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Potato production faces major challenges from inadequate soil fertility, and nematode infestation, yet synthetic fertilizers and nematicides are costly and harmful to the environment. This study explored the potential of chitin-fortified black soldier fly-composted organic fertilizer (BSFCOF) as a multipurpose organic fertilizer amendment for enhancing potato yield and suppressing potato cyst nematodes (PCN). The BSFCOF was applied at a rate equivalent to 150 kg N ha -1 and fortified with chitin from black soldier fly pupal exuviae at inclusion rates equivalent to 0.5, 1, 2, 3, 4 and 5% chitin. Data were collected on potato growth characteristics, PCN population densities, and soil chemical properties for two growing cycles. Results showed that chitin fortified BSFCOF significantly improved potato growth parameters, chlorophyll concentration, marketable tuber yield and number of marketable tubers. The marketable tuber yield achieved using chitin-fortified BSFCOF was 70 - 362%, and 69 - 238% higher than the values achieved using unfertilized soil during the first and second growing cycles, respectively. Soil amendment with chitin-fortified BSFCOF significantly reduced the number of cysts per 200 g soil -1 , number of eggs and J2 per cyst -1 , eggs g -1 soil and reproduction rate by 32 - 87%, 9 - 92%, 31- 98% and 31 - 98%, respectively. The PCN suppression increased with chitin inclusion rates. There were significantly higher values for soil pH, ammonium nitrogen, nitrate nitrogen, available phosphorus, calcium, magnesium, potassium, and cation exchange capacity in soil amended with BSFCOF compared to unamended soil. This study demonstrates that BSFCOF fortified with 5% chitin is an effective soil enhancer with multiple benefits, including improved soil fertility, potato performance, and effective management of potato cyst nematodes., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Anedo, Beesigamukama, Mochoge, Korir, Haukeland, Cheseto, Subramanian, Kelemu and Tanga.)

Acidic soils pose a major challenge for crop production in heavily weathered tropical soils, especially due to the high toxicity of aluminum (Al), low cation exchange capacity, and low availability of phosphorus (P) to plants. Lime application was recommended to alleviate soil acidity problems. Granular CaCO 3 lime was introduced into the Kenyan market as an alternative to powdered CaCO 3 and CaO-lime for small Kenyan farms, providing uniform distribution and efficient application. The aim of this study was therefore to investigate the effectiveness of different types of powdered and granular lime individually and in combination with mineral fertilizers in improving soil properties and maize yield. The study was conducted at two sites, Kirege (extremely acidic) and Kangutu (moderately acidic). Experiments were conducted in a randomized complete block design repeated four times in two consecutive seasons: long rain (LR) in 2016 and short rain (SR) in 2016. Three types of lime were applied before planting. Selected chemical properties of the soil were analyzed before and after the experiment. Maize and stover yield data were collected and analyzed. Results showed that lime application significantly increased soil pH and decreased exchangeable acidity. Powdered calcium carbonate (CaCO 3 ) showed the highest pH increase in both extreme (+19%) and moderate (+14%) acid sites. All types of lime and fertilizer applications alone significantly increased the available soil P at both the seasonal and site levels. However, maize grain yield was lower with fertilizer alone or lime alone than with lime and fertilizer combination. Powdered CaCO 3 + fertilizer was found to give the highest grain yields on both very acidic (5.34 t ha -1 ) and moderately (3.71 t ha -1 ) acid sites. In the study, combining powdered CaCO 3 lime with fertilizers was most effective in improving acidic soils by decreasing soil acidity and increasing available phosphorus, which ultimately increased grain yield. The results of this study recommend the use of powdered CaCO 3 as an effective and practical solution for farmers facing soil acidification problems., Competing Interests: The authors declare the following financial interests/personal relationships which may be considered as potential competing interests:Peter Kibet reports equipment, drugs, or supplies was provided by Alliance for a Green Revolution in Africa., (© 2023 The Authors.)

Worldwide, French beans ( Phaseolus vulgaris L.), tomato ( Solanum lycopersicum L.), and kales ( Brassica oleracea L. var. acephala ) are considered economically important food crops. There is a rapid decline in their yield due to severe soil degradation. Thus, high commercial fertilizer inputs are crucial, though they remain expensive and inaccessible to resource poor farmers. We investigated the comparative performance of composted black soldier fly frass fertilizer (BSFFF), conventionally composted brewer's spent grain (BSG), commercial organic fertilizer (Evergrow), and mineral [nitrogen, phosphorus, and potassium (NPK)] fertilizer on growth, yield, N use efficiency, and nutritional quality (crude protein, crude fiber, crude fats, ash, and carbohydrate concentrations) of tomatoes, kales, and French beans under greenhouse and open-field conditions for two seasons. The fertilizers were applied at rates equivalent to 371 kg of N ha -1 . For each crop, the plots were treated with sole rates of BSFFF, BSG, Evergrow, and NPK to supply 100% of the N required. Additional treatments included a combination of BSFFF and NPK, and BSG and NPK so that each fertilizer supplies 50% of the N required. The control treatment consisted of unfertilized soil. Results show that vegetable yields achieved using a combination of BSFFF and NPK were 4.5, 2.4, and 5.4-folds higher than the yield from the control treatment for tomatoes, kales, and French beans, respectively. The combined application of BSFFF and NPK produced 22-135%, 20-27%, and 38-50% higher yields than sole NPK for tomatoes, kales, and French beans, respectively, under both greenhouse and open-field conditions. The highest agronomic N use efficiency was achieved in sole BSFFF-treated plots compared to sole BSG and Evergrow. The N taken up by the vegetables was significantly higher when BSFFF and NPK were integrated. Vegetables grown using a combination of BSFFF and NPK had the highest crude protein and ash concentrations. Our findings demonstrate that the integration of BSFFF and NPK in vegetable cropping systems at the recommended rate of 1.24 t ha -1 BSFFF and 322 kg ha -1 NPK would improve soil health, boost yield, and nutritional quality of vegetable crops., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Anyega, Korir, Beesigamukama, Changeh, Nkoba, Subramanian, van Loon, Dicke and Tanga.)

Efforts to recycle organic waste using black soldier fly (BSF) larvae into high-quality alternative protein ingredients in animal feeds and organic fertilizers have gained momentum worldwide. However, there is limited information on waste manipulation to increase nutrient retention for enhanced larval performance and frass fertilizer quality. In the present study, brewer's spent grain with a carbon to nitrogen (C/N) ratio of 11 (control) was amended with sawdust to obtain substrates with C/N ratios of 15, 20, 25 and 30. The effects of substrate C/N ratios on BSF larval yield, waste degradation, biomass conversion efficiency, compost maturity and nutrient levels of frass fertilizer were evaluated. Substrates amended with sawdust did not significantly affect waste degradation efficiency and biomass conversion rates of BSF larvae. The wet and dried larval yields were significantly higher for substrates with C/N ratio of 15 compared to the other amended substrates. An amended substrate with C/N ratio of 15 enhanced nutrients uptake by BSF larvae, and increased nitrogen (N) and phosphorus retention in frass compost by 21 and 15%, respectively. Compost maturation time was shortened to five weeks, as indicated by the stable C/N ratios and high seed germination indices. This study has demonstrated that the amendment of the substrate with sawdust to C/N ratio of 15 could generate compost with desirable nutrients for use as high-quality fertilizer for organic farming., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Black soldier fly frass fertilizer (BSFFF) is increasingly gaining momentum worldwide as organic fertilizer. However, research on its performance on crop production remains largely unknown. Here, we evaluate the comparative performance of BSFFF and commercial organic fertilizer (SAFI) on maize (H513) production. Both fertilizers were applied at the rates of 0, 2.5, 5, and 7.5 t ha -1 , and 0, 30, 60, and 100 kg nitrogen (N) ha -1 . Mineral fertilizer (urea) was also applied at 0, 30, 60 and 100 kg N ha -1 to establish the N fertilizer equivalence (NFE) of the organic fertilizers. Maize grown in plots treated with BSFFF had the tallest plants and highest chlorophyll concentrations. Plots treated with 7.5 t ha -1 of BSFFF had 14% higher grain yields than plots treated with a similar rate of SAFI. There was a 27% and 7% increase in grain yields in plots treated with 100 kg N ha -1 of BSFFF compared to those treated with equivalent rates of SAFI and urea fertilizers, respectively. Application of BSFFF at 7.5 t ha -1 significantly increased N uptake by up to 23% compared to the equivalent rate of SAFI. Likewise, application of BSFFF at 100 kg N ha -1 increased maize N uptake by 76% and 29% compared to SAFI and urea, respectively. Maize treated with BSFFF at 2.5 t ha -1 and 30 kg N ha -1 had higher nitrogen recovery efficiencies compared to equivalent rates of SAFI. The agronomic N use efficiency (AE N ) of maize treated with 2.5 t ha -1 of BSFFF was 2.4 times higher than the value achieved using an equivalent rate of SAFI. Also, the AE N of maize grown using 30 kg N ha -1 was 27% and 116% higher than the values obtained using equivalent rates of SAFI and urea fertilizers, respectively. The NFE of BSFFF (108%) was 2.5 times higher than that of SAFI. Application rates of 2.5 t ha -1 and 30 kg N ha -1 of BSFFF were found to be effective in improving maize yield, while double rates of SAFI were required. Our findings demonstrate that BSFFF is a promising and sustainable alternative to commercial fertilizers for increased maize production., (Copyright © 2020 Beesigamukama, Mochoge, Korir, Fiaboe, Nakimbugwe, Khamis, Subramanian, Dubois, Musyoka, Ekesi, Kelemu and Tanga.)

Black soldier fly (BSF) (Hermetia illucens L.) is one of the most efficient bio-waste recyclers. Although, waste substrate amendments with biochar or gypsum during composting process are known to enhance nutrient retention, their impact on agro-industrial waste have not been documented. Hence, this study focuses on a comparative effect of agro-industrial waste amended with biochar and gypsum on BSF larval performance, waste degradation, and nitrogen (N) and potassium retention in frass fertilizer. Brewery spent grain was amended with biochar or gypsum at 0, 5, 10, 15 and 20% to determine the most effective rates of inclusion. Amending feedstock with 20% biochar significantly increased wet (89%) and dried (86%) larval yields than the control (unamended feedstock). However, amendment with 15% gypsum caused decrease in wet (34%) and dried (30%) larval yields but conserved the highest amount of N in frass. Furthermore, the inclusion of 20% biochar recorded the highest frass fertilizer yield and gave a 21% increase in N retention in frass fertilizer, while biomass conversion rate was increased by 195% compared to the control. Feedstock amendment with 5% biochar had the highest waste degradation efficiency. Potassium content in frass fertilizer was also significantly enhanced with biochar amendment. At maturity, frass compost with more than 10% inclusion rate of biochar had the highest cabbage seed germination indices (>100%). The findings of this study revealed that initial composting of biochar amended feedstocks using BSF larvae can significantly shorten compost maturity time to 5 weeks with enhanced nutrient recycling compared to the conventional composting methods., Competing Interests: The authors have declared that no competing interests exist.

MicroRNAs (miRNAs) are a group of non-coding RNAs that have functions in post-transcriptional gene regulation in plants. Although the most important economic component of peach trees (Prunus persica) is the fruit, not much is known about miRNAs in this organ. In this study, miRNAs and their targets were identified and characterized from libraries of small RNAs of peach fruit through Solexa based-sequencing and bioinformatics approaches. A total of 557 known peach miRNAs belonging to 34 miRNA families were identified, and some of these miRNAs were found to be highly conserved in at least four other plant species. Using the most current criteria for miRNA annotation, 275 putative novel miRNAs were predicted, and the sequencing frequencies of these novel miRNAs were less than those of the conserved miRNAs. In total, 3959 and 1614 target genes for 349 known and 193 novel miRNAs, respectively, were predicted with the criteria that a single target gene can be targeted by different miRNAs and that a single miRNA can also have a large number of target genes. Three targets were even found to be targeted by 13 novel miRNAs that contained the same complete miRNA sequence at different locations and had different scaffolds. The proteins predicted to be targeted by the miRNAs identified in this study encompass a wide range of transcription factors and are involved in many biological processes and pathways, including development, metabolism, stress responses and signal transduction. A total of 115 and 101 target genes were identified to be cleaved by 60 known miRNAs and 27 novel miRNAs through degradome sequencing, respectively. These miRNAs induce cleavage of their targets precisely at the position between nucleotides 10 and 11 of the miRNA sequences from the 5' to the 3' end. Thirty conserved miRNAs and 19 novel miRNAs exhibited differential expression profiles in the peach, and the expression patterns of some miRNAs appeared to be tissue- or developmental stage-specific. The findings of this study provide an important basis for the analysis of miRNAs, their targets and the functions of these targets in peach fruit.

Developments in the field of molecular biology and genetics, such as microarray, gene transfer and discovery of small regulatory RNAs, have led to significant advances in plant biotechnology. Among the small RNAs, microRNAs (miRNAs) have elicited much interest as key post-transcriptional regulators in eukaryotic gene expression. Advances in genome and transcriptome sequencing of plants have facilitated the generation of a huge wealth of sequence information that can find much use in the discovery of novel miRNAs and their target genes. In this review, we present an overview of the developments in the strategies and methods used to identify and study miRNAs, their target genes and the mechanisms by which these miRNAs interact with their target genes since the discovery of the first miRNA. The approaches discussed include both reverse and forward genetics. We observed that despite the availability of advanced methods, certain limitations ranging from the cost of materials, equipment and personnel to the availability of genome sequences for many plant species present a number of challenges for the development and utilization of modern scientific methods for the elucidation and development of miRNAs in many important plant species., (© 2014 Scandinavian Plant Physiology Society.)

In this study, 33 homeodomain-leucine zipper (HD-ZIP) genes were identified in peach using the HD-ZIP amino acid sequences of Arabidopsis thaliana as a probe. Based on the phylogenetic analysis and the individual gene or protein characteristics, the HD-ZIP gene family in peach can be classified into 4 subfamilies, HD-ZIP I, II, III, and IV, containing 14, 7, 4, and 8 members, respectively. The most closely related peach HD-ZIP members within the same subfamilies shared very similar gene structure in terms of either intron/exon numbers or lengths. Almost all members of the same subfamily shared common motif compositions, thereby implying that the HD-ZIP proteins within the same subfamily may have functional similarity. The 33 peach HD-ZIP genes were distributed across scaffolds 1 to 7. Although the primary structure varied among HD-ZIP family proteins, their tertiary structures were similar. The results from this study will be useful in selecting candidate genes from specific subfamilies for functional analysis.

In plants, microRNAs (miRNAs) play significant roles in post-transcriptional gene regulation and have been found to control many genes involved in different biological and metabolic processes. Extensive studies were carried out to discover miRNAs and analyze their functions in model plant species, such as in Arabidopsis and rice that have been reported. In this research, we used bioinformatics to predict microRNAs in an important strawberry rootstock cultivar to discover and validate precise sequences of microRNAs in strawberry. By adopting a range of filtering criteria, we obtained 59 potential miRNAs belonging to 40 miRNA families from the Fragaria vesca genome. Using two specific 5' and 3' miRNA RACE PCR reactions and a sequence-directed cloning method, we accurately determined 34 precise sequences of candidate miRNAs, while six other sequences exhibited some minor divergence in their termini nucleotides, and 19 miRNAs that could not be cloned owing to expression abundance may be too low or these mirRNAs predicted could not be existing in strawberry. Potential target genes were further predicted for the miRNAs above. The expression of the 16 miRNAs unreported and having exact sequences and their targets by experiment could be detected in different tissues of strawberry ranging from roots, stems, leaves, flowers and fruits by qRT-PCR and some of them showed differential expression in various tissues. The functional analysis of 16 miRNAs and their targets was carried out. Finally, we conclude that there are 34 mirRNAs in strawberry and their targets play vital roles not only in growth and development, but also in diverse physiological processes. These results show that regulatory miRNAs exist in agronomically important strawberry and might have an important function in strawberry growth and development., (Copyright © 2013 Elsevier B.V. All rights reserved.)

The genetic diversity and relationship of 42 tomato varieties sourced from different geographic regions was examined with EST-SSR markers. The genetic diversity was between 0.18 and 0.77, with a mean of 0.49; the polymorphic information content ranged from 0.17 to 0.74, with a mean of 0.45. This indicates a fairly high degree of diversity among these tomato varieties. Based on the cluster analysis using unweighted pair-group method with arithmetic average (UPGMA), all the tomato varieties fell into 5 groups, with no obvious geographical distribution characteristics despite their diverse sources. The principal component analysis (PCA) supported the clustering result; however, relationships among varieties were more complex in the PCA scatterplot than in the UPGMA dendrogram. This information about the genetic relationships between these tomato lines helps distinguish these 42 varieties and will be useful for tomato variety breeding and selection. We confirm that the EST-SSR marker system is useful for studying genetic diversity among tomato varieties. The high degree of polymorphism and the large number of bands obtained per assay shows that SSR is the most informative marker system for tomato genotyping for purposes of rights/protection and for the tomato industry in general. It is recommended that these varieties be subjected to identification using an SSR-based manual cultivar identification diagram strategy or other easy-to-use and referable methods so as to provide a complete set of information concerning genetic relationships and a readily usable means of identifying these varieties.

MicroRNAs (miRNAs) regulate target gene expression by mediating target gene cleavage or inhibition of translation at transcriptional and post-transcriptional levels in higher plants. Until now, many grapevine microRNAs (Vv-miRNAs) have been identified and quite a number of miRNA target genes were also verified by various analysis. However, global interaction of miRNAs with their target genes still remained to perform more research. We reported experimental validation of a number of miRNA target genes in table grapevine that had been previously identified by bioinformatics in our earlier studies. To verify more predicted target genes of Vv-miRNAs and elucidate the modes by which these Vv-miRNAs work on their target genes, 31 unverified potential target genes for 18 Vv-miRNAs were experimentally verified by a new integrated strategy employing a modified 5'-RLM-RACE (RNA ligase-mediated 5' rapid amplification of cDNA ends), 3'-PPM-RACE (poly(A) polymerase-mediated 3' rapid amplification of cDNA ends) and qRT-PCRs of cleavage products. The results showed that these Vv-miRNAs negatively regulated expression of their target messenger RNAs (mRNAs) through guiding corresponding target mRNA cleavage, of which about 94.4% Vv-miRNAs cleaved their target mRNAs mainly at the tenth nucleotide of 5'-end of miRNAs. Expression levels of both miRNAs and their target mRNAs in eight tissues exhibited inverse relationships, and expressions both of cleaved targets and miRNAs indicated a cleavage mode of Vv-miRNAs on their target genes. Our results confirm the importance of Vv-miRNAs in grapevine growth and development, and suggest more study on Vv-miRNAs and targets can enrich the knowledge of miRNA mediated-regulation in grapevine., (Copyright © 2013 Elsevier GmbH. All rights reserved.)

Tomato breeding and variety development have led to the generation of a large number of varieties in many countries worldwide. This has created a growing and urgent need for an improved strategy for genotyping and identification since the traditional methods based on phenotype are growing unreliable. DNA markers could provide distinct benefits in tomato variety identification; however, DNA fingerprint analyses have not made DNA marker data readily usable for identification of varieties in tomato and other crops. A manual cultivar and/or variety identification diagram (MCID) strategy has been developed and has been found to make DNA markers more usable for the identification of genotyped plant individuals. We adopted this strategy, using modified RAPD markers to identify 42 tomato varieties from different geographical origins and seed merchants. All of the varieties were clearly separated and individually identified by reproducible fingerprints of only 6 RAPD primers. The tomato MCID that is generated is usable for the identification of any two or more tomato varieties. In addition, fewer primers can be used to make a distinction between varieties using this approach, since the selected fingerprints from each primer are used after they have been generated. The information in this first version of the tomato MCID can be enriched through identification and incorporation of more varieties and adaptation to other molecular markers in order to provide a more comprehensive tomato variety identification service for the horticultural industry.

In plant and animal species FK506-binding protein (FKBP) family genes are important conserved genes and it is defined as the receptors of FK506 and rapamycin, where they work as PPIase and protein folding chaperones. FKBP have been isolated from Arabidopsis thaliana, Oryza sativa, and Zea mays. In grape, twenty-three genes containing the FK506-binding domain (FKBP_C) were first time identified by HMMER and blast research, they were classified into three groups and 17 out of the 23 genes were located on 11 chromosomes (Chr1, 3, 5, 7, 8, 14, 15, 16, 17, 18, and 19). The predicted gene expression pattern and semi-quantitative RT-PCR results revealed that five VvFKBPs were expressed in all tissues, while seven VvFKBPs were expressed only in some of the tissues, and the remaining VvFKBPs were not expressed in leaf, stem, inflorescences, flowers, and a mixture of fruit tissues (small, medium and big-sized fruits). Most of the VvFKBPs in grapevine 'Summer Black' were similar to those predicted one in 'Pinot Noir' except for VvFKBP16-4 and VvFKBPa. VvFKBP12, FaFKBP12 and PpFKBP12 were cloned from 'Summer Black', 'Sweet Charlie' and 'Xiahui 6'. Protein structure analysis confirmed that homologous genes have some differences during the process of protein structure construction. In this study, we characterized and verified 23 FKBP family genes in grapevine (Vitis vinifera L.) as well as their sub-cellular and chromosome location. The successful cloning of CDS regions and protein structural analysis of VvFKBP12, FaFKBP12, and PpFKBP12 can provide useful information for further study.

Plant variety and cultivar identification is one of the most important aspects in agricultural systems. The large number of varieties or landraces among crop plants has made it difficult to identify and characterize varieties solely on the basis of morphological characters because they are non stable and originate due to environmental and climatic conditions, and therefore phenotypic plasticity is an outcome of adaptation. To mitigate this, scientists have developed and employed molecular markers, statistical tests and software to identify and characterize the required plant cultivars or varieties for cultivation, breeding programs as well as for cultivar-right-protection. The establishment of genome and transcriptome sequencing projects for many crops has led to generation of a huge wealth of sequence information that could find much use in identification of plants and their varieties. We review the current status of plant variety and cultivar identification, where an attempt has been made to describe the different strategies available for plant identification. We have found that despite the availability of methods and suitable markers for a wide range of crops, there is dearth of simple ways of making both morphological descriptors and molecular markers easy, referable and practical to use although there are ongoing attempts at making this possible. Certain limitations present a number of challenges for the development and utilization of modern scientific methods in variety or cultivar identification in many important crops.

Presence of selected tomato (Solanum lycopersicon) microRNAs (sly-miRNAs) was validated and their expression profiles established in roots, stems, leaves, flowers and fruits of tomato variety Jiangshu14 by quantitative RT-PCR (qRT-PCR). In addition conservation characteristics these sly-miRNAs were analyzed and target genes predicted bioinformatically. Results indicate that some of these miRNAs are specific to tomato while most are conserved in other plant species. Predicted sly-miRNA targets genes were shown to be targeted by either by a single or more miRNAs and are involved in diverse processes in tomato plant growth and development. All the 36 miRNAs were present in the cDNA of mixed tissues and qRT-PCR revealed that some of these sly-miRNAs are ubiquitous in tomato while others have tissue-specific expression. The experimental validation and expression profiling as well target gene prediction of these miRNAs in tomato as done in this study can add to the knowledge on the important roles played by these sly-miRNAs in the growth and development, environmental stress tolerance as well as pest and disease resistance in tomatoes and related species. In addition these findings broaden the knowledge of small RNA-mediated regulation in S. lycopersicon. It is recommended that experimental validation of the target genes be done so as to give a much more comprehensive information package on these miRNAs in tomato and specifically in the selected variety.

Microarray analysis is a technique that can be employed to provide expression profiles of single genes and new insights to elucidate the biological mechanisms responsible for fruit development. To evaluate expression of genes mostly engaged in fruit development between Prunus mume and Prunus armeniaca, we first identified differentially expressed transcripts along the entire fruit life cycle by using microarrays spotted with 10,641 ESTs collected from P. mume and other Prunus EST sequences. A total of 1418 ESTs were selected after quality control of microarray spots and analysis for differential gene expression patterns during fruit development of P. mume and P. Armeniaca. From these, 707 up-regulated and 711 down-regulated genes showing more than two-fold differences in expression level were annotated by GO based on biological processes, molecular functions and cellular components. These differentially expressed genes were found to be involved in several important pathways of carbohydrate, galactose, and starch and sucrose metabolism as well as in biosynthesis of other secondary metabolites via KEGG. This could provide detailed information on the fruit quality differences during development and ripening of these two species. With the results obtained, we provide a practical database for comprehensive understanding of molecular events during fruit development and also lay a theoretical foundation for the cloning of genes regulating in a series of important rate-limiting enzymes involved in vital metabolic pathways during fruit development., (Copyright © 2012 Elsevier GmbH. All rights reserved.)

We identified 131 AP2/ERF (APETALA2/ethylene-responsive factor) genes in material from peach using the gene sequences of AP2/ERF amino acids of Arabidopsis thaliana (Brassicaceae) as probes. Based on the number of AP2/ERF domains and individual gene characteristics, the AP2/ERF superfamily gene in peach can be classified broadly into three families, ERF (ethylene-responsive factor), RAV (related to ABI3/VP1), and AP2 (APETALA2), containing 104, 5, and 21 members, respectively, along with a solo gene (ppa005376m). The 104 genes in the ERF family were further divided into 11 groups based on the group classification made for Arabidopsis. The scaffold localizations of the AP2/ERF genes indicated that 129 AP2/ERF genes were all located on scaffolds 1 to 8, except for two genes, which were on scaffolds 17 and 10. Although the primary structure varied among AP2/ERF superfamily proteins, their tertiary structures were similar. Most ERF family genes have no introns, while members of the AP2 family have more introns than genes in the ERF and RAV families. All sequences of AP2 family genes were disrupted by introns into several segments of varying sizes. The expression of the AP2/ERF superfamily genes was highest in the mesocarp; it was far higher than in the other seven tissues that we examined, implying that AP2/ERF superfamily genes play an important role in fruit growth and development in the peach. These results will be useful for selecting candidate genes from specific subgroups for functional analysis.

MicroRNAs (miRNAs) are an extensive class of newly identified small RNAs that regulate gene expression at post-transcription level by mRNA cleavage or translation. In our study, we used qRT-PCR and found that Vv-miR164 is expression in grapevine leaves, stems, tendrils, inflorescences, flowers and fruits. In addition, two potential target genes for Vv-miR164 were also found and verified by PPM-RACE and RLM-RACE. The results not only maps the cleavage site of the target mRNA but allowed for detection the expression pattern of cleaved fragments that can indicate the regulatory function of this miRNA on its target genes. These target genes were explored by qRT-PCR where some exhibited different expression patterns from their corresponding miRNA, indicating the cleavage mode of the miRNA on its target genes. The efficient and powerful approach used in this study can help in further understanding of how miRNAs cleaved their target mRNAs. Results from this study prove the importance of Vv-miR164 in regulating development and growth of grapes, and adds to the existing knowledge of small RNA-mediated regulation in grapes.

Background: MicroRNAs (miRNAs) play a critical role in post-transcriptional gene regulation and have been shown to control many genes involved in various biological and metabolic processes. There have been extensive studies to discover miRNAs and analyze their functions in model plant species, such as Arabidopsis and rice. Deep sequencing technologies have facilitated identification of species-specific or lowly expressed as well as conserved or highly expressed miRNAs in plants., Results: In this research, we used Solexa sequencing to discover new microRNAs in trifoliate orange (Citrus trifoliata) which is an important rootstock of citrus. A total of 13,106,753 reads representing 4,876,395 distinct sequences were obtained from a short RNA library generated from small RNA extracted from C. trifoliata flower and fruit tissues. Based on sequence similarity and hairpin structure prediction, we found that 156,639 reads representing 63 sequences from 42 highly conserved miRNA families, have perfect matches to known miRNAs. We also identified 10 novel miRNA candidates whose precursors were all potentially generated from citrus ESTs. In addition, five miRNA* sequences were also sequenced. These sequences had not been earlier described in other plant species and accumulation of the 10 novel miRNAs were confirmed by qRT-PCR analysis. Potential target genes were predicted for most conserved and novel miRNAs. Moreover, four target genes including one encoding IRX12 copper ion binding/oxidoreductase and three genes encoding NB-LRR disease resistance protein have been experimentally verified by detection of the miRNA-mediated mRNA cleavage in C. trifoliata., Conclusion: Deep sequencing of short RNAs from C. trifoliata flowers and fruits identified 10 new potential miRNAs and 42 highly conserved miRNA families, indicating that specific miRNAs exist in C. trifoliata. These results show that regulatory miRNAs exist in agronomically important trifoliate orange and may play an important role in citrus growth, development, and response to disease.