RNAseq of diverse spring wheat cultivars released during last 110 years

awais rasheed Huihui Li (2023, [Artículo])

CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA RNA SEQUENCE SPRING WHEAT ROOT ARCHITECTURE GENES

Influence of conservation agriculture-based production systems on bacterial diversity and soil quality in rice-wheat-greengram cropping system in eastern Indo-Gangetic Plains of India

Anup Das virender kumar Peter Craufurd Andrew Mcdonald Sonam Sherpa (2023, [Artículo])

Introduction: Conservation agriculture (CA) is gaining attention in the South Asia as an environmentally benign and sustainable food production system. The knowledge of the soil bacterial community composition along with other soil properties is essential for evaluating the CA-based management practices for achieving the soil environment sustainability and climate resilience in the rice-wheat-greengram system. The long-term effects of CA-based tillage-cum-crop establishment (TCE) methods on earthworm population, soil parameters as well as microbial diversity have not been well studied. Methods: Seven treatments (or scenarios) were laid down with the various tillage (wet, dry, or zero-tillage), establishment method (direct-or drill-seeding or transplantation) and residue management practices (mixed with the soil or kept on the soil surface). The soil samples were collected after 7 years of experimentation and analyzed for the soil quality and bacterial diversity to examine the effect of tillage-cum-crop establishment methods. Results and Discussion: Earthworm population (3.6 times), soil organic carbon (11.94%), macro (NPK) (14.50–23.57%) and micronutrients (Mn, and Cu) (13.25 and 29.57%) contents were appreciably higher under CA-based TCE methods than tillage-intensive farming practices. Significantly higher number of OTUs (1,192 ± 50) and Chao1 (1415.65 ± 14.34) values were observed in partial CA-based production system (p ≤ 0.05). Forty-two (42) bacterial phyla were identified across the scenarios, and Proteobacteria, Actinobacteria, and Firmicutes were the most dominant in all the scenarios. The CA-based scenarios harbor a high abundance of Proteobacteria (2–13%), whereas the conventional tillage-based scenarios were dominated by the bacterial phyla Acidobacteria and Chloroflexi and found statistically differed among the scenarios (p ≤ 0.05). Composition of the major phyla, i.e., Proteobacteria, Actinobacteria, and Firmicutes were associated differently with either CA or farmers-based tillage management practices. Overall, the present study indicates the importance of CA-based tillage-cum-crop establishment methods in shaping the bacterial diversity, earthworms population, soil organic carbon, and plant nutrient availability, which are crucial for sustainable agricultural production and resilience in agro-ecosystem.

Metagenomics Bacterial Diversity Rice-Wheat-Greengram CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA CONSERVATION AGRICULTURE DNA SEQUENCES EARTHWORMS METAGENOMICS SOIL QUALITY AGROECOSYSTEMS

Molecular characterization of divergent isolates of Citrus bent leaf viroid (CBLVd) from citrus cultivars of Punjab, Pakistan

Abdelfattah DABABAT Yong Suk Chung (2023, [Artículo])

Biological Indexing Sequencing Analysis Citrus Orchards CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA PHYLOGENETIC ANALYSIS CITRUS RNA DNA

Celebrating Professor Rajeev K. Varshney's transformative research odyssey from genomics to the field on his induction as Fellow of the Royal Society

Vanika Garg Rutwik Barmukh Manish Roorkiwal Chris Ojiewo Abhishek Bohra MAHENDAR THUDI Vikas Kumar Singh Himabindu Kudapa Reyaz Mir Chellapilla Bharadwaj Xin Liu Manish Pandey (2024, [Artículo])

Agricultural Biotechnology Crop Genomics Genome Sequencing CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA BIOTECHNOLOGY CROPS GENOMICS PLANT BREEDING AGRICULTURE GENETIC IMPROVEMENT

Wheat seed demand assessment assisted by genotyping in Ethiopia

Moti Jaleta Kindie Tesfaye Olaf Erenstein (2023, [Artículo])

This study examines the extent to which wheat varieties supplied by the formal seed system align with the varieties demanded and used by farmers in Ethiopia. The framework of stated and revealed preferences drawn from the consumer preference theory is used to analyze farmer demand for different wheat varieties. We used official data from the formal seed sector and representative survey data from wheat farm households in Ethiopia. The survey data allow to contrast the farmer reported varietal use with genotyping by sequencing (also known as DNA fingerprinting). Farmers' reliance on informal seed sources and own saved seed, among others, contributes to the misidentification of the varieties they grow. Consequently, farmers are likely to misinform the formal seed demand assessment leading to either an over- or underestimation of actual seed demand for specific wheat varieties. Genotyping by sequencing, as opposed to farmer reports, established the persistence of old varieties. This also implies vulnerability of wheat production to disease dynamics depending on the longevity of disease resistance by the variety in use. Apart from narrowing the gap between the actual and stated demand and ensuring timely replacement of wheat varieties, genotyping-assisted estimates can save seed carry-over cost. Genotyping by sequencing is increasingly used as the new benchmark and gold standard for identifying and tracking the adoption of crop varieties. The technique has potential to enhance the performance of the seed sector through effective planning that can optimize resource commitments and accelerate the rate of varietal replacement.

Seed Demand Varietal Replacement CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA GENOTYPING-BY-SEQUENCING SEEDS WHEAT

Draft Genome Sequence of Pediococcus pentosaceus Strain PP16CC, Isolated from Oyster Crassostrea corteziensis

JULIO ANTONIO HERNANDEZ GONZALEZ RICARDO VAZQUEZ JUAREZ Jose Manuel Vazquez-Guillen Carlos Rangel Dávalos MARIA CRISTINA RODRIGUEZ PADILLA MAURILIA ROJAS CONTRERAS (2022, [Artículo])

"Pediococcus pentosaceus strain PP16CC comes from the intestine of Crassostrea corteziensis. A 1.82-Mbp draft genome of this strain was assembled using A5-miseq from illumina reads, resulting in 4 contigs and 1,856 predicted protein coding genes. Additionally, 23 proteins belonging to various glycosyl hydrolase families and 6 prophage regions were identified."

Genome Sequence, Pediococcus pentosaceus BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOLOGÍA ANIMAL (ZOOLOGÍA) GENÉTICA ANIMAL GENÉTICA ANIMAL

Editorial: Genome wide association studies and genomic selection for crop improvement in the era of Big Data

Alison Bentley Charles Chen Nunzio D'Agostino (2022, [Artículo])

Allele Mining High-Throughput Phenotyping Genomic Estimated Breeding Value CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA CROP IMPROVEMENT DNA CHROMOSOME MAPPING GENETIC LINKAGE GENOMES GENOTYPING GERMINATION HEAT STRESS QUALITY CONTROL SINGLE NUCLEOTIDE POLYMORPHISM TRITICUM AESTIVUM GENETIC DIVERSITY (AS RESOURCE) HIGH-THROUGHPUT SEQUENCING

Comparison of sequencing-based and array-based genotyping platforms for genomic prediction of maize hybrid performance

XUECAI ZHANG Zefeng Yang Yang Xu (2022, [Artículo])

Genotyping by Sequencing Genomic Selection SNP Array Marker Density CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA MARKER-ASSISTED SELECTION MAIZE SINGLE NUCLEOTIDE POLYMORPHISM HYBRIDS

Genotyping by sequencing advancements in barley

Naeela Qureshi Mohammad Pourkheirandish (2022, [Artículo])

Genotyping by Sequencing Target Enrichment CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA BARLEY GENOTYPING RESTRICTION ENZYMES SINGLE NUCLEOTIDE POLYMORPHISM

miRNAs contained in extracellular vesicles cargo contribute to the progression of idiopathic pulmonary fibrosis: an in vitro aproach

JOVITO CESAR SANTOS ALVAREZ JUAN MANUEL VELAZQUEZ ENRIQUEZ ROSENDO GARCÍA CARRILLO CESAR RODRIGUEZ BEAS ALMA AURORA RAMIREZ HERNANDEZ EDILBURGA REYES JIMENEZ KARINA GONZÁLEZ GARCÍA ARMANDO LOPEZ MARTINEZ LAURA PEREZ CAMPOS MAYORAL SERGIO ROBERTO AGUILAR RUIZ MARIA DE LOS ANGELES ROMERO TLALOLINI HONORIO TORRES AGUILAR LUIS ALBERTO CASTRO SANCHEZ JAIME ARELLANES ROBLEDO VERONICA ROCIO VASQUEZ GARZON RAFAEL BALTIERREZ HOYOS (2022, [Artículo])

Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive lung disease. Lesions in the lung epithelium cause alterations in the microenvironment that promote fibroblast accumulation. Extracellular vesicles (EVs) transport proteins, lipids, and nucleic acids, such as microRNAs (miRNAs). The aim of this study was to characterize the differentially expressed miRNAs in the cargo of EVs obtained from the LL97 and LL29 fibroblast cell lines isolated from IPF lungs versus those derived from the CCD19 fibroblast cell line isolated from a healthy donors. We characterized EVs by ultracentrifugation, Western blotting, and dynamic light scattering. We identified miRNAs by small RNA-seq, a total of 1144 miRNAs, of which

1027 were known miRNAs; interestingly, 117 miRNAs were novel. Differential expression analysis showed that 77 miRNAs were upregulated and 68 were downregulated. In addition, pathway enrichment analyses from the Gene Ontology and Kyoto Encyclopedia of Genomes identified several miRNA target genes in the categories, cell proliferation, regulation of apoptosis, pathways in cancer, and proteoglycans in cancer. Our data reveal that miRNAs contained in EVs cargo could be helpful as biomarkers for fibrogenesis, diagnosis, and therapeutic intervention of IPF.

MEDICINA Y CIENCIAS DE LA SALUD Idiopathic pulmonary fibrosis Extracellular vesicles Fibroblasts Small-RNA seq