Genetic diversity of Moroccan date palm revealed by microsatellite markers.

The genetic diversity between 23 Moroccan date palm cultivars collected from the National Palm Collection at the INRA (National Agricultural Research Institute) experimental field in Zagora was assessed using SSR markers that are specifically designed for date palm. Among the 16 tested SSR, 13 were successfully amplified, and were selected to carry out this study. 208 bands were amplified, ranging from 10 to 25 bands per cultivar with an average of 16 alleles per cultivar. The value of heterozygosity of the studied markers ranged from 0.11 to 0.30. The pairwise genetic distances between those cultivars ranged from 0.06 to 0.46. The hierarchical cluster analysis distributed the 23 genotypes into four different groups of one to ten cultivars.

Characterization of centromeric DNA of Gossypium anomalum reveals sequence-independent enrichment dynamics of centromeric repeats.

Centromeres in eukaryotes are composed of highly repetitive DNAs, which evolve rapidly and are thought to achieve a favorable structure in mature centromeres. However, how the centromeric repeat evolves into an adaptive structure is largely unknown. We characterized the centromeric sequences of Gossypium anomalum through chromatin immunoprecipitation against CENH3 antibodies. We revealed that the G. anomalum centromeres contained only retrotransposon-like repeats but were depleted in long arrays of satellites. These retrotransposon-like centromeric repeats were present in the African-Asian and Australian lineage species, suggesting that they might have arisen in the common ancestor of these diploid species. Intriguingly, we observed a substantial increase and decrease in copy numbers among African-Asian and Australian lineages, respectively, for the retrotransposon-derived centromeric repeats without apparent structure or sequence variation in cotton. This result indicates that the sequence content is not a decisive aspect of the adaptive evolution of centromeric repeats or at least retrotransposon-like centromeric repeats. In addition, two active genes with potential roles in gametogenesis or flowering were identified in CENH3 nucleosome-binding regions. Our results provide new insights into the constitution of centromeric repetitive DNA and the adaptive evolution of centromeric repeats in plants.

Characterization of Repetitive DNA in Saccharum officinarum and Saccharum spontaneum by Genome Sequencing and Cytological Assays.

In most plant species, DNA repeated elements such as satellites and retrotransposons are composing the majority of their genomes. Saccharum officinarum (2n = 8x = 80) and S. spontaneum (2n = 40-128) are the two fundamental donors of modern sugarcane cultivars. These two species are polyploids with large genome sizes and are enriched in repetitive elements. In this work, we adopted a de novo strategy to isolate highly repetitive and abundant sequences in S. officinarum LA Purple and S. spontaneum SES208. The findings obtained from alignment to the genome assemblies revealed that the vast majority of the repeats (97.9% in LA Purple and 96.5% in SES208) were dispersed in the respective genomes. Fluorescence in situ hybridization assays were performed on 27 representative repeats to investigate their distributions and abundances. The results showed that the copies of some highly repeated sequences, including rDNA and centromeric or telomeric repeats, were underestimated in current genome assemblies. The analysis of the raw read mapping strategy showed more copy numbers for all studied repeats, suggesting that copy number underestimation is common for highly repeated sequences in current genome assemblies of LA Purple and SES208. In addition, the data showed that the centromeric retrotransposons in all SES208 centromeres were absent in certain S. spontaneum clones with different ploidies. This rapid turnover of centromeric DNA in sugarcane provides new clues regarding the pattern of centromeric retrotransposon formation and accumulation.

Chromosome Painting Provides Insights Into the Genome Structure and Evolution of Sugarcane.

The genus Saccharum is composed of species with high polyploidy and highly varied chromosome numbers, laying a challenge for uncovering its genomic structure and evolution. We developed a chromosome 2 painting (CP2) probe by designing oligonucleotides covering chromosome 2 of Saccharum spontaneum (2n = 8x = 64). Fluorescence in situ hybridization (FISH) using this CP2 probe revealed six types of ploidies from twenty S. spontaneum clones, including 6x, 8x, 10x, 11x, 12x, and 13x clones. The finding of S. spontaneum clones with uneven of ploid suggested that certain S. spontaneum clones come from hybridization. It renews our knowledge that S. spontaneum is derived from autopolyploidization. Combined with a S. spontaneum-specific probe, chromosome 2-derived chromosome or fragments from either S. spontaneum or Saccharum officinarum can be identified in sugarcane modern cultivars. We revealed unexpected high level of interspecific recombination from introgressive S. spontaneum chromosomes (>50.0%) in cultivars ROC22 and ZZ1, indicating frequent chromosome exchange in cultivars. Intriguingly, we observed interspecific recombination recurring among either homoeologous or non-homoeologous chromosomes in sugarcane cultivars. These results demonstrated that chromosome painting FISH is a powerful tool in the genome dissection of sugarcane and provide new insights into the genome structure and evolution of the complex genus Saccharum.

Foliar application of silicon improves growth of soybean by enhancing carbon metabolism under shading conditions.

An experiment was set up to investigate physiological responses of soybeans to silicon (Si) under normal light and shade conditions. Two soybean varieties, Nandou 12 (shade resistant), and Nan 032-4 (shade susceptible), were tested. Our results revealed that under shading, the net assimilation rate and the plant growth were significantly reduced. However, foliar application of Si under normal light and shading significantly improved the net photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (Tr), and decreased intercellular carbon dioxide concentration (Ci). The net photosynthetic rate of Nandou 12 under normal light and shading increased by 46.4% and 33.3% respectively with Si treatment (200 mg/kg) compared to controls. Si application also enhanced chlorophyll content, soluble sugars, fresh weight, root length, root surface area, root volume, root-shoot ratio, and root dry weight under both conditions. Si application significantly increased the accumulation of some carbohydrates such as soluble sugar and sucrose in stems and leaves ensuring better stem strength under both conditions. Si application significantly increased the yield by increasing the number of effective pods per plant, the number of beans per plant and the weight of beans per plant. After Si treatment, the yield increased 24.5% under mono-cropping, and 17.41% under intercropping. Thus, Si is very effective in alleviating the stress effects of shading in intercropped soybeans by increasing the photosynthetic efficiency and lodging resistance.

Changes in the Soil Microbiome in Eggplant Monoculture Revealed by High-Throughput Illumina MiSeq Sequencing as Influenced by Raw Garlic Stalk Amendment.

The incorporation of plant residues into soil can be considered a keystone sustainability factor in improving soil structure function. However, the effects of plant residue addition on the soil microbial communities involved in biochemical cycles and abiotic stress phenomena are poorly understood. In this study, experiments were conducted to evaluate the role of raw garlic stalk (RGS) amendment in avoiding monoculture-related production constraints by studying the changes in soil chemical properties and microbial community structures. RGS was applied in four different doses, namely the control (RGS0), 1% (RGS1), 3% (RGS2), and 5% (RGS3) per 100 g of soil. The RGS amendment significantly increased soil electrical conductivity (EC), N, P, K, and enzyme activity. The soil pH significantly decreased with RGS application. High-throughput Illumina MiSeq sequencing revealed significant alterations in bacterial community structures in response to RGS application. Among the 23 major taxa detected, Anaerolineaceae, Acidobacteria, and Cyanobacteria exhibited an increased abundance level. RGS2 increased some bacteria reported to be beneficial including Acidobacteria, Bacillus, and Planctomyces (by 42%, 64%, and 1% respectively). Furthermore, internal transcribed spacer (ITS) fungal regions revealed significant diversity among the different treatments, with taxa such as Chaetomium (56.2%), Acremonium (4.3%), Fusarium (4%), Aspergillus (3.4%), Sordariomycetes (3%), and Plectosphaerellaceae (2%) showing much abundance. Interestingly, Coprinellus (14%) was observed only in RGS-amended soil. RGS treatments effectively altered soil fungal community structures and reduced certain known pathogenic fungal genera, i.e., Fusarium and Acremonium. The results of the present study suggest that RGS amendment potentially affects the microbial community structures that probably affect the physiological and morphological attributes of eggplant under a plastic greenhouse vegetable cultivation system (PGVC) in monoculture.

An Era of CRISPR/ Cas9 Mediated Plant Genome Editing.

Recently the engineered nucleases have revolutionized genome editing to perturb gene expression at specific sites in complex eukaryotic genomes. Three important classes of these genome editing tools are Moreover, the more recent type II Clustered Regularly Inter-spaced Short Palindromic Repeats/Crispr associated protein (CRISPR/Cas9) system has become the most favorite plant genome editing tool for its precision and RNA based specificity unlike its counterparts which rely on protein based specificity. Plasmid-mediated co-delivery of multiple sgRNAs and Cas9 to the Plant cell can simultaneously alter more than one target loci which enable multiplex genome editing. In this review, we discuss recent advancements in the CRISPR/ Cas9 technology mechanism, theory and its applications in plants and agriculture. We also suggest that the CRISPR/ Cas9 as an effective genome editing tool, has vast potential for crop improvement and studying gene regulation mechanism and chromatin remodeling.

Exploring Durable Genetic Resistance against Leaf Rust through Phenotypic Characterization and Lr34Linked STS Marker in Wheat Germplasm / Explorando a resistência genética duradoura contra a ferrugem da folha através da caracterização fenotípica e do STS marker relacionado ao (GENE) LR34 do germoplasma do trigo

Present study was aimed to screening the population of 25 wheat genotypes from Baluchistan region of Pakistan along with five commercial cultivars for leaf rust adult plant resistance (APR) through gene postulation using natural inoculation of Puccinia triticina Erikss local pathotype. Infection severity was recorded on scale in comparison with susceptible control "Morroco" cultivar. On the basis of phenotypic score, seven accessions and four varieties (Zardana-89, Sariab-92, Zarlashta-99 and Raskoh-05) with AUDPC values up to 20% were characterized as resistant genotypes. Coefficient of infection (CI) score ranged from 0-10 for some accessions and cultivars showing high level of adult plant resistance. Furthermore, bi-allelic STS marker csLV34 having close linkage with Lr34 (0.4cM). This marker amplified one gene specific allele of 150bp in 21 genotypes, including 19 accessions and two commercial varieties (Sariab-92 and Zarghoon-79) which confirmed presence of Lr34 gene conferring adult plant resistance against leaf rust. The rust pathogenicity scale varied for accessions from resistant to moderately susceptible. However, beside Lr34, phenotypic gene postulation, in combination with marker assisted selection for leaf rust resistance, has revealed presence of some other unknown resistance genes in local wheat germplasm which signified its use in wheat improvement programs both locally and abroad.

O presente estudo teve como objetivo a triagem da população de 25 genótipos de trigo do Baluchistão, região do Paquistão, juntamente com cinco cultivares comerciais para o estudo da resistência à ferrugem da folha em plantas adultas (leaf rust adult plant resistance, APR, em inglês) através da postulação gênica usando a inoculação natural do patótipo local da Puccinia triticina Erikks. A gravidade da infecção foi registrada na escala em comparação ao cultivar de controle suscetível "Morroco". Com base na pontuação fenotípica, sete acessões e quatro variedades (Zardana-89, Sariab-92, Zarlashta-99 and Raskoh-05) com valores de AUDPC (area under the disease progress curve, em inglês) até 20% foram caracterizados como genótipos resistentes. A pontuação do coeficiente de infecção (CI) variou no intervalo de 0-10 para algumas acessões e cultivares evidenciando uma elevada resistência nas plantas adultas. Além disso, o STS marker para o csLV34 bi-alélico demonstrou uma ligação estreita com o Lr34 (0.4cM). Este marcador amplificou um alelo específico do gene do 150bp em 21 genótipos, incluindo 19 acessões e duas variedades comerciais (Sariab-92 and Zarghoon-79) o que confirmou a presença do gene Lr34 conferindo resistência às plantas adultas contra a ferrugem da folha. A escala de patogenicidade da ferrugem para as acessões de resistente a moderadamente suscetível. Contudo, além do Lr34, a postulação gênica fenotípica, em combinação com a seleção auxiliada (ou assistida) por marcadores para a resistência da ferrugem da folha, revelou a presença de outros genes resistentes desconhecidos no germoplasma do trigo local o que justifica a sua utilização em programas de melhoramento do trigo tanto a nível local quanto a nível internacional.