Haplotype-Based Genotyping in Polyploids

Clevenger, Josh; Korani, Walid; Ozias‐Akins, Peggy; Jackson, Scott A.

doi:10.3389/fpls.2018.00564

Cited by 67 publications

(74 citation statements)

References 17 publications

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“…There is currently no simple solution to identify misaligned SNPs within GBS datasets, though increasingly reliable methods for identifying non-allelic SNPs in polyploids are under development (e.g. [84,85]). Finally, although the availability of a reference genome has greatly aided the interpretation of GWAS studies in wheat, it should be noted that the causal variants underlying the majority of significant MTAs identified in this study remain unknown.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide association studies for yield-related traits in soft red winter wheat grown in Virginia

Ward

Brown‐Guedira

Kolb

et al. 2018

Preprint

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Grain yield is a trait of paramount importance in the breeding of all cereals. In wheat (Triticum aestivum L.), yield has steadily increased since the Green Revolution, though the current rate of increase is not forecasted to keep pace with demand due to growing world population and affluence. While several genome-wide association studies (GWAS) on yield and related component traits have been performed in wheat, the previous lack of a reference genome has made comparisons between studies difficult. In this study, a GWAS for yield and yield-related traits was carried out on a population of 324 soft red winter wheat lines across a total of four rain-fed environments in the state of Virginia using single-nucleotide polymorphism (SNP) marker data generated by a genotyping-by-sequencing (GBS) protocol. Two separate mixed linear models were used to identify significant marker-trait associations (MTAs). The first was a single-locus model utilizing a leave-one-chromosome-out approach to estimating kinship. The second was a sub-setting kinship multi-locus method (FarmCPU). The single-locus model identified nine significant MTAs for various yield-related traits, while the FarmCPU model identified 74 significant MTAs. The availability of the wheat reference genome allowed for the description of MTAs in terms of both genetic and physical positions, and enabled more extensive post-GWAS characterization of significant MTAs. The results indicate promising avenues for increasing grain yield by exploiting variation in traits relating to the number of grains per unit area, as well as phenological traits influencing grain-filling duration of genotypes.

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Section: Discussionmentioning

confidence: 99%

Genome-wide association studies for yield-related traits in soft red winter wheat grown in Virginia

Ward

Brown‐Guedira

Kolb

et al. 2018

Preprint

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“…It is notable that erroneous SNP calling is a common problem in polyploids and especially in the AD-genome allotetraploid cotton because of homoeologous and paralogous sequences. This issue has been addressed through several methods 89,93,94 . In this study, we used the published method 89 to avoid erroneous genotype calling and to provide accurate chromosome-specific and homoeologous haplotype structure.…”

Section: Fluorescence In Situ Hybridization Of a And D Homoeologous Cmentioning

confidence: 99%

Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement

et al. 2020

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olyploidy or whole-genome duplication provides genomic opportunities for evolutionary innovations in many animal groups and all flowering plants 1-5 , including most important crops such as wheat, cotton and canola or oilseed rape 6-8. The common occurrence of polyploidy may suggest its advantage and potential for selection and adaptation 2,3,9 , through rapid genetic and genomic changes as observed in newly formed Brassica napus 10 , Tragopogon miscellus 11 and polyploid wheat 12 , and/or largely epigenetic modifications as in Arabidopsis and cotton polyploids 5,13. Cotton is a powerful model for revealing genomic insights into polyploidy 3 , providing a phylogenetically defined framework of polyploidization (~1.5 million years ago (Ma)) 14 , followed by natural diversification and crop domestication 15. The evolutionary history of the polyploid cotton clade is longer than that of some other allopolyploids, such as hexaploid wheat (~8,000 years) 12 , tetraploid canola (~7,500 years) 16 and tetraploid Tragopogon (~150 years) 11. Polyploidization between an A-genome African species (Gossypium arboreum (Ga)-like) and a D-genome American species (G. raimondii (Gr)-like) in the New World created a new allotetraploid or amphidiploid (AD-genome) cotton clade (Fig. 1a) 14 , which has diversified into five polyploid lineages, G. hirsutum (Gh) (AD) 1 , G. barbadense (Gb) (AD) 2 , G. tomentosum (Gt) (AD) 3 , G. mustelinum (Gm) (AD) 4 and G. darwinii (Gd) (AD) 5. G. ekmanianum and G. stephensii are recently characterized and closely related to Gh 17. Gh and Gb were separately domesticated from perennial shrubs to become annualized Upland and Pima cottons 15. To date, global cotton production provides income for ~100 million families across ~150 countries, with an annual economic impact of ~US$500 billion worldwide 6. However, cotton supply is reduced due to aridification, climate change and pest emergence. Future improvements in cotton and sustainability will involve use of the genomic resources and gene-editing tools becoming available in many crops 9,18,19. Cotton genomes have been sequenced for the D-genome (Gr) 20 and A-genome (Ga) 21 diploids and two cultivated tetraploids 22-26. These analyses have shown structural, genetic and gene expression variation related to fiber traits and stress responses in cultivated

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“…The sorting of these variants could be done manually, as for example shown in Eriksson et al (2018), but this is only feasible for a small number of loci, while NGS tools in general generate thousands of loci. Clevenger et al (2018) used haplotype based genotyping for high-accurate SNP calling of polyploid subgenomes. However, both methods require long fragments and/or a reference genome.…”

Section: Introductionmentioning

confidence: 99%

Relationships and genome evolution of polyploid Salix species revealed by RAD sequencing data

Wagner

Hörandl

2019

Preprint

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14Despite the general progress in using next generation sequencing techniques for 15 evolutionary research questions, the analysis of polyploid species is still hampered by the lack 16 of suitable analytical tools and the statistical difficulties of dealing with more than two alleles 17 per locus. Polyploidization and especially allopolyploidy leads to new combinations of traits 18 by combining genomes of two or more parental species. This enhances the adaptive potential 19 and often results in speciation. However, multiple origins of polyploids, backcrossing to the 20 parental species and post-origin evolution can strongly influence the genome composition of 21 polyploid species. Here, we used RAD sequencing, which revealed 23,393 loci and 320,010 22 high quality SNPs, to analyze the relationships and origin of seven polyploid species of the 23 diverse genus Salix by utilizing a phylogenomic and a network approach, as well as analyzing 24 the genetic structure and composition of the polyploid genome in comparison to putative 25 parental species. We adapted the SNiPloid pipeline that was originally developed to analyse 26 SNP composition of recently established allotetraploid crop lineages to RAD sequencing data 27 by using concatenated RAD loci as reference. Our results revealed a well-resolved phylogeny 28 of 35 species of Eurasian shrub willows (Salix subg. Chamaetia/Vetrix), including 28 diploid 29 and 7 polyploid species. Polyploidization in willows appears to be predominantly connected 30 to hybridization, i.e. to an allopolyploid origin of species. More ancient allopolyploidization 31 events involving hybridization of more distantly related, ancestral lineages were observed for 32 two hexaploid and one octoploid species. Our data suggested a more recent allopolyploid 33 origin for the included tetraploids within the major subclades and identified putative parental 34 taxa that appear to be plausible in the context of geographical, morphological and ecological 35 patterns. SNiPloid and HyDe analyses disentangled the different genomic signatures resulting 36 from hybrid origin, backcrossing, and secondary post-origin evolution in the polyploid 37 species. All tetraploids showed a considerable post-origin, species-specific proportion of 38 Origin of polyploid Salix species 3 SNPs. The amount of extant hybridization appears to be related to the degree of geographical 39 and ecological isolation of species. Our data demonstrate that high-quality RAD sequencing 40 data are suitable and highly informative for the analysis of the origin and relationships of 41 polyploid species. The combination of the traditional tools RAxML, STRUCTURE, 42 SplitsTree and recently developed programs like SNAPP, HyDe and SNiPloid established a 43 bioinformatic pipeline for unraveling the complexity of polyploid genomes.44

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Haplotype-Based Genotyping in Polyploids

Cited by 67 publications

References 17 publications

Genome-wide association studies for yield-related traits in soft red winter wheat grown in Virginia

Genome-wide association studies for yield-related traits in soft red winter wheat grown in Virginia

Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement

Relationships and genome evolution of polyploid Salix species revealed by RAD sequencing data

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