The Potential Role of Genic-SSRs in Driving Ecological Adaptation Diversity in Caragana Plants

Caragana, a xerophytic shrub genus widely distributed in northern China, exhibits distinctive geographical substitution patterns and ecological adaptation diversity. This study employed transcriptome sequencing technology to investigate 12 Caragana species, aiming to explore genic-SSR variations in the Caragana transcriptome and identify their role as a driving force for environmental adaptation within the genus. A total of 3666 polymorphic genic-SSRs were identified across different species. The impact of these variations on the expression of related genes was analyzed, revealing a significant linear correlation (p < 0.05) between the length variation of 264 polymorphic genic-SSRs and the expression of associated genes. Additionally, 2424 polymorphic genic-SSRs were located in differentially expressed genes among Caragana species. Through weighted gene co-expression network analysis, the expressions of these genes were correlated with 19 climatic factors and 16 plant functional traits in various habitats. This approach facilitated the identification of biological processes associated with habitat adaptations in the studied Caragana species. Fifty-five core genes related to functional traits and climatic factors were identified, including various transcription factors such as MYB, TCP, ARF, and structural proteins like HSP90, elongation factor TS, and HECT. The roles of these genes in the ecological adaptation diversity of Caragana were discussed. Our study identified specific genomic components and genes in Caragana plants responsive to heterogeneous habitats. The results contribute to advancements in the molecular understanding of their ecological adaptation, lay a foundation for the conservation and development of Caragana germplasm resources, and provide a scientific basis for plant adaptation to global climate change.

Simulation and prediction of the geographical distribution of five Caragana species in the north temperate zone

The shrub encroachment caused by Caragana species (mainly C. microphylla, C. korshinskii, C. tibetica, C. stenophylla, and C. pygmaea) in the north temperate zone has significant impacts on ecosystems. Understanding the distribution of Caragana species' responses to climate change is increasingly relevant to the dynamic of shrub encroachment. In this study, we gathered 1124 geographical distribution records for 5 Caragana species. Through principal component analysis and Pearson correlation analysis, 11 environmental variables were identified. We employed the maximum entropy (MaxEnt) model and utilized the current and future climate dataset from 2041 to 2060 based on two extreme climate scenarios (RCP2.6 and RCP8.5) and atmospheric circulation models (BCC_CSM1.1 and IPSLCM5A-LR) to assess the potential distribution patterns and dynamic change with global warming. The results showed the following: (1) Currently, the five Caragana species are mainly distributed in the central and western parts of the Inner Mongolia Autonomous Region, Mongolia, and the southern parts of Russia. (2) In the future, the habitable zone of C. microphylla and C. korshinskii will expand gradually, while the distribution probability of C. stenophylla, C. tibetica, and C. pygmaea will shrink significantly in 60-80% of the area, and the habitable area will fluctuate sharply. (3) The range of the five species of Caragana expansion area is projected to be 1229.43×106 km2-1412.32×106 km2, with the suitable habitats expected to extend northward in the future, primarily concentrated in central Mongolia and around Lake Baikal in Russia. This research provides guidance for protecting grassland resources and ensuring sustainable development under shrub encroachment.

under Water Deficit

To evaluate the physiological responses of Korshinsk peashrub (Caragana korshinskii Kom.) to water deficit, photosynthetic gas exchange, chlorophyll fluorescence, and the levels of superoxide anion (O₂^•-), hydrogen peroxide (H₂O₂), malondialdehyde (MDA), antioxidant enzymes, and endogenous hormones in its leaves were investigated under different irrigation strategies during the entire growth period. The results showed that leaf growth-promoting hormones were maintained at a higher level during the stages of leaf expansion and vigorous growth, and zeatin riboside (ZR) and gibberellic acid (GA) gradually decreased with an increase in water deficit. At the leaf-shedding stage, the concentration of abscisic acid (ABA) dramatically increased, and the ratio of ABA to growth-promoting hormones increased to a high level, which indicated that the rate of leaf senescence and shedding was accelerated. At the stages of leaf expansion and vigorous growth, the actual efficiency of photosystem II (PSII) (Φ_PSii) was downregulated with an increment in non-photochemical quenching (NPQ) under moderate water deficit. Excess excitation energy was dissipated, and the maximal efficiency of PSII (F_v/F_m) was maintained. However, with progressive water stress, the photo-protective mechanism was inadequate to avoid photo-damage; F_v/F_m was decreased and photosynthesis was subject to non-stomatal inhibition under severe water deficit. At the leaf-shedding stage, non-stomatal factors became the major factors in limiting photosynthesis under moderate and severe water deficits. In addition, the generation of O₂^•- and H₂O₂ in the leaves of Caragana was accelerated under moderate and severe water deficits, which caused an enhancement of antioxidant enzyme activities to maintain the oxidation-reduction balance. However, when the protective enzymes were insufficient in eliminating excessive reactive oxygen species (ROS), the activity of catalase (CAT) was reduced at the leaf-shedding stage. Taken all together, Caragana has strong drought resistance at the leaf expansion and vigorous growth stages, but weak drought resistance at the leaf-shedding stage.

[Differences in Bacterial Community Structure in Rhizosphere Soil of Three Caragana Species and Its Driving Factors in a Common Garden Experiment]

The soil bacterial diversity and community structures in rhizosphere soil of Caragana microphylla, Caragana liouana, and Caragana roborovskyi in a common garden experiment were measured using the high-throughput sequencing technique, with the aim of investigating the factors driving the variation in the bacterial community structure. The results indicated that 42 phyla, 55 classes, 123 orders, 244 families, and 558 genera were obtained from the rhizosphere soil. The dominant phyla in all sample sites were Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, Firmicutes, and Acidobacteria (relative abundance>1%). At the genus level, Phenylobacterium, Ensifer, and Chitinophaga were dominant. Two-way analysis of variance showed that species had a significant effect on the Shannon index and Simpson index of rhizosphere soil bacteria of the three Caragana species, whereas the Chao1 index, Shannon index, and Simpson index were significantly affected by the interaction of provenances and species. There was a significant difference among the three species in the composition of bacterial communities, and the cluster analysis indicated that the composition of the soil bacterial community significantly differed among provenances in C. liouana and C. roborovskyi. Based on the redundancy analysis, mean annual precipitation and altitude were the dominant factors influencing the rhizosphere soil bacterial community structure. Overall, the present results indicated that there were intraspecific and interspecific differences in the diversity and community structures of rhizosphere soil bacteria, and the bacterial community structure was mainly affected by the provenance climate. These results provide a theoretical basis for understanding the adaptation strategies and ecological restoration of the three Caragana species.

as a partial substitution for sheep forage on intake, digestibility, growth, carcass features, and the rumen bacterial community

The aim of this study was to verify that Caragana korshinskii Kom. (CK) as a component of sheep forage influences lamb digestibility and rumen fermentation by altering the rumen microbial community. Hence, 12 female Tan sheep were allocated into 2 groups: receiving (CK group) or not (control group) 10% of the diet forage fraction with CK. During the 60-day experiment, growth performance, apparent digestibility, rumen volatile fatty acids (VFAs), and nitrogen balance were measured. Meanwhile, the rumen bacterial community diversity and composition were detected by the 16S rRNA sequence. The results indicated that the apparent digestibility of acid detergent fibre (ADF) tended to be higher (0.05 < P < 0.10), and the feed conversion efficiency was improved (P < 0.05) when CK was offered. Compared to those under alfalfa, the composition and abundance of the rumen microbial community were altered in the CK group, and the phylum Firmicutes, which is involved in promoting fibre digestion, increased in abundance. Moreover, VFAs tended to decrease (0.05 < P < 0.10), and the molar proportion of butyrate declined; similarly, levels of hypoxanthine and xanthine were lower (P < 0.05) in the sheep fed CK and may have been responsible for the decreased abundance of Fibrobacter spp., which are cellulolytic ruminal bacteria associated with VFA production.

Host-Specific Effects of Arbuscular Mycorrhizal Fungi on Two Caragana Species in Desert Grassland

Arbuscular mycorrhizal fungi (AMF), which form symbioses with most land plants, could benefit their hosts and potentially play important roles in revegetation of degraded lands. However, their application in revegetation of desert grasslands still faces challenges and uncertainties due to the unclear specificity of AMF-plant interactions. Here, Caragana korshinskii and Caragana microphylla were inoculated with either conspecific (home) or heterospecific (away) AM fungal communities from the rhizosphere of three common plant species (C. korshinskii, C. microphylla and Hedysarum laeve) in Kubuqi Desert, China. AMF communities of the inocula and their home and away effects on growth and nutrition status of two Caragana species were examined. Results showed that AMF communities of the three inocula from C. korshinskii, H. laeve and C. microphylla were significantly different, and were characterized by high abundance of Diversispora, Archaeospora, and Glomus, respectively. The shoot biomass, photosynthetic rate, foliar N and P contents of C. korshinskii only significantly increased under home AMF inoculation by 167.10%, 73.55%, 9.24%, and 23.87%, respectively. However, no significant effects of AMF on C. microphylla growth were found, regardless of home or away AMF. Positive correlations between C. korshinskii biomass and the abundance of AMF genus Diversispora were found. Our study showed strong home advantage of using native AMF community to enhance C. korshinskii growth in the desert and presented a potentially efficient way to use native AMF in restoration practices.

Water permeability/impermeability in seeds of 15 species of Caragana (Fabaceae)

Majority legumes in the temperate and arctic zones have water-impermeable seeds (physical dormancy, PY). However, various authors have reported that seeds of some Caragana species are water-permeable and thus non-dormant. We (1) tested seeds of 15 species of Caragana matured in the same site in 2014, 2016 and/or 2017 for presence of PY, (2) determined if dry storage decreased or increased the percentage of seeds with PY and (3) located the site on the seed coat of 11 species where water enters the seed. Sixty-three percent and 45% of the seeds of C. roborovskyi had PY in 2016 and 2017, respectively, but only 0-14% of the seeds of the other 14 species had PY. The palisade layer in the seed coat of water impermeable seeds had no cracks in it, whereas cracks were present in the palisade layer of water-permeable seeds. Year of collection and dry storage had significant effects on imbibition of two species (C. acanthophylla and C. roborovskyi). In two (C. acanthophylla and C. roborovskyi) of the 11 species tested, the hilum was the site of water entry into seeds (control seeds, not any dormant broken treatments), but for the other nine species tested water entered through all parts of the seed coat.

Comparative analyses of different biogenic CO2 emission accounting systems in life cycle assessment

The biomass-derived CO₂ emission is usually treated as neutral to climate change. However, due to the stay of biomass-derived CO₂ in the atmosphere, many researchers believe that biomass-derived CO₂ also has climate change benefit. Therefore, many methods to account the global warming potential of biomass-derived CO₂ (GWP_bio) were proposed. Based on those new methods, we developed an accounting system for climate change impact of biomass utilization in this study, and compared it with the conventional accounting system which follows the carbon neutral assumption. A case study of caragana-to-pellet bioenergy production system was simulated to test the performance of the GWP_bio accounting system. The CENTURY model was used to simulate carbon dynamics of caragana plantation in the Loess Plateau in China, and life cycle assessment (LCA) model was developed to estimate the life cycle emissions of the caragana-to-pellet system. Attributed to short rotation of caragana plantation and fast biomass accumulation after harvest, the GWP_bio values around 0.044 were obtained. When the GWP_bio was applied to LCA, significant high life cycle CO₂ emission was found in comparison to the conventional method. However, the GWP_bio accounting system has lower positive climate change impact than the conventional accounting system in assessing the overall impact of biomass utilization. This indicated that the application of GWP_bio accounting system would encourage the utilization of biomass and allow a fair comparison with fossil fuels. In the sensitivity analysis, we found the accounting system was sensitive to biomass accumulation and all the corresponding factor affecting biomass accumulation.

rosea

To exploit the drought-resistant Caragana species, we performed a comparative study of the plastomes from four species: Caragana rosea, C. microphylla, C. kozlowii, and C. Korshinskii. The complete plastome sequence of the C. rosea was obtained using the next generation DNA sequencing technology. The genome is a circular structure of 133,122 bases and it lacks inverted repeat. It contains 111 unique genes, including 76 protein-coding, 30 tRNA, and four rRNA genes. Repeat analyses obtained 239, 244, 258, and 246 simple sequence repeats in C. rosea, C. microphylla, C. kozlowii, and C. korshinskii, respectively. Analyses of sequence divergence found two intergenic regions: trnI-CAU-ycf2 and trnN-GUU-ycf1, exhibiting a high degree of variations. Phylogenetic analyses showed that the four Caragana species belong to a monophyletic clade. Analyses of Ka/Ks ratios revealed that five genes: rpl16, rpl20, rps11, rps7, and ycf1 and several sites having undergone strong positive selection in the Caragana branch. The results lay the foundation for the development of molecular markers and the understanding of the evolutionary process for drought-resistant characteristics.

Evolutionarily Conserved nodE, nodO, T1SS, and Hydrogenase System in Rhizobia of Astragalus membranaceus and Caragana intermedia

Mesorhizobium species are the main microsymbionts associated with the medicinal or sand-fixation plants Astragalus membranaceus and Caragana intermedia (AC) in temperate regions of China, while all the Mesorhizobium strains isolated from each of these plants could nodulate both of them. However, Rhizobium yanglingense strain CCBAU01603 could nodulate AC plants and it's a high efficiency symbiotic and competitive strain with Caragana. Therefore, the common features shared by these symbiotic rhizobia in genera of Mesorhizobium and Rhizobium still remained undiscovered. In order to study the genomic background influencing the host preference of these AC symbiotic strains, the whole genomes of two (M. silamurunense CCBAU01550, M. silamurunense CCBAU45272) and five representative strains (M. septentrionale CCBAU01583, M. amorphae CCBAU01570, M. caraganae CCBAU01502, M. temperatum CCBAU01399, and R. yanglingense CCBAU01603) originally isolated from AC plants were sequenced, respectively. As results, type III secretion systems (T3SS) of AC rhizobia evolved in an irregular pattern, while an evolutionarily specific region including nodE, nodO, T1SS, and a hydrogenase system was detected to be conserved in all these AC rhizobia. Moreover, nodO was verified to be prevalently distributed in other AC rhizobia and was presumed as a factor affecting the nodule formation process. In conclusion, this research interpreted the multifactorial features of the AC rhizobia that may be associated with their host specificity at cross-nodulation group, including nodE, nodZ, T1SS as the possible main determinants; and nodO, hydrogenase system, and T3SS as factors regulating the bacteroid formation or nitrogen fixation efficiency.

Drought responses of three closely related Caragana species: implication for their vicarious distribution

Drought is a major environmental constraint affecting growth and distribution of plants in the desert region of the Inner Mongolia plateau. Caragana microphylla, C. liouana, and C. korshinskii are phylogenetically close but distribute vicariously in Mongolia plateau. To gain a better understanding of the ecological differentiation between these three species, we examined the leaf gas exchange, growth, water use efficiency, biomass accumulation and allocation by subjecting their seedlings to low and high drought treatments in a glasshouse. Increasing drought stress had a significant effect on many aspects of seedling performance in all species, but the physiology and growth varied with species in response to drought. C. korshinskii exhibited lower sensitivity of photosynthetic rate and growth, lower specific leaf area, higher biomass allocation to roots, higher levels of water use efficiency to drought compared with the other two species. Only minor interspecific differences in growth performances were observed between C. liouana and C. microphylla. These results indicated that faster seedling growth rate and more efficient water use of C. korshinskii should confer increased drought tolerance and facilitate its establishment in more severe drought regions relative to C. liouana and C. microphylla.

Drought responses of three closely related Caragana species: implication for their vicarious distribution

Drought is a major environmental constraint affecting growth and distribution of plants in the desert region of the Inner Mongolia plateau. Caragana microphylla, C. liouana, and C. korshinskii are phylogenetically close but distribute vicariously in Mongolia plateau. To gain a better understanding of the ecological differentiation between these three species, we examined the leaf gas exchange, growth, water use efficiency, biomass accumulation and allocation by subjecting their seedlings to low and high drought treatments in a glasshouse. Increasing drought stress had a significant effect on many aspects of seedling performance in all species, but the physiology and growth varied with species in response to drought. C. korshinskii exhibited lower sensitivity of photosynthetic rate and growth, lower specific leaf area, higher biomass allocation to roots, higher levels of water use efficiency to drought compared with the other two species. Only minor interspecific differences in growth performances were observed between C. liouana and C. microphylla. These results indicated that faster seedling growth rate and more efficient water use of C. korshinskii should confer increased drought tolerance and facilitate its establishment in more severe drought regions relative to C. liouana and C. microphylla.

A molecular phylogeny of Caraganeae (Leguminosae, Papilionoideae) reveals insights into new generic and infrageneric delimitations

Based on sequence data of nuclear ITS and plastid matK, trnL-F and psbA-trnH markers, the phylogeny of the subtribes Caraganinae and Chesneyinae in tribe Caraganeae was inferred. The results support the monophyly of each of the subtribes. Within subtribes Caraganinae, Calophaca and Halimodendron are herein transferred into Caragana to ensure its generic monophyly. The subtribe Chesneyinae is composed of four well-supported genera: Chesneya, Chesniella, Gueldenstaedtia and Tibetia. Based on phylogenetic, morphological, distributional and habitat type evidence, the genus Chesneya was divided into three monophyletic sections: Chesneya sect. Chesneya, Chesneya sect. Pulvinatae and Chesneya sect. Spinosae. Chesneya macrantha is herein transferred into Chesniella. Spongiocarpella is polyphyletic and its generic rank is not maintained. The position of Chesneya was incongruent in the nuclear ITS and the plastid trees. A paternal chloroplast capture event via introgression is hypothesized for the origin of Chesneya, which is postulated to have involved the common ancestor of Chesniella (♂) and that of the Gueldenstaedtia - Tibetia (GUT) clade (♀) as the parents.

Distribution of three congeneric shrub species along an aridity gradient is related to seed germination and seedling emergence

Environmental tolerance of a species has been shown to correlate positively with its geographical range. On the Ordos Plateau, three Caragana species are distributed sequentially along the precipitation gradient. We hypothesized that this geographical distribution pattern is related to environmental tolerances of the three Caragana species during seed germination and seedling emergence stages. To test this hypothesis, we examined seed germination under different temperature, light and water potentials, and monitored seedling emergence for seeds buried at eight sand depths and given different amounts of water. Seeds of C. korshinskii germinated to high percentages at 5 : 15 to 25 : 35 °C in both light and darkness, while those of C. intermedia and C. microphylla did so only at 15 : 25 and 25 : 35 °C, respectively. Nearly 30 % of the C. korshinskii seeds germinated at -1.4 MPa at 20 and 25 °C, while no seeds of the other two species did so. Under the same treatments, seedling emergence percentages of C. korshinskii were higher than those of the other two species. The rank order of tolerance to drought and sand burial of the three species is C. korshinskii > C. intermedia > C. microphylla. The amount of precipitation and sand burial depth appear to be the main selective forces responsible for the geographical distribution of these species.