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Copyright of Revista de la Academia Colombiana de Ciencias Exactas, Físicas y Naturales is the property of Academia Colombiana de Ciencias Exactas, Fisicas y Naturales and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein (Cas)-mediated genome editing has greatly accelerated progress in plant genetic research and agricultural breeding by enabling targeted genomic modifications. Moreover, the prime editing system, derived from the CRISPR/Cas system, has opened the door for even more precise genome editing. Prime editing has the capability to facilitate all 12 types of base-to-base conversions, as well as desired insertions or deletions of fragments, without inducing double-strand breaks and requiring donor DNA templet. In a short time, prime editing has been rapidly verified as functional in various plants, and can be used in plant genome functional analysis as well as precision breeding of crops. In this review, we summarize the emergence and development of prime editing, highlight recent advances in improving its efficiency in plants, introduce the current applications of prime editing in plants, and look forward to future prospects for utilizing prime editing in genetic improvement and precision molecular breeding. [ABSTRACT FROM AUTHOR]

In a recent article, we presented evidence demonstrating the existence of hidden γ-stories within the genomes of humans and canines. These stories were found not only in the non-protein-coding regions but also within the genetic regions and the sequence of exons. Consequently, we are now exploring whether these discoveries are unique to humans and dogs or if they are more widely distributed throughout the cellular world. To approach this question, we embarked on an investigation of the genomes of various species across Whittaker's five kingdoms, namely Animalia, Plantae, Fungi, Protista, and Monera. Through online resources, we obtained and analysed whole-genome sequences of one avian species, one fish species, one reptile species, and one invertebrate species within the Animalia kingdom. Furthermore, we examined the genomes of one plant species, one fungus species, one protozoan species, and two bacterial species. Employing the same methods as in our prior studies, our findings in this study align with our proto knowledge hypothesis, suggesting that all living cells possess a repository of hidden γ-information which determines the cellular design, sustains its overall functionality, and governs its performance and behaviour throughout its lifespan until death. We briefly explain life as a bio-linguistic phenomenon and future projects. [ABSTRACT FROM AUTHOR]

[Display omitted] • The study presents chromosome-length genome assemblies of six legume species. • Evolutionary events that shaped the present day legumes are inferred. • Expansion of gene families contributing to unique traits in legumes is explored. • Demonstrated the utility of improved assemblies as better references. Legume crops are an important source of protein and oil for human health and in fixing atmospheric N 2 for soil enrichment. With an objective to accelerate much-needed genetic analyses and breeding applications, draft genome assemblies were generated in several legume crops; many of them are not high quality because they are mainly based on short reads. However, the superior quality of genome assembly is crucial for a detailed understanding of genomic architecture, genome evolution, and crop improvement. Present study was undertaken with an objective of developing improved chromosome-length genome assemblies in six different legumes followed by their systematic investigation to unravel different aspects of genome organization and legume evolution. We employed in situ Hi-C data to improve the existing draft genomes and performed different evolutionary and comparative analyses using improved genome assemblies. We have developed chromosome-length genome assemblies in chickpea, pigeonpea, soybean, subterranean clover, and two wild progenitor species of cultivated groundnut (A. duranensis and A. ipaensis). A comprehensive comparative analysis of these genome assemblies offered improved insights into various evolutionary events that shaped the present-day legume species. We highlighted the expansion of gene families contributing to unique traits such as nodulation in legumes, gravitropism in groundnut, and oil biosynthesis in oilseed legume crops such as groundnut and soybean. As examples, we have demonstrated the utility of improved genome assemblies for enhancing the resolution of " QTL-hotspot " identification for drought tolerance in chickpea and marker-trait associations for agronomic traits in pigeonpea through genome-wide association study. Genomic resources developed in this study are publicly available through an online repository, 'Legumepedia'. This study reports chromosome-length genome assemblies of six legume species and demonstrates the utility of these assemblies in crop improvement. The genomic resources developed here will have significant role in accelerating genetic improvement applications of legume crops. [ABSTRACT FROM AUTHOR]

Background: DNA markers improved the productivity and accuracy of classical plant breeding by means of marker-assisted selection (MAS). The enormous number of quantitative trait loci (QTLs) mapping read for different plant species have given a plenitude of molecular marker-gene associations. In this review, we have discussed the positive aspects of molecular marker-assisted selection and its precise applications in plant breeding programmes. Molecular marker-assisted selection has considerably shortened the time for new crop varieties to be brought to the market. To explore the information about DNA markers, many reviews have been published in the last few decades; all these reviews were intended by plant breeders to obtain information on molecular genetics. In this review, we intended to be a synopsis of recent developments of DNA markers and their application in plant breeding programmes and devoted to early breeders with little or no knowledge about the DNA markers. The progress made in molecular plant breeding, plant genetics, genomics selection, and editing of genome contributed to the comprehensive understanding of DNA markers and provides several proofs on the genetic diversity available in crop plants and greatly complemented plant breeding devices. Short conclusion: MAS has revolutionized the process of plant breeding with acceleration and accuracy, which is continuously empowering plant breeders around the world. [ABSTRACT FROM AUTHOR]

We present the complete genome sequences of 3 Erwinia rhapontici strains, MAFF 311153, 311154, and 311155. These chromosome sequences contained variety types of luxI / luxR gene pair involved in acylhomoserine lactone biosynthesis and reception. Large-scale insertion sequence was observed in the indigenous plasmid of MAFF 311154 and contained eraI3 / eraR3 gene pair that make possible to produce acylhomoserine lactone. [ABSTRACT FROM AUTHOR]

The Australian tree malletwood (Rhodamnia argentea) is unique. The genome of malletwood is the only known plant genome that contains a gene coding for an α‐actinin‐like protein. Several organisms predating the animal‐plant bifurcation express an α‐actinin or α‐actinin‐like protein. Therefore, it appears that plants in general, but not malletwood, have lost the α‐actinin or α‐actinin‐like gene during evolution. In order to characterize its structure and function, we synthesized the gene and expressed the recombinant R. argentea protein. The results clearly show that this protein has all properties of genuine α‐actinin. The N‐terminal actin‐binding domain (ABD), with two calponin homology motifs, is very similar to the ABD of any α‐actinin. The C‐terminal calmodulin‐like domain, as well as the intervening rod domain, are also similar to the corresponding regions in other α‐actinins. The R. argentea α‐actinin‐like protein dimerises in solution and thereby can cross‐link actin filaments. Based on these results, we believe the R. argentea protein represents a genuine α‐actinin, making R. argentea unique in the plant world. [ABSTRACT FROM AUTHOR]

Transgenic walnuts (Juglans regia L.) were produced in the presence of the Agrobacterium strain LBA4404 and the plasmid pBI121. This plasmid contains a BADH gene driven by a CaMV 35S promoter. It further includes an NPTII gene as a selectable marker which, in turn, is driven by a NOS promoter. Somatic embryos of the walnut cultivar 'Chandler' were inoculated using an Agrobacterium suspension. Secondary embryos that developed on a selection medium were driven towards germination so as to develop micro-shoot cultures. The regeneration rate was 5.5%. PCRand southern blot analysis were used for confirming that the BADH transgene is successfully integrated into the plant genome. Transgenic and wild-type plants raised from somatic embryos were exposed to four osmotic stress levels (i.e. 0%, 2%, 4%, and 8% PEG) and four salinity levels (i.e. 0, 50, 100, and 200 mM NaCl). After 21 days, the transgenic plants grew almost vigorously in saline and drought-stress conditions, whereas the wild-type ones showed retarded levels of growth and did not survive after the cradle stage. These results show that the BADH gene can be expressed effectively in transgenic plantlets of walnut and can be used for breeding walnuts against drought and salinity. [ABSTRACT FROM AUTHOR]

The 2020 Nobel Prize for Chemistry has been awarded for research on bacterial defense against viruses and plasmids, popularly known as CRISPR/Cas9 system. One half of the Prize has been awarded to Professor Emmanuelle Charpentier of the Max Planck Unit for the Science of Pathogens (Berlin, Germany), and the other half to Professor Jennifer A. Doudna of the University of California (Berkeley, USA). These two scientists have dedicated their research to understanding the molecular mechanisms of CRISPR/Cas9 function in bacteria and for facilitating their use as genome editing tools in animals and plants. [ABSTRACT FROM AUTHOR]

To evaluate crops generated by new breeding techniques, it is important to confirm the removal of recombinant DNAs (rDNAs) derived from foreign genes including unintentionally introduced short rDNA(s). We attempted to develop a sensitive detection method for such short rDNAs using Southern blot analysis and performed a model study targeting single-copy endogenous genes in plants. To increase the detection sensitivity, the general protocol for Southern blot analysis was modified. In the model study, we used endogenous-gene-targeting probes in which complementary sequences were serially replaced by dummy sequences, and detected complementary sequences as well as 30 bp. We further evaluated the sensitivity using short rDNAs derived from GM sequences as pseudoinsertions, and the results demonstrated that rDNA-insertions as small as 30 bp could be detected. The results suggested that unintentionally introduced rDNA-insertions were 30 bp or more in length could be detected by the Southern blot analysis. Short sequences, equal to or longer than 30 bp, could be detected by a modified Southern blot analysis. The method would be used for an evaluation of crops generated by new breeding techniques. [ABSTRACT FROM AUTHOR]

Three transgenic soybean lines expressing the Cry1Ia5 gene were developed using the Agrobacterium transformation system. The integration of the Cry1Ia5 gene in the genome of the transgenic plants was approved using specific primers for PCR and real time PCR analysis, respectively. The insecticidal activity of three transgenic lines (L1, L2 and L3) against 2nd larval instars Spodoptera littoralis was tested. The data indicate that L2 exhibited the highest mortality percentage 9 days post feeding (60%) followed by L3 (40%) then L1 (20%) while the control showed 0% mortality. The larvae fed transgenic material appeared smaller in size than compared to the control larvae. The reduction in insect size and weight was due to the accumulation of higher phenoloxidase activity in insect tissues. The higher mortality observed in L2 was due to a significant decrease in the acetylcholine esterase activity that leads to accumulation of acetylcholin at higher levels which causes paralysis and death. The developed transgenic line 2 could be used to construct an insect resistant soybean cultivar. [ABSTRACT FROM AUTHOR]

Increased plant genotypic diversity in crop fields can promote ecosystem services including pest control, but understanding of mechanisms behind herbivore population responses to cultivar mixtures is limited. We studied aphid settling on barley plants exposed to volatiles from different cultivars, aphid population development in monocultures and two‐cultivar mixtures, and differences in volatile composition between studied cultivars. Aphid responses to one cultivar in a mixture were neighbor‐specific and this was more important for pest suppression than the overall mixture effect, aphid colonization patterns, or natural enemy abundance. Aphid populations decreased most in a mixture where both cultivars showed a reduced aphid–plant acceptance after reciprocal volatile exposure in the laboratory, and reduced population growth compared to monocultures in the field. Our findings suggest that herbivore population responses to crop genotypic diversity can depend on plant–plant volatile interactions, which can lead to changes in herbivore response to individual cultivars in a mixture, resulting in slower population growth. The impact of plant–plant interaction through volatiles on associated herbivore species is rarely considered, but improved understanding of these mechanisms would advance our understanding of the ecological consequences of biodiversity and guide development of sustainable agricultural practices. Combining cultivars in mixtures based on how they interact with each other is a promising strategy for sustainable pest management. [ABSTRACT FROM AUTHOR]

Abstract The cross-genome transferability of 101 simple sequence repeats (SSR) markers of finger millet and 26 SSR markers of foxtail millet were analyzed in 8 other millets. In total, 33 finger millet and 2 foxtail millet SSR markers showed 100% cross-genome transferability in other millets. The cross-genome transferability of 101 finger millet and 26 foxtail millet SSR markers ranged from 47.52% to 61.38% and from 30.76% to 69.23% respectively. Expressed sequence tags SSR (EST-SSR) markers of finger millet showed higher level of cross-genome transferability than genomic SSR (gSSR) markers. The observed polymorphic information content (PIC) values were the same for finger millet and foxtail millet SSR markers which ranged from 0.14 to 1.00. Further, these data were also used for genetic diversity analysis among 8 millets using the software version 2.1 of NTSYSpc tool and PAST version 2. All millet species were grouped into one major cluster based on finger millet SSR markers, through UPGMA analysis. But two major clusters were observed by the analysis using foxtail millet SSR markers. Similarity value ranged from 0.238 to 0.714. Higher bootstrap values were observed in all cluster nodes. Successful analysis of genetic diversity was also confirmed by PCO and PCA analyses. This study would pave the way to understand the genetic structure of many nutritionally important millets lacking genomic resources. The SSR markers can also be used for further studies on analysis of genetic variation, population structure and germplasm characterization of millets. [ABSTRACT FROM AUTHOR]

Preservation of elite key lime (Citrus aurantifolia) genotypes using efficient micropropagation and regeneration protocols is very important for new breeding programmes. The objective of the present study was to develop an efficient protocol for micropropagation and maintenance of elite genotypes of key lime based on slow growth and starvation strategy. To do this, regenerated shoots were starved, and the growth was compromised via avoiding subcultures for 4, 8, 12 and 24 months. The numbers of responsive explants and adventitious shoots per each explant were evaluated in the presence of benzylaminopurine (BAP). The results showed that the 12- and 24-month starved explants treated with 1 mg/l BAP were able to produce four times more shoots than the control. In addition, the influences of horizontal or vertical layering explants over medium were evaluated. The results indicated that all horizontally layered explants significantly produced 25% adventitious shoots more than vertical explants, most likely owing to more contact with the surface medium. Finally, it could be concluded that application of slow growth, starvation strategy and also horizontally layering of the explants could efficiently enhance micropropagation and maintenance of threatened elite key lime genotypes with a low cost. [ABSTRACT FROM AUTHOR]

The occurrence of phosphoenolpyruvate carboxykinase (PEPCK) and pyruvate orthophosphate dikinase (PPDK) was determined in the ripe pericarps of several grape genotypes. Moreover, the abundance pattern of PEPCK during the development of grape berries was studied in a range of cultivars. In addition, the presence of PEPCK in grape leaves and the location/abundance of PEPCK in developing grape seeds were investigated. PEPCK was present in the pericarp of all the cultivars of Vitis vinifera studied and in that of the hybrid 420A (Vitis berlandieri × Vitis riparia). By contrast, PPDK was either not present or present at very low abundance. The results strongly indicated that the PEPCK and not the PPDK pathway is the predominant one utilised in gluconeogenesis in the berry pericarp of grape genotypes. Further, the results showed that the abundance of PEPCK increased greatly at the start of ripening in all the cultivars, showing a similar pattern in all of them. PEPCK was not present (or at very low abundance) in grape leaves throughout their development. In developing grape seeds, the results indicated a similar abundance of PEPCK in both the seed coat and the tissues enclosed by it. [ABSTRACT FROM AUTHOR]

Transgenic chrysanthemum plants harbouring the genes producing small interfering RNAs (siRNAs) whose sequence was designed based on the chrysanthemum stunt viroid (CSVd) genome were established. The siRNAs are expected to target and decompose CSVd RNA through a silencing mechanism. The CSVd-infected plants were grafted as scions onto the stocks of either non-transgenic or transgenic plants, and axial shoots that elongated from the stocks were rooted and grown to investigate if the plants are resistant to CSVd under greenhouse conditions. The non-transgenic plants infected with CSVd showed severe disease symptoms, i.e. stunted growth and spotty chlorotic lesions on leaves, but no such symptoms were observed in the transgenic plants. The real-time quantitative reverse transcription PCR for monitoring the amounts of CSVd indicated that CSVd equally accumulated in both non-transgenic and transgenic plants. The present results suggest that the resistant feature of the transgenic plants to CSVd was due to interference with the pathway of symptom development, and not the inhibition of CSVd replication. [ABSTRACT FROM AUTHOR]

Two Gram-positive, catalase-positive, oxidase-negative, motile, endospore-forming, rod-shaped bacteria, designated as 0911MAR22V3T and 0911TES10J4, were isolated from air samples collected in two show caves, located in Andalusia, Southern Spain. Phylogenetic analysis based on 16S rRNA gene sequences indicated that both strains were indistinguishable and they were most closely related to Bacillus humi DSM 16318T (98%). DNA–DNA hybridization values of the strain 0911MAR22V3T with respect to strain 0911TES10J4 and B. humi DSM 16318T were 76.8% (73.9%, reciprocal) and 56.9% (63.3%, reciprocal analysis), respectively. Whole genome average nucleotide identity (ANI) values of both strains were in the threshold value for species delineation and less than 85% with B. humi . Strains 0911MAR22V3T and 0911TES10J4 grew at 10–47 °C (optimum 37 °C), at pH 6–9.5 and with 0–8% (w/v) NaCl (optimum 1%). In both strains the dominant isoprenoid quinone was MK-7, the major cellular polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and two more phospholipids, the predominant fatty acids were iso-C15:0 and anteiso-C15:0 and the DNA G + C content was 38 mol%. On the basis of their phylogenetic relatedness and their phenotypic and genotypic features, the strains 0911MAR22V3T and 0911TES10J4 should be attributed to a novel species within the genus Bacillus, for which the name Bacillus onubensis sp. nov. is proposed. The type strain is 0911MAR22V3T (=LMG 27963T = CECT 8479T); and strain 0911TES10J4 (CECT 8478) is a reference strain. [ABSTRACT FROM AUTHOR]

Next-generation sequencing techniques provide a new insight into the genetic bases of the most important commercial traits in fruit trees. The genomic deep sequencing results of peach cultivar ‘Xiaobaitao’ and its bud variation type ‘Jinliuzaohong’ are reported here. The numbers of detected Single nucleotide polymorphisms (SNPs) in wild type and in mutant were 591,485 and 593,484, with that of InDel as 113,934 and 115,065, respectively. Interestingly, the numbers of SNPs and InDels that differentiate ‘Jinliuzaohong’ from ‘Xiaobaitao’ were 50,217 and 19,368, respectively. The number of genes with non-synonymous mutation was 887, which involved in 109 pathways. The authors found dozens of genes involved in the important commercial traits of peach fruit which are of variations in Coding sequence (CDS) regions, including 3 NAC family genes, i.e. NAC66, NAC68, and NAC78. The relevant commercial traits of peach fruit include colour coverage, maturity date, fruit size, and sugar content. A phylogenetic tree of homological NAC proteins indicated relationship among the species. Genome sequence data suggested that a series of genes and several genetic pathways were likely involved in the formation of the important traits in peach fruits. The findings provide new evidence for the functions of the candidate genes controlling peach fruit traits which were proposed previously by researchers using QTL analysis. [ABSTRACT FROM AUTHOR]

Plant genome stability can be altered by exposure to stress. Many stresses that are not directly mutagenic can alter genome stability. Our recent work showed that stresses such as salt, heat and drought can change the frequency of homologous recombination. We showed that exposure to stress triggers changes in methylation, and that these changes are important for the establishment of transgenerational response to stress. Here, we tested whether exposure to zebularine or 5-azaC, two chemicals interfering with normal cytosine methylation patterns, would destabilize the genome and lead to transgenerational changes. Exposure to both chemicals resulted in a dose-dependent decrease in global DNA methylation, with changes at symmetrical CNG cytosines being the most pronounced. The analysis of genome instability showed a dose-dependent increase in microsatellite instability and to a lesser degree in recombination frequency in somatic cells of exposed plants. The analysis of the progeny showed that the spontaneous non-induced recombination frequency was decreased in response to zebularine and did not change in response to 5-azaC, whereas the frequency of microsatellite instability increased profoundly in response to both chemicals. At the same time, the analysis of cytosine methylation in progeny of plants exposed to zebularine and 5-azaC showed a more pronounced decrease at CNG cytosines. Our work shows that the maintenance of DNA methylation is likely important for the prevention of microsatellite instability and that hypomethylation may affect genome stability in progeny differently in different genomic regions with genomic regions containing microsatellites being more prone to destabilization. [ABSTRACT FROM AUTHOR]

Copyright of Cryptogamie Mycologie is the property of Museum National d'Histoire Naturelle, Paris and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

SWEET proteins play an indispensable role as a sugar efflux transporter in plant development and stress responses. The SWEET genes have previously been characterized in several plants. Here, we present a comprehensive analysis of this gene family in the rubber tree, Hevea brasiliensis. There are 36 members of the SWEET gene family in this species, making it one of the largest families in plant genomes sequenced so far. Structure and phylogeny analyses of these genes in Hevea and in other species demonstrated broad evolutionary conservation. RNA-seq analyses revealed that SWEET2, 16, and 17 might represent the main evolutionary direction of SWEET genes in plants. Our results in Hevea suggested the involvement of HbSWEET1a, 2e, 2f, and 3b in phloem loading, HbSWEET10a and 16b in laticifer sugar transport , and HbSWEET9a in nectary-specific sugar transport. Parallel studies of RNA-seq analyses extended to three other plant species ( Manihot esculenta, Populus trichocarpa, and Arabidopsis thaliana) produced findings which implicated MeSWEET10a, 3a, and 15b in M. esculenta storage root development, and the involvement of PtSWEET16b and PtSWEET16d in P. trichocarpa xylem development. RT-qPCR results further revealed that HbSWEET10a, 16b, and 1a play important roles in phloem sugar transport. The results from this study provide a foundation not only for further investigation into the functionality of the SWEET gene family in Hevea, especially in its sugar transport for latex production, but also for related studies of this gene family in the plant kingdom. [ABSTRACT FROM AUTHOR]

Narrowing the metabolic engineering divide between plants and microorganisms will require faster design-build-test cycles and better genome engineering tools. [ABSTRACT FROM AUTHOR]

The genus Cheirolophus constitutes one of the most striking cases of species radiation in Macaronesia, where it diversified into a lineage of ca. 20 endemic species at a rate that is amongst the fastest reported for oceanic islands. Whilst the cytogenetic dynamics of many of the Macaronesian Cheirolophus species have been comparatively well studied, an overall vision of chromosome and genome evolution has been hampered by the lack of data for the earliest--diverging species, Ch. crassifolius. In this study, we have completed the cytogenetic survey of Cheirolophus to investigate how different cytogenetic traits may have contributed to the dramatic radiation of the genus in Macaronesia. We provide new cytogenetic data (i.e., chromosome counts, genome size estimates and physical mapping of 35S rDNA loci) for several key species, including Ch. crassifolius, and then model trait evolution within a phylogenetic context. Our results reveal a trend of genome downsizing accompanied by a dramatic increase in number of 35S rDNA loci which started early in the evolutionary history of the genus, before its radiation in Macaronesia. It is notable that the increasing number of 35S rDNA loci has not been driven by polyploidisation, in contrast to the more typical trend observed in many angiosperms. In addition, the number of 35S rDNA loci was observed to negatively correlate with genome size, which is also very unusual in angiosperms. It is suggested that non-homologous and unequal homologous recombination are the most likely mechanisms to explain these observations and we discuss whether the unique genomic architectures of Cheirolophus could have predisposed the genus to its successful and rapid speciation in Macaronesia. [ABSTRACT FROM AUTHOR]

Two major bacterial blight (BB) resistance genes ( Xa21 and xa13 ) and a major gene for blast resistance ( Pi54 ) were introgressed into an Indian rice variety MTU1010 through marker-assisted backcross breeding. Improved Samba Mahsuri (possessing Xa21 and xa13 ) and NLR145 (possessing Pi54 ) were used as donor parents. Marker-assisted backcrossing was continued till BC 2 generation wherein PCR based functional markers specific for the resistance genes were used for foreground selection and a set of parental polymorphic microsatellite markers were used for background selection at each stage of backcrossing. Selected BC 2 F 1 plants from both crosses, having the highest recoveries of MTU1010 genome (90% and 92%, respectively), were intercrossed to obtain intercross F 1 (ICF 1 ) plants, which were then selfed to generate 880 ICF 2 plants possessing different combinations of the BB and blast resistance genes. Among the ICF 2 plants, seven triple homozygous plants ( xa13xa13Xa21Xa21Pi54Pi54 ) with recurrent parent genome recovery ranging from 82% to 92% were identified. All the seven ICF 2 plants showed high resistance against the bacterial blight disease with a lesion lengths of only 0.53–2.28 cm, 1%–5% disease leaf areas and disease scoring values of ‘1’ or ‘3’. The seven ICF 2 plants were selfed to generate ICF 3 , which were then screened for blast resistance, and all were observed to be highly resistant to the diseases. Several ICF 3 lines possessing high level of resistance against BB and blast, coupled with yield, grain quality and plant type on par with MTU1010 were identified and advanced for further selection and evaluation. [ABSTRACT FROM AUTHOR]

Advances in plant genomics have had an impact on the field of forensic botany. However, the use of pollen DNA profiling in forensic investigations has yet to be applied. Five volunteers wore a jacket with Pinus echinata pollen-containing cotton swatches for a 14-day period. Pollen decay was evaluated at days 0, 3, 6, 9 and 14 by microscopy. Pollen grains were then transferred to slides using a portable forensic vacuum handle. Ten single grains per swatch were isolated for DNA analysis. DNA was extracted using a high throughput extraction method. A nine-locus short tandem repeat (STR) multiplex system, including previously published primers from Pinus taeda , was developed. DNA was amplified by PCR using fluorescent dyes and analyzed by capillary electrophoresis. Pollen counts from cotton swatches in a 14-day period exhibited an exponential decay from 100% to 17%. The success rate of PCR amplification was 81.2%. Complete and partial STR profiles were generated from 250 pollen grains analyzed (44% and 37%, respectively). Due to the limited amount of DNA, drop-in events were observed (1.87%). However, the rate of contamination with pollen from other pine individuals originating from environmental sources was 4.4%. In conclusion, this study has shown that pollen can be a stable source of forensic DNA evidence, as a proof-of-principle, and that may persist on cotton clothing for at least 14 days of wear. This method can be applied in forensic cases where pollen grains larger than 10 μm (e.g., from herbs or trees) may be transferred to clothing (worn by suspect or victim) by primary contact. [ABSTRACT FROM AUTHOR]

The sustainable production of lignocellulosic biomass in Short Rotation Coppice (SRC) in the context of bioeconomic development in Europe demands an ever greater understanding of the plant material. Different species and, in some cases, different genotypes ( Populus deltoides ‘Baldo’, Populus x canadensis : ‘Orion’, ‘Oudenberg’, ‘Ballottino’ and ‘I-214’; Robinia pseudoacacia ‘Nyirsegi’, Salix matsudana x Salix spp. ‘ Levante’ and Platanus x hispanica ‘Girona’) were tested at four contrasting Mediterranean locations to determine the biomass yield after three years. Besides production, genotypic stability is a key factor in furthering our understanding of the plant material, with important implications for the management of plantations as well as for breeding. To study this factor, several stability models were compared (additive mixed model, Shukla’s stability variance model, Finlay–Wilkinson and Eberhart–Russell models) and differences in the response capacity of the material were evaluated in the different environments. This evaluation of genotypic stability, based on the measurement of variances, was complemented by an analysis of the mean genotypic value and the variability in genotype productivity. Intrinsic water use efficiency was also evaluated as it is an important trait of plant material destined for use in Mediterranean conditions. S. matsudana x Salix spp. ‘Levante’ exhibited the highest production and showed an intermediate reactivity (stability) as well as high intrinsic water use efficiency under the conditions in which it was tested. P. x canadensis ‘Orion’ also displayed a good overall performance and was highly sensitive to improving environmental conditions. Conversely, R. pseudoacacia and P. x hispanica presented yields well below the average as well as low responsiveness to improved environmental conditions. Our findings will contribute to a better understanding of plant material, enabling improved recommendations for plantations the Mediterranean area, including more precise large scale predictions. Furthermore, the information provided will be of particular value in future breeding programs. [ABSTRACT FROM AUTHOR]

In its broadest sense, Scirpus consists of a heterogeneous assemblage of up to 250 species, but modern circumscriptions suggest that only 40-50 species are part of the genus. Despite a narrower definition of the genus, atypical species continue to be segregated from Scirpus with a common pattern being the removal of Southern Hemisphere taxa to other genera and tribes. In South America, the morphology of remaining Scirpus species also suggests that they are not closely related to Scirpus s.str., but most of these taxa are only known from their types, making a detailed analysis of their generic affinities difficult. One notable exception is Scirpus asper, a species that is relatively common in the mountains and adjacent lowlands of Peru south to Argentina. Although this species possesses features used in the circumscription of Scirpus, such as cauline leaves, flat leaf blades and anthelate inflorescences, it is known to differ from Scirpus s.str. by its Schoenus-type embryo, and most of its presumed allies are now placed in different genera (e.g., Scirpus analecti = Cyprirtglea analecta; Scirpus giganteus = Androtrichum giganteum). In this study, we use DNA sequence data from the plastid (matK, ndhF) and nuclear (ETS-lf) genomes to demonstrate that Scirpus asper is not closely related to Scirpus s.str., but sister to Phylloscirpus within the predominantly South American Zameioscirpus clade (Amphiscirpus, Phylloscirpus, Zameioscirpus). When combined with morphological, anatomical and embryological data, results indicate that S. asper is best treated as the sole species of a new monotypic genus, Rhodoscirpus. The implications of these results on the taxonomy of tribe Scirpeae are discussed. [ABSTRACT FROM AUTHOR]

Colchicine-induced changes in ploidy levels provide an opportunity to improve the morphological and biochemical attributes of plants. Concentrations of metabolites have been shown to be affected by changing the ploidy level of the genome. Nigella sativa L. has long been used as a traditional spice and a medicinal herb, and recent scientific reports have increased its pharmaceutical and industrial applications. Ploidy effects were investigated following the application of 0.025, 0.05, or 0.10% (w/v) colchicine, and several changed levels of ploidy (aneuploidy, triploidy, or tetraploidy) were scored. The aneuploid seedling had one telocentric chromosome missing and did not survive beyond the juvenile stage. Triploids and tetraploids exhibited large-scale morphological characteristics such as thicker and darker-green leaves, and increased numbers of branches compared to diploid plants. Increased ploidy improved the morphogenetic behaviour of the tetraploid plants, but these plants exhibited stalk-lodging at maturity. Most of the triploid plants recovered by losing the extra chromosomes from their genome in succeeding generations, with the effect that seed-set returned to normal, as in the diploids. Other triploid plants did not set C2 seed. Tetraploid plants also revealed low levels of segregation in the C2 and later generations. Careful selection and screening, based on morphological and biochemical characteristics, established 32 tetraploid lines of N. sativa with approx. 46% higher concentrations of thymoquinone in the oil of their seed. [ABSTRACT FROM AUTHOR]

A hybrid between Berula erecta and Helosciadium nodiflorum is reported from Chippenham Fen National Nature Reserve, Cambridgeshire, England. Parentage was investigated using chromosome counts, a maternally inherited chloroplast marker (rpsl6-trnK), a biparentally inherited nuclear marker (ITS), and fluorescent in situ hybridisation (FISH) using labelled total genomic probes. Two parental genomes were identified in the putative hybrid (2n = 20), a maternal genome consisting of 9 chromosomes from B. erecta (2n = 18) and a paternal genome consisting of 11 chromosomes from H. nodiflorum (2n = 22). The implication of this hybrid for the taxonomy of the group is discussed, and a new hybrid genus is described: xBeruladium (= Berula x Helosciadium). In overall appearance the hybrid resembles a small, creeping H. nodiflorum, and can be identified in the wild by a combination of characters: (1) the absence of a ring-mark on the petiole below the lowest pair of leaflets that is characteristic of pure Berula, (2) lower leaves with up to five pairs of leaflets, (3) peduncles varying from shorter than to longer than rays, (4) umbels with several usually untoothed bracts, (5) a relatively long stigma and style, and (6) the absence of ripe fruits. The detection of this taxon is of considerable interest and, as far as we know, it is the first confirmed intergeneric hybrid in the Apiaceae within Europe. [ABSTRACT FROM AUTHOR]

For the past few decades continuous increase in the levels of tropospheric ozone (O 3 ) concentrations is posing to be a threat for agricultural productivity. Two high yielding tropical rice cultivars (Malviya dhan 36 and Shivani) were evaluated against different concentrations of O 3 under field conditions. Experimental design included filtered chambers, non-filtered chambers having ambient O 3 and 10 and 20 ppb elevated O 3 above the ambient. Study was conducted to assess differential response if any in induction of antioxidative defense system, genome stability, leaf proteome, yield and quality of the product in both the test cultivars. Superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), ascorbate peroxidase (APX), and glutathione reductase (GR) were induced under ambient and elevated levels of O 3 . Native polyacrylamide gel electrophoresis (PAGE) of SOD, CAT and POD also displayed increased enzymatic activity along with associated alterations in specific isoforms. Ascorbic acid, thiols and phenolics were also stimulated at ambient and elevated O 3 . Structural alterations in DNA of rice plants due to O 3 affecting its genome template stability (GTS) was examined using RAPD technique. 2-D PAGE revealed 25 differential spots in Malviya dhan 36 and 36 spots in Shivani after O 3 treatment with reductions in RuBisCO subunits. Reductions in yield and change in the quality of grains were also noticed. [ABSTRACT FROM AUTHOR]

Allopolyploidization in plants is an important event that enhances heterosis and environmental adaptation. Common wheat, Triticum aestivum (AABBDD), which is an allohexaploid that evolved from an allopolyploidization event between T. turgidum (AABB) and Aegilops tauschii (DD), shows more growth vigor and wider adaptation than tetraploid wheats. To better understand the molecular basis for the heterosis of hexaploid wheat, we systematically analyzed the genomewide gene expression patterns of two combinations of newly hybridized triploids (ABD), their chromosome-doubled hexaploids (AABBDD), stable synthetic hexaploids (AABBDD) and natural hexaploids, in addition to their parents, T. turgidum (AABB) and Ae. tauschii (DD), using a microarray to reconstruct the events of allopolyploidization and genome stabilization. Overall comparisons of gene expression profiles showed that the newly generated hexaploids exhibited gene expression patterns similar to those of their maternal tetraploids, irrespective of hybrid combination. With successive generations, the gene expression profiles of nascent hexaploids became less similar to the maternal profiles, and belonged to a separate cluster from the natural hexaploids. Triploids revealed characteristic expression patterns, suggesting endosperm effects. In the newly hybridized triploids (ABD) of two independent synthetic lines, approximately onefifth of expressed genes displayed non-additive expression; the number of these genes decreased with polyploidization and genome stabilization. Approximately 20% of the non-additively expressed genes were transmitted across generations throughout allopolyploidization and successive self-pollinations, and 43 genes overlapped between the two combinations, indicating that shared gene expression patterns can be seen during allohexaploidization. Furthermore, four of these 43 genes were involved in starch and sucrose metabolism, suggesting that these metabolic events play key roles in the hybrid vigor of hexaploid wheat. [ABSTRACT FROM AUTHOR]

Over the last 200 years, genetic resources of forest trees have been increasingly transferred, within and outside of species’ native distribution ranges, for forestry and for research and development (R&D). Transferred germplasm has been deployed to grow trees for numerous purposes, ranging from the production of wood and non-wood products to the provision of ecosystem services such as the restoration of forests for biodiversity conservation. The oldest form of R&D, provenance trials, revealed early on that seed origin has a major influence on the performance of planted trees. International provenance trials have been essential for selecting seed sources for reforestation and for improving tree germplasm through breeding. Many tree breeding programmes were initiated in the 1950s, but as one round of testing and selection typically takes decades, the most advanced of them are only in their third cycle. Recent advances in forest genomics have increased the understanding of the genetic basis of different traits, but it is unlikely that molecular marker-assisted approaches will quickly replace traditional tree breeding methods. Furthermore, provenance trials and progeny tests are still needed to complement new research approaches. Currently, seed of boreal and temperate trees for reforestation purposes are largely obtained from improved sources. The situation is similar for fast growing tropical and subtropical trees grown in plantations, but in the case of tropical hardwoods and many agroforestry trees, only limited tested or improved seed sources are available. Transfers of tree germplasm involve some risks of spreading pests and diseases, of introducing invasive tree species and of polluting the genetic make-up of already present tree populations. Many of these risks have been underestimated in the past, but they are now better understood and managed. Relatively few tree species used for forestry have become invasive, and the risk of spreading pests and diseases while transferring seed is considerably lower than when moving live plants. The implementation of the Nagoya Protocol on access to genetic resources and benefit sharing (ABS) may significantly change current transfer practices in the forestry sector by increasing transaction costs and the time needed to lawfully obtain forest genetic resources for R&D purposes. Many countries are likely to struggle to establish a well-functioning ABS regulatory system, slowing down the process of obtaining the necessary documentation for exchange. This is unfortunate, as climate change, outbreaks of pests and diseases, and continual pressure to support productivity, increase the need for transferring tree germplasm and accelerating R&D. [ABSTRACT FROM AUTHOR]

In the course of reconstructing Aegilops caudata from its own genome (CC) and its plasmon, which had passed half a century in common wheat (genome AABBDD), we produced alloplasmic Ae. cylindrica (genome CCDD) with the plasmon of Ae. caudata. This line, designated (caudata)-CCDD, was found to express male sterility in its second substitution backcross generation (SB2) of (caudata)-AABBCCDD pollinated three times with the Ae. cylindrica pollen. We repeatedly backcrossed these SB2 plants with the Ae. cylindrica pollen until the SB5 generation, and SB5F2 progeny were produced by self-pollination of the SB5 plants. Thirteen morphological and physiological characters, including pollen and seed fertilities, of the (caudata)-CCDD SB5F2 were compared with those of the euplasmic Ae. cylindrica. The results indicated that the male sterility expressed by (caudata)-CCDD was due to genetic incompatibility between the Ae. cylindrica genome and Ae. caudata plasmon that did not affect any other characters of Ae. cylindrica. Also, we report that the genome integrity functions in keeping the univalent transmission rate high. [ABSTRACT FROM AUTHOR]

Plant phenotyping investigates how a plant's genome, interacting with the environment, affects the observable traits of a plant (phenome). It is becoming increasingly important in our quest towards efficient and sustainable agriculture. While sequencing the genome is becoming increasingly efficient, acquiring phenotype information has remained largely of low throughput. Current solutions for automated image-based plant phenotyping, rely either on semi-automated or manual analysis of the imaging data, or on expensive and proprietary software which accompanies costly hardware infrastructure. While some attempts have been made to create software applications that enable the analysis of such images in an automated fashion, most solutions are tailored to particular acquisition scenarios and restrictions on experimental design. In this paper we propose and test, a method for the segmentation and the automated analysis of time-lapse plant images from phenotyping experiments in a general laboratory setting, that can adapt to scene variability. The method involves minimal user interaction, necessary to establish the statistical experiments that may follow. At every time instance (i.e., a digital photograph), it segments the plants in images that contain many specimens of the same species. For accurate plant segmentation we propose a vector valued level set formulation that incorporates features of color intensity, local texture, and prior knowledge. Prior knowledge is incorporated using a plant appearance model implemented with Gaussian mixture models, which utilizes incrementally information from previously segmented instances. The proposed approach is tested on Arabidopsis plant images acquired with a static camera capturing many subjects at the same time. Our validation with ground truth segmentations and comparisons with state-of-the-art methods in the literature shows that the proposed method is able to handle images with complicated and changing background in an automated fashion. An accuracy of 96.7% (dice similarity coefficient) was observed, which was higher than other methods used for comparison. While here it was tested on a single plant species, the fact that we do not employ shape driven models and we do not rely on fully supervised classification (trained on a large dataset) increases the ease of deployment of the proposed solution for the study of different plant species in a variety of laboratory settings. Our solution will be accompanied by an easy to use graphical user interface and, to facilitate adoption, we will make the software available to the scientific community. [ABSTRACT FROM AUTHOR]

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Wheat-rye translocations are widely used in wheat breeding to confer resistance against abiotic and biotic stress. Studying gene expression in wheat-rye translocations is complicated due to the presence of homoeologous genes in hexaploid wheat and high levels of synteny between wheat and rye chromatin. To distinguish transcripts expressed from each of the three wheat genomes and those from rye chromatin, genomic probes generated from diploid progenitors of wheat and rye were synthesized on a custom array. A total of 407 transcripts showed homoeologous genome ('A', 'B' or 'D' genome)- or rye genome ('R')-specific differential expression, based on unequal values of probe hybridization. In a 2BS.2RL wheat-rye translocation, thirteen of the 407 transcripts showed preferential expressions from rye chromatin. As well as quantifying variation in homoeologous transcript in wheat-rye translocations, this study also provides a potential aid to examine the contribution of the subgenomes to complex allohexapolyploids. [ABSTRACT FROM AUTHOR]

Despite remarkable recent progress in the analysis of plant genome organization and chromosome structure, there is a need for methods enabling DNA sequences to be mapped by fluorescence in situ hybridization (FISH) at high spatial resolution. We sorted mitotic metaphase chromosomes of wheat by flow cytometry and observed the occurrence of hyperexpanded chromosomes among them. However, this phenomenon was not reproducible in subsequent experiments. An investigation into the procedures of flow cytometry revealed that the hyperexpansion of chromosomes became reproducible when the concentration of formaldehyde used in sample fixation was reduced. We conducted FISH analysis with 45S rDNA, 5S rDNA and wheat centromeric repeat sequences as probes on flow-sorted chromosomes and also on chromosomes from squash preparations. We measured the length of chromosomes 1B and 6B, identified by FISH. On average, the hyperexpanded 1B and 6B chromosomes were 7.26 and 7.53 times longer, respectively, than the same chromosomes from the squash preparations. The most stretched 1B and 6B chromosomes both exceeded 100 micrometers. [ABSTRACT FROM AUTHOR]

Plasma membrane forms the barrier between the cell and the environment but also forms the passageway for information from the outside to the inside of the cell. Molecular and ionic movement from one location to another is known as transport. Local transport of solutes into or within cells is regulated mainly by membranes. Identification of anion channel in plants represents a goal for a better understanding of their central role in cell signaling, osmoregulation, nutrition, and metabolism. By separating the proteins in the plasma membrane fraction with ion exchange and reverse phase chromatography and analyzing the resulting fractions on a MALDI-TOF mass spectrometer, over 900 proteins could be detected. Of these proteins, 304 were annotated as membrane proteins, 70 transporter proteins and 35 important proteins in biotic and abiotic stresses were, distributed among the different protein families in proportions reflecting the distribution in the genome. Strong cation exchange and reverse phase chromatography and analysis of the resulting fractions on a MALDITOF mass spectrometer, are a powerful tool for retrieving plasma membrane proteins. [ABSTRACT FROM AUTHOR]

Cleomaceae is a small pantropical family that is emerging as a promising system to investigate C4 photosynthesis, floral evolution, and comparative genomics. However, our understanding of these phenomena is hindered by a lack of a strong phylogenetic hypothesis, despite a number of previous studies. We reconstructed the phylogeny of the family using data from all three genomes, including three cpDNA (ndhF, matK, ycfl), one mtDNA (rps3), and one nrDNA (ITS) regions. Analyses strongly supported 15 clades: (1) Clade 1, which includes two Old World species, Cleome khorassanica and C. turkmena; (2) Cleome s.str., which includes the type C. ornithopodioides and Old World species; (3) Droserifolia, corresponding to three Old World species, C. droserifolia, C.fimbriata, C. quinquenervia; (4) Polanisia, equivalent to this New World genus; (5) Angustifolia, which includes four Old World species; (6) North American cleomoids, which includes four genera, Cleomella, Peritoma, Oxystylis, and Wislizenia; (7) Australian, which includes Old world species and worldwide weed Arivela viscosa; (8) Gynandropsis, equivalent to this monotypic genus; (9) Clade 6, which includes Old World species of Cleome and Dipterygium; (10) Dactylaena, corresponding to this genus and Physostemon; (1l) African, which includes species distributed in Old World; (12) Andean, which includes Podandrogyne and tropical New World species of Cleome; (13) Melidiscus, which includes New World tropical species; (14) Cleoserrata, which includes New World tropical species; and (15) Tarenaya, a large New World clade. Major relationships amongst the clades are strongly supported for the first time, including North American cleomoids sister to all remaining Cleomaceae. While five genera are confirmed or newly identified here to be non-monophyletic (Cleome, Cleomella, Hemiscola, Peritoma, Tarenaya), six are supported (Cleoserrata, Dactylaena, Melidiscus, Physostemon, Podandrogyne, Polanisia). Thus, there are many taxonomic and evolutionary implications to our revised phylogenetic hypothesis. [ABSTRACT FROM AUTHOR]

Abstract: Precise modification of plant genomes provides powerful tools for understanding gene function. Furthermore, pinpoint modification of endogenous plant genes is also an attractive method in molecular plant breeding. One of the best methods currently available to induce specific DNA sequence changes into genomes is gene targeting (GT) via homologous recombination (HR). GT can induce a variety of mutations, including substitution of several nucleotides as well as insertions and deletions. Of the various approaches taken to improve GT efficiency, utilization of engineered sequence-specific endonucleases to create targeted DNA double-strand breaks (DSBs) that stimulate HR at breaking sites is one of the most effective. As a universal selection system for GT cells, a target-gene-independent selection system such as positive–negative selection with subsequent elimination of the positive selection marker using piggyBac transposon or HR combined with mega-nuclease allows retention of the desired mutation without any trace of additional exogenous nucleotides. Furthermore, a novel GT system named in planta GT seems to have effectively overcome problems due to low transformation efficiency of the HR template into plant nuclei, and can adjust the timing of DSB induction at the target locus. In the in planta system, an HR template flanked by a nuclease recognition site is stably integrated into the plant genome; subsequent expression of nuclease simultaneously releases the HR template from the genome and induces a DSB at the target site. Here, we review recent developments in GT, giving examples of new techniques improving the efficiency of GT in plants. [Copyright &y& Elsevier]

Abstract: Abiotic stresses present major challenges in sustaining crop yield. They trigger responses involving molecular mechanisms for cellular adjustments, including signal perception and transduction cascades, transcriptional networks and adaptive metabolic pathways. The past decade has witnessed the completion of genome projects of several model plant species and many candidate genes involved in stress tolerance have been identified, expanding the germplasm pool to facilitate genetic engineering. Transgenic technology has accelerated the production of novel stress-tolerant varieties in parallel with conventional breeding. In this review article, various transcription factors, metabolic pathways and effector molecules that are candidates for genetic manipulation to achieve abiotic stress tolerance are discussed. [Copyright &y& Elsevier]

Abstract: Necessity is the mother of invention and has always been a vital key to the progress of humanity, with science as one of the major driving forces. From the perspective of agriculture, modern molecular genetics coupled with plant biotechnology has set a stage for the advancement of agricultural practices, delivering high quality crops that will be able to meet the changing lifestyle, global food and health demands. Agro biotechnology enables the manipulation of the plant genome and the production of genetically modified plants by means of metabolic engineering and genomics. Oilseed crops not only serve as a source of edible oils and bio-lubricants but also find their use in a myriad of applications, the most exciting being biofuels for sustainable energy production. A better understanding of the lipid synthesis metabolism and storage, transgenic technology that goes hand in hand with conventional plant breeding approaches and the domestication of plants that synthesize useful fatty acids will allow for a real breakthrough in the manipulation of oil crops for sustainable development. [Copyright &y& Elsevier]

Abstract: Seed development represents an important phase in the life cycle of flowering plants including the majority of the crop plants. During this phase, developmental and metabolic programs are coordinated to produce the seed that contains the germline information and storage reserves. Although seed developmental patterns vary significantly between the monocots and dicots, they share several conserved developmental programs. The embryo is the major component of the seed in dicots whereas the endosperm is predominant in monocot seeds. The formation of the dormant seed that protects the embryo and provides nutrition during germination is a key characteristic adaptive feature in the evolution of the angiosperms and a determining factor of yield in crop plants. From a crop perspective, the metabolites and especially the storage products deposited in the seed defines the value of the seed. Despite progress in fundamental understanding of seed development, the global genetic and metabolic programs involved in the making of the seed and their implications to genetic improvement of the seed is yet to be fully exploited in crop plants. So, the major goal of several recent studies is to develop comprehensive systems-level insights into molecular and biochemical programs associated with gene expression, protein and metabolite profiles during seed development in model and crop plants. These integrated systems approaches and studies are producing foundational and comprehensive datasets. In this review, we will present an overview of advances in the developmental, genetic and genomic studies of seed biology and their implications to improve seed characteristics in crop plants. [Copyright &y& Elsevier]

Abstract: Microspore culture is not only a valuable system for the study of developmental plant biology, but can also be effectively exploited for biotechnological purposes. Microspore culture is an established platform for the production of large numbers of doubled haploid plants in a few crop species. The unique characteristics of this haploid cell and the rapid advancement of genome sequencing technology make the microspore a special target for genetic engineering. DNA and/or protein delivery into these cells has been studied during the past 25 years with mitigated success, and was often limited to daughter cells. A novel delivery method using short peptide nanocarriers has rendered microspore transformation more achievable and opened new opportunities for crop development. [Copyright &y& Elsevier]

Abstract: Site-specific nucleases create DNA double stranded breaks which, during repair, can be used to introduce site-specific point mutations, insertions and deletions into the plant genome. Identification of novel nucleases and further characterization of known nucleases, including Zinc finger nucleases, TAL effector-like endonucleases, Meganucleases and CRISPR–Cas, have increased the range and level of precision of methods available for modifying plant genomes. Precision, site-specific modification of plant genomes, known as genome editing, is emerging as a powerful tool for the improvement of crop species. This review discusses the functional and structural details of these nucleases and their potential applications for the genetic modification of plants. [Copyright &y& Elsevier]

Chromosome mutations occur in common wheat carrying a monosome of gametocidal (Gc) chromosomes 2C and 3CSAT. These Gc chromosomes have been known to induce chromosomal breakage in a rye chromosome 1R added to common wheat. We attempted to introduce the two Gc chromosomes into the other six rye chromosome (2R to 7R) addition or substitution lines of common wheat to establish a set of chromosomal rearrangement-inducing lines for rye chromosomes. We obtained critical plants that had a pair of rye chromosomes and one Gc chromosome for 2R, 3R, 4R and 6R, and semi-critical plants that were monotelodisomic and monosomic for 5R. Chromosomal aberrations are expected to occur in the progeny of these plants. Besides we established self-fertile disomic 2C addition lines of common wheat that were disomic substitution for 3R, disomic addition for 6R, monotelodisomic for 5R, and monosomic for 7R. We can produce the critical plants of the respective rye chromosomes by crossing above lines to the respective wheat-rye disomic addition or substitution lines. During the cytological screening in this study, we found Gc-induced chromosomal aberrations for every rye chromosome. The stocks reported here can be used to produce dissection lines for each of the rye chromosomes in common wheat by the Gc system. [ABSTRACT FROM AUTHOR]

Next-generation sequencing (NGS) has revolutionized molecular systematics as well as population and conservation genetics. It is now possible to obtain enormous amounts of gene sequence data from any species in a short time at low cost. More technological advances are on the horizon, ensuring that this trend will continue throughout the coming decade. These rapid advances provide unprecedented opportunities in systematics; they also pose new challenges, requiring that the next generation of systematists be well-versed in new skill sets (e.g., bioinformatics). As examples of the potential of NGS, it is now possible to develop genetic resources for any plant system that poses intriguing evolutionary questions. During the next decade many new "evolutionary model systems" will become available as systematists rapidly develop the necessary genetic/genomic frameworks for many previously unstudied plants. Phylogenetic reconstruction will be conducted at an unprecedented pace at both deep and fine scales with datasets of numerous taxa and genes--this includes rapid progress on assembling a more com-prehensive Tree of Life for green plants. For example, complete plastid genome sequencing is now routinely facilitating analyses of hundreds of taxa at deep levels, as well as enabling complete plastid genome phylogeographic analyses at the population level. Gene capture methods hold enormous promise for the rapid and inexpensive analyses of complete plastid genomes, as well as studies of hundreds of selected (targeted) nuclear loci. NGS has also had a big impact on population genetics, initially by dramatically simplifying microsatellite marker development, but more recently by opening new possibilities through vari-ous genotyping-by-sequencing (GBS) approaches that have great potential to expand on the types of questions that can be addressed at the population level. Transcriptome sequencing has enabled the construction of large datasets of nuclear genes while also providing a wealth of plastid and mitochondrial genes. NGS has also facilitated probe development for studies of chromosomes using FISH (fluorescence in situ hybridization). NGS is also making the rapid sequencing of complete nuclear genomes routine, thus transforming our field and opening up new avenues of systematic endeavor in comparative genomics. However, even as sequencing costs drop and technological advances make complete nuclear genome sequencing more com-monplace, genome assembly will remain a major challenge. [ABSTRACT FROM AUTHOR]

The biodegradation of hazardous petroleum hydrocarbons has recently received a lot of attention because of its many possible applications. Bacillus marsiflavi strain was isolated from oil contaminated soil of Rawalpindi, Pakistan. Initial sequencing was done by 16s rRNA sequencing technique. Bac 144 had shown 78% emulsification index and 72% hydrophobicity content. Further, the strain displayed production of 15.5 mg/L phosphate sloubilization and 30.25 μg/ml indole acetic acid (IAA) in vitro assay. The strain showed 65% biodegradation of crude oil within 5 days by using Gas Chromatography-Mass Spectrometry (GC-MS) analysis. Whole Genome analysis of Bac 144 was performed by PacBio sequencing and results indicated that Bacillus marsiflavi Bac144 strain consisted of size of 4,417,505bp with closest neighbor Bacillus cereus ATCC 14579. The number of the coding sequence was 4662 and number of RNAs was 141. The GC content comprised 48.1%. Various genes were detected in genome responsible for hydrocarbon degradation and plant defense mechanism. The toxic effect of petroleum hydrocarbons in soil and its mitigation with Bac 144 was tested by soil experiment with three levels of oil contamination (5%, 10% and 15%). Soil enzymatic activity such as dehydrogenase and fluorescein diacetate (FDA) increased up to 49% and 40% with inoculation of Bac 144, which was considered to be correlated with hydrocarbon degradation recorded as 46%. An increase of 20%, 14% and 9% in shoot length of plant at 5%, 10% and 15% level of oil was recorded treated with Bac 144 as compared to untreated plants. A percent increase of 14.89%, 16.85%, and 13.87% in chlorophyll, carotenoid, and proline content of plant was observed by inoculation with Bac 144 under oil stress. Significant reduction of 14% and 18%, 21% was recorded in the malondialdehyde content of plant due to inoculation of Bac 144. A considerable increase of 21.33%, 19.5%, and 24.5% in super oxide dismutase, catalase, and peroxidase dismutase activity was also observed in plants inoculated with strain Bac 144. These findings suggested that Bac-144 can be considered as efficient candidate for bioremediation of hydrocarbons. • Bacillus marsiflavi Bac 144 strain was isolated from oil contaminated soil of Rawalpindi, Pakistan which showed plant growth-promoting attributes. • Whole genome sequencing of strain indicated the presence of genes involved in hydrocarbon degradation. • Bac 144 had shown a positive impact on the growth of maize plant and hydrocarbon degradation at three levels of oil contamination (5%, 10% and 15%). [ABSTRACT FROM AUTHOR]