GBS-SNP-CROP: a reference-optional pipeline for SNP discovery and plant germplasm characterization using variable length, paired-end genotyping-by-sequencing data

Background: With its simple library preparation and robust approach to genome reduction, genotyping-by-sequencing (GBS) is a flexible and cost-effective strategy for SNP discovery and genotyping, provided an appropriate reference genome is available. For resource-limited curation, research, and breeding programs of underutilized plant genetic resources, however, even low-depth references may not be within reach, despite declining sequencing costs. Such programs would find value in an open-source bioinformatics pipeline that can maximize GBS data usage and perform high-density SNP genotyping in the absence of a reference. Results: The GBS SNP-Calling Reference Optional Pipeline (GBS-SNP-CROP) developed and presented here adopts a clustering strategy to build a population-tailored “Mock Reference” from the same GBS data used for downstream SNP calling and genotyping. Designed for libraries of paired-end (PE) reads, GBS-SNP-CROP maximizes data usage by eliminating unnecessary data culling due to imposed read-length uniformity requirements. Using 150 bp PE reads from a GBS library of 48 accessions of tetraploid kiwiberry (Actinidia arguta), GBS-SNP-CROP yielded on average three times as many SNPs as TASSEL-GBS analyses (32 and 64 bp tag lengths) and over 18 times as many as TASSEL-UNEAK, with fewer genotyping errors in all cases, as evidenced by comparing the genotypic characterizations of biological replicates. Using the published reference genome of a related diploid species (A. chinensis), the reference-based version of GBS-SNP-CROP behaved similarly to TASSEL-GBS in terms of the number of SNPs called but had an improved read depth distribution and fewer genotyping errors. Our results also indicate that the sets of SNPs detected by the different pipelines above are largely orthogonal to one another; thus GBS-SNP-CROP may be used to augment the results of alternative analyses, whether or not a reference is available. Conclusions: By achieving high-density SNP genotyping in populations for which no reference genome is available, GBS-SNP-CROP is worth consideration by curators, researchers, and breeders of under-researched plant genetic resources. In cases where a reference is available, especially if from a related species or when the target population is particularly diverse, GBS-SNP-CROP may complement other reference-based pipelines by extracting more information per sequencing dollar spent. The current version of GBS-SNP-CROP is available at https://github.com/halelab/GBS-SNP-CROP.gi

Acclimatization of Tapeinochilos ananassae plantlets in association with arbuscular mycorrhizal fungi.

The objective of this work was to assess the potential of three isolates of arbuscular mycorrhizal fungi to promote growth of micropropagated plantlets of Tapeinochilos ananassae during acclimatization. The experiment was carried out in greenhouse, in a completely randomized block design, with four inoculation treatments: non-inoculated control and plants inoculated with Glomus etunicatum, Acaulospora longula or Gigaspora albida, with ten replicates. After 90 days, the following parameters were evaluated: survival rate, height, leaf and tiller number, leaf area, fresh and dry biomass, contents of macro- and micronutrients in the root and shoot, glomerospore number, and mycorrhizal colonization. The survival percentage was 100%, except for plants inoculated with G. albida (80%). The isolate G. etunicatum is more suitable for plant development, since it improves survival, growth, dry matter production, nutritional status, and vigor of T. ananassae micropropagated plants

Eficiência de uso de nitrogênio por genótipos de feijão.

O objetivo deste estudo foi avaliar a resposta e eficiência de uso de N por genótipos de feijoeiro.CONAFE

Fungos micorrízicos arbusculares (FMA) e rizobactérias promotoras de crescimento de plantas (RPCP) na aclimatização de Zingiber spectabile Griff. micropropagado (Zingiberaceae).

O objetivo do trabalho foi avaliar o potencial de FMA e RPCP, isolados e/ou combinados (em dupla inoculação) na aclimatização de Z. spectabi/e

Avaliação de linhagens intermediárias de feijoeiro comum do grupo comercial carioca no agreste nordestino.

Este trabalho teve por objetivo avaliar o comportamento produtivo de linhagens intermediárias de feijoeiro comum do grupo comercial preto em áreas do Agreste nordestino

Caracterização morfométrica da área de drenagem de cinco açudes a partir de técnicas de sensoriamento remoto.

Este trabalho apresenta estudos realizados na Bacia Hidrográfica do Rio Pontal, onde foram aplicadas técnicas de geoprocessamento e sensoriamento remoto para a geração de dados para a caracterização morfométrica. Através de imagens do satélite SRTM, foi possível extrair informações como curvas de nível, forma do relevo, rede de drenagem e declividade para as análises morfométricas de cinco açudes: Gavião, Comprida, Jatobá de Comprida, Mandi e Poço do Canto. Todos se localizam no rio principal - Pontal - e em sequência, onde realizou-se estudo das suas estruturas de drenagem. A partir dos dados morfométricos, foram gerados dados das microbacias alimentadas por estes açudes como a área de captação, perímetro, densidade de drenagem e forma superficial de cada microbacia. As cinco microbacias apresentaram baixo grau de desenvolvimento do sistema de drenagem. Observou-se que as microbacias variam de área superficial de 18,47 km² a 246,22 km², e com comprimento da área de drenagem de 4,26 km a 32,13 km. A forma das microbacias são irregulares e menos sujeitas a enchentes e, consequentemente, com baixa capacidade de captação de água de chuva, principalmente os dois açudes que localizam-se na parte central da sequência