 18 rice stress associated protein (SAP) genes have been shown to be regulated by multiple abiotic stresses. In the present study, expression pattern of all the 18 OsSAP genes have been analysed in response to different biotic stress simulators, in order to get insights into their possible involvement in biotic stress tolerance. Our results showed the upregulation of OsSAP1 and OsSAP11 by all biotic stress simulator treatments. Furthermore, the functional role of OsSAP1 in plant defence responses has been explored through overexpression in transgenic plants. Constitutive expression of OsSAP1 in transgenic tobacco resulted into enhanced disease resistance against virulent bacterial pathogen, together with the upregulation of known defence-related genes. Present investigation suggests that rice SAPs are responsive to multiple biotic stresses and OsSAP1 plays a key role in basal resistance against pathogen infection. This strongly supports the involvement of rice SAPs in cross-talk between biotic and abiotic stress signalling pathways, which makes them ideal candidate to design strategies for protecting crop plants against multiple stresses. [ABSTRACT FROM AUTHOR]

Ca2+ homeostasis is required to maintain a delicate balance of cytosolic Ca2+ during normal and adverse growth conditions. Various Ca2+ transporters actively participate to maintain this delicate balance especially during abiotic stresses and developmental events in plants. In this study, we present a genome-wide account, detailing expression profiles, subcellular localization and functional analysis of rice Ca2+ transport elements. Exhaustive in silico data mining and analysis resulted in the identification of 81 Ca2+ transport element genes, which belong to various groups such as Ca2+- ATPases (pumps), exchangers, channels, glutamate receptor homologs and annexins. Phylogenetic analysis revealed that different Ca2+ transporters are evolutionarily conserved across different plant species. Comprehensive expression analysis by gene chip microarray and quantitative RT- PCR revealed that a substantial proportion of Ca2+ transporter genes were expressed differentially under abiotic stresses (salt, cold and drought) and reproductive developmental stages (panicle and seed) in rice. These findings suggest a possible role of rice Ca2+ transporters in abiotic stress and development triggered signaling pathways. Subcellular localization of Ca2+ transporters from different groups in Nicotiana benthamiana revealed their variable localization to different compartments, which could be their possible sites of action. Complementation of Ca2+ transport activity of K616 yeast mutant by Ca2+- ATPase Os ACA7 and involvement in salt tolerance verified its functional behavior. This study will encourage detailed characterization of potential candidate Ca2+ transporters for their functional role in planta. [ABSTRACT FROM AUTHOR]

Abstract: Sugarcane (Saccharum spp. hybrid) with complex polyploid genome requires a large number of informative DNA markers for various applications in genetics and breeding. Despite the great advances in genomic technology, it is observed in several crop species, especially in sugarcane, the availability of molecular tools such as microsatellite markers are limited. Now-a-days EST-SSR markers are preferred to genomic SSR (gSSR) as they represent only the functional part of the genome, which can be easily associated with desired trait. The present study was taken up with a new set of 351 EST-SSRs developed from the 4085 non redundant EST sequences of two Indian sugarcane cultivars. Among these EST-SSRs, TNR containing motifs were predominant with a frequency of 51.6%. Thirty percent EST-SSRs showed homology with annotated protein. A high frequency of SSRs was found in the 5′UTR and in the ORF (about 27%) and a low frequency was observed in the 3′UTR (about 8%). Two hundred twenty-seven EST-SSRs were evaluated, in sugarcane, allied genera of sugarcane and cereals, and 134 of these have revealed polymorphism with a range of PIC value 0.12 to 0.99. The cross transferability rate ranged from 87.0% to 93.4% in Saccharum complex, 80.0% to 87.0% in allied genera, and 76.0% to 80.0% in cereals. Cloning and sequencing of EST-SSR size variant amplicons revealed that the variation in the number of repeat-units was the main source of EST-SSR fragment polymorphism. When 124 sugarcane accessions were analyzed for population structure using model-based approach, seven genetically distinct groups or admixtures thereof were observed in sugarcane. Results of principal coordinate analysis or UPGMA to evaluate genetic relationships delineated also the 124 accessions into seven groups. Thus, a high level of polymorphism adequate genetic diversity and population structure assayed with the EST-SSR markers not only suggested their utility in various applications in genetics and genomics in sugarcane but also enriched the microsatellite marker resources in sugarcane. [Copyright &y& Elsevier]

Stress associated proteins (SAPs), novel A20/AN1 zinc-finger domain-containing proteins, are fast emerging as potential candidates for biotechnological approaches in order to improve abiotic stress tolerance in plants - the ultimate aim of which is crop-yield protection. Until relatively recently, such proteins had only been identified in humans, where they had been shown to be key regulators of innate immunity. Their phylogenetic relationship and recruitment of diverse protein domains reflect an architectural and mechanistic diversity. Emerging evidence suggests that SAPs may act as ubiquitin ligase, redox sensor, and regulator of gene expression during stress. Here, we evaluate the new knowledge on SAPs with a view to understand their mechanism of action. Furthermore, we set an agenda for investigating hitherto unexplored roles of these proteins. [ABSTRACT FROM AUTHOR]

Cicer arietinum L. (chickpea) is the third most important food legume crop. We have generated the draft sequence of a desi-type chickpea genome using next-generation sequencing platforms, bacterial artificial chromosome end sequences and a genetic map. The 520-Mb assembly covers 70% of the predicted 740-Mb genome length, and more than 80% of the gene space. Genome analysis predicts the presence of 27 571 genes and 210 Mb as repeat elements. The gene expression analysis performed using 274 million RNA-Seq reads identified several tissue-specific and stress-responsive genes. Although segmental duplicated blocks are observed, the chickpea genome does not exhibit any indication of recent whole-genome duplication. Nucleotide diversity analysis provides an assessment of a narrow genetic base within the chickpea cultivars. We have developed a resource for genetic markers by comparing the genome sequences of one wild and three cultivated chickpea genotypes. The draft genome sequence is expected to facilitate genetic enhancement and breeding to develop improved chickpea varieties. [ABSTRACT FROM AUTHOR]

Background: Phospholipase C (PLC) is one of the major lipid hydrolysing enzymes, implicated in lipid mediated signaling. PLCs have been found to play a significant role in abiotic stress triggered signaling and developmental processes in various plant species. Genome wide identification and expression analysis have been carried out for this gene family in Arabidopsis, yet not much has been accomplished in crop plant rice. Methodology/Principal Findings: An exhaustive in-silico exploration of rice genome using various online databases and tools resulted in the identification of nine PLC encoding genes. Based on sequence, motif and phylogenetic analysis rice PLC gene family could be divided into phosphatidylinositol-specific PLCs (PI-PLCs) and phosphatidylcholine- PLCs (PC-PLC or NPC) classes with four and five members, respectively. A comparative analysis revealed that PLCs are conserved in Arabidopsis (dicots) and rice (monocot) at gene structure and protein level but they might have evolved through a separate evolutionary path. Transcript profiling using gene chip microarray and quantitative RT-PCR showed that most of the PLC members expressed significantly and differentially under abiotic stresses (salt, cold and drought) and during various developmental stages with condition/stage specific and overlapping expression. This finding suggested an important role of different rice PLC members in abiotic stress triggered signaling and plant development, which was also supported by the presence of relevant cis-regulatory elements in their promoters. Sub-cellular localization of few selected PLC members in Nicotiana benthamiana and onion epidermal cells has provided a clue about their site of action and functional behaviour. Conclusion/Significance: The genome wide identification, structural and expression analysis and knowledge of sub-cellular localization of PLC gene family envisage the functional characterization of these genes in crop plants in near future. [ABSTRACT FROM AUTHOR]

Chickpea (Cicer arietinum L.) is an important crop legume plant with high nutritional value. The transcriptomes of desi and wild chickpea have already been sequenced. In this study, we sequenced the transcriptome of kabuli chickpea, C. arietinum (genotype ICCV2), having higher commercial value, using GS-FLX Roche 454 and Illumina technologies. The assemblies of both Roche 454 and Illumina datasets were optimized using various assembly programs and parameters. The final optimized hybrid assembly generated 43,389 transcripts with an average length of 1065 bp and N50 length of 1653 bp representing 46.2 Mb of kabuli chickpea transcriptome. We identified a total of 5409 simple sequence repeats (SSRs) in these transcript sequences. Among these, at least 130 and 493 SSRs were polymorphic with desi (ICC4958) and wild (PI489777) chickpea, respectively. In addition, a total of 1986 and 37,954 single nucleotide polymorphisms (SNPs) were predicted in kabuli/desi and kabuli/wild genotypes, respectively. The SNP frequency was 0.043 SNP per kb for kabuli/desi and 0.821 SNP per kb for kabuli/wild, reflecting very low genetic diversity in chickpea. Further, SSRs and SNPs present in tissue-specific and transcription factor encoding transcripts have been identified. The experimental validation of a selected set of polymorphic SSRs and SNPs exhibited high intra-specific polymorphism potential between desi and kabuli chickpea, suggesting their utility in large-scale genotyping applications. The kabuli chickpea gene index assembled, and SSRs and SNPs identified in this study will serve as useful genomic resource for genetic improvement of chickpea. [ABSTRACT FROM AUTHOR]

Perceived by Charles Darwin in many vegetable plants and rediscovered by George H Shull and Edward M East in maize, heterosis or hybrid vigour is one of the most widely utilized phenomena, not only in agriculture but also in animal breeding. Although, numerous studies have been carried out to understand its genetic and/or molecular basis in the past 100 years, our knowledge of the underlying molecular processes that results in hybrid vigour can best be defined as superficial. Even after century long deliberations, there is no consensus on the relative/individual contribution of the genetic/epigenetic factors in the manifestation of heterosis. However, with the recent advancements in functional genomics, transcriptomics, proteomics, and metabolomics-related technologies, the riddle of heterosis is being reinvestigated by adopting systems-level approaches to understand the underlying molecular mechanisms. A number of intriguing hypotheses are converging towards the idea of a cumulative positive effect of the differential expression of a variety of genes, on one or several yield-affecting metabolic pathways or overall energy-use efficiency, as the underlying mechanism for the manifestation of heterosis. Presented here is a brief account of clues gathered from various investigative approaches targeted towards better scientific understanding of this process. [ABSTRACT FROM AUTHOR]

The transcriptome of cultivated chickpea ( Cicer arietinum L.), an important crop legume, has recently been sequenced. Here, we report sequencing of the transcriptome of wild chickpea, C. reticulatum (PI489777), the progenitor of cultivated chickpea, by GS-FLX 454 technology. The optimized assembly of C. reticulatum transcriptome generated 37 265 transcripts in total with an average length of 946 bp. A total of 4072 simple sequence repeats (SSRs) could be identified in these transcript sequences, of which at least 561 SSRs were polymorphic between C. arietinum and C. reticulatum. In addition, a total of 36 446 single-nucleotide polymorphisms (SNPs) were identified after optimization of probability score, quality score, read depth and consensus base ratio. Several of these SSRs and SNPs could be associated with tissue-specific and transcription factor encoding transcripts. A high proportion (92-94%) of polymorphic SSRs and SNPs identified between the two chickpea species were validated successfully. Further, the estimation of synonymous substitution rates of orthologous transcript pairs suggested that the speciation event for divergence of C. arietinum and C. reticulatum may have happened approximately 0.53 million years ago. The results of our study provide a rich resource for exploiting genetic variations in chickpea for breeding programmes. [ABSTRACT FROM AUTHOR]

Summary [ABSTRACT FROM AUTHOR]