Nature Communications: Wang Jing/Mao Kangshan/Liu Jianquan's research group collaborates to reveal the genetic mechanism of environmental adaptation of forest tree species and future climate change...

With the intensification of the greenhouse effect and increasingly severe climatic conditions, climate change has posed a serious threat
to biodiversity and the stability of natural ecosystems.
As the main body of the earth's terrestrial ecosystem, forests carry many ecological functions
such as soil and water conservation, climate regulation, and biodiversity maintenance.
General Secretary Xi Jinping also proposed that "forests and grasslands play a fundamental and strategic role in national ecological security, and forests and grasslands prosper ecology" when participating in the capital's
voluntary tree-planting activities 。 In addition, how to help China achieve the goals of "carbon peak" and "carbon neutrality" based on nature?; How to identify tree species or ecotypes suitable for planting in different regions that are suitable for future climate change?; And how to achieve the purpose of optimizing forest carbon sinks of "suitable forests and forests, suitable trees in the right place, and optimal management"? In order to answer and solve the above key scientific questions, systematic excavation and utilization of wild forest germplasm resources adapted to different climatic conditions is the fundamental way
to ensure the development and ecological security of China's forest seed industry from the source.
Wild forest genetics and germplasm resources are not only the foundation of the development of modern forestry seed industry, but also the basic strategic resources of the country, providing important support
for the future creation and selection of new forest germplasm adapted to different climatic conditions.

On November 1, 2022, Nature Communications published online the title "Genomic insights into local adaptation and future climate-induced vulnerability of a keystone forest tree in" co-authored by Professor Wang Jing, Professor Mao Kangshan and Professor Liu Jianquan's research group from the School of Life Sciences, Sichuan University East Asia"
.
In this study, Populus koreana, an important forest tree species distributed in temperate coniferous mixed forests in northeast China, was used as the research object, de novo was assembled and annotated the reference genome at the chromosome level of Populus chinensis, and 230 individuals from 24 natural populations of Populus chinensis collected in the wild were resequenced
whole-genome 。 Ecology, genomics, population genetics, combined with climate factor correlation analysis, molecular biology experimental verification and machine learning algorithms were used to explore the molecular genetic mechanism of P.
chinensis adapting to different climatic environments, and the genome vulnerability of different populations of P.
chinensis was further evaluated
.
The study highlights the importance of
using interdisciplinary approaches to predict species responses to climate and environmental change and coping strategies.

1.
Assembly of genomes at the chromosome level of Populus chinensis

The researchers first integrated data from three sequencing methods: Nanopore long-read sequencing (106×, 42.
42 Gb), Illumina sequencing (74×, 29.
82 Gb), and Hi-C paired-end reads (137×, 54.
22 Gb) to assemble the Yang genome
。 The resulting assembled genome contained 19 chromosomes with a size of 401.
6 Mb, a contig N50 of 6.
41 Mb, and a BUSCO of 97.
4% (Fig 1).

Of these, 37.
2% of the genome sequences were identified as duplicate elements
.
By combining transcriptome, homology sequences, and de novo prediction, the authors annotated a total of 37,072 protein-coding genes
.

2.
Population structure, genetic diversity and population history dynamics of the natural population of Populus chinensis

First, the researchers performed high-depth whole genome resequencing (Fig2) using 230 individuals from 24 natural populations of Populus chinensis in northeast China to identify 16,619,620 SNPs, 2,663,202 Indels, and 90,357 SVs (Fig 1),
respectively.
The ADMIXTURE results and NJ trees showed that the population was mainly divided into two subgroups
: south (Changbaishan area) and north (Daxing'anling area).
However, the results of 2D-SFS suggest that the North-South subpopulations share a large amount of genetic variation, indicating a relatively weak population genetic structure
.
In addition, genetic differentiation was small between the two subpopulations (Fst: 0.
02125; DXY:0.
01098) and nucleotide diversity and linkage attenuation distance are also relatively close
.
PSMC analysis showed that the historical dynamics of the two groups were similar, diverging around the last glacial period (LGM), after which the effective population size of the northern group gradually shrank and the southern group expanded
slightly.

3.
Identification of climate adaptation association sites in Populus chinensis populations

In order to explore the genetic basis of the climatic adaptability of different populations of P.
chinensis, the researchers used two environmental association methods to detect genetic variants associated with climate factors at the genome-wide level: first, based on 19 environmental variables (BIO1-19), the correlation between genomic variant sites and environmental variables was tested by the LFMM (latent factor mixed model) model under the condition of excluding population structure, and 3013, 3013, respectively detected 378 and 44 SNPs, Indels and SVs associated with the environment (q< 0.
05) (Fig3).

Since LFMM is a univariate detection method, the researchers further adopted the multivariate landscape genome method (RDA) for climate factor association
.
Consider gradient forests; GF) after ranking importance and correlation between environment variables, the authors retained 6 |r| The environmental variables (BIO1, 3, 5, 13, 15, 19) < 0.
6 (Spearman correlation coefficient) were analyzed for RDA
.
Of the standard deviation >3 identified by RDA analysis, 1,779 sites intersected with the LFMM results, and these variants are considered "core climate adaptation sites" and are widely distributed on the genome (Fig1).

Compared with genomic neutral sites, the identified core adaptation sites have larger Fst between populations, and the environment has a higher degree of explanation for the variation of the adaptive site (partial RDA analysis; 41.
2% VS 10.
4%), and the IBE (isolation by environment) partial Mantel test after excluding geographical distance still showed a significant pattern of environmental isolation (Fig 2d), indicating that the variation between populations at these adaptation sites is indeed mainly driven
by the environment 。 For the core adaptive variants detected by LFMM and RDA, only 3.
2% were nonsynonymous, 2.
0% were synonymous, and the rest were noncoding mutations, and these variants were significantly enriched in the 5' UTR region and TE(p < 0.
001 compared with the genomic background), indicating that the regulatory region sequence variation played an important role
in the climate adaptation of Populus chinensis.
Combined with iHS analysis, the authors found that adaptive variants did not have significant positive selection characteristics compared to genomic background, suggesting that climate adaptation may be largely determined
by a large number of multigenic loci with small effects.

4.
Geographical distribution of allele associated with climate adaptation of Populus chinensis

In this study, multiple key genes and allele variants
associated with different climatic factors were identified.
For example, the Arabidopsis homologous gene CRL1 (Fig 3a, b),
which is closely related to BIO13 (precipitation in the wettest month).
The researchers identified 2 tandem repeat genes of CRL1 (Pokor12247 and Pokor12248) and 104 potential adaptive variant sites (Fig 3b) on chromosome 4 of Xiangyang, and patterned the adaptive SNP:LG04:25159299 in the UTR region of Pokor122475' UTR: T haplotype was mainly distributed in high precipitation areas, while C haplotype was fixed in the area with relatively little precipitation (Fig 3c).

。 The authors further detected these two haplotypes of Pokor12247 by qRT-PCR with significant expression differences under flooding stress (Fig 3e).

Compared with CC genotype individuals, TC genotype individuals had enhanced gene expression in flood stress, suggesting that the T allele may be related to
flood tolerance.
In addition, the researchers did not observe a strong short-term selection signal at this site, and there was no significant difference in the degree of extended haplotype homozygosity at this SNP site (Fig 3d, |iHS|= 1.
693), again supporting the polygenic adaptation pattern
of Populus.

In addition, the authors identified multiple temperature-related genes and allele variants, such as genes homologous to Arabidopsis HMG1, PGP4, HSP60-3A (Fig 3a, f).

An example of a significant correlation with BIO5 (the highest temperature of the warmest month) is Pokor17228, which encodes a heat shock protein
homologous to Arabidopsis HSP60-3A.
and identified 62 potential adaptive variants
from this gene.
The researchers chose an SNP: LG07:4796402 located in the intron for demonstration (Fig 3f): genotype G is mainly distributed in relatively warmer regions, while genotype A is mainly distributed in regions
with lower temperatures.
Similarly, the expression of GG genotype after 2 h of heat stress was significantly higher than that of AA genotype (Fig 3i), indicating that Pokor17228 may be related to
the thermal stress response of Pokor17228.
The authors also did not observe a strong near-term selection signal (Fig 3h)
at this site.

5.
Adaptive prediction of Xiangyang to cope with the future environment

Based on the established contemporary genotype-climate relationship and the identified climate-associated genetic loci, the researchers used four CMIP6 climate prediction models (2061-2080 and 2081-2100, two emission scenarios: SSP126 and SSP370) to predict the vulnerability of the Populus population to future climate change
.

The authors first calculated the risk of non-adaptedness; RONA), which predicts allele frequency changes required to adapt to future climatic conditions after establishing a linear relationship with contemporary climate variables based on allele frequencies, and the greater the need for change on the genome, the worse the adaptation potential
.
The results show that although the values of RONA differ numerically across the next four climate models, the trends are highly correlated
.
Therefore, the authors used the average RONA values of different models to compare their differences
between populations.
For most environmental variables, RONA continues to increase with the intensity of climate change (Fig 4).

The authors selected predictions for the two variables BIO5 and BIO13 as representative results and found that populations located in areas with more severe environmental change had larger RONA values (Fig 4a, c): both northern and southern groups had a lower potential to cope with future temperature changes (Fig 4, b), while southern groups that were likely to experience heavy rainfall or extreme precipitation events in the future had higher RONA values (Fig 4c, d)
in the face of precipitation.

Next, the researchers used gradient forests (GF) to model allele frequency changes along current environmental gradients and predict genetic shifts
under future climate conditions.
In contrast to RONA, which is estimated at the level of a single locus at a single environmental variable, GF can make genetic bias predictions
based on the association between the composite effects of adaptive loci and multivariate climate variables.
Consistent with the RONA results: the Yalu Basin groups in the south are most vulnerable to future climate change (Fig 5a, b).

Finally, in addition to the classical (local) genetic bias, the researchers integrated migration into the prediction, further evaluating the reverse and forward genetic bias
of Populus 。 First, the researchers assumed that the poplar population would be able to migrate to any location within the existing distribution, using the predicted minimum offset as a reverse offset; Then, the maximum migration distance of Populus fragrant is defined to estimate the forward offset, and the authors find that the forward offset trend of the population is basically the same
under different maximum migration distances (100, 250, 500, 1000 km and infinity).
While the predicted local, forward, and reverse genetic shifts varied across the distribution, southern populations had relatively high local, forward, and reverse genetic shifts (Fig 5c, d).

In summary, the southern poplar population (especially the Yalu River basin population) is relatively vulnerable to the future environment, and considering that this group contains many genetic resources adapted to the climate and carries many genes adapted to precipitation, the population in this area may need to attract additional attention and focus on conservation
.

discuss

At present, many studies focus on the study of adaptability to a certain level of short-generation species, and it is often difficult to explore the adaptability of species through traditional homogeneous garden experiments and mutual transplantation adaptation experiments, and it is often not feasible
for species with long generation cycles and imperfect experimental systems.
Through the resequencing data of 230 P.
chinensis from East Asia, combined with genomics and population genetics theory, this paper innovatively uses a variety of methods to comprehensively elucidate the adaptive model of P.
chinensis to the contemporary and future environment, which provides important information
for breeding and germplasm preservation.
At the same time, the study emphasizes the importance of integrating genomic and environmental data to predict the adaptive ability of species to rapid future climate changes, and has certain implications
for the study of the adaptive evolution mechanism of forest tree species.

Professor Wang Jing, Professor Mao Kangshan and Professor Liu Jianquan of the School of Life Sciences, Sichuan University are the corresponding authors, and Sang Yupeng, a doctoral student in Wang Jing's group, and Long Zhiqin, a master's student, are the co-first authors
of the paper.
Associate Professor Xiaoting Xu, Associate Professor Liu Zhuohuo, Associate Professor Jiang Yuanzhong of Sichuan University, Professor Pör K.
Ingvarsson of Swedish University of Agricultural Sciences and other researchers participated in the work
.
The research was supported
by the National Key Research and Development Program, the National Natural Science Foundation of China, and the Basic Operating Expenses of Central Universities.

In addition, Wang Jing's research group plans to recruit postdoctoral fellows in plant molecular biology (experience in forest tree species research is preferred), bioinformatics, genetics and other professional directions, interested parties please send resumes to email: wangjing2019@scu.
edu.
cn
.
Research group website: https://jingwanglab.
org
.