The genetic evolutionary history of soybean "Xia Nanyang"

The genetic evolutionary history of soybean "Xia Nanyang"

The genetic evolution history of soybean "Xia Nanyang" The genetic evolution history of soybean "Xia Nanyang"

Photo courtesy of Soy Childhood Respondents

 Photo courtesy of Soy Childhood Respondents

Photo courtesy of interviewees with soybean pod

Photo courtesy of interviewees with soybean pod

32-40 degrees north latitude, the Huanghuaihai region of China, the birthplace of soybean cultivation 5000 years ago
.

Today, low-latitude tropical regions account for more than half of the global soybean production

As a typical short-day crop with extremely sensitive photoperiods, how did soybeans that originated in the temperate zone “go south” to adapt to the tropical ecological environment? How does it affect soybean production and its worldwide planting and distribution?

On September 14, "Nature-Communications" published online the latest results of the research team of Guangzhou University professor Kong Fanjiang/Liu Baohui, which comprehensively analyzed the evolutionary trajectory and genetic basis of soybean adaptation to tropical regions, and solved this mystery
.

Each Break: The Key Gene Regulating Soybean Childhood Length

Each Break: The Key Gene Regulating Soybean Childhood Length

Cultivated soybeans occupies an important position in China's agricultural production and food security
.

However, soybeans are naturally more adaptable to short-day environments, and individual varieties or germplasm resources are generally only suitable for planting in areas with a small latitude span, which makes it difficult to increase soybean yields in low-latitude and long-day environments

Kong Fanjiang, the corresponding author of the paper, told the China Science Daily that the study found that about 2,000 years ago, soybeans spread from China’s Huanghuaihai area to Southeast Asia, such as the Philippines, Malaysia, Thailand, and India, and gradually adapted to the local short-day environment
.

In the 18th century, soybeans spread from Northeast China to North America, and then to Central and South America
.

"Soybeans spread to South America in a very short time, but they have developed rapidly
.

" Kong Fanjiang said

At present, Brazil has become the world's largest soybean producer
.

Soybean production in low-latitude regions has exceeded half of the world's total soybean production

However, scientists have not understood the genetic evolution process of soybeans in order to adapt to low-latitude and short-day environments
.

In order to explore this scientific problem, the Kong Fanjiang team conducted long-term systematic and in-depth research
.

According to Liu Baohui, the co-corresponding author of the paper, in 2017, the team reported on the key gene J of soybean long juvenile and its evolution mechanism, and clarified the mechanism by which the J gene improves soybean adaptability to low latitudes
.

They also found that E6, another important locus that controls long-term childhood traits in soybeans, is actually an allelic variant of the J gene

In 2021, they also reported two FT homologous genes, FT2a and FT5a, respectively encoding two QTL loci for soybean long-term childhood traits
.

The ft2a and ft5a double mutants can overcome the genetic compensation effect, show an enhanced phenotype of long childhood traits, and transform into higher yields under short-day conditions

 

"Southward" evolution track

"Southward" evolution track

Dong Lidong, the first author of the paper and lecturer at the Research Center for Molecular Genetics and Evolution of Guangzhou University, introduced that this time, they used genomics and other methods to discover a new site, Tof16, that controls the flowering period of soybeans in low-latitude regions under short-day conditions.

It is determined by the biological clock.

Under short-day conditions, the loss-of-function allelic variation of Tof16 significantly prolonged the flowering period and increased soybean yield
.

The molecular mechanism analysis showed that Tof16 directly regulates the expression of E1 gene, and then regulates the photoperiod flowering of soybean
.

"We found that more than 80% of soybean varieties in low latitude regions contain allelic variants of J gene and Tof16 gene, indicating that Tof16 and J played a very important role in the adaptation of soybeans to low latitude regions
.
" Liu Baohui said, the rest About 20% of the varieties carry another set of homologous genes (FT2a and FT5a) or some other unknown minor genes
.

Using gene editing technology, they obtained 15 mutants of the four homologous genes of Tof16 in soybeans
.
Phenotypic observation revealed that the four homologous genes have redundant functions in regulating the flowering period and yield of soybean, that is, their functions are partially the same, and mutation or silencing of one gene does not affect the phenotype of other genes
.

The phenotypes of various lhy mutants under short-day conditions are provided by interviewees

The phenotypes of various lhy mutants under short-day conditions are provided by interviewees

"Interestingly, we found that Tof16 and J gradually evolved and selected in the process of soybean adaptation to low-latitude regions
.
" Kong Fanjiang said
.

First, the weak loss-of-function allelic variants tof16-2 and j-11 were selected, but they could not meet people's demand for soybean yield in low-latitude regions
.
As a result, on the basis of weak allelic variants of loss-of-function type, soybeans have further developed allelic variants of complete loss-of-function type.
After being manually selected, soybeans are more adapted to low latitudes and provide yield
.

Specifically, the first mutation in soybean adaptability is a single amino acid substitution of Tof16 and J protein, which is a slightly weakened mutation, for example, it can make soybeans flower late by about a week
.
This step of mutation occurred as early as in wild soybeans, but it was not manually selected because it was not needed in the domestication process
.
However, cultivated species still carry this weaker mutation
.

After soybeans spread to lower-dimensional areas, it takes a longer period of childhood to adapt to the environment
.
As a result, the Tof16 and J genes of soybeans have allelic mutations with complete loss of function on the basis of weaker mutations, and they have been artificially selected to meet the needs of soybean growth and high yield in low-latitude regions
.

At this point, soybeans have completed the adaptive trajectory of "Southeast Asia"
.

 

Soybean flowering and yield achieved quantify design meter

Soybean flowering and yield achieved quantify design meter meter

"We found Tof16 and J at low latitudes zone control soybean flowering and the yield genetically independent, and with additive genetic effects
.
" Fan Jiang explained, Tof16 and J gene without disturbing each other, are able to influence and soybean flowering Yield
.
If both of them are placed in the same variety or germplasm resources to perform their functions, their effects on the length of childhood and yield can be superimposed
.

The area control soybean flowering period and yield are genetically independent, and have additive genetic effects
.
Kong Fanjiang explained that Tof16 and J genes do not interfere with each other and can respectively affect the flowering period and yield of soybeans
.
If both are placed in the same variety or germplasm resources to perform their functions, their impact on the length of childhood and yield can be significant.
Overlay
.

For example, the Tof16 gene mutant can extend the child period of soybeans by 10 days, and the J gene mutant can extend the child period by 15 days.
If the tof16 gene and the J gene are mutated at the same time, the child period can be extended by 25-30 days
.

Dong Lidong said that an analysis of the genome of soybean varieties from low-latitude tropical regions found that 80% of the varieties had at least one mutation at the Tof16 or J locus
.

"This shows that the natural variation of Tof16 or J locus is the main genetic basis for cultivated soybeans to adapt to tropical regions
.
" Dong Lidong said
.

More importantly, they can quantify the flowering period and yield of soybeans by combining various allelic variations of LHY, J, and E1
.

The working mechanism of Tof16 and J under short-day conditions.
Photo courtesy of the interviewee

The working mechanism of Tof16 and J under short-day conditions.
Photo courtesy of the interviewee

They aggregated these genes into one germplasm resource, and developed a series of germplasm materials with different flowering periods and yield gradients, such as from 30 days to 35 days, 40 days, 45 days.
.
.
and 60 days
.

Liu Baohui said that they will provide these germplasm materials free of charge, and breeders can select corresponding genotypes to carry out breeding work according to local soybean growth period restrictions
.

"This idea can not only be used in soybean breeding, and provide new strategies for improving the adaptability and yield of soybeans in tropical low-latitude regions, but the research also provides a theoretical basis for other crop molecular breeding
.
" Kong Fanjiang said
.
(Source: China Science News Li Chen)

Related paper information: https://doi.
org/10.
1038/s41467-021-25800-3

https://doi.
org/10.
1038/s41467-021-25800-3