Break the bottleneck of breeding and achieve excellent traits of “fish and bear paw”

Rice breeding experts often encounter some headaches: the number of panicles is larger and fewer, the yield of disease resistance is not high, and the high yield is not high quality… Excellent traits are compatible, and it is difficult to have both “fish and bear paws”.

Recently, the team of academician Li Jiayang of the Institute of Genetics and Developmental Biology of the Chinese Academy of Sciences revealed the molecular mechanism of mutual restriction between panicle weight and panicle number, which provides new genetic resources and research ideas for breaking through this breeding bottleneck. The results were published in Nature Biotechnology on 21 April.

The dilemma of “fish and bear paws”

Rice is one of the most important staple crops, feeding more than half of the world’s population. Rice yield is mainly determined by three core elements: the number of panicles, the number of grains per panicle, and the grain weight.

However, these three traits are usually negatively correlated in rice. For example, when the panicle increases, the number of panicles decreases.

“This phenomenon of trade-off between traits is called trade-off effect.” Song Xiaoguang, the first author of the paper and an associate researcher at the Institute of Genetic Development of the Chinese Academy of Sciences, explained to China Science News that it is obtained by plants in the process of long-term selection and evolution, because the resources available for plants to use when they grow in the natural environment are limited, and while enhancing certain traits, they have to weaken other traits.

Scientists have found that the trade-off effect between these different agronomic traits may be related to two factors — interlocking burdens or gene pleiotropy.

According to reports, the chain burden is in the traditional backcross breeding, and the introduction of favorable genes brings in the bad genes that are linked to it, resulting in inconsistencies between the representative type after breeding and the expected results. Currently, this problem can be solved by fine localization of genes and exchange recombination.

However, there is still no effective way to resolve the trade-off effects caused by gene pleiotropy. Current gene function research mainly focuses on the excellent phenotype produced by a gene, and often ignores the negative effects it brings at the same time, making this negative effect difficult to break in breeding practice, and only a small number of genes can be well utilized.

Is it possible to address the phenotypic trade-off effects caused by gene pleiotropy? In order to answer this question, the research team used gene editing technology to edit the IPA1 of the main regulator gene of the ideal plant type of rice, and achieved the combination of “fish and bear paw” with excellent phenotype of panicle weight and panicle number, breaking through the existing breeding bottleneck.

“Cut off” trait chains

IPA1 is a typical pluripotent gene previously identified by Li Jiayang’s team. It can regulate the growth and development process of rice in many aspects, and also has an important regulatory effect on anti-disease and environmental adaptability.

“Increasing the expression of IPA1 in rice can increase the number of grains per panicle of rice, making the panicle of rice larger, but at the same time reducing the number of panicles (tillers) grown per rice, which affects its yield potential.” Song Xiaoguang said, “If we can only improve the expression level of IPA1 in the panicle, so that it only increases the panicle, without affecting the panicle number, or even increase the panicle number, we can further increase the yield of rice.” ”

In order to break through the constraints of panicle and tillering caused by gene pleiotropy, the research team proposed a strategy to modify the expression regulation zone of IPA1 and regulate its expression level in various tissues such as young panicles and stem base, so as to achieve specific regulation of different phenotypes, thereby breaking the negative effect between yield factors.

Song Xiaoguang introduced that a gene can be divided into a coding region and an expression regulation region (cis regulation region), where the coding region determines the function of the gene coding product, and the expression regulation region determines the time and amount of expression of the gene in what tissues and organs.

“Variation in both the coding region and the expression control region play a key role in the domestication and improvement of crops. However, due to the limitations of technical methods, most of the previous research focused on the coding region, and the research on the expression regulation region was very lacking. He said.

Using the “gene scissors” CRISPR/Cas9 technology, the research team systematically sequenced the expression regulation region of the IPA1 gene to study its function.

“Gene editing tools are powerful and can edit any segment of a gene, but where to edit to break the negative effects, we need to identify these segments.” Yu Hong, the corresponding author of the paper and a researcher at the Institute of Genetic Development, said that for this reason, they divided the expression regulation region of the IPA1 gene into many segments like “tiles” and deleted them separately to infer that “which tile” contained important promoter regulatory elements.

In this way, they excavated a material IPA1-Pro10 that could simultaneously increase the panicle number and panicle size from the rice lines deleted from the expression regulatory region, which had fragment deletions of 54 bases in the IPA1 expression regulatory region, with a phenotype of simultaneous increase in panicle weight and panicle number, plant height height, and thick stem and root system.

How much will new materials increase production? In this regard, the research team conducted three field communities to measure and identify the yield, and the results showed that the new material IPA1-Pro10 could increase the yield by 15.9% compared with the control variety Of Flowers 11, which greatly improved the rice yield.

“This is one of the first studies to successfully use the ‘promoter tapping’ strategy in plants and is an important breakthrough in promoting rice yields.” A reviewer review.

To understand the mechanism behind this, the team further showed that the domestication of the key transcription factor An-1 can specifically regulate the expression level of IPA1 in young spikes by binding to a GCGCGTGT fundamental order in the 54bp key cis-acting element, and thus specifically regulate the panicle phenotype.


Molecular mechanisms for breaking through the bottleneck of rice yield by breaking the trait chain Courtesy of the interviewee

Leading new trends in breeding

Speaking of the biggest highlight of this research, Yu Hong said that traditional breeding uses the resources that exist in nature to aggregate excellent genes to create new germplasm. The premise is that there are excellent genes in a certain breed that we want. To break the “symbiosis” between the usual excellent traits such as panicle number and panicle weight, it is necessary to create new resources.

The new study successfully lifted the negative correlation between key elements of rice yield by editing and screening the expression control area of key genes of rice by “tile” tile deletion strategy, which provides an effective strategy for breaking the bottleneck of rice yield by creating new genetic resources.

“This is a research trend worth paying attention to, and an important advance in understanding the molecular mechanisms of interaction between multiple quantitative trait genes.” One reviewer said so. (Source: China Science Daily Feng Lifei)

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