BackgroundMicroRNAs (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.ResultsIn 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.ConclusionDeep 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.

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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.

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.

Fruit skin coloration is a unique phase in the life cycle of fruiting plants and is mainly attributed to anthocyanin pigments. Anthocyanins are the largest and most diverse group of plant pigments derived from the phenyl propanoid pathway. They are water-soluble phenolic compounds that form part of a large and common group of plant flavonoids. Coloration encompasses several physiological and biochemical changes that happen through differential expression of various developmentally regulated genes. Due to research importance and economic value, Arabidopsis thaliana (chromosome no. = 5) and Vitis vinifera (chromosome no. = 19) have been used for investigations of the structural genes involved in anthocyanin biosynthesis. Thus for this review, V. vinifera is used as a model crop. In anthocyanin biosynthesis, a wide range of constructive genes including phenylalanine ammonia lyase, chalcone synthase and anthocyanidin synthase that are regulated by MYB transcription factors are involved. These genes are coordinately expressed and their levels of expression are positively related to the anthocyanin concentrations. Expression or suppression of the constructive genes contributes to a variety of changes that make fruits visually attractive and edible. Transgenic approaches also have discovered a strong relationship between phenyl propanoid/flavonoid gene expressions for fruit skin coloration. In this study, various developments that have taken place in the last decade with respect to identifying and altering the function of color-related genes are described.

ABSTRACT. We identified 131 AP2/ERF (APETALA2/ethyleneresponsive 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 gene superfamily 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 C.H. Zhang et al. ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research (2012) Ahead of Print 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.

The use of black soldier fly frass fertilizer (BSFFF) is being promoted globally. However, information on nitrogen (N) fertilizer equivalence (NFE) value and synchrony of N mineralization for crop production remains largely unknown. Comparative studies between BSFFF and commercial organic fertilizer (SAFI) were undertaken under field conditions to determine synchrony of N release for maize uptake. The BSFFF, SAFI, and urea fertilizers were applied at the rates of 0, 30, 60, and 100 kg N ha−1. The yield data from urea treated plots were used to determine the NFE of both organic inputs. Results showed that maize from BSFFF treated plots had higher N uptake than that from SAFI treated plots. High N immobilization was observed throughout the active growth stages of maize grown in soil amended with BSFFF, whereas soil treated with SAFI achieved net N release at the silking stage. Up to three times higher negative N fluxes were observed in SAFI amended soils as compared with BSFFF treated plots at the tasseling stage. The BSFFF applied at 30 and 60 kg N ha−1 achieved significantly higher NFE than all SAFI treatments. Our findings revealed that BSFFF is a promising and sustainable alternative to SAFI or urea for enhanced maize production.

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.