Genomic conservation of crop wild relatives: A case study of citrus.

Conservation of crop wild relatives is critical for plant breeding and food security. The lack of clarity on the genetic factors that lead to endangered status or extinction create difficulties when attempting to develop concrete recommendations for conserving a citrus wild relative: the wild relatives of crops. Here, we evaluate the conservation of wild kumquat (Fortunella hindsii) using genomic, geographical, environmental, and phenotypic data, and forward simulations. Genome resequencing data from 73 accessions from the Fortunella genus were combined to investigate population structure, demography, inbreeding, introgression, and genetic load. Population structure was correlated with reproductive type (i.e., sexual and apomictic) and with a significant differentiation within the sexually reproducing population. The effective population size for one of the sexually reproducing subpopulations has recently declined to ~1,000, resulting in high levels of inbreeding. In particular, we found that 58% of the ecological niche overlapped between wild and cultivated populations and that there was extensive introgression into wild samples from cultivated populations. Interestingly, the introgression pattern and accumulation of genetic load may be influenced by the type of reproduction. In wild apomictic samples, the introgressed regions were primarily heterozygous, and genome-wide deleterious variants were hidden in the heterozygous state. In contrast, wild sexually reproducing samples carried a higher recessive deleterious burden. Furthermore, we also found that sexually reproducing samples were self-incompatible, which prevented the reduction of genetic diversity by selfing. Our population genomic analyses provide specific recommendations for distinct reproductive types and monitoring during conservation. This study highlights the genomic landscape of a wild relative of citrus and provides recommendations for the conservation of crop wild relatives.

Absolute tests of three flats for interferometer with 800 mm aperture.

In this study, absolute tests of three flats were performed by using an 800 mm Fizeau interferometer. The flats were installed by employing double-wedge rubber, and the deformation of the flats, primarily involving power and spherical aberrations, was analyzed by conducting finite element analysis. The measurement results revealed an astigmatism component that did not follow the rotation. The astigmatism was separated from the measurement result, and the remaining aberration was consistent with the simulation results, confirming that the astigmatism deformation did not originate from the rubber installation. Subsequently, an absolute test of an 800 mm flat was completed, and the results were compared with those of the traditional three-flat absolute test and Zygo interferometer. The directions of the vertical diameter lines were consistent. The peak-to-valley difference in the full-surface shape was less than 4 nm, and the root mean square was less than 1 nm. The surface errors of flats A and C were consistent with the result of replacing the reference flat, B, with the fourth flat, D, to perform an absolute test. The difference between flats A and C was similar to Zygo's results, thus eliminating the influence of the transmission flat. These results verified the accuracy of the results.

Short-term response of primary human meniscus cells to simulated microgravity.

BACKGROUND: Mechanical unloading of the knee articular cartilage results in cartilage matrix atrophy, signifying the osteoarthritic-inductive potential of mechanical unloading. In contrast, mechanical loading stimulates cartilage matrix production. However, little is known about the response of meniscal fibrocartilage, a major mechanical load-bearing tissue of the knee joint, and its functional matrix-forming fibrochondrocytes to mechanical unloading events. METHODS: In this study, primary meniscus fibrochondrocytes isolated from the inner avascular region of human menisci from both male and female donors were seeded into porous collagen scaffolds to generate 3D meniscus models. These models were subjected to both normal gravity and mechanical unloading via simulated microgravity (SMG) for 7 days, with samples collected at various time points during the culture. RESULTS: RNA sequencing unveiled significant transcriptome changes during the 7-day SMG culture, including the notable upregulation of key osteoarthritis markers such as COL10A1, MMP13, and SPP1, along with pathways related to inflammation and calcification. Crucially, sex-specific variations in transcriptional responses were observed. Meniscus models derived from female donors exhibited heightened cell proliferation activities, with the JUN protein involved in several potentially osteoarthritis-related signaling pathways. In contrast, meniscus models from male donors primarily regulated extracellular matrix components and matrix remodeling enzymes. CONCLUSION: These findings advance our understanding of sex disparities in knee osteoarthritis by developing a novel in vitro model using cell-seeded meniscus constructs and simulated microgravity, revealing significant sex-specific molecular mechanisms and therapeutic targets.

Population genomics highlights structural variations in local adaptation to saline coastal environments in woolly grape.

Structural variations (SVs) are a feature of plant genomes that has been largely unexplored despite their significant impact on plant phenotypic traits and local adaptation to abiotic and biotic stress. In this study, we employed woolly grape (Vitis retordii), a species native to the tropical and subtropical regions of East Asia with both coastal and inland habitats, as a valuable model for examining the impact of SVs on local adaptation. We assembled a haplotype-resolved chromosomal reference genome for woolly grape, and conducted population genetic analyses based on whole-genome sequencing (WGS) data from coastal and inland populations. The demographic analyses revealed recent bottlenecks in all populations and asymmetric gene flow from the inland to the coastal population. In total, 1,035 genes associated with plant adaptive regulation for salt stress, radiation, and environmental adaptation were detected underlying local selection by SVs and SNPs in the coastal population, of which 37.29% and 65.26% were detected by SVs and SNPs, respectively. Candidate genes such as FSD2, RGA1, and AAP8 associated with salt tolerance were found to be highly differentiated and selected during the process of local adaptation to coastal habitats in SV regions. Our study highlights the importance of SVs in local adaptation; candidate genes related to salt stress and climatic adaptation to tropical and subtropical environments are important genomic resources for future breeding programs of grapevine and its rootstocks.

Phylogenomic analyses using a new 1013-gene Vitaceae bait-set support major groups of North American Vitis.

A set of newly designed Vitaceae baits targeting 1013 genes was employed to explore phylogenetic relationships among North American Vitis. Eurasian Vitis taxa including Vitis vinifera were found to be nested within North American Vitis subgenus Vitis. North American Vitis subgenus Vitis can be placed into nine main groups: the Monticola group, the Occidentales group, the Californica group, the Vinifera group (introduced from Eurasia), the Mustangensis group, the Palmata group, the Aestivalis group, the Labrusca group, and the Cinerea group. Strong cytonuclear discordances were detected in North American Vitis, with many species non-monophyletic in the plastid phylogeny, while monophyletic in the nuclear phylogeny. The phylogenomic analyses support recognizing four distinct species in the Vitis cinerea complex in North America: V. cinerea, V. baileyana, V. berlandieri, and V. simpsonii. Such treatment will better serve the conservation of wild Vitis diversity in North America. Yet the evolutionary history of Vitis is highly complex, with the concordance analyses indicating conflicting signals across the phylogeny. Cytonuclear discordances and Analyses using the Species Networks applying Quartets (SNaQ) method support extensive hybridizations in North American Vitis. The results further indicate that plastid genomes alone are insufficient for resolving the evolutionary history of plant groups that have undergone rampant hybridization, like the case in North American Vitis. Nuclear gene data are essential for species delimitation, identification and reconstructing evolutionary relationships; therefore, they are imperative for plant phylogenomic studies.

Non-iterative phase tilt interferometry for the tilt shift calculation and phase extraction.

This study proposed a non-iterative phase tilt interferometry (NIPTI) for the tilt shift calculation and phase extraction, which can solve the random tilt-shift problem caused by external vibration. The method approximates the higher order terms of the phase to make it suitable for linear fitting. Then according to an estimated tilt, the accurate tilt shift can be obtained by least squares method without iteration, and the phase distribution can be calculated by it. The simulation results indicated that the root mean square error of the phase calculated by the NIPTI can reach up to 0.0002λ. The experimental results showed that the calculated phase exhibited no significant ripple when using the NIPTI for cavity measurements in a time-domain phase shift Fizeau interferometer. Moreover, the root mean square repeatability of the calculated phase reached up to 0.0006λ. It indicates that the NIPTI provides an efficient and high-precision solution for random tilt-shift interferometry under vibration.

System design and error correction of simultaneous phase-shifting point-diffraction interferometer for dynamic wavefront detection with 400 mm aperture.

In this paper, a simultaneous phase-shifting point-diffraction interferometer (SPS-PDI)  at 632.8 nm is designed with the assistance of an off-axis parabolic mirror (OAPM), through which the dynamic wavefront with 400 mm aperture can be detected. In the system, a polarization point-diffraction plate (P-PDP) is developed to modulate the polarization states of the reference light and the test light through a simultaneous phase-shifting system based on a chessboard phase grating and a retarder array, and four phase-shifting interferograms can be acquired to realize dynamic detection. Furthermore, the circular carrier squeezing interferometry (CCSI) is proposed to suppress the phase errors generated by position mismatch, intensity distortion, and phase-shift error. The detection result of the SPS-PDI is consistent with the 4D PhaseCam6000 dynamic interferometer. The difference of the peak-to-valley (PV) and root-mean-square (RMS) values are only 0.04λ and 0.008λ. Additionally, the capacity to detect dynamic wavefront is good.

Climate-influenced boreotropical survival and rampant introgressions explain the thriving of New World grapes in the north temperate zone.

The north temperate region was characterized by a warm climate and a rich thermophilic flora before the Eocene, but early diversifications of the temperate biome under global climate change and biome shift remain uncertain. Moreover, it is becoming clear that hybridization/introgression is an important driving force of speciation in plant diversity. Here, we applied analyses from biogeography and phylogenetic networks to account for both introgression and incomplete lineage sorting based on genomic data from the New World Vitis, a charismatic component of the temperate North American flora with known and suspected gene flow among species. Biogeographic inference and fossil evidence suggest that the grapes were widely distributed from North America to Europe during the Paleocene to the Eocene, followed by widespread extinction and survival of relicts in the tropical New World. During the climate warming in the early Miocene, a Vitis ancestor migrated northward from the refugia with subsequent diversification in the North American region. We found strong evidence for widespread incongruence and reticulate evolution among nuclear genes within both recent and ancient lineages of the New World Vitis. Furthermore, the organellar genomes showed strong conflicts with the inferred species tree from the nuclear genomes. Our phylogenomic analyses provided an important assessment of the wide occurrence of reticulate introgression in the New World Vitis, which potentially represents one of the most important mechanisms for the diversification of Vitis species in temperate North America and even the entire temperate Northern Hemisphere. The scenario we report here may be a common model of temperate diversification of flowering plants adapted to the global climate cooling and fluctuation in the Neogene.

Mechano-bioengineering of the knee meniscus.

The meniscus is a fibrocartilaginous structure of the knee joint that serves a crucial role in joint health and biomechanics. Degeneration or removal of the meniscus is known to lead to a chronic and debilitating disease known as knee osteoarthritis, whose prevalence is expected to increase in the next few decades. Meniscus bioengineering has been developed as a potential alternative to current treatment methods, wherein meniscus-like tissues are engineered using cells, materials, and biomechanical stimuli. The application of mechanical stimulation in meniscus bioengineering has presented varied results but, for the most part, it has been shown to enhance meniscus-like tissue formation. In this review, we summarized literature over the last 10 years of various mechanical stimuli applied in bioengineering meniscus tissues. The role of individual loading types is examined, and the effects on engineered meniscus are evaluated on both molecular and tissue levels. In addition, simulated microgravity is highlighted as a new area of interest in meniscus engineering, and its potential use as a disease-driving platform is discussed. Taken together, with the increased understanding of the effects of mechanical stimulation on bioengineered meniscus tissues, the most suitable loading regime could be developed for meniscus tissue engineering and osteoarthritis modeling.

Iterative correction method of a retrace error in interferometry.

In interferometer measurements, the inconsistency of the optical range through which the reference and test lights pass introduces a retrace error in the phase measurement. In this study, we propose an iterative retrace error correction method in interferometry. A black-box model is established based on the linear and squared relationships between the retrace error and the tilt of the testing surface. The error correction phase is obtained using the least-squares method; thereafter, the global tilt is determined to iteratively correct the retrace error. The root mean square (RMS) of the residuals was > 3.2 × 10-5λ, >6.4 × 10-3λ, and >1.4 × 10-3λ in the simulation, experimentally computed retrace error correction in the planar measurement, and spherical measurement, respectively, proving that the retrace error can be effectively corrected.

Phylogenomic relationships and character evolution of the grape family (Vitaceae).

The grape family consists of 16 genera and ca. 950 species. It is best known for the economically important fruit crop - the grape Vitis vinifera. The deep phylogenetic relationships and character evolution of the grape family have attracted the attention of researchers in recent years. We herein reconstruct the phylogenomic relationships within Vitaceae using nuclear and plastid genes based on the Hyb-Seq approach and test the newly proposed classification system of the family. The five tribes of the grape family, including Ampelopsideae, Cayratieae, Cisseae, Parthenocisseae, and Viteae, are each robustly supported by both nuclear and chloroplast genomic data and the backbone relationships are congruent with previous reports. The cupular floral disc (raised above and free from ovary at the upper part) is an ancestral state of Vitaceae, with the inconspicuous floral disc as derived in the tribe Parthenocisseae, and the state of adnate to the ovary as derived in the tribe Viteae. The 5-merous floral pattern was inferred to be the ancestral in Vitaceae, with the 4-merous flowers evolved at least two times in the family. The compound dichasial cyme (cymose with two secondary axes) is ancestral in Vitaceae and the thyrse inflorescence (a combination of racemose and cymose branching) in tribe Viteae is derived. The ribbon-like trichome only evolved once in Vitaceae, as a synapomorphy for the tribe Viteae.

Tunable Covalent Organic Frameworks with Different Heterocyclic Nitrogen Locations for Efficient Cr(VI) Reduction, Escherichia coli Disinfection, and Paracetamol Degradation under Visible-Light Irradiation.

Covalent organic frameworks (COFs) have great application potentials in photocatalytic water treatment. By using p-phenylenediamine with different numbers and locations of heterocyclic nitrogen atoms as a precursor, five types of COFs with different nitrogen positions were synthesized. We found that Cr(VI) photoreduction,Escherichia coli inactivation, and paracetamol degradation by COFs were heterocyclic nitrogen location-dependent. Particularly, the photocatalytic performance for all three tested pollutants by five types of COFs followed the order of the best performance for COF-PDZ with two ortho position heterocyclic N atoms, medium for COF-PMD with two meta position heterocyclic N atoms, and COF-PZ with two para position heterocyclic N atoms, and COF-PD with a single heterocyclic N atom, the worst performance for COF-1 without a heterocyclic N atom. Compared to the other COFs, COF-PDZ contained improved quantum efficiency and thus enhanced generation of electrons. The lower energy barriers and larger energy gaps of COF-PDZ contributed to its improved quantum efficiencies. The stronger affinity to Cr(VI) with lower adsorption energy of COF-PDZ also contributed to its excellent Cr(VI) reduction performance. By transferring into a more stable keto form, COF-PDZ showed great stability through five regeneration and reuse cycles. Overall, this study provided an insight into the synthesis of high-performance structure-dependent COF-based photocatalysts.

Testing morphological trait evolution and assessing species delimitations in the grape genus using a phylogenomic framework.

The grape genus (Vitis L.) is of great agronomic importance and represents an economically valuable resource. Researchers have explored the phylogenetic relationships of subgenus Vitis for decades. However, the evolutionary patterns of many morphological characters of subgenus Vitis have not yet been explored in the context of a robust phylogenetic framework. Within the East Asian clade, V. bryoniifolia and its closely related taxa form the V. bryoniifolia clade, which is taxonomically complex. The phylogenetic relationships and species delimitation within this clade remain poorly resolved, due to the limited sampling in prior studies. We tested morphological trait evolution based on ancestral character state reconstruction using a phylogenomic framework. With 89 accessions from the East Asian subgenus Vitis sampled, a robust phylogenetic relationship of the V. bryoniifolia clade is reconstructed using the restriction-site associated DNA sequencing (RAD-seq) data, which support the monophyly of most taxa of the V. bryoniifolia clade. Ancestral character state reconstructions suggest that the weak climbing ability and simplified tendrils of Vitis each evolved multiple times. This study provides a reliable phylogenomic framework for the V. bryoniifolia clade. Coupled with morphological analyses, we discuss the taxonomic status of some taxa in the V. bryoniifolia clade and untangle a taxonomic dilemma in the grape genus.

Transcriptomic and proteomic approaches to explore the differences in monoterpene and benzenoid biosynthesis between scented and unscented genotypes of wintersweet.

Wintersweet (Chimonanthus praecox L.) is an important ornamental plant in China with a pleasant floral scent. To explore the potential mechanisms underlying differences in the fragrances among genotypes of this plant, we analyzed floral volatile organic compounds (VOCs) from two different genotypes: SW001, which has little to no fragrance, and the scented genotype H29. The major VOCs in H29 were linalool, trans-ß-ocimene, benzyl acetate, methyl salicylate, benzyl alcohol (BAlc) and methyl benzoate. The most important aroma-active compound in H29, linalool, was emitted at a low concentration in SW001, which had markedly higher levels of trans-ß-ocimene than H29. Next, to investigate scent biosynthesis, we analyzed the transcriptome and proteome of fully open flowers of the two genotypes. A total of 14 443 differentially expressed unigenes and 196 differentially expressed proteins were identified. Further analyses indicated that 56 differentially expressed genes involved in the terpenoid and benzenoid biosynthesis pathways might play critical roles in regulating floral fragrance difference. Disequilibrium expression of four terpene synthase genes resulted in diverse emission of linalool and trans-ß-ocimene in both genotypes. In addition, the expressions of two CpMYC2 transcription factors were both upregulated in H29, implying that they may regulate linalool production. Notably, 16 of 20 genes in the benzenoid biosynthesis pathway were downregulated, corresponding to the relatively low level of benzenoid production in SW001. The lack of benzyl acetate might indicate that SW001 may lack substrate BAlc or functional acetyl-CoA:benzylalcohol acetyltransferase.

Phylogenomics, biogeography, and adaptive radiation of grapes.

The application of whole-genome resequencing based on next-generation sequencing technologies provides an unprecedented opportunity for researchers to resolve long-standing evolutionary problems. Taxa belonging to the grape genus (Vitis L.) represent important genetic resources for the improvement of cultivated grapes. However, it has been challenging to resolve the deep phylogenetic relationships within Vitis, limiting the current understanding of the evolutionary history of Vitis and preventing the use of valuable wild grape resources. In this study, we obtained whole-genome sequence data from 41 accessions representing most taxa within subgenus Vitis and aligned these sequences to the Vitis vinifera L. reference genome. We reconstructed deep phylogenetic relationships within subgenus Vitis based on 2068 single-copy orthologous genes, which led to a robust topology with bootstrap support values of 100% for almost all branches. Three main clades are recovered within subgenus Vitis reflecting their continental distribution through North America, Europe, and East Asia, respectively. Our results suggest that the most possible migration route of the East Asian Vitis is from northeastern Asia southward to South Asia and Southeast Asia. The East Asian Vitis seems to have experienced adaptive radiation during the Miocene. This study provides novel insights into the diversification history of the grape genus Vitis.

Optimizing Thermoelectric Performance of Hybrid Crystals Bi2O2Se1-xTex in the Bi2O2X System.

In addressing the global need for sustainable energy conversion, this study presents a breakthrough in thermoelectric materials research by optimizing the Bi2O2Se1-xTex system in the Bi2O2Se/Bi2O2Te pseudobinary series. Leveraging the principles of innovative transport mechanisms and defect engineering, we introduce tellurium (Te) doping into Bi2O2Se to enhance its thermoelectric properties synergistically. With the help of various advanced characterization tools such as XRD, SEM, TEM, XPS, FTIR, TGA, LFA, and DSC, combined with relevant resistance and density measurement techniques, we conducted an in-depth exploration of the complex interactions between various factors within thermoelectric materials. We recognize that the balance and synergy of these factors in the thermoelectric conversion process are crucial to achieving efficient energy conversion. Through systematic research, we are committed to revealing the mechanisms of these interactions and providing a solid scientific foundation for the optimal design and performance enhancement of thermoelectric materials. Finally, the advantage coefficient (ZT) of the thermoelectric material has been significantly improved. The crystallographic analysis confirms the formation of a continuous series of mixed crystals with varying Te concentrations, adhering to Vegard's law and exhibiting significant improvements in electrical and thermal conductivities. The Bi2O2Se1-xTex crystals, particularly the Bi2O2Se0.6Te0.4 composition, demonstrate a peak ZT of 0.86 at 373 K. This achievement aligns with recent advancements in defect-enabled mechanisms and band convergence and sets a new standard for high-performance thermoelectrics. The study's findings contribute significantly to the ongoing quest for efficient thermal-to-electrical energy conversion, offering a promising avenue for future sustainable energy technologies.

Double crosslinked hyaluronic acid and collagen as a potential bioink for cartilage tissue engineering.

The avascular nature of hyaline cartilage results in limited spontaneous self-repair and regenerative capabilities when damaged. Recent advances in three-dimensional bioprinting have enabled the precise dispensing of cell-laden biomaterials, commonly referred to as 'bioinks', which are emerging as promising solutions for tissue regeneration. An effective bioink for cartilage tissue engineering needs to create a micro-environment that promotes cell differentiation and supports neocartilage tissue formation. In this study, we introduced an innovative bioink composed of photocurable acrylated type I collagen (COLMA), thiol-modified hyaluronic acid (THA), and poly(ethylene glycol) diacrylate (PEGDA) for 3D bioprinting cartilage grafts using human nasal chondrocytes. Both collagen and hyaluronic acid, being key components of the extracellular matrix (ECM) in the human body, provide essential biological cues for tissue regeneration. We evaluated three formulations - COLMA, COLMA+THA, and COLMA+THA+PEGDA - for their printability, cell viability, structural integrity, and capabilities in forming cartilage-like ECM. The addition of THA and PEGDA significantly enhanced these properties, showcasing the potential of this bioink in advancing applications in cartilage repair and reconstructive surgery.

De novo assembling a high-quality genome sequence of Amur grape (Vitis amurensis Rupr.) gives insight into Vitis divergence and sex determination.

To date, there has been no high-quality sequence for genomes of the East Asian grape species, hindering biological and breeding efforts to improve grape cultivars. This study presents ~522 Mb of the Vitis amurensis (Va) genome sequence containing 27 635 coding genes. Phylogenetic analysis indicated that Vitis riparia (Vr) may have first split from the other two species, Va and Vitis vinifera (Vv). Divergent numbers of duplicated genes reserved among grapes suggests that the core eudicot-common hexaploidy (ECH) and the subsequent genome instability still play a non-negligible role in species divergence and biological innovation. Prominent accumulation of sequence variants might have improved cold resistance in Va, resulting in a more robust network of regulatory cold resistance genes, explaining why it is extremely cold-tolerant compared with Vv and Vr. In contrast, Va has preserved many fewer nucleotide binding site (NBS) disease resistance genes than the other grapes. Notably, multi-omics analysis identified one trans-cinnamate 4-monooxygenase gene positively correlated to the resveratrol accumulated during Va berry development. A selective sweep analysis revealed a hypothetical Va sex-determination region (SDR). Besides, a PPR-containing protein-coding gene in the hypothetical SDR may be related to sex determination in Va. The content and arrangement order of genes in the putative SDR of female Va were similar to those of female Vv. However, the putative SDR of female Va has lost one flavin-containing monooxygenase (FMO) gene and contains one extra protein-coding gene uncharacterized so far. These findings will improve the understanding of Vitis biology and contribute to the improvement of grape breeding.

Comparative population genomics reveals convergent and divergent selection in the apricot-peach-plum-mei complex.

The economically significant genus Prunus includes fruit and nut crops that have been domesticated for shared and specific agronomic traits; however, the genomic signals of convergent and divergent selection have not been elucidated. In this study, we aimed to detect genomic signatures of convergent and divergent selection by conducting comparative population genomic analyses of the apricot-peach-plum-mei (APPM) complex, utilizing a haplotype-resolved telomere-to-telomere (T2T) genome assembly and population resequencing data. The haplotype-resolved T2T reference genome for the plum cultivar was assembled through HiFi and Hi-C reads, resulting in two haplotypes 251.25 and 251.29 Mb in size, respectively. Comparative genomics reveals a chromosomal translocation of ~1.17 Mb in the apricot genomes compared with peach, plum, and mei. Notably, the translocation involves the D locus, significantly impacting titratable acidity (TA), pH, and sugar content. Population genetic analysis detected substantial gene flow between plum and apricot, with introgression regions enriched in post-embryonic development and pollen germination processes. Comparative population genetic analyses revealed convergent selection for stress tolerance, flower development, and fruit ripening, along with divergent selection shaping specific crop, such as somatic embryogenesis in plum, pollen germination in mei, and hormone regulation in peach. Notably, selective sweeps on chromosome 7 coincide with a chromosomal collinearity from the comparative genomics, impacting key fruit-softening genes such as PG, regulated by ERF and RMA1H1. Overall, this study provides insights into the genetic diversity, evolutionary history, and domestication of the APPM complex, offering valuable implications for genetic studies and breeding programs of Prunus crops.

Evolutionary genomics of climatic adaptation and resilience to climate change in alfalfa.

Given the escalating impact of climate change on agriculture and food security, gaining insights into the evolutionary dynamics of climatic adaptation and uncovering climate-adapted variation can empower the breeding of climate-resilient crops to face future climate change. Alfalfa (Medicago sativa subsp. sativa), the queen of forages, shows remarkable adaptability across diverse global environments, making it an excellent model for investigating species responses to climate change. In this study, we performed population genomic analyses using genome resequencing data from 702 accessions of 24 Medicago species to unravel alfalfa's climatic adaptation and genetic susceptibility to future climate change. We found that interspecific genetic exchange has contributed to the gene pool of alfalfa, particularly enriching defense and stress-response genes. Intersubspecific introgression between M. sativa subsp. falcata (subsp. falcata) and alfalfa not only aids alfalfa's climatic adaptation but also introduces genetic burden. A total of 1671 genes were associated with climatic adaptation, and 5.7% of them were introgressions from subsp. falcata. By integrating climate-associated variants and climate data, we identified populations that are vulnerable to future climate change, particularly in higher latitudes of the Northern Hemisphere. These findings serve as a clarion call for targeted conservation initiatives and breeding efforts. We also identified pre-adaptive populations that demonstrate heightened resilience to climate fluctuations, illuminating a pathway for future breeding strategies. Collectively, this study enhances our understanding about the local adaptation mechanisms of alfalfa and facilitates the breeding of climate-resilient alfalfa cultivars, contributing to effective agricultural strategies for facing future climate change.