Solve a century-old genetic problem and help corn molecular breeding

The hybrid offspring of a crop show greater biomass, greater stress tolerance, and higher yields than its parents, which is the hybrid advantage. For more than a hundred years, geneticists have been struggling to find the genetic mechanism behind it, looking for gene loci that can make offspring more “outstanding” than their parents, but it is difficult to uncover its mystery.

Recently, Nature Genetics published the research results jointly completed by a team of Chinese breeding scientists and geneticists online, and made significant progress in constructing the pan-genome of maize core inbred lines and analyzing the formation mechanism of maize hybrid dominance.

The paper reviewers believe that the maize genome assembled by the institute is very important, useful and informative, and will play a key role in promoting the research and breeding efficiency of maize, a world-important crop.

Different maize germplasm. Photo courtesy of interviewee

Mysterious mechanism of hybrid dominance

“Heterodominance is a common phenomenon in the biological world, and the use of heterogeneity is one of the main methods of crop breeding.” Wang Haiyang, co-corresponding author of the paper and professor of South China Agricultural University, told China Science News that at present, the genetic mechanism of plant heterogeneity is still lagging behind as a whole, although scientists have carried out research related to heterogeneity site mining and genetic mechanism analysis, but the mechanism of heterogeneity has not been fully explained.

Zhao Jiuran, co-corresponding author of the paper and researcher at the Beijing Academy of Agriculture and Forestry Sciences, said that corn is currently the world’s largest food crop with the highest total output in China, accounting for about 36% of global cereal production. At the same time, corn is also one of the crops with the strongest hybrid advantage and the most successful application in crops, and almost all the corn varieties used in China’s production are hybrids based on hybrid advantages.

As a breeding scientist, Zhao Jiuran calls himself “Maize Regiment Leader” and is also a co-initiator of the research. He led the team to cultivate and scale up the quality corn varieties approved in more than 100 countries. “Two corn inbred lines are not good on their own, and they have to find a good pairing.” Zhao Jiuran told China Science News that the probability of truly encountering a strong hybrid advantage in breeding is still not high.

In breeding practice, scientists like Zhao Jiuran can already rely on a large number of phenotypic observation and breeding practice experience to select suitable parent groups for hybrid experiments, but the process requires a lot of energy and time, “plant by plant matching, and then test the traits of hybrids”. Zhao Jiuran stressed to reporters that the practical experience of breeding must rise to the theoretical level, and then use theory to guide breeding practice.

However, the question of why corn has a strong hybrid advantage has not been solved. “This is a question that researchers who do genetics research want to answer.” Wang Haiyang said that the phenomenon itself is very complex, and the reasons for it may be diverse. Some current hypotheses may simply try to answer this question from a certain side or angle. “What exactly is the mechanism of heterogeneity, which is probably the most difficult question in genetics to answer.”

Hybrids are F1 generations produced by hybridization of two homozygous materials, the so-called inbred parents. “The breeding process often speculates empirically which two parents can produce better advantages, but it is not known how strong the hybrid offspring of two specific parent plants will produce.” Wang Haiyang said that if you know in advance which two parent hybrids can produce a strong hybrid advantage, you may not have to do such a large-scale, high-cost hybrid breeding process.

Wang Baobao, the first author of the paper and a researcher at the Institute of Biotechnology of the Chinese Academy of Agricultural Sciences, said in an interview with China Science News that although the academic community generally believes that the heterogeneity of corn is related to the genetic differences of both parents, because the genetic differences between corn inbred lines of different groups are very large, a common corn material is traditionally used as a reference genome for genetic analysis, and it is often easy to miss the genetic information specific to many maize groups.

Wang Baobao said that due to the lack of accurate genomic information of maize core germplasm, it is difficult to deepen the research on the advantages of maize hybrids, and most of the research only stays in the stage of hypothesis speculation and rough quantitative trait site estimation. This makes the current selection and breeding of corn hybrids mainly dependent on experience, long breeding cycle, low efficiency, and lack of breakthrough new varieties.

First verification of the “genetic complementarity hypothesis” at the genomic level

The next popular hypothesis is that the advantage of corn hybrids arises because the original advantages and disadvantages of the two parents complement each other, and the hybrid offspring retain the advantages of both sides. To test this hypothesis, it is impossible to understand the differences in genetic information between maize taxa.

In view of this, Wang Haiyang’s team united the scientific research teams of South China Agricultural University, Institute of Biotechnology, Chinese Academy of Agricultural Sciences, China Agricultural University, Beijing Academy of Agriculture and Forestry Sciences, Henan Agricultural University and other maize research advantageous units to assemble the high-quality genomes of 12 backbone inbred parents widely used worldwide through third-generation sequencing and other technologies, and combined with the published maize genome to construct a pan-genome of temperate maize core germplasm. This pan-genome represents virtually all maize hybrid dominant populations currently used in production.

“Previous studies have shown that the genetic differences between corn inbred lines are greater than the differences between humans and gorillas, and our analysis further suggests that the differences between inbred lines may be even greater than we expected.” Wang said they found that the average DNA sequence between the two corn inbred lines was only 56.3 percent highly similar, which means that more than 40 percent of the sequences between the corn inbred lines were different.

Analysis of genetic tools showed that “there is a wide range of genetic variation between inbred lines of maize.” Wang Haiyang said that these corn inbred lines not only have obvious genetic differences, but also look very different in appearance.

Further studies found that maize hybrid dominance was significantly positively correlated with the number of structural variation between the genomes of both parents, but negatively correlated with the degree of collinearity between the genomes of both parents. This indicates that maize hybrid dominance is closely related to the genetic complementarity of both parents at the genome-wide level, which provides strong support for the genetic complementarity model of heterogeneous dominance.

“That is, the higher the similarity between corn genomes, the smaller the heterogeneous advantage, and the more differences (structural variation) in the DNA sequences of large fragments, the stronger the heterogeneous advantage.” Wang Baobao explained that large DNA sequence differences generally mean that a large DNA fragment is present in one inbred line, not in another, or exists in the form of another sequence, or has undergone an inversion or position change.

Complementarity occurs when two inbred lines with such differences are hybridized. “We found that the more large DNA sequences between two inbred genomes complement each other, the stronger the hybrid dominance of F1 hybrids produced by their hybridization. Therefore, the genetic complementarity of the parents at the genome-wide level may be the most important reason for the formation of corn hybrid dominance. Wang Baobao said.

Wang Haiyang said that this work is the first to provide strong evidence at the genomic level for the hypothesis that genetic complementarity leads to corn hybrid dominance.

For the first time, the heterogeneity gene for corn was found

“In addition to complementarity at the genome-wide level, we were fortunate to find two dominant super-relative maize hybrid dominance sites.” Wang Baobao said that the dominant site of dominant super-relative heterozygous refers to the fact that the heterozygous genotype of a certain site in the genome will have a better effect than both parents for a certain trait. This is also another hybrid dominance mechanism hypothesis popular in the academic community.

After extensive work, combining genetic and molecular biology evidence, they unearthed two key yielding heterodominance genes, ZmACO2 (encoding an ethylene synthetase) and ZAR1 (encoding an ethylene signaling-related protein). It was demonstrated that the different genotype combinations of these two sites in hybrids can produce a heterozygous effect that is superior to the expression of homozygous genotypes of both parents. ”

Wang Haiyang said that because of the large differences between maize populations, there are millions of different sites between the two genomes. It is a difficult challenge to find a certain point in such a large difference site and prove that it is stronger and more prominent than the heterogeneous advantage produced by other sites.

Zhao Jiuran said that this work provides clear molecular and genetic data support for the hypothesis of unit point superdominant effect of maize hybrid dominance, and for the first time proves that both genetic complementarity and superdominant effects of specific sites contribute to maize heterogeneous dominance. “This key site of heterogeneity is also sought and pursued by breeding scientists.” 

The first reference genome of maize is the B73 genome published in 2009, which greatly promotes the mining of functional genes of maize and the analysis of the genetic mechanism of important traits. Wang Haiyang believes that the core inbred complete genome assembled by this study will also greatly promote the advancement of maize functional genome research worldwide. Zhao Jiuran pointed out that using this achievement to guide the selection process of maize parents, more combinations with strong hybrid advantages can be found.

Lai Jinsheng, co-corresponding author of the paper and a professor at China Agricultural University, told China Science News that this work has provided a relatively good analysis of the maize pan-genome, and to a certain extent, it outlines an explanation of the genomic dimension for the mechanism of heterogeneity. Multiple hypotheses about the mechanism of heterodominance are not necessarily mutually exclusive, but compatible to a certain extent, but there is still a long way to go to fully explain the mechanism of heterodominance, and there are still great challenges.

Wang Haiyang stressed that no matter which crop has tens of thousands of genes, scientists cannot study all the genes of a crop with the strength of their lifetime. The excellent traits of crops are the result of polygenic polymerization, “we can’t figure out every gene and then polymerize and breed.” In the future, we want to explain the aggregation effect of genes at the genome-wide level, and develop digital breeding techniques to guide the breeding of strong dominant maize hybrids. (Source: Li Chen, China Science News)

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