On the usefulness of mock genomes to define heterotic pools, testers, and hybrid predictions in orphan crops

Machado, Ingrid Pinheiro; DoVale, Júlio César; Sabadin, Felipe; Fritsche‐Neto, Roberto

doi:10.3389/fpls.2023.1164555

Cited by 3 publications

(1 citation statement)

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“…The same panel also showed diversity in previous studies involving stress conditions due to low doses of nitrogen (Sant'Ana et al 2020) and symbiosis with growth-promoting bacteria (Yassue et al 2021). In addition, a genetic diversity study involving only genomic information grouped these lines into which six clusters (Machado et al 2023), coinciding with the results found in this study (Fig. 2A).…”

Section: Panel Discrimination and Variabilitysupporting

confidence: 89%

Breeding trials in water-stress conditions: identification of sensitive traits in early stages and characterization of a tropical maize public panel

Machado

Pontes

Silveira

et al. 2023

Preprint

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One of the major goals of modern agriculture is to achieve increased crop yield using less water. Despite the significant advances in genomics, a phenotypic characterization efficient is essential for the success of a modern breeding program, which wants to speed up the genetic gains by deploying selection in the early stages. Thus, this study aimed to identify which traits are most important to discriminate the maize genotypes to support early selection under contrasting water availability conditions. For this, we used a public diversity panel consisting of 360 tropical maize inbred lines, involving two conditions, well-watered (WW) and water-stress (WS), in eight trials. Evaluations were carried out in the phenological stage V6 for shoot and root traits. There was a significant variation in the panel performance, mainly for root traits under WS conditions, composing six clusters. However, the traits showed a similar pattern of clustering evidenced by principal components in WW and WS conditions. Moreover, a strong relationship was found among the roots' length, surface area, and volume. Based on this, we suggest discarding the most error-prone ones. Our results showed via Redundancy Analysis (RDA) that plant height, stalk diameter, and lateral roots length are traits more sensitive to WS and, therefore, may be considered in early selection in breeding programs aiming for water use efficiency.

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Section: Panel Discrimination and Variabilitysupporting

confidence: 89%

Breeding trials in water-stress conditions: identification of sensitive traits in early stages and characterization of a tropical maize public panel

Machado

Pontes

Silveira

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

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Fine-Tuning GBS Data with Comparison of Reference and Mock Genome Approaches for Advancing Genomic Selection in Less Studied Farmed Species

Fischer,

Tapio,

Bitz

et al. 2023

Preprint

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BackgroundDiversifying animal cultivation demands efficient genotyping for enabling genomic selection, but non-model species lack efficient genotyping solutions. The aim of this study was to optimize a genotyping-by-sequencing (GBS) double-digest RAD-sequencing (ddRAD) pipeline. Bovine data was used to automate the bioinformatic analysis. The application of the optimization was demonstrated on non-model European whitefish data.ResultsDdRAD data generation was designed for a reliable estimation of relatedness and is scalable to up to 384 samples. The GBS sequencing yielded approximately one million reads for each of the around 100 assessed samples. Optimizing various strategies to create a de-novo reference genome for variant calling (mock reference) showed that using three samples outperformed other building strategies with single or very large number of samples. Adjustments to most pipeline tuning parameters had limited impact on high-quality data, except for the identity criterion for merging mock reference genome clusters. For each species, over 15k GBS variants based on the mock reference were obtained and showed comparable results with the ones called using an existing reference genome. Repeatability analysis showed high concordance over replicates, particularly in bovine while in European whitefish data repeatability did not exceed earlier observations.ConclusionsThe proposed cost-effective ddRAD strategy, coupled with an efficient bioinformatics workflow, enables broad adoption of ddRAD GBS across diverse farmed species. While beneficial, a reference genome is not obligatory. The integration of Snakemake streamlines the pipeline usage on computer clusters and supports customization. This user-friendly solution facilitates genotyping for both model and non-model species.

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Fine-Tuning GBS Data with Comparison of Reference and Mock Genome Approaches for Advancing Genomic Selection in Less Studied Farmed Species

Fischer,

Tapio,

Bitz

et al. 2024

Preprint

View full text Add to dashboard Cite

Background Diversifying animal cultivation demands efficient genotyping for enabling genomic selection, but non-model species lack efficient genotyping solutions. The aim of this study was to optimize a genotyping-by-sequencing (GBS) double-digest RAD-sequencing (ddRAD) pipeline. Bovine data was used to automate the bioinformatic analysis. The application of the optimization was demonstrated on non-model European whitefish data. Results DdRAD data generation was designed for a reliable estimation of relatedness and is scalable to up to 384 samples. The GBS sequencing yielded approximately one million reads for each of the around 100 assessed samples. Optimizing various strategies to create a de-novo reference genome for variant calling (mock reference) showed that using three samples outperformed other building strategies with single or very large number of samples. Adjustments to most pipeline tuning parameters had limited impact on high-quality data, except for the identity criterion for merging mock reference genome clusters. For each species, over 15k GBS variants based on the mock reference were obtained and showed comparable results with the ones called using an existing reference genome. Repeatability analysis showed high concordance over replicates, particularly in bovine while in European whitefish data repeatability did not exceed earlier observations. Conclusions The proposed cost-effective ddRAD strategy, coupled with an efficient bioinformatics workflow, enables broad adoption of ddRAD GBS across diverse farmed species. While beneficial, a reference genome is not obligatory. The integration of Snakemake streamlines the pipeline usage on computer clusters and supports customization. This user-friendly solution facilitates genotyping for both model and non-model species.

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On the usefulness of mock genomes to define heterotic pools, testers, and hybrid predictions in orphan crops

Cited by 3 publications

References 94 publications

Breeding trials in water-stress conditions: identification of sensitive traits in early stages and characterization of a tropical maize public panel

Breeding trials in water-stress conditions: identification of sensitive traits in early stages and characterization of a tropical maize public panel

Fine-Tuning GBS Data with Comparison of Reference and Mock Genome Approaches for Advancing Genomic Selection in Less Studied Farmed Species

Fine-Tuning GBS Data with Comparison of Reference and Mock Genome Approaches for Advancing Genomic Selection in Less Studied Farmed Species

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