New maize reference genome may help grow genetically modified lines of corn more easily

The ugly duckling of corn may hold the key to having better grains in the future.

Maize, also known as corn, is widely cultivated for a variety of uses such as human consumption, fuel and feed. Unraveling the amazing diversity of maize has fascinated geneticists for decades and has helped improve one of the main crops that feed the world. Now, a group of scientists has added a new chapter to the genetic encyclopedia of this indispensable cereal. Their work will help improve regeneration of transformed plants, a major bottleneck in the advancement of crop biotechnology.

Scientists turn to plant transformation, the insertion of DNA from other organisms into a plant’s genome, to study a certain gene or to make a more useful crops for humans. Take diseases, for example. Scientists and growers may be interested in having maize that is resistant to leaf blight. For this, they could introduce genetic instructions to resist the disease along with genes of Agrobacterium tumefaciens, a sort of engineer that integrates the genetic instructions to the maize’s genome. This resistant plant is now transformed. But how can scientists ensure the genetic change is passed on to new plants in the most cost and time effective way?

Biologists use tissue culture to re-grow a clone of the same plant containing the genetic changes in a process called regeneration. Regeneration is difficult to achieve in most maize lines and almost impossible in most other crops.

That is where a line of a low-yielding corn known as A188 comes in. Last month, a group of researchers published in The Crop Journal a new reference genome for A188 that holds in its genome clues that might help improve plant regeneration in other varieties of maize.

A188 is like the ugly duckling of maize: It has poor agronomic traits because it is much shorter, flowers earlier, and has lower yield compared to other varieties. So, if A188 does not perform as well in the field as other more productive varieties, why would it be of value to annotate its genome? It is exactly these dramatic differences that make A188 valuable to study.

“[T]he A188 genome may add information about flowering time, which is important for maize productivity and seed quality,” says Jiahn-Chou Guan, a maize researcher at the University of Florida. “Also, comparative analysis of genome sequences can give us new information on controls for plant architecture because of its short stature.”

Another astonishing difference is that A188 is much better at regenerating, or re-growing from stem cells. Scientists found A188 has a 91% chance of regenerating plants from tissue culture compared to other popular research varieties: 1.67% in W22, 6.94% in Mo17 and 0% in B73. It is not understood why or how certain genotypes are more or less efficient in regenerating in tissue culture, but it is thought that analysis of the A188 genome will be helpful in improving regeneration capacity in other maize lines.

Another novel aspect of this research lies in the methodology. Most techniques for DNA sequencing produce highly accurate short “reads” or sentences, and other methods produce long reads but are prone to error. However, the group of researchers from the Maize Research Institute in Sichuan Agricultural University of China and the Berry Genomics Corp. in Beijing, China used  PacBio’s single molecule sequencing platform instead, allowing them to have the best of both worlds in long and highly accurate reads. This new method increased the resolution and accuracy compared to previously released maize genomes. After the genome was assembled, researchers compared side by side the chromosomes of A188 withB73, Mo17 and W22, and found that about 30% of A188 genes had large structural variations, or changes in the structure of their genes. These changes could be potential genetic causes that explain the physical differences of A188 and why it is so much better at regeneration than other maize varieties.

The researchers narrowed down their analysis to a list of 10 candidate genes that may be responsible for A188’s high-capacity of regeneration. These candidate genes are valuable genetic resources for improving maize genetic transformation and regeneration.

Interestingly, most transgenic maize has some part of its DNA coming from A188 since the most popular maize line being used for transformation and regeneration is called Hi-II, which is descended from a cross with A188.

“Even after multiple back-crosses, the transgenics and CRISPRs will carry some of the A188 genome. It will be good to know what’s in there!” says Karen E. Koch, a maize researcher at the University of Florida. “Additionally, our understanding of white corn behavior is potentially enhanced by knowing more about A188. The genome is potentially useful for tracking its role in post-domestication improvement of maize that involved repeated selections for white vs. yellow kernels by different cultures for different reasons”.

The Human Genome Project is currently adding genomes from people from across the globe to build a reference pangenome that is more representative of human genetic diversity for medical research. Similarly, the maize pangenome will be better representative of maize genetic diversity with the new addition of the A188 reference genome and aid in much more discovery.


Fei Ge, Jingtao Qu, Peng Liu, Lang Pan, Chaoying Zou, Guangsheng Yuan, Cong Yang, Guangtang Pan, Jianwei Huang, Langlang Ma, Yaou Shen. Genome assembly of the maize inbred line A188 provides a new reference genome for functional genomics. The Crop Journal. 2021.

Nadia Mourad Silva is a Ph.D. student at the University of Florida studying maize genetics and physiology. She is currently working on understanding sugar metabolism in the kernel. Nadia strives to be a lifelong learner and enjoys explaining complicated concepts in ways anyone can understand. When she is not in the field or the lab, she helps run her tropical plant nursery with her partner.

Spanish translation by Lorena Villanueva Almanza

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