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<jats:p>Developing wheat varieties with durable resistance is a core objective of the International Maize and Wheat Improvement Center (CIMMYT) and many other breeding programs worldwide. The CIMMYT advanced wheat line “Mucuy” displayed high levels of resistance to stripe rust (YR) and leaf rust (LR) in field evaluations in Mexico and several other countries. To determine the genetic basis of YR and LR resistance, 138 F<jats:sub>5</jats:sub> recombinant inbred lines (RILs) derived from the cross of Apav#1× Mucuy were phenotyped for YR responses from 2015 to 2020 at field sites in India, Kenya, and Mexico, and LR in Mexico. Seedling phenotyping for YR and LR responses was conducted in the greenhouse in Mexico using the same predominant races as in field trials. Using 12,681 polymorphic molecular markers from the DArT, SNP, and SSR genotyping platforms, we constructed genetic linkage maps and QTL analyses that detected seven YR and four LR resistance loci. Among these, a co-located YR/LR resistance loci was identified as <jats:italic>Yr29/Lr46</jats:italic>, and a seedling stripe rust resistance gene <jats:italic>YrMu</jats:italic> was mapped on the 2AS/2NS translocation. This fragment also conferred moderate adult plant resistance (APR) under all Mexican field environments and in one season in Kenya. Field trial phenotyping with <jats:italic>Lr37</jats:italic>-virulent <jats:italic>Puccinia triticina</jats:italic> races indicated the presence of an APR QTL accounting for 18.3–25.5% of the LR severity variation, in addition to a novel YR resistance QTL, <jats:italic>QYr.cim-3DS</jats:italic>, derived from Mucuy. We developed breeder-friendly KASP and indel molecular markers respectively for <jats:italic>Yr29</jats:italic>/<jats:italic>Lr46</jats:italic> and <jats:italic>YrMu</jats:italic>. The current study validated the presence of known genes and identified new resistance loci, a QTL combination effect, and flanking markers to facilitate accelerated breeding for genetically complex, durable rust resistance.</jats:p>

<jats:p>Stripe rust and powdery mildew are devastating diseases that have severe effects on wheat production. Introducing resistant genes/loci from wheat-related species into the wheat genome is an important method to improve wheat resistance. Rye (<jats:italic>Secale cereale</jats:italic> L.) is a cross-pollinating plant and is the most important related species for wheat genetic improvement. In this study, we developed three 6RS ditelosomic addition lines, three 6RL ditelosomic addition lines, and two 6R disomic addition lines by crossing common wheat cultivar Chuannong 25 and rye inbred line QL2. The chromosome composition of all new lines was confirmed by non-denaturing fluorescence <jats:italic>in situ</jats:italic> hybridization (ND-FISH) and molecular marker analyses. Disease responses to different <jats:italic>Puccinia striiformis</jats:italic> f. sp. <jats:italic>tritici</jats:italic> (<jats:italic>Pst</jats:italic>) races and <jats:italic>Blumeria graminis</jats:italic> f. sp. <jats:italic>tritici</jats:italic> (<jats:italic>Bgt</jats:italic>) isolates and cytogenetic analysis showed that the resistance of the new lines was derived from the rye chromosome 6R of QL2, and both arms (6RS and 6RL) may harbor resistance genes against <jats:italic>Pst</jats:italic> and <jats:italic>Bgt</jats:italic>. These new lines could be used as a promising bridging parent and valuable genetic resource for wheat disease resistance improvement.</jats:p>

<jats:p>The <jats:italic>bZIP</jats:italic> gene family is one of the largest transcription factor families and has important roles in plant growth, development, and stress responses. However, <jats:italic>bZIP</jats:italic> genes in the Solanaceae family have not been extensively investigated. Here, we conducted genome-wide re-annotation in nine Solanaceae species and <jats:italic>Arabidopsis thaliana</jats:italic>. We annotated 935 <jats:italic>bZIP</jats:italic> genes, including 107 (11%) that were newly identified. Structural analyses of <jats:italic>bZIP</jats:italic> genes in the Solanaceae family revealed that the bZIP domain displayed two types of architectures depending on the presence of an additional domain, suggesting that these architectures generate diversified structures and functions. Motif analyses indicated that the two types of <jats:italic>bZIP</jats:italic> genes had distinct sequences adjacent to the bZIP domain. Phylogenetic analyses suggested that the two types of <jats:italic>bZIP</jats:italic> genes distinctly evolved and ultimately adapted in different lineages. Transcriptome analyses in pepper (<jats:italic>Capsicum annuum</jats:italic>) and tomato (<jats:italic>Solanum lycopersicum</jats:italic>) revealed putative functional diversity between the two types of <jats:italic>bZIP</jats:italic> genes in response to various abiotic stresses. This study extensively updated <jats:italic>bZIP</jats:italic> gene family annotations and provided novel evolutionary and functional evidence for the role of <jats:italic>bZIP</jats:italic> genes in Solanaceae plants. Our findings provide evolutionary and functional characteristics of <jats:italic>bZIP</jats:italic> genes for a better understanding of their roles in Solanaceae plants.</jats:p>

<jats:p>Legume alfalfa (<jats:italic>Medicago sativa</jats:italic> L.) is extensively planted to reduce chemical fertilizer input to the soil and remedy damaged fields. The soil mechanism of these effects is potentially related to the variations in alfalfa-mediated interactions of the soil microbial community. To understand the impact of planting alfalfa on the soil microbial community in degraded black soil cultivated land, a 4-year experiment was conducted in degraded black soil cultivated land. We assessed soil parameters and characterized the functional and compositional diversity of the microbial community by amplicon sequencing that targeted the 16S rDNA gene of bacteria and ITS of fungi in four systems under corn cultivation at the Harbin corn demonstration base (Heilongjiang, China): multiyear corn planting (more than 30 years, MC1); 2 years of alfalfa-corn rotation (OC); 3 years of alfalfa planting (TA); and 4 years of alfalfa planting (FA). It was found out that alfalfa led to changes in the alpha diversity of soil bacteria rather than in fungi in the degraded arable land. The abundance of the bacterial groups Gemmatimonadetes, Actinobacteria, Planctomycetes, and Chloroflexi was increased in OC, while Proteobacteria and Acidobacteria and the fungal group Glomeromycota were increased in TA and FA. OC, TA, and FA significantly increased the pH level but reduced soil electrical conductivity, but they had no impact on soil available nitrogen and soil available potassium at the 0–15 cm soil depth. However, with the years of alfalfa planting, soil available nitrogen and soil available potassium were reduced at the 15–30 cm soil depth. OC, TA, and FA significantly reduced the soil available phosphorus and soil total phosphorus at the 15–30 cm soil depth. There was no significant impact made on soil total nitrogen. FA significantly reduced the soil organic matter at the 15–30 cm soil depth. Planting alfalfa in degraded black soil cultivated land can reduce the salt content of the soil, and the nutrient content of soil planted with alfalfa without fertilization was equivalent to that of degraded corn cultivated land with annual fertilization. Besides, alfalfa recruited and increased contained taxa with the capacity to improve soil nutrient utilization and inhibit the harmful influences of pathogens for subsequent crops. Meanwhile, the planting of alfalfa can modify soil conditions by promoting the proliferation of specific beneficial microbiota groups.</jats:p>

<jats:p>Cherries are one of the important fruit trees. The growth of cherry is greatly affected by abiotic stresses such as drought, which hinders its development. Chalcone synthase (CHS, EC 2.3.1.74) is a crucial rate-limiting enzyme in the flavonoid biosynthetic pathway that plays an important role in regulating plant growth, development, and abiotic stress tolerance. In the current study, three genes encoding chalcone synthase were identified in the genome of sweet cherry (<jats:italic>Prunus avium</jats:italic> L.). The three genes contained fewer introns and showed high homology with CHS genes of other Rosaceae members. All members are predicted to localize in the cytoplasm. The conserved catalytic sites may be located at the Cys163, Phe214, His302, and Asn335 residues. These genes were differentially expressed during flower bud dormancy and fruit development. The total flavonoid content of Chinese cherry (<jats:italic>Cerasus pseudocerasus</jats:italic> Lindl.) was highest in the leaves and slightly higher in the pulp than in the peel. No significant difference in total flavonoid content was detected between aborted kernels and normally developing kernels. Overexpression of Chinese cherry <jats:italic>CpCHS1</jats:italic> in tobacco improved the germination frequency of tobacco seeds under drought stress, and the fresh weight of transgenic seedlings under drought stress was higher than that of the wild type, and the contents of SOD, POD, CAT, and Pro in OE lines were significantly increased and higher than WT under drought stress. These results indicate cherry CHS genes are conserved and functionally diverse and will assist in elucidating the functions of flavonoid synthesis pathways in cherry and other Rosaceae species under drought stress.</jats:p>

<jats:p>Understanding the potential mechanisms and processes of leaf photosynthesis in response to elevated CO<jats:sub>2</jats:sub> concentration ([CO<jats:sub>2</jats:sub>]) and temperature is critical for estimating the impacts of climatic change on the growth and yield in crops such as maize (<jats:italic>Zea mays</jats:italic> L.), which is a widely cultivated C<jats:sub>4</jats:sub> crop all over the world. We examined the combined effect of elevated [CO<jats:sub>2</jats:sub>] and temperature on plant growth, leaf photosynthesis, stomatal traits, and biochemical compositions of maize with six environmental growth chambers controlling two CO<jats:sub>2</jats:sub> levels (400 and 800 μmol mol<jats:sup>−1</jats:sup>) and three temperature regimes (25/19°C, 31/25°C, and 37/31°C). We found that leaf photosynthesis was significantly enhanced by increasing growth temperature from 25/19°C to 31/25°C independent of [CO<jats:sub>2</jats:sub>]. However, leaf photosynthesis drastically declined when the growth temperature was continually increased to 37/31°C at both ambient CO<jats:sub>2</jats:sub> concentration (400 μmol mol<jats:sup>−1</jats:sup>, <jats:italic>a</jats:italic>[CO<jats:sub>2</jats:sub>]) and elevated CO<jats:sub>2</jats:sub> concentration (800 μmol mol<jats:sup>−1</jats:sup>, <jats:italic>e</jats:italic>[CO<jats:sub>2</jats:sub>]). Meanwhile, we also found strong CO<jats:sub>2</jats:sub> fertilization effect on maize plants grown at the highest temperature (37/31°C), as evidenced by the higher leaf photosynthesis at <jats:italic>e</jats:italic>[CO<jats:sub>2</jats:sub>] than that at <jats:italic>a</jats:italic>[CO<jats:sub>2</jats:sub>], although leaf photosynthesis was similar between <jats:italic>a</jats:italic>[CO<jats:sub>2</jats:sub>] and <jats:italic>e</jats:italic>[CO<jats:sub>2</jats:sub>] under the other two temperature regimes of 25/19°C and 31/25°C. Furthermore, we also found that <jats:italic>e</jats:italic>[CO<jats:sub>2</jats:sub>] resulted in an increase in leaf soluble sugar, which was positively related with leaf photosynthesis under the high temperature regime of 37/31°C (<jats:italic>R</jats:italic><jats:sup>2</jats:sup> = 0.77). In addition, our results showed that <jats:italic>e</jats:italic>[CO<jats:sub>2</jats:sub>] substantially decreased leaf transpiration rates of maize plants, which might be partially attributed to the reduced stomatal openness as demonstrated by the declined stomatal width and stomatal area. These results suggest that the CO<jats:sub>2</jats:sub> fertilization effect on plant growth and leaf photosynthesis of maize depends on growth temperatures through changing stomatal traits, leaf anatomy, and soluble sugar contents.</jats:p>

<jats:p>Cropland reactive nitrogen losses (Nr) are of the greatest challenges facing sustainable agricultural intensification to meet the increases in food demand. The environmental impacts of Nr losses and their yield responses to the mitigation strategies were not completely evaluated. We assessed the environmental impacts of Nr losses in China and decoupled the efficiency of mitigation actions with yield responses. Datasets about Nr losses in China were collected, converted into potentials of acidification (AP), global warming (GWP), and aquatic eutrophication (AEP), and analyzed by a meta-analysis program. Results showed that producing 1 Mg of rice grains had the highest AP (153 kg acid equiv.), while wheat had the highest GWP and AEP (74 kg CO<jats:sub>2</jats:sub> equiv. and 0.37 kg PO<jats:sub>4</jats:sub> equiv., respectively). Using the conventional rates (averagely, 200, 230, and 215 kg N ha<jats:sup>−1</jats:sup>) of urea as a surface application to produce 131.4, 257.2, and 212.1 Tg of wheat, maize, and rice resulted in 17–33 Tg, 7–10 Tg, and 6–87 Gg of AP, GWP, and AEP, respectively. For their balanced effect on reducing AP, GWP, and AEP while maximizing yields, inhibitors, and subsurface application could be set as the best mitigation strategies in wheat production. Inhibitors usage and biochar are strongly recommended strategies for sustainable production of maize. None of the investigated strategies had a balanced effect on rice yield and the environment, thus new mitigation technologies should be developed.</jats:p>

<jats:p><jats:italic>Zanthoxylum bungeanum</jats:italic> Maxim. as an important economic forest, its epidermis bears prickles which complicate the harvesting process and increase the labor costs. To explore the developmental mechanism of prickles, three varieties of <jats:italic>Zanthoxylum bungeanum</jats:italic> (PZB, SZB, GSZB) were selected for morphological and multi-omics analyses. The absorption spectra of prickles and stems were detected using Fourier-transform infrared spectroscopy (FTIR), and they were found different at 1617, 1110, 3319, and 1999 cm<jats:sup>–1</jats:sup>. The morphology of prickles and stems were observed using light microscopy and transmission electron microscopy (TEM). The growth direction of cells on the prickle side and stem side were perpendicular to each other, and there was a resembling abscission zone (RAZ) between them. The vacuolar deposits of prickle cells were much more than stem cells, indicating that the lignification degree of prickles was higher than stems. In addition, 9 candidate genes (<jats:italic>ZbYABBY2</jats:italic>, <jats:italic>ZbYABBY1</jats:italic>, <jats:italic>ZbYABBY5</jats:italic>, <jats:italic>ZbWRKY</jats:italic>, <jats:italic>ZbLOG5</jats:italic>, <jats:italic>ZbAZG2</jats:italic>, <jats:italic>ZbGh16</jats:italic>, <jats:italic>ZbIAA33</jats:italic>, and <jats:italic>ZbGh16X1</jats:italic>) were screened out and validated base on transcriptome and qRT-PCA. As well as, 30 key metabolites were found related to prickle development base on metabolome analysis. Among them, 4-hydroxy-2-oxopentanoate, trans-2-hydroxy-cinnamate, trans-cinnamate, polyhydroxy-fatty acid, 10,16-dihydroxypalmitate, cinnamic acid were related to the biosynthesis of cutin, suberine and wax. Indole-3-acetate, tryptamine, anthranilate, fromylanthranilate, N6-(delta2-isopentenyl)-adenine were related to plant hormone signal transduction. Generally, this is the first study to reveal the developmental mechanism of prickles. The results of this study lay the foundation for the breeding of non-prickle <jats:italic>Zanthoxylum bungeanum</jats:italic>.</jats:p>

<jats:p>The holoparasitic dodder (<jats:italic>Cuscuta</jats:italic> spp.) is able to transfer mRNA and certain plant pathogens (e.g., viruses and bacteria) from the host plant. “<jats:italic>Candidatus</jats:italic> Liberibacter asiaticus,” the phloem-limited causative agent of citrus Huanglongbing, can be transferred from citrus to periwinkle (<jats:italic>Catharanthus roseus</jats:italic>) mediated by dodder. However, characterization of mRNA transport between dodder and citrus/periwinkle remains unclear. In this study, we sequenced transcriptomes of dodder and its parasitizing host, sweet orange (<jats:italic>Citrus sinensis</jats:italic> “Newhall”) and periwinkle (<jats:italic>Catharanthus roseus</jats:italic>), to identify and characterize mRNA transfer between dodder and the host plant during parasitism. The mRNA transfer between dodder and citrus/periwinkle was bidirectional and most of the transfer events occurred in the interface tissue. Compared with the citrus–dodder system, mRNA transfer in the periwinkle–dodder system was more frequent. Function classification revealed that a large number of mRNAs transferred between dodder and citrus/periwinkle were involved in secondary metabolism and stress response. Dodder transcripts encoding proteins associated with microtubule-based processes and cell wall biogenesis were transferred to host tissues. In addition, transcripts involved in translational elongation, plasmodesmata, and the auxin-activated signaling pathway were transmitted between dodder and citrus/periwinkle. In particular, transcripts involved in shoot system development and flower development were transferred between the host and dodder in both directions. The high abundance of dodder-origin transcripts, encoding MIP aquaporin protein, and <jats:italic>S</jats:italic>-adenosylmethionine synthetase 1 protein, in citrus and periwinkle tissues indicated they could play an important biological role in dodder–host interaction. In addition, the uptake of host mRNAs by dodder, especially those involved in seed germination and flower development, could be beneficial for the reproduction of dodder. The results of this study provide new insights into the RNA-based interaction between dodder and host plants.</jats:p>

<jats:p>Low temperatures in the spring often lead to a decline in the emergence rate and uniformity of maize, which can affect yield in northern regions. This study used 365 recombinant inbred lines (RILs), which arose from crossing Qi319 and Ye478, to identify low-temperature resistance during the germination stage by measuring eight low-temperature-related traits. The quantitative trait locis (QTLs) were mapped using <jats:italic>R/qtl</jats:italic> software by combining phenotypic data, and the genotyping by sequencing (GBS) method to produce a high-density genetic linkage map. Twenty QTLs were detected during QTL mapping, of which seven QTLs simultaneously detected a consistent 197.10–202.30 Mb segment on chromosome 1. The primary segment was named <jats:italic>cQTL1-2</jats:italic>, with a phenotypic variation of 5.18–25.96% and a physical distance of 5.2 Mb. This combines the phenotype and genotype with the identification of seven chromosome segment substitution lines (CSSLs), which were derived from Ye478*Qi319 and related to <jats:italic>cQTL1-2</jats:italic>. The physical distance of <jats:italic>cQTL1-2</jats:italic> was reduced to approximately 1.9 Mb. The consistent meta-QTL <jats:italic>mQTL1</jats:italic> was located at 619.06 cM on chromosome 1, had a genetic distance of 7.27 cM, and overlapped with <jats:italic>cQTL1-2</jats:italic>. This was identified by combining the results of previous QTL studies assessing maize tolerance to low temperatures at the germination stage. An assessment of the results of the RIL population, CSSLs, and <jats:italic>mQTL1</jats:italic> found the consistent QTL to be <jats:italic>LtQTL1-1</jats:italic>. It was identified in bin1.06-1.07 at a confidence interval of between 200,400,148 and 201,775,619 bp. In this interval, qRT-PCR found that relative expression of the candidate genes <jats:italic>GRMZM2G082630</jats:italic> and <jats:italic>GRMZM2G115730</jats:italic> were both up-regulated in low-temperature tolerant lines and down-regulated in sensitive lines (<jats:italic>P</jats:italic> &amp;lt; 0.01).</jats:p>