Population-tailored mock genome enables genomic studies in species without a reference genome

Sabadin, Felipe; Carvalho, Humberto Fanelli; Galli, Giovanni; Fritsche‐Neto, Roberto

doi:10.1007/s00438-021-01831-9

Cited by 5 publications

(29 citation statements)

References 67 publications

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“…However, few studies still address how genotyping platforms in uence single-crosses' prediction and, more speci cally, regarding the mock genome as a tool for more sophisticated analyses, such as genomic prediction. Only one recent study shows the mock genome's e ciency in predicting maize single-crosses, which may be an alternative for crops that do not yet have a reference genome (Sabadin et al, 2022). However, our study is more complete and more representative because getting approaches from the population structure phase is crucial for the intended use of germplasm through the division of heterotic groups, the de nition of testers, and, nally, the genomic prediction of single-crosses.…”

Section: Discussionmentioning

confidence: 99%

“…All this progress, including well-characterized genes and vast collections of genetic and genomic resources, focuses on a small group of crops (Tester and Langridge, 2010) to the detriment of smaller agricultural species, considered orphans, historically poorly researched (Mayes et al, 2012), in that the large majority do not have a reference genome. Sabadin et al (2022) showed that using mock genomes could be a worthy strategy that permits using SNP markers for genomic selection in orphan crops.…”

Section: Discussionmentioning

confidence: 99%

“…The second purpose was to build a simulated reference genome (mock genome), according to the GBS-SNP-CROP pipeline proposed by Melo et al (2016), and use it to perform the SNP calling. More details about the mock reference can found in (Sabadin et al, 2022).…”

Section: Genotypic Data and Analysismentioning

confidence: 99%

“…The term "orphan" is derived from the condition of neglect and helplessness of these crops by the scienti c community, leading to the designation of such species as underused, neglected, or minor crops (Tadele and Assefa, 2012). GBS also appears as an option for genomic studies in these crops, especially when they do not have a reference genome (Sabadin et al, 2022). With these data, it is possible to build a mock reference to perform the SNP calling, where the discovery of polymorphisms will be intrinsic to the study population without using an external genome (Melo et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

“…With these data, it is possible to build a mock reference to perform the SNP calling, where the discovery of polymorphisms will be intrinsic to the study population without using an external genome (Melo et al, 2016). This pipeline has already been successfully used in several genomic studies (Holloway et al, 2018;Munjal et al, 2018;Adhikari et al, 2018;Matias et al, 2019;Sabadin et al, 2022). Adopting this technology in poorly studied crops has a tangible impact on the progress of the breeding process (Ye and Fan, 2021).…”

Section: Introductionmentioning

confidence: 99%

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

Machado

DoVale

Sabadin

et al. 2022

Preprint

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The advances in genomics in recent years have increased the accuracy and efficiency of breeding programs for many crops. Nevertheless, the adoption of genomic enhancement for several other crops essential in developing countries is still limited, especially for those that do not have a reference genome. These crops are more often called orphans. This is the first report to show how the results provided by different platforms, including the use of a simulated genome called the mock genome, can generate in population structure and genetic diversity studies, especially when the intention is to use this information to support the formation of heterotic groups, choice of testers and genomic prediction of single-crosses. For that, we used a method to assemble a reference genome to perform the SNP calling without needing an external genome. Thus, we compared the analysis results using the mock genome with the standard approaches (Array and GBS). The results showed that the GBS-Mock presented similar results to the standard methods of genetic diversity studies, division of heterotic groups, the definition of testers, and genomic prediction. These results showed that a mock genome constructed from the population's intrinsic polymorphisms to perform the SNP calling is an effective alternative for conducting genomic studies of this nature in orphan crops, especially those that do not have a reference genome.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Genotypic Data and Analysismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

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

Machado

DoVale

Sabadin

et al. 2022

Preprint

Self Cite

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Life on a beach leads to phenotypic divergence despite gene flow for an island lizard

et al. 2023

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Limited spatial separation within small islands suggests that observed population divergence may occur due to habitat differences without interruption to gene flow but strong evidence of this is scarce. The wall lizard Teira dugesii lives in starkly contrasting shingle beach and inland habitats on the island of Madeira. We used a matched pairs sampling design to examine morphological and genomic divergence between four beach and adjacent (<1 km) inland areas. Beach populations are significantly darker than corresponding inland populations. Geometric morphometric analyses reveal divergence in head morphology: beach lizards have generally wider snouts. Genotyping-by-sequencing allows the rejection of the hypothesis that beach populations form a distinct lineage. Bayesian analyses provide strong support for models that incorporate gene flow, relative to those that do not, replicated at all pairs of matched sites. Madeiran lizards show morphological divergence between habitats in the face of gene flow, revealing how divergence may originate within small islands.

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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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Population-tailored mock genome enables genomic studies in species without a reference genome

Cited by 5 publications

References 67 publications

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

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

Life on a beach leads to phenotypic divergence despite gene flow for an island lizard

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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