Alfalfa is the most important leguminous forage grass, with strong adaptability, high protein content, and is known as the "king of forage", and is one of the best quality forages for dairy cows and other livestock, with more than 45 million hectares planted worldwide. However, global climate change has led to frequent extreme weather events, posing a serious threat to global food security. Therefore, the cultivation of new stress-tolerant and high-yielding plant varieties that are resilient to climate change is an important measure to ensure food security.
On April 26, 2024, Yang Qingchuan's team from the Beijing Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, and Zhou Yongfeng's team from the Shenzhen Institute of Agricultural Genomics, Chinese Academy of Agricultural Sciences, published a research paper entitled "Evolutionary genomics of climatic adaptation and resilience to climate change in alfalfa" online at Molecular Plant. A total of 1671 candidate genes related to environmental adaptation were identified, and the adaptation of alfalfa populations to climate change in different regions was predicted based on machine learning models. This work identified several important genes for climate adaptation of alfalfa species, which laid the foundation for alfalfa genome-wide design and breeding, and was of great significance for cultivating excellent new alfalfa varieties with climate change adaptability in the context of global climate change.
https://doi.org/10.1016/j.molp.2024.04.013
Fig. 1 Global distribution of 704 alfalfa materials used in the study
In this study, genomic data analysis was performed on 704 alfalfa (Figure 1) materials from around the world, covering 24 annual and perennial species of the genus Alfalfa, including 473 alfalfa complex materials. By assessing the genetic differences and gene infiltration among different species of the genus Alfalfa, it was found that the alfalfa complex was distantly related to other annual alfalfa species, but gene exchange information could still be detected between different alfalfa species (Fig. 2). A total of 1094 genes infiltrated into the alfalfa complex were detected by genome-wide introgression segment scanning, and these genes were enriched in the processes of stress stress, development and metabolism.
Fig.2 Genetic relationship between different species of Alfalfa (left) and gene introgression (right)
In order to estimate the regional adaptability and genomic variation of alfalfa during global dispersal, this study analyzed the nucleotide diversity, introgression ratio, and deleterious mutation sites among different populations of alfalfa (Fig. 3). The results showed that alfalfa had increased nucleotide diversity during its spread to East Asia, Europe and the United States, which was due to the introgression of alfalfa, which led to a high genetic load in alfalfa in addition to the introduction of genetic loci for climate adaptation. However, the opposite trend occurred in the process of spreading to Africa and South America, with a decrease in the proportion of introgression, a decrease in nucleotide diversity, and a decrease in genetic load. But this process can also lead to deleterious mutation homozygosity, which affects the adaptability of alfalfa.
Fig. 3 Changes in gene infiltration, genetic diversity and genetic load during the global spread of alfalfa
A total of 490 candidate genes related to climate adaptation, including CYP450 and DREB, and 1181 candidate genes related to climate adaptation were identified by population differentiation analysis (PBS). All 1671 candidate genes related to climate adaptation were not uniformly distributed on chromosomes, and were mainly enriched in biological processes such as stress response and reproductive development (Fig. 4).
Fig.4 Exploration of candidate genes related to climate adaptation. (A, B) LFMM analysis results, (C, D) PBS analysis results.
In this study, we combined genetic loci related to climate adaptation, future climate factors, and machine learning algorithms to systematically evaluate the ability of alfalfa populations in different regions to respond to climate change. The results suggest that most alfalfa growing areas in the northern hemisphere will be affected to varying degrees by climate change. However, there are also populations in some regions that are more climate-adaptable, including those from the southern center of origin in the Caucasus Mountains, central North America, and Central Asia (Figure 5).
Fig.5 Assessment of the genetic vulnerability of alfalfa in response to future climate change (the darker the color, the more vulnerable)
Zhang Fan, a postdoctoral fellow at the Shenzhen Institute of Agricultural Genomics, Chinese Academy of Agricultural Sciences, and Long Ruicai, associate researcher from the Beijing Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, are the first authors of the paper, and researcher Yang Qingchuan and researcher Zhou Yongfeng are the co-corresponding authors. Professor Zhiwu Zhang from Washington State University, Professor Longxi Yu and Professor Ming Li from the U.S. Department of Agriculture, Associate Professor Tiejun Zhang from Beijing Forestry University, Dr. Zhiyao Ma, Dr. Xiaodong Xu, Dr. Hua Xiao, Dr. Zhongjie Liu, and Dr. Yiwen Wang from the Institute of Genomics participated in the study. The research of the project has been supported by the National Forage Industry Technology System, the Innovation Project of the Chinese Academy of Agricultural Sciences, and the Overseas Excellent Youth Project. In recent years, Yang Qingchuan's team has been engaged in alfalfa genetics and breeding related research, and has successively bred 8 national alfalfa varieties of "Chinese Alfalfa", which have been popularized and planted in more than 10 provinces and regions in mainland China.
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