The genome of Lespedeza potaninii reveals biased subgenome evolution and drought adaptation

Lespedeza potaninii, a xerophytic subshrub belonging to the legume family, is native to the Tengger Desert and is highly adapted to drought. It has important ecological value due to its drought adaptability, but the underlying molecular mechanisms remain largely unknown. Here, we report a 1.24 Gb chromosome-scale assembly of the L. potaninii genome (contig N50=15.75 Mb). Our results indicate that L. potaninii underwent an allopolyploid event with two subgenomes, A and B, presenting asymmetric evolution and B subgenome dominance. We estimate that the two diploid progenitors of L. potaninii diverged around 3.6 MYA and merged around 1.0 MYA. We revealed that the expansion of hub genes associated with drought responses, such as the binding partner 1 of accelerated cell death 11 (ACD11) (BPA1), facilitated environmental adaptations of L. potaninii to desert habitats. We found a novel function of the BPA1 family in abiotic stress tolerance in addition to the known role in regulating the plant immune response, which could improve drought tolerance by positively regulating reactive oxygen species homeostasis in plants. We revealed that bZIP transcription factors could bind to the BPA1 promoter and activate its transcription. Our work fills the genomic data gap in the Lespedeza genus and the tribe Desmodieae, which should provide both theoretical support in the study of drought tolerance and in the molecular breeding of legume crops.

Nitraria sibirica adapts to long-term soil water deficit by reducing photosynthesis, stimulating antioxidant systems, and accumulating osmoregulators

Amid climate change and shifts in precipitation patterns, drought conditions are expanding worldwide. Drought stress severely threatens plant growth in arid and semi-arid regions, wherein shrubs play a crucial role in maintaining ecological stability. Despite its ecological significance, studies are lacking on how Nitraria sibirica adapts to long-term drought stress. Therefore, in this study, to elucidate the mechanism of drought stress adaptation in N. sibirica, we analysed morphological, physiological, and transcriptional characteristics of plants in two soil habitats: riparian (moist) and desert (arid). The results showed that in desert soils, as soil water content decreased, leaf thickness increased, while plant height and leaf area decreased. Physiologically, photosynthesis decreased; soluble sugar, starch, proline, and hydrogen peroxide content increased significantly; while soluble proteins decreased significantly. Additionally, membrane lipid peroxidation products and antioxidant enzyme activities significantly increased under drought stress. Then, Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment analysis identified 313 key genes, which were considered the most significantly enriched in the photosynthesis and photosynthetic antenna protein pathways. Further, we found that the proteins encoding photosystem II (PsbP, PsbQ, PsbR, PsbY, and Psb27), photosystem I (PsaD, PsaF, PsaG, PsaH, PsaK, and PsaO), photosynthetic electron transport (PetF), and light-trapping antenna proteins were significantly downregulated under drought stress. Taken together, these results suggest that N. sibirica adapts to long-term drought conditions by suppressing photosynthesis, activating antioxidant systems, and recruiting osmoregulators. This study provides a basis for elucidating the growth mechanisms of N. sibirica under long-term drought stress conditions.

Combined effects of shade and drought on physiology, growth, and yield of mature cocoa trees

Climate models predict decreasing precipitation and increasing air temperature, causing concern for the future of cocoa in the major producing regions worldwide. It has been suggested that shade could alleviate stress by reducing radiation intensity and conserving soil moisture, but few on-farm cocoa studies are testing this hypothesis. Here, for 33 months, we subjected twelve-year cocoa plants in Ghana to three levels of rainwater suppression (full rainwater, 1/3 rainwater suppression and 2/3 rainwater suppression) under full sun or 40 % uniform shade in a split plot design, monitoring soil moisture, physiological parameters, growth, and yield. Volumetric soil moisture (ϴw) contents in the treatments ranged between 0.20 and 0.45 m3m-3 and increased under shade. Rainwater suppression decreased leaf water potentials (ѱw), reaching -1.5 MPa in full sun conditions indicating severe drought. Stomatal conductance (gs) was decreased under the full sun but was not affected by rainwater suppression, illustrating the limited control of water loss in cocoa plants. Although pre-dawn chlorophyll fluorescence (Fv/Fm) indicated photoinhibition, rates of photosynthesis (Pn) were highest in full sun. On the other hand, litter fall was highest in the full sun and under water stress, while diameter growth and carbon accumulation increased in the shade but was negatively affected by rainwater suppression. Abortion of fruits and damage to pods were high under shade, but dry bean yield was higher compared to under the full sun. The absence of interactions between shade treatments and rainwater suppression suggests that shade may improve the performance of cocoa, but not sufficiently to counteract the negative effects of water stress under field conditions.

Leaf trait modification in European beech trees in response to climatic and edaphic drought

Leaf morphological and physiological traits control the carbon and water relations of mature trees and are determinants of drought tolerance, but it is not well understood how they are modified in response to water deficits. We analysed five sun-canopy leaf traits (mean leaf size (LS), specific leaf area (SLA), Huber value (HV), water potential at turgor loss point (Ψ_tlp ) and foliar carbon isotope signature (δ¹³ C)) in European beech (Fagus sylvatica L.) across three precipitation gradients sampled in moist (2010), dry (2019) and very dry (2018) summers, and tested their response to short-term water deficits (climatic water balance (CWB) preceding sample collection) and long-term water availability (mean annual precipitation (MAP), plant-available soil water capacity (AWC) and neighbourhood competition). Across the 34 sites, LS varied seven-fold (3.9-27.0 cm² ), SLA four-fold (77.1-306.9 cm²·g^-1 ) and HV six-fold (1.0-6.65 cm² ·m^-2 ). In the 2018 dataset, LS showed a negative and HV a positive relationship to MAP, which contradicts relations found in multi-species samples. Average Ψ_tlp ranged from -1.90 to -2.62 MPa and decreased across the sites with decreasing CWB in the month prior to measurement, as well as with decreasing MAP and AWC in 2019. Studied leaf traits varied considerably between years, suggesting that mast fruiting and the severe 2018 drought caused the formation of smaller leaves. We conclude that sun-canopy leaf traits of European beech exhibit considerable plasticity in response to climatic and edaphic aridity, and that osmotic adjustment may be an important element in the drought response strategy of this anisohydric tree species.

Genome-wide analysis reveals selection signatures for body size and drought adaptation in Liangzhou donkey

Liangzhou donkey is a domestic animal breed distributed on the edge of the Tengger Desert in Gansu Province of China. It has small body size and strong adaptability to dry environments. Here, we sequenced 10 Liangzhou donkey genomes and compared them to the 55 genomes of 8 representative donkey breeds worldwide. The population structure analysis revealed that Liangzhou donkey harboured the ancestry with the Asian domestic donkeys (0.863) and European domestic donkeys (0.137). Three methods (nucleotide diversity, linkage disequilibrium decay and runs of homozygosity) implied the genetic diversity in Liangzhou donkey. In addition, we analyzed the genetic basis of the small body size and drought adaptation of Liangzhou donkey by using F_st, θπ-ratio, XP-EHH, CLR and θπ methods. We found that the NCAPG-LCORL on chromosome 3 may be a candidate region for small body size trait of Liangzhou donkey. The CYP4A11 gene located on chromosome 5 showed strong sign of selection sweep. CYP4A11 can convert arachidonic acid into 19(S)-HETE, which can promote water reabsorption in renal tubule and enhance the ability of Liangzhou donkey to adapt to dry environment. These results contribute to a better understanding of the underlying population structure of Liangzhou donkeys and provides a valuable resource for future research on donkey breeding in response to climate change.

Drought changes litter quantity and quality, and soil microbial activities to affect soil nutrients in moso bamboo forest

Drought would significantly influence the forest soils through changing the litterfall production and decomposition process. However, comprehensive in situ studies on drought effects in subtropical forests, especially in bamboo forests, have rarely been conducted. Here, we conducted a throughfall exclusion experiment with a rainfall reduction of ~80% in moso bamboo (Phyllostachys edulis) forests to investigate effects of drought on litter quantity, quality, soil microbial and enzyme activities, and soil nutrients across two years in subtropical China. We observed that throughfall exclusion (TE) treatment significantly decreased soil moisture by 63% compared to ambient control treatment (CK). Drought significantly decreased the annual litterfall in the second treatment year, and the leaf litter decomposition rate (-30% relative to CK) over 2 years of decomposition. TE treatment significantly decreased net release rate of litter carbon (C) and the amount of litter nitrogen (N) immobilization during a 360-day decomposition period, leading an increased litter C: N ratio in TE compared to CK. There was a distinct difference in soil microbial community composition between TE and CK treatments, showing higher bacteria biomass in TE but no difference in fungal biomass between TE and CK. Structural equation modelling revealed that drought decreased the contribution of litter quantity to soil nutrients but increased that of litter quality and soil microbial community to soil nutrients. Our results suggest that increasing drought events in subtropical China will directly reduce litterfall quantity and quality on the one hand, and alter the soil enzyme activities and microbial composition on the other hand, all of which will consequently decrease litter decomposition rate, soil nutrient availability, growth rate and productivity, leading to changes in the functioning and services of subtropical bamboo forests.

Leaf size as a key determinant of contrasting growth patterns in closely related Limonium (Plumbaginaceae) species

This study aims to analyze the importance of leaf size on plant growth capacity among an array of closely related Limonium species, and its impact on the underlying determinants of growth reduction under extreme water deficit conditions. To do so, thirteen Balearic Limonium species with contrasting leaf size were grown under long-term well-watered (WW) and severe water-deficit (WD) conditions in a common garden experiment. Fundamental growth traits were measured, including relative growth rate (RGR), net assimilation rate (NAR), leaf area ratio (LAR), leaf mass area (LMA) and leaf mass ratio (LMR). WD promoted small changes in leaf size, and species with larger leaves had higher RGR than species with smaller leaves, irrespective of the water treatment. Most RGR variation across species and treatments was explained by NAR, with comparatively much lower importance of LAR. The factorization of LAR underlying components denoted the importance of LMA in explaining RGR, whereas the impact of LMR on RGR was negligible in Limonium. Further, species with larger leaves had higher water consumption but also higher water use efficiency, especially under WD. Therefore, contrary to general trends in species from dry environments, increased leaf size is linked to increased growth capacity and also increased water use efficiency across closely related Limonium species.

Enriched networks 'nucleoside/nucleotide and ribonucleoside/ribonucleotide metabolic processes' and 'response to stimulus' potentially conferred to drought adaptation of the epiphytic orchid Dendrobium wangliangii

Dendrobium wangliangii is an endangered and epiphytic orchid with tolerance to seasonally extreme arid conditions and occurs exclusively in the hot-dry valley area of southwestern China. To reveal its molecular basis responsible for ecological adaptation, large-scale transcriptome sequencing was performed using Illumina sequencing with pooled mRNA extracted from whole plants and pseudobulbs during drought and rainy seasons. Based on the target transcript selection, the differentially expressed genes were related to 8 well-known drought-tolerant categories, and to morphological traits in resistance to water stress including pseudobulbs and roots. Further gene ontology enrichment analysis revealed that 'nucleoside/nucleotide and ribonucleoside/ribonucleotide metabolic processes' and 'response to stimulus' were the two most important aspects in resistance to drought stress with respect to the whole plant. In addition, the difference in the number and category of differentially expressed genes in whole plant and stem suggested the involvement of genes specifically localized in the stem, such as GTP-binding protein, lipases, signaling related transcripts and those involved in the ATP metabolic process. The comprehensive analysis of the epiphytic orchid in response to water deprivation indicates that integral tactics lead to active adaptation as a basal defense response to drought stress by the endangered epiphyte, including the collaboration of metabolic processes, responses to a various stimulus and other candidate genes contribute to its extreme drought tolerance. Insights from this study can be further utilized to understand stress-responsive genes in other medicinally important species and to improve the drought tolerance of food crops.

Speed breeding for multiple quantitative traits in durum wheat

BACKGROUND

Plant breeding requires numerous generations to be cycled and evaluated before an improved cultivar is released. This lengthy process is required to introduce and test multiple traits of interest. However, a technology for rapid generation advance named 'speed breeding' was successfully deployed in bread wheat (Triticum aestivum L.) to achieve six generations per year while imposing phenotypic selection for foliar disease resistance and grain dormancy. Here, for the first time the deployment of this methodology is presented in durum wheat (Triticum durum Desf.) by integrating selection for key traits, including above and below ground traits on the same set of plants. This involved phenotyping for seminal root angle (RA), seminal root number (RN), tolerance to crown rot (CR), resistance to leaf rust (LR) and plant height (PH). In durum wheat, these traits are desirable in environments where yield is limited by in-season rainfall with the occurrence of CR and epidemics of LR. To evaluate this multi-trait screening approach, we applied selection to a large segregating F₂ population (n = 1000) derived from a bi-parental cross (Outrob4/Caparoi). A weighted selection index (SI) was developed and applied. The gain for each trait was determined by evaluating F₃ progeny derived from 100 'selected' and 100 'unselected' F₂ individuals.

RESULTS

Transgressive segregation was observed for all assayed traits in the Outrob4/Caparoi F₂ population. Application of the SI successfully shifted the population mean for four traits, as determined by a significant mean difference between 'selected' and 'unselected' F₃ families for CR tolerance, LR resistance, RA and RN. No significant shift for PH was observed.

CONCLUSIONS

The novel multi-trait phenotyping method presents a useful tool for rapid selection of early filial generations or for the characterization of fixed lines out-of-season. Further, it offers efficient use of resources by assaying multiple traits on the same set of plants. Results suggest that when performed in parallel with speed breeding in early generations, selection will enrich recombinant inbred lines with desirable alleles and will reduce the length and number of years required to combine these traits in elite breeding populations and therefore cultivars.

Studies of life history of Gagea graeca (Liliaceae) based on morphological and molecular methods

BACKGROUND

We studied the life history of Gagea graeca (L.) A. Terracc. (sect. Anthericoides) by field surveys on the Greek island of Crete, including quantitative analyses of 405 individuals, estimation of resource allocation by measuring the nitrogen content of different plant organs, assessing seed set and recording genetic diversity via amplified fragment length polymorphism (AFLP) analyses. In contrast to most species of the genus G. graeca seems to be a short-lived perennial, developing several characters that are rather typical for annual plants.

RESULTS

Although seed set varies largely, flowering plants produce many (68 ± 79) small, flattened seeds (mean weight 73 ± 22 µg) in comparison to a single bulbil. If measured as nitrogen content of the respective plant parts, investment in seeds (25%) is much higher than that in bulbils (4%). In addition, the threshold for flower formation (expressed as bulb size where 50% of the plants form the respective structure) is with 2.17 ± 0.05 mm lower than that for bulbils with 2.80 ± 0.16 mm. This is in accordance with AFLP analyses revealing predominantly sexual reproduction (only 9.1% of 110 investigated plants belonged to clones).

CONCLUSION

In the genus Gagea early, predominantly sexual reproduction seems to be characteristic for species from arid habitats, coupled with a low proportion of clonal plants.

Artemisia dominant species succession relating to the soil moisture decrease in abandoned land of the Loess Plateau (China): comparative study of drought-adaptive characteristics

Artemisia scoparia, Artemisia sacrorum and Artemisia giraldii were three dominant Artemisia species which successive grew in the secondary succession on abandoned land of the Loess Plateau. The succession accompanied the soil moisture steady decrease with field age after their abandonment. To elucidate the relationship between the Artemisia species succession and their drought-adaptation, three dominant species and a contrastive species Artemisia annua (mesophyte), were selected to compare their drought-resistant characteristics, including morphological and anatomical traits of leaf and root. Then physiological responses were investigated in mature plants after drought treatment. The results indicated that three dominant species leaf presented drought-adaptive structures, such as bushy trichomes, transitional or isolateral leaf cells, thick cuticles and epidermal cells. However, A. annua had no leaf traits involved in drought-adaptation. In addition, A. sacrorum and A. giraldii contained large root systems, while A. scoparia and A. annua utilized succulent roots. The physiological responses to drought suggested that A. giraldii had strong regulation in water using strategy, growth, as well as superoxide dismutase and catalase activity. A. sacrorum and A. giraldii could maintain high ascorbate peroxidase activity and malondialdehyde content, while A. scoparia and A. giraldii presented higher peroxidase activity, ascorbate and soluble sugar content. A. annua exhibited high proline and carotenoid contents under drought. The drought-resistant of the four Artemisia species presented the order of A. giraldii > A. sacrorum > A. scoparia > A. annua, which was consistent with their succession on abandoned land.

Keeping wetlands wet in the western United States: adaptations to drought in agriculture-dominated human-natural systems

Water is critical to protecting wetlands in arid regions, especially in agriculture-dominated watersheds. This comparative case study analyzes three federal wildlife refuges in the Bear River Basin of the U.S. West where refuge managers secured water supplies by adapting to their local environmental context and their refuge's relationship to agriculture in being either irrigation-dependent, reservoir-adjacent or diked-delta wetlands. We found that each refuge's position confers different opportunities for securing a water supply and entails unique management challenges linked to agricultural water uses. Acquiring contextually-appropriate water rights portfolios was important for protecting these arid region wetlands and was accomplished through various strategies. Once acquired, water is managed to buffer wetlands against fluctuations caused by a dynamic climate and agricultural demands, especially during droughts. Management plans are responsive to needs of neighboring water users and values of the public at large. Such context-specific adaptations will be critical as the West faces climate change and population growth that threaten wetlands and agricultural systems to which they are linked.