Unveiling corn's 'selfish' gene

Helps curb pollen drift and provides a new isolation-free solution for seed and fresh corn production

White corn is a new variety that is incompatible with one-way hybridization, and there is no "cross-pollination" phenomenon with the neighboring yellow corn.

Corn is a favorite of many whole grain lovers. Careful "foodies" will find that the price of "pure" corn on the market is higher.

Unlike wheat and rice, which are self-pollinating, corn, one of the three major staple foods, is a typical cross-pollinating crop, although it is "monoecious". This makes it difficult for corn in the field to maintain its "pure" characteristics due to "cross-pollination". In order to produce pure corn with better appearance and taste, isolation measures such as time or space have to be taken, which brings difficulties to production and increases costs.

Miraculously, there are some "selfish" corn types in nature, whose pollen can spread outward but do not accept foreign pollen. This naturally occurring biological isolation barrier provides a new non-isolation solution for purebred corn production and seed production.

Scientists discovered this "unidirectional hybrid incompatibility" (UCI) between corn more than 100 years ago. However, due to the complexity of its genetic mechanism and the differences in genome structure between different types of corn, the gene cloning and mechanism research that controls this phenomenon has been extremely slow and difficult, and it can be called the "problem of the century."

After more than ten years of unremitting efforts, Chen Huabang's research team from the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, has once again made a breakthrough in the field of one-way hybrid incompatibility in corn, unveiling the mystery of corn UCI, systematically expounding its molecular mechanism, and cultivating my country's first new combination of one-way hybrid incompatibility fresh corn. The relevant results were published in Nature Communications on April 15.

"Excellent" and "important" are the comments given by the three reviewers unanimously.

Solving the mystery of the century

In 1902, German botanist Correns discovered a non-Mendelian inheritance phenomenon when studying the offspring of the mutant gene su in sweet corn - an extreme form of uniparental inheritance. When this gene material is hybridized with other materials, its offspring will show the "selfish" phenomenon described at the beginning of this article, which is to only expand their own genes and reject foreign pollen.

"The compatibility of species determines and balances the diversity and stability of plant populations on Earth." Chen Huabang said that incompatibility is an important mechanism for various species such as corn, rice, and sorghum to maintain their own characteristics. However, in the process of natural variation and human domestication, incompatibility genes between some species or their subspecies will gradually be lost, and genetic materials will be exchanged with each other, so that plants have population diversity and the traits that people need.

Since UCI affects the direction of pollen gamete transmission, the gene that controls this phenomenon was first called the gametophyte gene (Ga). The first UCI site discovered by Collens was named Ga1, which is one of the most thorough sites of unidirectional hybrid incompatibility.

For a long time, people believed that UCI was dominated by the behavior of male gametes, pollen, while ignoring the role of female gametes. It was not until 1965 that researchers gradually realized that female gametes were also involved.

Despite this, the genetic laws of UCI have not been revealed.

Through genetic analysis of large-scale populations, Chen Huabang's team revealed the mode of joint action of male and female determining factors behind the Ga1 locus in 2018. "In fact, there is a pair of determining factors. The female gametophyte forms a 'shield' to block foreign male gamete pollen, but its own pollen produces a 'spear' that can penetrate its own 'shield'." He metaphorically said that now they have found that another gene locus Ga2 also controls the UCI phenomenon through this mechanism.

"In fact, Ga1 and Ga2 are both 'old genes'. Their male-female determining factors both encode pectin methylesterase (PME). Adding it to fruit products such as jams, sauces, and fruit pulp can increase hardness, improve viscosity and taste, and affect the composition and structure of cell walls." Chen Huabang said, but it has never been reported before that it is related to crop incompatibility.

The new study discovered new functions of the old gene, indicating that PME can regulate the methylation level of pectin in the pollen tube cell wall. The content of methylated pectin at the top of the incompatible pollen tube is higher than that of the compatible corn.

Since UCI materials are generally derived from popcorn and ancestral teosinte, they are quite different from the genome sequence of common corn, and their heterozygous homologous chromosomes have poor pairing and less recombination between chromosomes, which greatly increases the difficulty of fine positioning and positional cloning of UCI sites. For more than a century since the discovery of the UCI phenomenon in corn, the key genes of the UCI site have not been cloned.

To address this challenge, the team constructed a bacterial artificial chromosome data library (BAC) of UCI materials, and with the help of whole-genome association analysis and de novo splicing of genome transcription data, they were the first to map and clone the relevant male and female determining factors, and verified their functions through gene complementation and overexpression of transgenics.

"The determinants of maize gametophyte incompatibility have been a hot topic for nearly 100 years, and I think this is an excellent result on this important topic by UCI. I am familiar with other studies by these authors, and I have been impressed by the quality and level of their past research, and this paper is no exception," commented a reviewer.

New combination of fresh corn

If this theoretical mechanism is mapped to breeding practice, it will undoubtedly help solve the "pollen cross-fertilization" problem in corn production.

Based on the genetic analysis and precise positioning of the UCI locus, Chen Huabang's team simultaneously developed functional molecular markers. Using backcrossing and molecular marker-assisted selection, they introduced the UCI locus into the parents of JKN2000, the largest glutinous corn variety in my country, and cultivated the first new "UCI fresh corn" combination.

"Its out-crossing rate is less than one thousandth, which can realize the non-isolation seed production and non-isolation production of JKN2000." Chen Huabang introduced that the relevant technology has effectively solved the practical problem of a Chinese seed company exporting this variety abroad, which was caused by "cross-pollination" and thus affected the price.

Traditional corn planted next to each other will have "pollination" phenomenon, resulting in impure corn kernels (left picture), while the new corn material containing UCI loci (right picture) is not contaminated by "pollination" of foreign pollen.

At the same time, he said that the UCI system of corn is independently controlled by multiple loci, such as Ga1, Ga2 and Tcb1 loci, which will not accept foreign pollen and are also incompatible with each other. In order to reduce the risk of a single UCI locus being "penetrated" by individual materials for pollination, they aggregated these incompatible UCI loci together to create germplasm resources that do not exist in nature.

"In nature, it takes a long time for such germplasm resources to be aggregated together, or it may never be completed," said Chen Huabang.

So, how did they make these incompatible genes come together through artificial intervention? Chen Huabang introduced that the female gametophyte of corn is located at the base of the filament, while the pollen tube produced by pollen grows in the filament. Fertilization can only be achieved when the pollen tube successfully enters the filament and transports the male gametophyte to combine with the female gametophyte egg cell at the base of the filament. The reason why corn is incompatible is that the filament blocks the pollen tube from going to the female gametophyte.

In response to this characteristic, they created a "cut filament" pollination method, which directly delivers pollen to the base of the filament, breaking the reproductive barriers between different UCI sites and cultivating the first "poly-UCI" new germplasm, laying the material foundation for the subsequent cultivation of related new combinations.

According to reports, another innovative point of the research is the invention of a "homogeneous population" positioning method. Based on the analysis of the genetic laws of UCI, the team created a unique positioning strategy for the UCI male-determining factor. Without identifying the plant phenotype, the male-determining factor can be located directly by measuring the genotype, which improves the positioning efficiency of the UCI locus. According to conventional methods, one-to-one pollination of the positioning group is required to observe the fruit-bearing phenotype, which limits the expansion of the positioning group and has low positioning efficiency.

New “non-isolation” seed production solution

Corn is the crop that has made the most effective use of hybrid vigor in the world. Since the 1930s, the use and promotion of hybrids has led to a qualitative leap in global corn production.

my country's corn-growing areas are widely distributed, the natural conditions of each producing area vary significantly, and the microclimate within the producing areas is complex and changeable, resulting in a rich variety of corn hybrid types in my country.

"The isolation between seed fields of different varieties is a major problem in my country's corn seed production, which has long troubled my country's seed industry workers." Researcher Chen Huabang gave an example, in Zhangye, Gansu, my country's "seed production holy land", about one million mu of land is required to undertake the task of seed production of about hundreds of varieties every year. The coordination and layout of the "isolation zone" has become one of the most severe challenges facing local seed production.

The application of UCI and the scientific layout between related sites will make "seed production without isolation" possible.

At the same time, as people's living standards improve and the demand for special corn in medical and industrial production increases, the purity of special corn is an important criterion for measuring its economic value. "The application of UCI will also become an effective means to prevent special corn from being contaminated by ordinary corn," said researcher Chen Huabang.

"This is an excellent study that provides valuable insights into one-way hybrid incompatibility systems in corn. They are important and will be of great value to the popcorn industry as well as the organic/non-GMO markets," said another reviewer.

The white fresh corn grown in the north is a new variety of one-way hybrid incompatibility, and has not been found to be "cross-pollinating" with the neighboring yellow corn.

Scientific research is never achieved overnight. It is precisely because of more than ten years of persistence and accumulation that Chen Huabang's team has achieved several innovative research results in the field of corn UCI from "zero to one" and from simple to in-depth, refreshing people's understanding of UCI over the past century.

"Now, we can say with confidence that Chinese scholars are at the forefront of the world in the research of one-way hybrid incompatibility in corn." Chen Huabang hopes to further combine theoretical research with practical application to promote industrial development and the upgrading of seed production technology.

Related paper information:

https://doi.org/10.1038/s41467-022-29729-z.

https://doi.org/10.1038/s41467-018-06139-8