Tackling breeding challenges for polyploid crops

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Time to read:   5 minute read

Updated : Tue, November 23, 2021 @ 3:00 PM

Originally published : Tue, Nov 23, 2021 @ 07:00 AM

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Many cultivated crops with agronomic significance, including wheat, peanut, oat, banana, potato, coffee and strawberry, are polyploid angiosperms with complex genomes. While polyploidy often generates the potential for more genetic, genomic and phenotypic novelty, linking genotype and phenotype can be more challenging compared to diploid crops.1 

Fortunately, recent research and genomic technology are helping plant breeders unravel complex genomes, such as the octoploid strawberry, to improve genetic gain for traits of interest. For example, the latest genotyping by sequencing (GBS) technology can increase efficiency, reduce operating costs and improve the data quality for complex plant breeding applications.

What is polyploidy?

Polyploidy results when two or more genomes within one nucleus fuse, resulting in more than two pairs of homologous chromosomes within each cell.2 Strawberry, the most widely cultivated fruit crop, arose from the hybridisation of two wild octoploid species, formed from the fusion of four diploid subgenomes into a single nucleus more than one million years ago.3 

Breeding challenges for polyploid crops

With a complex, highly heterozygous genome, achieving breeding success in polyploids is challenging using traditional breeding methods.4 In diploid crops, only two alleles of the same gene at the same loci on homologous chromosomes contribute to gene expression and the corresponding phenotype. That makes identifying and selecting a trait of interest relatively straightforward, even if multiple genes contribute to the phenotype.

However, in polyploids, multiple alleles are associated with a single locus, making segregation more complex than diploids. Homeoalleles of a given gene can contribute to complex interactions with a substantial effect on phenotype. For example, in the octoploid strawberry, determining which allele or combination of up to eight different homeoalleles regulates the expression of a trait of interest can be extremely difficult.5 Polyploid plant cells have complex regulatory mechanisms to unify gene expression between the homeologs and define their relative contributions to the final phenotype.1 

Marker-assisted selection is one way to improve breeding efficiency for polyploid crops. However, developing and analysing molecular markers and performing sequencing projects can be complicated due to the high sequence homology between sub-genomes in polyploids.2 

In the past decade, next generation sequencing (NGS) has revolutionised the exploration of polyploid genomes. NGS technologies reduce sequencing costs, increase throughputs and expand fragment assembly complexity due to its short-sequence read output. A reference genome is used to observe variations across different individuals within a species to aid genome assembly.1 While a step in the right direction, challenges associated with GBS and other NGS platforms have historically limited their widespread application in octoploid strawberry. Uneven and inadequate sequencing depth, copy number uncertainty, heterozygote miscalling, missing data and sequencing errors have limited data quality and useful application for plant breeders.6

Recent research helps overcome breeding challenges in strawberry

As mentioned, a complex octoploid genome has historically challenged genotyping and genetic mapping progress for strawberry breeding. Recent research efforts to address some of the significant technical challenges include: 

  • the development of a high-quality octoploid genome assembly,
  • whole genome sequencing of numerous octoploid individuals to better understand intra- and inter-homoeologous nucleotide variation,
  • identification and physical mapping of DNA variants across the octoploid genome and comparative genetic mapping of the wild octoploid progenitors.6 

This information helps breeders employ genomic tools to generate more reliable data for decision making. Strawberry breeding programs can now use genome-wide prediction for parent selection to improve yield and quality traits. Studies have shown that markers are more effective than pedigrees for estimating breeding values, even when phenotypic information is present.6 In addition, phenotyping effort can be reduced when advanced selections are used as training populations.6 Another benefit to genomic breeding tools is that individuals with high predicted performance can be used as parents earlier in the breeding cycle, getting products to market sooner.6 

SeqSNP: An efficient, economical solution for genotyping polyploids

Assays for single nucleotide polymorphism (SNP) detection such as competitive allele-specific polymerase chain reaction (KASP) have become popular for strawberry breeding applications due to an abundance of SNP information from array genotyping, accuracy and ease of scoring and resilience to crude DNA extracts.6 But, major limitations of arrays include the length of time for production and lack of scalability. It can take three to six months to design and manufacture a fixed set of markers, which may not be practical for fast-moving breeding cycles. 

LGC, Biosearch Technologies‘ SeqSNP targeted GBS technology is a refinement of targeted GBS technology and addresses some critical genotyping challenges breeders face. SeqSNP provides a cost-efficient, flexible and scalable mid-plex genotyping platform as a service or as bespoke kits for in-house targeted sequence-based genotyping.7 With planning, SeqSNP's process flow enables the design and manufacture of probe libraries, DNA purification, sequencing and data analysis to fit into plant breeding cycles. 

seqsnp-project-workflow

SeqSNP technology allows complex trait assessment in modern breeding programs and is an ideal option for highly heterotic species or segregating populations in crossing programs. SeqSNP’s probe design offers flexibility for target sequences, avoiding variability in DNA due to heterosis. SeqSNP is an excellent solution for genotyping polyploid crops, including strawberry, as long as a reference genome and SNP locations are available. 

Biosearch Technologies’ SeqSNP HT (high-throughput) technology builds on the benefits of standard SeqSNP genotyping and offers the most cost-effective solution for large scale breeding programs that require more than 2,000 samples screened with 500 to 5,000 markers. SeqSNP HT supports applications in marker-assisted selection such as sample screening, marker discovery, genomic selection, QTL mapping, germplasm profiling and sequence-based genotyping. After the initial library design phase is complete (typically 4-8 weeks), researchers can expect data delivery in just two weeks for most projects.  

Comprehensive tools to increase genetic gain

Improving genome sequencing of polyploid crops will have a fundamental impact on genetic research and plant breeding outcomes. With a more thorough understanding of plant genomes, and the ability to efficiently identify genomic variants and tie them to economic, physiological, and morphological agronomic traits, plant breeders will more effectively meet market needs for agronomic crops.1

As an industry leader in the agrigenomics space, Biosearch Technologies has the expertise, experience and products to support complex plant breeding objectives. We offer customised consultations to help recommend the right solutions for each unique plant breeding project. Leaders in the plant breeding industry have vetted our diverse portfolio of products and services. 

Download an application note to learn more about how SeqSNP genotyping can help support your breeding objectives.

The main advantages of SeqSNP over existing targeted GBS technologies include: 

  • Lower setup costs. Costs are dependent on SNP and sample number, with no solid array setup. 
  • Flexible marker selection. Up to 100K SNPs per sample in a single run.
  • De novo variants (including structural variants) detected in target SNP region.
  • Cost-effective. Highly efficient enrichment methods reduce day-to-day operating costs.
  • Shorter turnaround times for probe library production when compared to the manufacture of arrays. 
  • Access to sequencers and high throughput purification instrumentation without capital investment. 
  • gDNA fragmentation replaces mechanical shearing. Simultaneous digestion and labelling of DNA fragments simplify the workflow. 
  • Single primer target enrichment technology (SPET) enables highly flexible and scalable custom panel design.
  • Dual-index sample barcoding enables multiplex sequencing of more than 3,000 samples in a single sequencing lane, allowing further scalability without limitations.

Download application note

References

  1. Kyriakidou M, Tai HH, Anglin NL, et al. Current strategies of polyploid plant genome sequence assembly. Frontiers in Plant Science. 9, 1660. Published November 2018. Accessed September 17, 2021. https://doi.org/10.3389/fpls.2018.01660 
  2. van Dijk, T. The allo-octoploid strawberry: simply complex. Thesis Wageningen University. Published November 2016. Accessed September 17, 2021. https://edepot.wur.nl/392822 
  3. Edger PP, Poorten TJ, VanBuren R, et al. Origin and evolution of the octoploid strawberry genome. Nat Genet. 51, 541–547. Published February 2019. Accessed September 19, 2021. https://doi.org/10.1038/s41588-019-0356-4 
  4. Schaart JG, van de Wiel CCM and Smulders MJM. Genome editing of polyploid crops: prospects, achievements and bottlenecks. Transgenic Res 30, 337–351. Published April 2021. Accessed September 17, 2021. https://doi.org/10.1007/s11248-021-00251-0 
  5. Gaston A, Osorio S, Denoyes B, et al. Applying the Solanaceae strategies to strawberry crop improvement. Trends in Plant Science. 25, 2. 130-140. Published February 2020. Accessed September 17, 2021. https://doi.org/10.1016/j.tplants.2019.10.003 
  6. Whitaker VM, Knapp SJ, Hardigan MA, et al. A roadmap for research in octoploid strawberry. Hortic Res 7, 33. Published March 2020. Accessed September 17, 2021. https://doi.org/10.1038/s41438-020-0252-1 
  7. LGC, Biosearch Technologies. SeqSNP targeted GBS as alternative for array genotyping in routine breeding programs. Published September 2021. Accessed September 16, 2021. https://biosearch-cdn.azureedge.net/assetsv6/seqsnp-tgbs-alternative-genotyping-routine-breeding-programs.pdf 

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LGC, Biosearch Technologies is the complete Genomics portfolio from LGC. Providing genomic analysis tools, instrumentation and services to the genomic scientific discovery sector worldwide, with focus on across ag bio, pharma and molecular diagnostics. Visit our home page to view our products and services.

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