Timely and accurate forecasting of crop yields is critical for food management and trade.  However, only limited research has explored the impact of integrating crop phenotypic parameters (CPPs) with unmanned aerial vehicle (UAV) data across different phenological stages on maize yield prediction.  The extent to which multi-temporal data enhances the accuracy and reliability of yield projections compared to mono-temporal data has yet to be systematically investigated.  To attain the proper balance between accuracy and cost in crop yield estimation, this study proposed a structured framework for identifying the optimal phenological periods for summer maize yield prediction using UAV-based multispectral data.  Three classical methods of custom mean decrease accuracy (C-MDA), optimal parameters-based geographical detector (OPGD), and grey relational analysis (GRA) were first used to sort and screen both the CPPs and vegetation indices (VIs) derived from UAV-based information over six growth stages.  Ridge regression models based on multi-temporal data combinations and mono-temporal data were established separately, and their performance in yield prediction were compared to identify the optimal phenological stages and the corresponding key factors.  Our results showed that C-MDA was much better at factor screening and ranking compared to OPGD and GRA.  The green normalized difference vegetation index (GNDVI), normalized difference vegetation index (NDVI), and normalized difference red edge index (NDRE) emerged as the top-performing VIs, while the leaf area index (LAI) and above ground biomass (AGB) proved to be the most effective CPPs.  When predicting yield using only mono-temporal data, the dough stage delivered the highest predictive accuracy (R²=0.871, RMSE=0.407 t ha^–1), while the tasseling stage was the earliest that achieved yield estimates with acceptable precision (R²=0.810, RMSE=0.493 t ha^–1).  In contrast, the integration of UAV data from different crop growth stages markedly enhanced the accuracy of yield estimation.  Combinations of data from the tasseling, silking, and dough stages were recommended as the best option (R²=0.942, RMSE=0.291 t ha^–1).  These findings indicate that the precise estimation of maize yields in smallholder fields may be attainable, and present both substantial theoretical insights and practical benefits for the advancement of precision agriculture.

Drought stress negatively affects grapevine growth and development.  Grafting with rootstock is widely used to improve the quality of grape fruits and confer drought stress tolerance, but the underlying genetics and regulatory mechanisms are unclear.  Hence, we investigated the physiologic and transcriptomic profiles in the leaves of grafted SM/1103P (SM shoot/1103P root) and self-rooted SM (‘Shine Muscat’) as well as roots of grafted SM/1103P and self-rooted 1103P under drought stress conditions.  The results indicated that grafted grapevine effectively attenuated drought damage in grape leaves by increasing phytohormone levels and antioxidant enzyme activities, reducing H₂O₂ and MDA contents.  Transcriptomic profiling revealed a total of 11,855 and 11,197 differentially expressed genes (DEGs) were identified in grape leaves and roots respectively.  Weighted correlation network analysis (WGCNA) was performed based on the RNA-seq data, and five modules (greenyellow, black, turquoise, salmon and blue) were significantly correlated to drought stress.  Pathway analysis showed that DEGs were enriched in the plant hormone signal transduction and MAPK signaling pathway.  916 transcription factor genes (TFs) belonging to different gene families were detected that may participate in regulating the drought stress.  Quantitative real-time PCR (qRT-PCR) expression analysis of twelve drought stress responsive DEGs was used to verify the transcriptome data.  Furthermore, overexpression of VvMYBPA1 in Arabidopsis thaliana and grape callus tissues improved drought tolerance.  Our findings provided new insights into to the regulatory mechanism for improving grapevine adaptation to drought.  

Adjustment of the sowing date is a widely used measure in rice production for adapting to high-temperature conditions.  However, the impact of a delayed sowing date (DS) on rice quality may vary by variety and ecological conditions.  In this study, we conducted experiments using four different sowing dates, the conventional sowing date 1 (CS1), CS2 (10 d later than CS1), DS1 (30 d later than CS1), and DS2 (30 d later than CS2), and three rice varieties, i.e., Yixiangyou 2115, Fyou 498, and Chuanyou 6203.  This experiment was conducted at four sites in the Sichuan Basin in 2018 and 2019 to evaluate the influence of DS on the pasting properties of rice, which are a proxy for the eating and cooking quality (ECQ).  In DS1 and DS2, the rice had a significantly greater amylose content (AC) but a lower protein content (PC), peak viscosity (PKV), cool paste viscosity (CPV), and hot paste viscosity (HPV) than in CS1 and CS2.  Moreover, except for CS2 and DS1 in 2018, DS1 and DS2 led to 2.15–11.19% reductions in breakdown viscosity (BDV) and 23.46–108.47% increases in setback viscosity (SBV).  However, the influence of DS on rice pasting properties varied by study site and rice variety.  In 2019, DS1 and DS2 led to BDV reductions of 2.35–9.33, 2.61–8.61, 10.03–17.78, and 2.06–8.93%, and SBV increases of 2.32–60.93, 63.74–144.24, 55.46–91.63, and –8.28–65.37% at the Dayi, Anzhou, Nanbu, and Shehong (except for SBV in CS2 and DS1) sites, respectively.  DS resulted in greater reductions in PKV, HPV, CPV, and BDV and greater increases in the AC and SBV for Yixiangyou 2115 than for Chuanyou 6203 and Fyou 498.  The correlation analysis indicated that PKV and HPV were significantly and positively related to the mean, maximum, and minimum temperatures after heading.  These temperatures must be greater than 25.9, 31.2, and 22.3°C, respectively, to increase the relative BDV and reduce the relative SBV of rice, thereby enhancing ECQ.  In conclusion, DS might contribute to a significant deterioration in ECQ in machine-transplanted rice in the Sichuan Basin.  A mean temperature above 25.9°C after heading is required to improve the ECQ of rice.

Germplasm resources are essential for the sustainable development of biodiversity and husbandry of local chickens, as well as for the breeding and industry of superior quality chickens.  Unfortunately, many local and indigenous chicken breeds are at risk of declining numbers, emphasizing the need to conserve breed resources for endangered chickens.  Primordial germ cells (PGCs) are crucial for preserving germplasm resources by inheriting genetic information from parents to offspring and ensuring stability of genetic material between germlines.  In this study, PGCs were isolated from chicken embryos’ gonads and cultured in FAcs medium without feeder cells.  Over a period of approximately 40 d, the cells proliferated to a number of up to 10⁶, establishing various cell lines.  Particularly, 18 PGC lines were created from Rugao Yellow chicken and Shouguang chicken, with an efficiency ranging from 39.1 to 45%.  Furthermore, PGCs that had been cultured for 40 passages exhibited typical PGC characteristics, such as glycogen staining reaction, and expression of pluripotency and reproductive markers.  These results confirm that PGCs maintain stem cell properties even after long-term in vitro culture.  Additionally, PGCs cryopreserved for up to 120 d remained viable, maintained typical PGC morphologies, and possessed stable cell proliferation ability.  Through intravascular injection into chicken embryos, green fluorescent protein (GFP)-PGCs were found in the recipient embryos’ gonads and could develop into gametes to produce offspring, indicating that even after extended culture, PGCs retain their migratory and lineage-transmitting capabilities.  This research offers valuable insights into the in vitro cultivation and preservation of PGCs of Chinese indigenous chickens.  The findings of this study can be applied in transgenic chicken production and the preservation of genetic resources of indigenous chicken breeds.

Genetic transformation has been an effective technology for improving the agronomic traits of maize.  However, it is highly reliant on the use of embryonic callus (EC) and shows a serious genotype dependence.  In this study, we performed genomic sequencing for 80 core maize germplasms and constructed a high-density genomic variation map using our newly developed pipeline (MQ2Gpipe).  Based on the induction rate of EC (REC), these inbred lines were categorized into three subpopulations.  The low-REC germplasms displayed more abundant genetic diversity than the high-REC germplasms.  By integrating a genome-wide selective signature screen and region-based association analysis, we revealed 95.23 Mb of selective regions and 43 REC-associated variants.  These variants had phenotypic variance explained values ranging between 21.46 and 49.46%.  In total, 103 candidate genes were identified within the linkage disequilibrium regions of these REC-associated loci.  These genes mainly participate in regulation of the cell cycle, regulation of cytokinesis, and other functions, among which MYB15 and EMB2745 were located within the previously reported QTL for EC induction.  Numerous leaf area-associated variants with large effects were closely linked to several REC-related loci, implying a potential synergistic selection of REC and leaf size during modern maize breeding.

Broody behavior is regulated by hypothalamic prolactin secretion, which seriously affects egg production in poulty production.  Numerous studies have provided evidence that animal behavior is governed by dynamic bidirectional communication between specific gut bacteria and their host via the brain–gut–microbiome axis.  However, little research focused on how the gut microbiota influence broody behavior in poultry.  In this study, Zhedong white geese in laying and brooding phases were selected.  Ten differentially abundant bacteria in cecum were detected between brooding and laying geese through metagenomic analyses and 16S rRNA sequencing (P<0.05), and Bacteroides fragilis was specifically identified as a key driver species in the brooding geese.  Moverover, the serum metabolites were quantified, and the 313 differentially abundant metabolites were found between the two groups of different physiological geese.  They were primarily enriched in the tryptophan metabolism pathways.  Pearson correlation analyses revealed there was a significant positive correlation between B. fragilis abundance and the context of 11 tryptophan metabolism-related metabolites (such as serotonin, etc.) in broody geese, which hinted that those tryptophan metabolites might be produced or driven by B. fragilis.  Finally, the serum hormone levels were also measured.  We found there was a positive correlation between B. fragilis abundance and content of serotonin.  Besides, prolactin secreted by the pituitary gland was greater in brooding geese than that in laying geese, which was also highly correlated with B. fragilis abundance.  This result implied that B. fragilis could promote the secretion of prolactin by the pituitary gland.  Together, the current study findings provided the information on gut microbiota influencing broody behavior, B. fragilis produced or driven more serum serotonin, and stimulated the pituitary gland to secret more prolactin, which potentially offered a new enlightenment for the intervention of broody behavior in poultry.

The Chinese crested duck is a unique duck breed having a bulbous feather shape on its duck head.  However, the mechanisms involved in its formation and development are unclear.  In the present study, RNA sequencing analysis was performed on the crested tissues of 6 Chinese crested ducks and the scalp tissues of 6 cherry valley ducks (CVs) from 2 developmental stages.  This study identified 261 differentially expressed genes (DEGs), 122 upregulated and 139 downregulated, in the E28 stage and 361 DEGs, 154 upregulated and 207 downregulated in the D42 stage between CC and CV ducks.  The subsequent results of weighted gene co-expression network analysis (WGCNA) revealed that the turquoise and cyan modules were associated with the crest trait in the D42 stage, meanwhile, the green, brown, and pink modules were associated with the crest trait in the E28 stage.  Venn analysis of the DEGs and WGCNA showed that 145 and 45 genes are associated between the D42 and E28 stages, respectively.  The expression of WNT16, BMP2, SLC35F2, SLC6A15, APOBEC2, ABHD6, TNNC2, MYL1, and TNNI2 were verified by real-time quantitative PCR.  This study provides an approach to reveal the molecular mechanisms underlying the crested trait development.

^{Eukaryotic genomes are hierarchically packaged into cell nucleus, affecting gene regulation.  The genome is organized into multiscale structural units, including chromosome territories, compartments, topologically associating domains (TADs), and DNA loops.  The identification of these hierarchical structures has benefited from the development of experimental approaches, such as 3C-based methods (Hi-C, ChIA-PET, etc.), imaging tools (2D-FISH, 3D-FISH, Cryo-FISH, etc.) and ligation-free methods (GAM, SPRITE, etc.).  In recent two decades, numerous studies have shown that the 3D organization of genome plays essential roles in multiple cellular processes via various mechanisms, such as regulating enhancer activity and promoter-enhancer interactions.  However, there are relatively few studies about the 3D genome in livestock species.  Therefore, studies for exploring the function of 3D genomes in livestock are urgently needed to provide a more comprehensive understanding of potential relationships between the genome and production traits.  In this review, we summarize the recent advances of 3D genomics and its biological functions in human and mouse studies, drawing inspiration to explore the 3D genomics of livestock species.  We then mainly focus on the biological functions of 3D genome organization in muscle development and its implications in animal breeding.}

Leaf rust is a highly destructive foliar disease in wheat, causing major constraints in wheat production worldwide.  In this study, we conducted a comprehensive assessment of adult plant resistance to leaf rust in 590 accessions from the advanced backcross-nested association mapping plus inter-crossed (AB-NAMIC) population. We used 660K genotype data to perform a genome-wide association study (GWAS), identifying significant quantitative trait loci (QTLs) on chromosomes 1B, 2A, 2B, and 7D, with particular emphasis on the candidate gene TaRLK-1B on chromosome 1B.  A cleaved amplified polymorphic sequence (CAPS) marker was developed based on TaRLK-1B haplotypes and effectively differentiated between resistant and susceptible varieties.  This gene encodes a membrane-localized leucine-rich repeat receptor-like kinase (LRR-RLK) that is upregulated in response to the fungal infection that causes leaf rust.  Targeted knockout of TaRLK-1B in wheat led to reduced resistance to leaf rust, underscoring its essential role as a positive regulator in defense against this disease.  Additionally, we propose that TaRLK-1B interacts with the receptor-like cytoplasmic kinase TaRLCK1B, potentially facilitating immune signal transduction.  Our findings also demonstrate that pyramiding minor effect QTLs significantly increases resistance to leaf rust.  This study provides novel insights into resistance genes and valuable QTL information, which could improve marker-assisted wheat breeding efforts.

Fusarium crown rot (FCR), primarily caused by Fusarium pseudograminearum and other Fusarium species, is a devastating wheat disease that has led to substantial yield losses worldwide. In this study, a xyloglucan endotransglucosylase/hydrolase gene, TaXTH3A associated with FCR resistance was identified by integrating bulked segregant exome capture sequencing (BSE-Seq) and transcriptome sequencing (RNA-Seq) analyses. Functional characterization revealed that TaXTH3A encodes a secreted protein localized to the cell wall, demonstrated by a yeast signal sequence trap system and subcellular localization assays. Transgenic validation confirmed that TaXTH3A overexpression significantly enhances FCR resistance, accompanied by reduced H₂O₂ accumulation, increased catalase activity, and improved disease resistance. Transcriptome profiling further indicated that TaXTH3A regulates the expression of genes involved in plant defense and xyloglucan metabolism during F. pseudograminearum infection. Furthermore, TaXTH3A-overexpressing lines exhibited increased xyloglucan endotransglucosylase (XET) activity and elevated hemicellulose content in leaf sheaths upon infection. Collectively, these findings suggest that, TaXTH3A enhances wheat resistance to F. pseudograminearum by regulating cell wall remodeling and associated defense responses. This study provides new insights into the molecular mechanisms underlying FCR resistance and offers a potential target for the genetic improvement of disease-resistant wheat cultivars.

Potassium (K) improves the grain yield and stress resistance of crops; however, its effect on rice under shading stress is unclear.  In this study, a two-factor split-plot experiment was conducted in Sichuan, China, to evaluate the influence of K management methods on the morphological and physiological characteristics of leaves and grain yield under shading stress.  The results showed that leaf morphological and physiological traits had a greater relationship with grain yield under shading stress than under full sunlight.  Compared to full sunlight control, shading stress significantly increased the leaf area index (LAI) by improving the green leaf number and leaf area of rice.  Shading stress also significantly increased the chlorophyll, K⁺, and Na⁺ contents, but decreased the specific leaf weight, ratios of grain-to-leaf area and chlorophyll a/b, net photosynthetic rate (P_n), and sucrose and starch contents.  This resulted in a 16.21–29.71% reduction in grain yield by reducing the seed setting rate and 1,000-grain weight.  Compared to the no potassium application control (K_0-0), the green leaf number and leaf area of rice were significantly increased by K fertilizer, resulting in 15.61–29.88% and 13.46–22.20% increases in the total LAI under full sunlight control and shading stress, respectively.  K fertilizer significantly improved the chlorophyll b, K⁺, and K⁺/Na⁺ contents, but decreased the chlorophyll a/b ratio under shading stress, thereby enhancing P_n and increasing the sucrose and starch contents of flag leaves.  Therefore, K fertilizer significantly increased the grain yield by 5.57–17.35% under shading stress.  Compared to 90 kg ha^-1 of K₂O single use as basal fertilizer (K_90-0), 90 kg ha^-1 of K₂O single use as panicle fertilizer at panicle initiation stage (K_0-90) significantly increased the P_n and starch content of flag leaves under shading stress.  Furthermore, there was no significant difference between the grain yields of K_0-90 and 180 kg ha^-1 of K₂O equal-spilt applicated as basal and panicle fertilizers (K_90-90) in 2021 (except under shading stress) and 2022.  Overall, K fertilizer, particularly panicle K, improved the LAI and photosynthetic performance of rice, resulting in an improved rice grain yield under shading stress.