From Lab to Field: How Molecular Genotyping Improves Agriculture


The last few decades have seen dramatic improvements agricultural technology, in part thanks to the implementation of techniques that harness the power of genetic analysis.

The use of molecular genotyping in agricultural breeding programs is ushering in a new era of possibilities, from the rapid analysis of crops and livestock to the identification of traits via DNA sequencing. In this blog, we will explore the methods and impact of molecular genotyping in agricultural genomics.

Improving Food Stability

Molecular genotyping is a tool that enables scientists to gain insight into the genetic makeup of crop plants. By studying these genes and understanding how they affect key traits such as growth, yield, or disease resistance, more advanced breeding programs can be developed to create new crop varieties with desired qualities. This process is called marker-assisted breeding, and it underlies the modern capability to breed crops with improved traits.1

One example of successful marker-assisted breeding is rice, which is a dietary staple for billions of people around the world. Scientists have bred rice varieties that are resistant to diseases such as bacterial leaf blight and blast, thus preventing devastating yield losses. Scientists have also developed Swarna-Sub1, a rice variety shown to be tolerant to submergence for up to two weeks while still able to produce a good yield.2 This variety has been particularly important for farmers in flood-prone areas of India.

Another example of marker-assisted breeding is the development of drought-tolerant maize in sub-Saharan Africa, where more than 80% of the population relies on the crop as a staple food source.3 Using molecular markers, researchers created new strains of drought-tolerant maize that can maintain yields even when water is limited.

Breeding new crop varieties like these, which are more productive, disease-resistant, and adaptable to different environmental conditions, is crucial to ensuring food security amid threats like climate change and disease.

Revolutionizing Agricultural Breeding

The use of molecular tools for genotyping in agricultural breeding has had a relatively short history, with the first molecular markers developed in the 1980s.4 These early markers were primarily used for mapping and identifying genes of interest in crop plants, such as disease-resistant genes.

In the 1990s and early 2000s, the development of high-throughput genotyping methods, such as restriction fragment length polymorphism and amplified fragment length polymorphism, allowed for rapid analysis of large numbers of markers in multiple individuals. This made it possible to conduct genome-wide association studies and quantitative trait locus mapping, which are used to identify genes associated with important agronomic traits.

The advent of microarray-based genotyping, in the late 1990’s, created a subsequent revolutionary improvement in high-throughput genotyping and the ability to measure thousands of markers per sample at the same time. Microarray technology can be used to detect a wider range of genetic variations, including single nucleotide polymorphisms, copy number variations, and structural variations. While microarray genotyping has advantages over other genotyping methods – particularly in terms of cost per marker detected – the technology also has some limitations, such as the fact that it can only directly detect known variations that are built into the array.

Expanding Boundaries of Agriculture Genotyping

In recent years, next-generation sequencing (NGS) technologies have further expanded the boundaries of genotyping in agricultural breeding by providing cost-effective and high-throughput methods for sequencing entire genomes or large portions of genomes.

New breeding techniques include genomic selection, which uses genome-wide marker data to predict the breeding value of individuals. NGS has also facilitated the development of reference genomes for a wide range of crop plants, which has greatly improved our understanding of crop genetics and has been used to pinpoint specific genes and regions associated with desired traits.

Some of these methods include:

  • Genotyping by sequencing (GBS), which is a powerful technique used to identify genetic variation across individuals.5 This method combines the power of NGS technologies with a strategy called reduced representation to selectively sequence a subset of the genome. GBS works by first cutting the genome into small pieces and then only sequencing a subset of those pieces. This subset is chosen because it contains a lot of genetic variation across different individuals. By only sequencing this subset, the process is faster and cheaper than sequencing the entire genome.
  • Low-coverage whole genome sequencing (or “low-pass” WGS) improves on GBS and other methods.6 Sequencing at a low depth typically permits the variation in the genome to be observed at enough locations that even unsequenced bases can be imputed or predicted by their proximity or linkage to neighboring variants. Depending on the application, sequencing depth as low as 0.01x can be used to impute genotypes as accurately as microarray or PCR genotyping. This allows for potentially hundreds or thousands of samples to be analyzed simultaneously.


From improving food stability to mapping and identifying genes of interest in plants, molecular genotyping and NGS technologies have helped shape agriculture. Advances in molecular genotyping have led us to a better, deeper understanding of the plants and animals at the heart of this industry.

At seqWell, we are dedicated to revolutionizing NGS library prep so the full potential of today’s DNA sequencing instruments can be realized. Our plexWell and purePlex technologies allow for simple, scalable multiplexing of samples without time- and cost-consuming normalization. So it becomes easier to sequence human, plant, animal, and microbial genomes.7, 8