A Standardized Framework for Better Understanding of Phenotypic Differences within Bacterial Phyla Based on Protein Domain.

We propose a standardized framework to classify target species based on their protein domains, which can be utilized in different contexts, like eukaryotes and prokaryotes. In this study, by applying the framework to the bacterial kingdom as an implementation example and comparing the results with the current taxonomy standards at the phylum level, we came to the conclusion that the sequence of domains rather than the content of domains in a protein and the presence of one domain rather than the number of occurrences of one domain play more important roles in deciding bacterial phenotypes as well as matching the current taxonomy. In addition, the comparison also helps us to better focus on the species that conflict with the current phylum category, as well as to further investigate their phenotypic or genotypic differences. IMPORTANCE A 3-step framework was designed which can be applied to clustering species based on their protein domains, and different candidate models are proposed in each step for better adaptation of various scenarios. We show its implementation for the bacterial kingdom as an example, which helps us to find the most appropriate model combination that will best reflect the relationship between domains and phenotypes in this context. In addition, identifying species that are distant in the results but should be closely related phylogenetically can help us to focus on the mismatch for better understanding of their key phenotypic or genotypic differences.

Multiomics reveals an essential role of long-distance translocation in regulating plant cadmium resistance and grain accumulation in allohexaploid wheat (Triticum aestivum).

Cadmium (Cd) is a highly toxic heavy metal that readily enters cereals, such as wheat, via the roots and is translocated to the shoots and grains, thereby posing high risks to human health. However, the vast and complex genome of allohexaploid wheat makes it challenging to understand Cd resistance and accumulation. In this study, a Cd-resistant cultivar of wheat, 'ZM1860', and a Cd-sensitive cultivar, 'ZM32', selected from a panel of 442 accessions, exhibited significantly different plant resistance and grain accumulation. We performed an integrated comparative analysis of the morpho-physiological traits, ionomic and phytohormone profiles, genomic variations, transcriptomic landscapes, and gene functionality in order to identify the mechanisms underlying these differences. Under Cd toxicity, 'ZM1860' outperformed 'ZM32', which showed more severe leaf chlorosis, poorer root architecture, higher accumulation of reactive oxygen species, and disordered phytohormone homeostasis. Ionomics showed that 'ZM32' had a higher root-to-shoot translocation coefficient of Cd and accumulated more Cd in the grains than 'ZM1860'. Whole-genome re-sequencing (WGS) and transcriptome sequencing identified numerous DNA variants and differentially expressed genes involved in abiotic stress responses and ion transport between the two genotypes. Combined ionomics, transcriptomics, and functional gene analysis identified the plasma membrane-localized heavy metal ATPase TaHMA2b-7A as a crucial Cd exporter regulating long-distance Cd translocation in wheat. WGS- and PCR-based analysis of sequence polymorphisms revealed a 25-bp InDel site in the promoter region of TaHMA2b-7A, and this was probably responsible for the differential expression. Our multiomics approach thus enabled the identification of a core transporter involved in long-distance Cd translocation in wheat, and it may provide an elite genetic resource for improving plant Cd resistance and reducing grain Cd accumulation in wheat and other cereal crops.

Strontium uptake and antioxidant capacity comparisons of low accumulator and high accumulator oat (Avena sativa L.) genotypes.

The main object of the present study is to investigate genotypic differences in strontium (Sr) resistance of two oat varieties, including Neimengkeyi-1 (high accumulator) and Bayou-3 (low accumulator). The growth and antioxidant enzyme responses to five Sr concentrations (0, 25, 100, 500, and 1000 mg kg-1) were compared after 30-day Sr treatment. The shoot-Sr concentrations of Neimengkeyi-1 were higher than those of Bayou-3 in all treatments. The translocation factors of Neimengkeyi-1 in all treatments were greater than 1 and significantly higher than those of Bayou-3. Sr ions did not affect the growth of Neimengkeyi-1. The H2O2 contents and the leaf malondialdehyde contents of Neimengkeyi-1 were lower than those of Bayou-3. The activities of superoxide dismutase (SOD), catalase (CAT), and peroxidase of Neimengkeyi-1 were significantly higher than those of Bayou-3. Significant negative correlations were found between H2O2 contents and SOD and CAT activities in Neimengkeyi-1. The results of this study suggest that Sr accumulation patterns have significant genotypic differences, and SOD and CAT may play a pivotal role in the detoxification mechanism of Sr.

Management of trace element-contaminated agricultural land by in situ stabilization combined with phytoexclusion over a three years crop rotation.

This study assessed in situ stabilization combined with phytoexclusion in practical application on agricultural land contaminated strongly, and spatially heterogeneous, with metals (Cd, Pb, and Zn) and As. Single and combined lime marl and phosphate treatments were consecutively planted with two cultivars each of rape, wheat, and barley differing in trace elements (TE) accumulation. The effects on soil acidity, NH4NO3-soluble, and straw and grain TE concentrations were evaluated. The combined fertilizer treatment most effectively reduced metals mobility, but neither amendment mitigated plant TE status, which correlated more with pseudo-total than NH4NO3-soluble TE in soil. The cultivar choice reduced grain Cd by 39 or 21% in barley or wheat, respectively, simultaneously decreased grain Zn, but conversely affected As uptake in wheat grains. The lack of correlations between grain TE concentrations suggests the potential for breeding cultivars with low Cd and As accumulation without causing Zn malnutrition. The cereals had relatively low yields, particularly on highly polluted areas, and only rape and barley grains unexceptionally suited for animal consumption. Agricultural measures and climatic conditions influenced TE mobility. The cultivars' TE uptake varied less than in greenhouse studies, stressing the importance of field studies for an adequate estimation of phytoexclusion potentials.

Genetics of mycorrhizal symbiosis in winter wheat (Triticum aestivum).

Bread wheat (Triticum aestivum) is a major staple food and therefore of prime importance for feeding the Earth's growing population. Mycorrhiza is known to improve plant growth, but although extensive knowledge concerning the interaction between mycorrhizal fungi and plants is available, genotypic differences concerning the ability of wheat to form mycorrhizal symbiosis and quantitative trait loci (QTLs) involved in mycorrhization are largely unknown. Therefore, a diverse set of 94 bread wheat genotypes was evaluated with regard to root colonization by arbuscular mycorrhizal fungi. In order to identify genomic regions involved in mycorrhization, these genotypes were analyzed using the wheat 90k iSelect chip, resulting in 17 823 polymorphic mapped markers, which were used in a genome-wide association study. Significant genotypic differences (P < 0.0001) were detected in the ability to form symbiosis and 30 significant markers associated with root colonization, representing six QTL regions, were detected on chromosomes 3A, 4A and 7A, and candidate genes located in these QTL regions were proposed. The results reported here provide key insights into the genetics of root colonization by mycorrhizal fungi in wheat.

Differences between winter oilseed rape (Brassica napus L.) cultivars in nitrogen starvation-induced leaf senescence are governed by leaf-inherent rather than root-derived signals.

Nitrogen (N) efficiency of winter oilseed rape (Brassica napus L.) line-cultivars (cvs.), defined as high grain yield under N limitation, has been primarily attributed to maintained N uptake during reproductive growth (N uptake efficiency) in combination with delayed senescence of the older leaves accompanied with maintained photosynthetic capacity (functional stay-green). However, it is not clear whether genotypic variation in N starvation-induced leaf senescence is due to leaf-inherent factors and/or governed by root-mediated signals. Therefore, the N-efficient and stay-green cvs. NPZ-1 and Apex were reciprocally grafted with the N-inefficient and early-senescing cvs. NPZ-2 and Capitol, respectively and grown in hydroponics. The senescence status of older leaves after 12 days of N starvation assessed by SPAD, photosynthesis and the expression of the senescence-specific cysteine protease gene SAG12-1 revealed that the stay-green phenotype of the cvs. NPZ-1 and Apex under N starvation was primarily under the control of leaf-inherent factors. The same four cultivars were submitted to N starvation for up to 12 days in a time-course experiment. The specific leaf contents of biologically active and inactive cytokinins (CKs) and the expression of genes involved in CK homeostasis revealed that under N starvation leaves of early-senescing cultivars were characterized by inactivation of biologically active CKs, whereas in stay-green cultivars synthesis, activation, binding of and response to biologically active CKs were favoured. These results suggest that the homeostasis of biologically active CKs was the predominant leaf-inherent factor for cultivar differences in N starvation-induced leaf senescence and thus N efficiency.

Variations in Root Characteristics and Cadmium Accumulation of Different Rice Varieties under Dry Cultivation Conditions.

Variations in the cadmium (Cd) accumulation and root characteristics of different genotypes of rice during three developmental periods of dry cultivation were investigated in pot experiments in which two levels of Cd were added to the soil (0 and 10 mg kg-1). The results show that the Cd concentration in each organ of the different rice genotypes decreased in both the order of roots > shoots > grains and during the three developmental periods in the order of the maturity stage > booting stage > tillering stage. The lowest bioaccumulation factor (BCF) and translocation factor (TF) were found in Yunjing37 (YJ37) under Cd stress. At maturity, Cd stress inhibited the root length of Dianheyou34 (DHY34) the most and that of Dianheyou 918 (DHY918) the least, also affecting the root volume of DHY34 and Dianheyou615 (DHY615) the most and that of YJ37 and Yiyou 673 (YY673) the least; the inhibition rates were 41.80, 5.09, 40.95, and 10.51%, respectively. The exodermis showed the greatest thickening in YY673 and the lowest thickening in DHY615, while the endodermis showed the opposite result. The rates of change were 16.48, 2.45, 5.10, and 8.49%, respectively. The stele diameter of DHY615 decreased the most, and that of YY673 decreased the least, while the secondary xylem area showed the opposite result; the rates of change were -21.50, -14.29, -5.86, and -26.35%, respectively. Under Cd stress treatment at maturity, iron plaque was extracted using the dithionite-citrate-bicarbonate (DCB) method. The concentration of iron (DCB-Fe) was highest in YJ37, and the concentration of cadmium (DCB-Cd) was lowest in DHY34. YJ37 was screened as a low Cd-accumulating variety. The concentration of available Cd in the rhizosphere soil, iron plaque, root morphology, and anatomy affect Cd accumulation in rice with genotypic differences. Our screening of Cd-accumulating rice varieties provides a basis for the dry cultivation of rice in areas with high background values of Cd in order to avoid the health risks of Cd intake.

Investigating aluminum toxicity effects on callose deposition, oxidative stress, and nutrient homeostasis in banana genotypes.

Aluminum (Al) toxicity poses a significant challenge to agricultural productivity, particularly in acidic soils. The banana crop, predominantly cultivated in tropical and subtropical climates, often grapples with low pH and Al toxicity. This study seeks to explore the differential responses of two banana genotypes with varying Al tolerance (Baodao and Baxi) to Al exposure (100 and 500 µM) for 24 h. Microscopic analysis uncovered distinctive structural modifications in root cells, with Baodao displaying more severe alterations in response to Al stress. There was higher superoxide (O2-.) and hydrogen peroxide (H2O2) production and lipid peroxidation in Baodao indicating enhanced oxidative stress and membrane damage. Al accumulation in root tips was higher in Baxi than Baodao, while the roots of Baodao had a higher accumulation of callose. Nutrient content analysis revealed alterations in ion levels, highlighting the impact of Al exposure on nutrient uptake and homeostasis. In summary, Al differentially affects callose deposition, which, in turn, leads to Al uptake and nutrient homeostasis alteration in two contrasting banana genotypes. This intricate interplay is a key factor in understanding plant responses to aluminum toxicity and can inform strategies for crop improvement and soil management in aluminum-stressed environments.

Geographic differences and variation of functional components of brown rice in 690 mini-core collections from global germplasms.

Objective: To understand the geographic differences and variations in the functional components of brown rice cores collected from global rice germplasms. Methods: Four functional components, γ-aminobutyric acid (GABA), resistant starch (RS), total flavonoids, and alkaloids, in brown rice from 690 mini-core collections from 31 countries from five continents and the International Rice Research Institute, were analyzed using a spectrophotometry colorimetric method, and the results were statistically validated. Conclusion: The highest average amounts of functional components were obtained in Asian germplasms, except for GABA, and total flavonoids were highest in brown rice from Europe and Oceania, followed by Asia. The highest coefficient of variation for GABA was observed in Asia; that for RS and total flavonoids was observed in Africa, followed by Asia; and that for alkaloids was observed in America, followed by Asia. Overall, Asian countries were the most prominent and representative zones with the highest genotypic potential for functional components of brown rice. Forty-one rice accessions with enriched functional components originated mostly from biodiversity-rich areas in China, followed by those in the Philippines. Late sowing favored the enrichment of these components in brown rice. The current study provides a reference for rice breeding with enriched functional constituents, and guidelines for screening functional rice that could be used for human chronic disease research.

Transcriptomic analysis of nitrogen starvation- and cultivar-specific leaf senescence in winter oilseed rape (Brassica napus L.).

High nitrogen (N) efficiency, characterized by high grain yield under N limitation, is an important agricultural trait in Brassica napus L. cultivars related to delayed senescence of older leaves during reproductive growth (a syndrome called stay-green). The aim of this study was thus to identify genes whose expression is specifically altered during N starvation-induced leaf senescence and that can be used as markers to distinguish cultivars at early stages of senescence prior to chlorophyll loss. To this end, the transcriptomes of leaves of two B. napus cultivars differing in stay-green characteristics and N efficiency were analyzed 4 days after the induction of senescence by either N starvation, leaf shading or detaching. In addition to N metabolism genes, N starvation mostly (and specifically) repressed genes related to photosynthesis, photorespiration and cell-wall structure, while genes related to mitochondrial electron transport and flavonoid biosynthesis were predominately up-regulated. A kinetic study over a period of 12 days with four B. napus cultivars differing in their stay-green characteristics confirmed the cultivar-specific regulation of six genes in agreement with their senescence behavior: the senescence regulator ANAC029, the anthocyanin synthesis-related genes ANS and DFR-like1, the ammonium transporter AMT1;4, the ureide transporter UPS5, and SPS1 involved in sucrose biosynthesis. The identified genes represent markers for the detection of cultivar-specific differences in N starvation-induced leaf senescence and can thus be employed as valuable tools in B. napus breeding.

Seed mass, genotype, and density effects on growth and yield of Oenothera biennis L.

Seed mass and genotypic effects on the growth and reproduction of Oenothera biennis L. over a gradient of intraspecific density were examined in a greenhouse experiment. By using genetically identical seeds from five parental genotypes we were able to examine independently the effects of seed mass and genotype on seedling and adult performance. Seedling size was significantly correlated with seed mass for the first five weeks but had no effect on adult size or reproductive output. In contrast, genotype differences became increasingly apparent with time. In particular, there were striking differences in reproductive output among genotypes. Plants grown from two of the genotypes consistently produced more, but lighter, seeds and a greater proportion flowered at high density than the other three genotypes. In all five genotypes, seed number was much more variable than seed mass across the density gradient. Initial seed mass accounted for a significant proportion of the variation in progeny seed mass, and mean seed mass produced in the greenhouse was positively correlated with mean seed mass of the parent (in the field). This result, together with the observed constancy of seed mass within a genotype across the density gradient, indicates the differences in reproductive output among these genotypes are genetically determined.