From Phylogenomics to Breeding: Can Universal Target Capture Probes Be Used in the Development of SNP Markers for Kinship Analysis?

Overview

Journal Appl Plant Sci

Date 2025 Feb 5

PMID 39906492

Authors

Kedra M Ousmael

Ole K Hansen

Affiliations

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Abstract

Premise: Leveraging DNA markers, particularly single-nucleotide polymorphisms (SNPs), in parentage analysis, sib-ship reconstruction, and genomic relatedness analysis can enhance plant breeding efficiency. However, the limited availability of genomic information, confined to the most commonly used species, hinders the broader application of SNPs in species of lower economic interest (e.g., most tree species). We explored the possibility of using universal target capture probes, namely Angiosperms353, to identify SNPs and assess their effectiveness in genomic relatedness analysis.

Methods: We tested the approach in 11 tree species, six of which had a half-sib family structure. Variants were called within species, and genomic relatedness analysis was conducted in species with two or more families. Scalability via amplicon sequencing was tested by designing primers and testing them in silico.

Results: Adequate SNPs for relatedness analysis were identified in all species. Relatedness values from Angiosperms353-based SNPs highly correlated with those from thousands of genome-wide DArTseq SNPs in , one of the species with a family structure. The in silico performance of designed primers demonstrated the potential for scaling up via amplicon sequencing.

Discussion: Utilizing universal target capture probes for SNP identification can help overcome the limitations of genomic information availability, thereby enhancing the application of genomic markers in breeding plant species with lower economic interest.

References

Johnson M, Gardner E, Liu Y, Medina R, Goffinet B, Shaw A . HybPiper: Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment. Appl Plant Sci. 2016; 4(7). PMC: 4948903. DOI: 10.3732/apps.1600016. View

Amadeu R, Garcia A, Munoz P, Ferrao L . AGHmatrix: genetic relationship matrices in R. Bioinformatics. 2023; 39(7). PMC: 10371492. DOI: 10.1093/bioinformatics/btad445. View

Wang J . Estimating pairwise relatedness in a small sample of individuals. Heredity (Edinb). 2017; 119(5):302-313. PMC: 5637371. DOI: 10.1038/hdy.2017.52. View

Soto Gomez M, Pokorny L, Kantar M, Forest F, Leitch I, Gravendeel B . A customized nuclear target enrichment approach for developing a phylogenomic baseline for yams (Dioscoreaceae). Appl Plant Sci. 2019; 7(6):e11254. PMC: 6580989. DOI: 10.1002/aps3.11254. View

Flanagan S, Jones A . The future of parentage analysis: From microsatellites to SNPs and beyond. Mol Ecol. 2018; 28(3):544-567. DOI: 10.1111/mec.14988. View

Johnson M, Pokorny L, Dodsworth S, Botigue L, Cowan R, Devault A . A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-Medoids Clustering. Syst Biol. 2018; 68(4):594-606. PMC: 6568016. DOI: 10.1093/sysbio/syy086. View

Meek M, Larson W . The future is now: Amplicon sequencing and sequence capture usher in the conservation genomics era. Mol Ecol Resour. 2019; 19(4):795-803. DOI: 10.1111/1755-0998.12998. View

McLay T, Birch J, Gunn B, Ning W, Tate J, Nauheimer L . New targets acquired: Improving locus recovery from the Angiosperms353 probe set. Appl Plant Sci. 2021; 9(7). PMC: 8312740. DOI: 10.1002/aps3.11420. View

Wolf P, Robison T, Johnson M, Sundue M, Testo W, Rothfels C . Target sequence capture of nuclear-encoded genes for phylogenetic analysis in ferns. Appl Plant Sci. 2018; 6(5):e01148. PMC: 5991577. DOI: 10.1002/aps3.1148. View

10.

Hale H, Gardner E, Viruel J, Pokorny L, Johnson M . Strategies for reducing per-sample costs in target capture sequencing for phylogenomics and population genomics in plants. Appl Plant Sci. 2020; 8(4):e11337. PMC: 7186906. DOI: 10.1002/aps3.11337. View

11.

Ousmael K, Whetten R, Xu J, Nielsen U, Lamour K, Hansen O . Identification and high-throughput genotyping of single nucleotide polymorphism markers in a non-model conifer (Abies nordmanniana (Steven) Spach). Sci Rep. 2023; 13(1):22488. PMC: 10728141. DOI: 10.1038/s41598-023-49462-x. View

12.

Griesmann M, Chang Y, Liu X, Song Y, Haberer G, Crook M . Phylogenomics reveals multiple losses of nitrogen-fixing root nodule symbiosis. Science. 2018; 361(6398). DOI: 10.1126/science.aat1743. View

13.

Katoh K, Asimenos G, Toh H . Multiple alignment of DNA sequences with MAFFT. Methods Mol Biol. 2009; 537:39-64. DOI: 10.1007/978-1-59745-251-9_3. View

14.

Garrison E, Kronenberg Z, Dawson E, Pedersen B, Prins P . A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar. PLoS Comput Biol. 2022; 18(5):e1009123. PMC: 9286226. DOI: 10.1371/journal.pcbi.1009123. View

15.

Foster J, Allan G, Chan A, Rabinowicz P, Ravel J, Jackson P . Single nucleotide polymorphisms for assessing genetic diversity in castor bean (Ricinus communis). BMC Plant Biol. 2010; 10:13. PMC: 2832895. DOI: 10.1186/1471-2229-10-13. View

16.

Eserman L, Thomas S, Coffey E, Leebens-Mack J . Target sequence capture in orchids: Developing a kit to sequence hundreds of single-copy loci. Appl Plant Sci. 2021; 9(7):e11416. PMC: 8312744. DOI: 10.1002/aps3.11416. View

17.

Neale D, Martinez-Garcia P, De La Torre A, Montanari S, Wei X . Novel Insights into Tree Biology and Genome Evolution as Revealed Through Genomics. Annu Rev Plant Biol. 2017; 68:457-483. DOI: 10.1146/annurev-arplant-042916-041049. View

18.

Liu Y, Johnson M, Cox C, Medina R, Devos N, Vanderpoorten A . Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes. Nat Commun. 2019; 10(1):1485. PMC: 6445109. DOI: 10.1038/s41467-019-09454-w. View

19.

Ousmael K, Cappa E, Hansen J, Hendre P, Hansen O . Genomic evaluation for breeding and genetic management in Cordia africana, a multipurpose tropical tree species. BMC Genomics. 2024; 25(1):9. PMC: 10759591. DOI: 10.1186/s12864-023-09907-z. View

20.

Wang J, Scribner K . Parentage and sibship inference from markers in polyploids. Mol Ecol Resour. 2013; 14(3):541-53. DOI: 10.1111/1755-0998.12210. View