Discover how tiny genetic variations called indels are revolutionizing maize breeding and improving global food security
In the intricate blueprint of life, sometimes the most crucial information lies not in the genes themselves, but in the tiny, hidden spaces between them.
Imagine you have two nearly identical instruction manuals for building a complex machine. They are the same, word for word, except that in one manual, a single sentence is missing. That small difference could change everything about how the machine functions.
This is the world of indels—short for insertions and deletions—which are tiny bits of genetic material that are either added or removed from a DNA sequence 1 . In the quest to improve one of the world's most important crops, maize, scientists have embarked on a treasure hunt, using the power of modern DNA sequencing to find these microscopic differences. Their goal is to create powerful new tools, called genetic markers, that can speed up the development of corn that can better feed our growing world 1 .
To understand the significance of this genetic treasure hunt, we first need to appreciate the sheer scale and importance of the maize genome. Maize, known as corn in many parts of the world, is not just a simple snack; it is a cornerstone of global agriculture, a source of food, animal feed, and biofuel.
Its genetic code, or genome, is a massive and complex instruction manual. Scientists first fully decoded this manual for a reference variety called B73 in 2009 1 . This was a monumental achievement, but it was only the beginning. To truly improve corn, we need to understand how the manual differs between various types of corn.
This is where Next-Generation Sequencing (NGS) comes in. Think of it as a super-powered photocopier that can read and digitize millions of pages of DNA instructions from hundreds of different corn varieties at an unprecedented speed and low cost 1 7 . By comparing these hundreds of digital blueprints to the original B73 reference manual, scientists can spot the differences—the genetic variations that make one corn plant more drought-resistant or another more nutritious.
For a long time, most genetic research focused on a different type of variation called SNPs (Single Nucleotide Polymorphisms), which are single-letter changes in the genetic code, like a typo (e.g., "cat" vs. "bat"). However, indels are now recognized as an equally important and abundant source of natural variation 1 . An indel might be the insertion or deletion of a few letters, or even a whole paragraph of DNA.
These small changes can have big consequences. In humans, indels are known to cause diseases like cystic fibrosis 1 . In plants, they can dramatically alter a plant's appearance, its ability to resist pests, or its yield. For example, key genes responsible for the domestication of maize from its wild ancestor, teosinte, involve indel variations 1 . This makes them incredibly valuable for both understanding plant biology and for guiding breeding efforts.
Indels represent a major class of genetic variation alongside SNPs
Addition of genetic material into the DNA sequence
Removal of genetic material from the DNA sequence
Can alter gene function, regulation, and protein structure
To unlock the potential of indels, a team of researchers designed a comprehensive study to find and catalog these variations on a genome-wide scale. They used an innovative computational strategy to sift through the DNA of 345 different maize varieties, including inbred lines and traditional landraces from around the world 1 .
The researchers started by designing millions of virtual "hooks," known as primers, that could latch onto unique spots all across the B73 reference genome. This was like creating a unique tag for every interesting paragraph in the instruction manual 1 .
Instead of doing physical experiments in a lab, they used a clever computer simulation called electronic PCR (e-PCR). They took the massive amount of sequencing data from the 344 other maize varieties and virtually "fished" for matches to their primers. If a primer from one plant matched the reference manual but the DNA fragment between the primers was a different size, it signaled a potential indel 1 .
This high-tech fishing expedition was a huge success. They discovered a staggering 1,973,746 unique indels scattered throughout the maize genome 1 . To ensure these weren't just computer errors, they selected 100 of the most promising markers and tested them in a real lab. The results confirmed their digital findings with an accuracy of about 90%, proving the method was both powerful and reliable 1 .
The analysis revealed several fascinating insights into the maize genome:
| Feature | Finding | Significance |
|---|---|---|
| Total Unique Indels | 1,973,746 | Shows maize has a very high level of natural genetic diversity 1 |
| Overall Density | 958.79 indels/Mbp | Indicates how common these variations are throughout the genome 1 |
| Highly Polymorphic Indels (PIC ≥ 0.5) | 264,214 (13.39% of total) | Represents the subset most useful for genetic studies and breeding 1 |
| Average Number of Alleles | 2.76 | Suggests most indels have two or three common variants in the population 1 |
| Genomic Region | Relative Indel Density (from highest to lowest) |
|---|---|
| Region upstream of Transcription Start Site (TSS_up_0.5Kb) | Highest |
| 5'-Untranslated Region (5'-UTR) | ↑ |
| 3'-Untranslated Region (3'-UTR) | ↑ |
| Region downstream of Transcription End Site (TES_down_0.5Kb) | ↑ |
| Introns (non-coding parts of genes) | ↑ |
| Intergenic Regions (between genes) | ↑ |
| Code Determining Sequences (CDSs) | Lowest 1 |
What does it take to run such a sophisticated genetic analysis? Here are some of the essential tools and reagents that power this research.
| Tool/Reagent | Function in the Experiment |
|---|---|
| Reference Genome (B73) | The standard genetic "map" or blueprint against which all other varieties are compared 1 |
| Next-Generation Sequencer | The high-tech machine that reads the DNA sequences of hundreds of maize samples, generating billions of data points 1 7 |
| Restriction Enzymes (e.g., Ape KI) | Molecular "scissors" that cut the DNA into manageable-sized fragments for sequencing, a technique often used in genotyping-by-sequencing (GBS) 7 |
| e-PCR Primers | Short, single-stranded DNA sequences designed to bind to specific, unique locations in the genome, acting as anchors for finding indels 1 |
| Bioinformatics Software (e.g., GATK, SAMtools) | The sophisticated computer programs and pipelines that analyze the massive amounts of sequencing data to identify and characterize indels 1 |
Modern bioinformatics tools are essential for processing the massive datasets generated by next-generation sequencing.
Despite computational advances, physical validation in the lab remains crucial to confirm findings.
The development of these genome-wide indel markers is far more than an academic exercise; it is a practical tool that is already enhancing the efficiency of maize breeding. By using these markers, breeders can quickly and accurately select parent plants with desirable traits, such as disease resistance or improved yield, without having to wait for the plants to grow to maturity. This process, known as marker-assisted selection, significantly speeds up the breeding cycle 1 .
The implications are profound. In a world facing the dual challenges of climate change and a growing population, the ability to rapidly develop more resilient and productive crop varieties is critical. The humble indel, once a hidden part of the genetic landscape, is now in the spotlight, helping scientists and breeders write a new, more promising future for global food security—one tiny genetic variation at a time.
This research contributes to food security for a growing global population
This article is a popular science adaptation of the research published in BMC Genomics in 2015: "Development of genome-wide insertion and deletion markers for maize, based on next-generation sequencing data."