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Overcoming challenges in variant calling: exploring sequence diversity in candidate genes for plant development in perennial ryegrass (Lolium perenne).

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Abstract
Revealing DNA sequence variation within the Lolium perenne genepool is important for genetic analysis and development of breeding applications. We reviewed current literature on plant development to select candidate genes in pathways that control agronomic traits, and identified 503 orthologues in L. perenne. Using targeted resequencing, we constructed a comprehensive catalogue of genomic variation for a L. perenne germplasm collection of 736 genotypes derived from current cultivars, breeding material and wild accessions. To overcome challenges of variant calling in heterogeneous outbreeding species, we used two complementary strategies to explore sequence diversity. First, four variant calling pipelines were integrated with the VariantMetaCaller to reach maximal sensitivity. Additional multiplex amplicon sequencing was used to empirically estimate an appropriate precision threshold. Second, a de novo assembly strategy was used to reconstruct divergent alleles for each gene. The advantage of this approach was illustrated by discovery of 28 novel alleles of LpSDUF247, a polymorphic gene co-segregating with the S-locus of the grass self-incompatibility system. Our approach is applicable to other genetically diverse outbreeding species. The resulting collection of functionally annotated variants can be mined for variants causing phenotypic variation, either through genetic association studies, or by selecting carriers of rare defective alleles for physiological analyses.
Keywords
: genomic diversity, targeted resequencing, variant calling, allele reconstruction, natural variation

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Chicago
Veeckman, Elisabeth, Sabine Van Glabeke, Annelies Haegeman, Hilde Muylle, Frederik R D van Parijs, Stephen L Byrne, Torben Asp, et al. 2019. “Overcoming Challenges in Variant Calling: Exploring Sequence Diversity in Candidate Genes for Plant Development in Perennial Ryegrass (Lolium Perenne).” DNA Research.
APA
Veeckman, Elisabeth, Van Glabeke, S., Haegeman, A., Muylle, H., van Parijs, F. R. D., Byrne, S. L., Asp, T., et al. (2019). Overcoming challenges in variant calling: exploring sequence diversity in candidate genes for plant development in perennial ryegrass (Lolium perenne). DNA Research.
Vancouver
1.
Veeckman E, Van Glabeke S, Haegeman A, Muylle H, van Parijs FRD, Byrne SL, et al. Overcoming challenges in variant calling: exploring sequence diversity in candidate genes for plant development in perennial ryegrass (Lolium perenne). DNA Research. 2019;
MLA
Veeckman, Elisabeth, Sabine Van Glabeke, Annelies Haegeman, et al. “Overcoming Challenges in Variant Calling: Exploring Sequence Diversity in Candidate Genes for Plant Development in Perennial Ryegrass (Lolium Perenne).” DNA Research (2019): n. pag. Print.
@article{8587988,
  abstract     = {Revealing DNA sequence variation within the Lolium perenne genepool is important for genetic analysis and development of breeding applications. We reviewed current literature on plant development to select candidate genes in pathways that control agronomic traits, and identified 503 orthologues in L. perenne. Using targeted resequencing, we constructed a comprehensive catalogue of genomic variation for a L. perenne germplasm collection of 736 genotypes derived from current cultivars, breeding material and wild accessions. To overcome challenges of variant calling in heterogeneous outbreeding species, we used two complementary strategies to explore sequence diversity. First, four variant calling pipelines were integrated with the VariantMetaCaller to reach maximal sensitivity. Additional multiplex amplicon sequencing was used to empirically estimate an appropriate precision threshold. Second, a de novo assembly strategy was used to reconstruct divergent alleles for each gene. The advantage of this approach was illustrated by discovery of 28 novel alleles of LpSDUF247, a polymorphic gene co-segregating with the S-locus of the grass self-incompatibility system. Our approach is applicable to other genetically diverse outbreeding species. The resulting collection of functionally annotated variants can be mined for variants causing phenotypic variation, either through genetic association studies, or by selecting carriers of rare defective alleles for physiological analyses. },
  author       = {Veeckman, Elisabeth and Van Glabeke, Sabine and Haegeman, Annelies and Muylle, Hilde and van Parijs, Frederik R D and Byrne, Stephen L and Asp, Torben and Studer, Bruno and Rohde, Antje and Roldan-Ruiz, Isabel and Vandepoele, Klaas and Ruttink, Tom},
  issn         = {1756-1663},
  journal      = {DNA Research},
  keyword      = {: genomic diversity,targeted resequencing,variant calling,allele reconstruction,natural variation},
  language     = {eng},
  title        = {Overcoming challenges in variant calling: exploring sequence diversity in candidate genes for plant development in perennial ryegrass (Lolium perenne).},
  url          = {http://dx.doi.org/10.1093/dnares/dsy033},
  year         = {2019},
}

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