GBS & Marker-Assisted Selection

GBS & Marker-Assisted Selection Overview

Our GBS & Marker-Assisted Selection provides a comprehensive and cutting - edge approach to modern agricultural breeding. GBS is a high - throughput, cost - effective genotyping method that allows for the simultaneous discovery and genotyping of thousands of genetic markers across the genome. The AgriSeq Panel provides a targeted approach, focusing on a curated set of key genetic markers. When combined with broader genomic analyses, these technologies work together to give us a complete and precise picture of genetic makeup. This integrated strategy enables faster, more efficient breeding by guiding selection with accuracy.

Our GBS & Targeted Panel Solution for Marker-Assisted Salection Empowers Your Agricultural Breeding with:

• Comprehensive Marker Discovery: GBS enables the identification of a vast number of single - nucleotide polymorphisms (SNPs) throughout the genome. This provides a detailed genetic fingerprint of each individual, allowing breeders to distinguish between closely related genotypes. For example, in crop breeding, it can help identify subtle genetic differences that contribute to variations in yield, quality, or stress tolerance.
• Accelerate breeding decisions: Our toolkit provides detailed genetic information to help breeders quickly identify parents carrying the optimal gene combination. This enables us to significantly shorten the breeding cycle, saving time while effectively reducing the cost of maintaining large-scale populations.
• Flexible customization on demand: Our targeted sequencing solution offers exceptional flexibility, allowing for the creation of custom panels tailored to specific species or breeding objectives. For example, in developing new tomato varieties, you can design a dedicated panel to precisely detect key genes governing fruit size, color, and flavor profiles, enabling highly focused selection.
• High-Throughput Genotyping: Both our GBS and custom panel services are engineered for high-throughput operation, empowering breeders to process thousands of samples efficiently. This scalability is vital for large-scale breeding programs. For instance, in a maize improvement project, our platform can genotype hundreds of seedling samples in a single streamlined run, providing rapid assessment of genetic potential and significantly accelerating the selection cycle.

What Is GBS & Marker-Assisted Selection

Genotyping-by-Sequencing (GBS) & Marker-Assisted Selection are vital in modern agri-research. GBS is a high-throughput genotyping method, discovering numerous genetic markers across the genome. Marker-assisted selection uses these markers to predict trait expression. By analyzing gene loci related to yield, quality, etc., it reveals gene-trait links. This combination accelerates breeding of high-yield varieties, boosting agricultural productivity and sustainability.

How We Deliver This Solution

Sample Collection & Preparation

1. Diverse Germplasm Collection & Phenotyping

We start by building a diverse germplasm panel that includes wild relatives, landraces, and elite varieties. Each sample is paired with high-quality phenotypic data for traits like yield and stress tolerance. Collected from various environments, these samples enable the discovery of locally adapted alleles. We also integrate multiple molecular layers (e.g., transcriptomics, metabolomics) from relevant tissues for a holistic, multi-omics view.

2.Multi-Tissue and Multi-Omics Integration

To build a holistic view of the genotype-to-phenotype map, we often employ a multi-omics strategy. During collection, we sample relevant tissues (e.g., roots under drought stress, seeds for quality analysis, animal blood or muscle). We integrate genomic data with other molecular layers, such as transcriptomics (gene expression) and metabolomics (biochemical profiles), alongside detailed environmental records.

Sequencing

1. Genotyping-by-Sequencing (GBS) for Discovery and Diversity

How We Deliver: GBS uses restriction enzymes to reduce genome complexity, followed by high-throughput sequencing to genotype thousands of markers across the genome. This is our go-to method for initial genetic diversity assessment, constructing genetic maps, and conducting genome-wide association studies (GWAS) in populations without a pre-existing reference panel.

Application: It is exceptionally cost-effective for screening large populations at the early stages of a breeding program. We use GBS to uncover novel genetic variants, analyze population structure, and identify genomic regions associated with traits in unstructured or highly diverse germplasm collections.

2. Custom Targeted Panels for High-Throughput, Application-Focused Genotyping

How We Deliver: Leveraging discoveries from our GBS data and public repositories, we design custom targeted genotyping panels. These panels utilize a highly multiplexed, amplicon-based sequencing approach to focus on a curated set of known, trait-relevant markers, ensuring exceptional genotyping accuracy, reproducibility, and cost-efficiency for large-scale screening.

Application: This method forms the core of our applied marker-assisted selection (MAS) pipeline. Once key marker-trait associations are validated, we deploy these custom panels for routine, high-throughput genotyping in advanced breeding generations. This facilitates the rapid and precise selection of superior individuals carrying desirable alleles for traits such as disease resistance, quality, and stress tolerance, thereby dramatically accelerating the breeding cycle.

Bioinformatics

1. Population Genomics & Genetic Architecture

We start with stringent quality control (using tools like PLINK) to clean the data. We then analyze population structure to clarify genetic relationships and ancestry. This allows you to make informed crossing decisions, manage genetic diversity, and avoid spurious associations in later analyses.

2. Selection Signature & Genomic Selection

We scan the genome for signatures of selection using statistical methods like XP-CLR (Cross-Population Composite Likelihood Ratio) and iHS (Integrated Haplotype Score). This reveals genomic regions that have been under historical selection pressure, highlighting genes that contributed to the improvement of traits like grain size or animal growth rate. Furthermore, we use the genome-wide marker profiles to build Genomic Selection (GS) models. These models calculate Genomic Estimated Breeding Values (GEBVs), allowing breeders to select individuals based on their total genetic potential at the seedling stage, long before phenotypic evaluation.

3. Gene-Trait Association & Functional Annotation

Which specific gene variants control my trait of interest? We perform GWAS to find statistically robust associations. We then annotate these variants to understand their potential biological effect (e.g., if they disrupt a protein), giving you a shortlist of high-confidence candidate genes to target in your program.

Service flowchart

Figure 1: How We Deliver This Solution: GBS & Marker-Assisted Selection Workflow

Our Advantages

Cost-Effectiveness for Genome-Wide Coverage

GBS uses restriction enzymes to reduce genome complexity, allowing for the sequencing and genotyping of thousands of markers across the genome at a fraction of the cost of whole-genome sequencing. This makes high-density genotyping accessible for large breeding populations, which is essential for powerful statistical analysis.

Discovery of Novel and Breed-Specific Markers

Unlike array-based technologies that rely on pre-defined markers, GBS is a discovery platform. It can identify novel SNPs and insertions/deletions (InDels) directly within any germplasm, including wild relatives and local landraces. This is crucial for uncovering unique alleles associated with valuable traits in underutilized or locally adapted genetic resources.

No Prior Genomic Information Required

GBS is exceptionally valuable for non-model organisms or crops with limited genomic resources. It does not require a pre-existing reference genome to generate a large number of markers, enabling the implementation of modern MAS in species that were previously lacking genetic tools.

Simultaneous Marker Discovery and Genotyping

The GBS protocol seamlessly integrates the discovery of new genetic variants with the genotyping of individuals in a single, streamlined workflow. This eliminates the need for separate, costly discovery phases and accelerates the transition from initial genetic studies to applied breeding.

High-Resolution Genetic Map Construction

The high density of markers generated by GBS allows for the construction of very precise genetic linkage maps. These improved maps enhance the accuracy of Quantitative Trait Loci (QTL) mapping, leading to the identification of candidate genes with higher confidence and a better understanding of complex trait architecture.

Effective Analysis of Population Structure and Diversity

GBS provides a genome-wide snapshot of genetic variation that is ideal for robust population genetics analyses. It allows breeders to accurately quantify genetic diversity, understand population structure, and identify genetic relationships, which informs decisions on parental selection and germplasm conservation.

Foundation for Genomic Selection (GS)

The dense, genome-wide marker data from GBS is the perfect input for building Genomic Selection models. These models use all markers to calculate Genomic Estimated Breeding Values (GEBVs), allowing for the selection of superior individuals based on their genetic potential alone, dramatically accelerating the breeding cycle for complex, polygenic traits.

Applications

Enhanced Reproductive Performance

Reproductive efficiency is a key factor in livestock production. GBS can help identify genetic variants related to reproductive traits in pigs, such as litter size and age at puberty. The AgriSeq Panel can be used to screen pig populations for these markers. Farmers can increase the number of piglets per sow and reduce the time to first breeding, thereby improving the overall productivity of the pig herd.

Genome-Wide Association Studies (GWAS)

GBS is a powerful tool for GWAS in diverse natural populations or association panels. It detects genome-wide markers that are significantly associated with specific phenotypes. This approach leverages historical recombination events to identify marker-trait associations with much higher resolution than traditional QTL mapping, facilitating the discovery of alleles for disease resistance or quality traits from diverse genetic backgrounds.

Genomic Selection (GS) for Complex Traits

For traits controlled by many genes with small effects (polygenic traits), GBS provides the genome-wide marker density required for Genomic Selection. Researchers use GBS data to build prediction models that calculate Genomic Estimated Breeding Values (GEBVs) for individuals. This allows for selection based on genetic potential early in the lifecycle (e.g., at the seedling stage), significantly accelerating the breeding cycle.

Marker-Assisted Backcrossing (MABC) and Gene Pyramiding

GBS facilitates the introgression of one or a few major genes (e.g., for disease resistance) from a donor into an elite recipient line. The dense markers allow for both foreground selection (to ensure the target gene is present) and background selection (to rapidly recover the recipient genome). Similarly, GBS data is used to pyramid multiple beneficial genes from different sources into a single elite genotype.

Demo

Figure 2: Comparison of mean annual aggregated genetic gain (a), total breeding value (TBV) and variance (b) across different parental selection strategies, including Stage 2 (STG2) with phenotypic selection (PS), and STG2, F6, F2, or F1 generations with genomic selection (GS) using single-seed-descent (SSD) or accelerated SSD (aSSD) methods. (Li, 2022)

Case Study

Marker-Assisted Introgression of the Salinity Tolerance Locus Saltol in Temperate Japonica Rice.

Journal: Rice (N Y)

Published：2023

• Challenge
• Solution
• Scientific Achievements

FAQ