The low egg production of goose greatly limits the development of the industry.  China possesses the most abundant goose breeds resources.  In this study, genome resequencing data of swan goose (Anser cygnoides) and domesticated high and low laying goose breeds (Anser cygnoides domestiation) were used to identify key genes related to egg laying ability in geese and verify their functions.  Selective sweep analyses revealed 416 genes that were specifically selected during the domestication process from swan geese to high laying geese.  Furthermore, SNPs and Indels markers were used in GWAS analyses between high and low laying breed geese.  The results showed that RTCB, BPIFC, SYN3, SYNE1, VIP, and ESR1 may be related to the differences in laying ability of geese.  Notably, only ESR1 was identified simultaneously by GWAS and selective sweep analysis.  The genotype of Indel_{chr3:54429172}, located downstream of ESR1, was confirmed to affect the expression of ESR1 in the ovarian stroma and showed significant correlation with body weight at first egg and laying frequency of geese.  CCK-8, EdU, and flow cytometry confirmed that ESR1 can promote the apoptosis of goose pre-hierarchical follicles ganulosa cells (phGCs) and inhibit their proliferation.  Combined with transcriptome data, it was found ESR1 involved in the function of goose phGCs may be related to MAPK and TGF-beta signaling pathways.  Overall, our study used genomic information from different goose breeds to identify an indel located in the downstream of ESR1 associated with goose laying ability.  The main pathways and biological processes of ESR1 involved in the regulation of goose laying ability were identified by cell biology and transcriptomics methods.  These results are helpful to further understand the laying ability characteristics of goose and improve the egg production of geese.

Population growth and growing demand for livestock products produce large amounts of manure, which can be harnessed to maintain soil sustainability and crop productivity. However, the impacts of excessive manure application on crop yields, nitrogen (N)-cycling processes and microorganisms remain unknown. Here, we explored the effects of 20-year of excessive rates (18 and 27 Mg ha^–1 yr^–1) of pig manure application on peanut crop yields, soil nutrient contents, N-cycling processes and the abundance of N-cycling microorganisms in an acidic Ultisol in summer and winter, compared with none and a regular rate (9 Mg ha^–1 yr^–1) of pig manure application. Long-term excessive pig manure application, especially at the high-rate, significantly increased soil nutrient contents, the abundance of N-cycling functional genes, potential nitrification and denitrification activity, while it had a weaker effect on peanut yield and plant biomass. Compared with manure application, seasonality had a much weaker effect on N-cycling gene abundance. Random forest analysis showed that available phosphorus (AP) content was the primary predictor for N-cycling gene abundance, with significant and positive associations with all tested N-cycling genes. Our study clearly illustrated that excessive manure application would increase N-cycling gene abundance and potential N loss with relatively weak promotion of crop yields, providing significant implications for sustainable agriculture in the acidic Ultisols.

The yellow seed trait is preferred by breeders for its potential to improve the seed quality and commercial value of Brassica napus.  In the present study, we produced yellow seed mutants using a CRISPR/Cas9 system when the two BnPAP2 homologs were knocked out.  Histochemical staining of the seed coat demonstrated that proanthocyanidin accumulation was significantly reduced in the pap2 double mutants and decreased specifically in the endothelial and palisade layer cells of the seed coat.  Transcriptomic and metabolite profiling analysis suggested that disruption of the BnPAP2 genes could reduce the expression of structural and regulated genes in the phenylpropanoid and flavonoid biosynthetic pathways.  The broad suppression of these genes might hinder proanthocyanidin accumulation during seed development, and thereby causing the yellow seed trait in B. napus.  These results indicate that BnPAP2 might play a vital role in the regulatory network controlling proanthocyanidin accumulation.

Straw return is a promising strategy for managing soil organic carbon (SOC) and improving yield stability.  However, the optimal straw return strategy for sustainable crop production in the wheat (Triticum aestivum L.)–cotton (Gossypium hirsutum L.) cropping system remains uncertain.  The objective of this study was to quantify the long-term (10 years) impact of carbon (C) input on SOC sequestration, soil aggregation and crop yields in a wheat–cotton cropping system in the Yangtze River Valley, China.  Five treatments were arranged with a single-factor randomized design as follows: no straw return (Control), return of wheat straw only (Wt), return of cotton straw only (Ct), return of 50% wheat and 50% cotton straw (Wh-Ch) and return of 100% wheat and 100% cotton straw (Wt-Ct).  In comparison to the Control, the SOC content increased by 8.4 to 20.2% under straw return.  A significant linear positive correlation between SOC sequestration and C input (1.42–7.19 Mg ha⁻¹ yr⁻¹) (P<0.05) was detected.  The percentages of aggregates of sizes >2 and 1–2 mm at the 0–20 cm soil depth were also significantly elevated under straw return, with the greatest increase of the aggregate stability in the Wt-Ct treatment (28.1%).  The average wheat yields increased by 12.4–36.0% and cotton yields increased by 29.4–73.7%, and significantly linear positive correlations were also detected between C input and the yields of wheat and cotton.  The average sustainable yield index (SYI) reached a maximum value of 0.69 when the C input was 7.08 Mg ha⁻¹ yr⁻¹, which was close to the maximum value (SYI of 0.69, C input of 7.19 Mg ha⁻¹ yr^–1) in the Wt-Ct treatment.  Overall, the return of both wheat and cotton straw was the best strategy for improving SOC sequestration, soil aggregation, yields and their sustainability in the wheat–cotton rotation system.

Light deficiency is a growing abiotic stress in rice production. However, few studies focus on shading effects on grain yield and quality of rice in East China. It is also essential to investigate proper nitrogen (N) application strategies that can effectively alleviate the negative impacts of light deficiency on grain yield and quality in rice. A two-year field experiment was conducted to explore the effects of shading (non-shading and shading from heading to maturity) and panicle N application (N_DP, decreased panicle N rate; N_MP, medium panicle N rate; N_IP, increased panicle N rate) treatments on rice yield- and quality-related characteristics. Compared with non-shading, shading resulted in a 9.5–14.8% yield loss (P<0.05), mainly due to lower filled-grain percentage and grain weight. N_MP and N_IP had higher (P<0.05) grain yield than N_DP under non-shading, and no significant difference was observed in rice grain yield among N_DP, N_MP, and N_IP under shading. Compared with N_MP and N_IP, N_DP achieved less yield loss under shading because of the increased filled-grain percentage and grain weight. Shading reduced leaf photosynthetic rate after heading, as well as shoot biomass weight at maturity, shoot biomass accumulation from heading to maturity, and nonstructural carbohydrate (NSC) content in the stem at maturity (P<0.05). The harvest index and NSC remobilization reserve of N_DP were increased under shading. Shading decreased (P<0.05) percentages of brown rice, milled rice, head rice, and amylose content while increasing (P<0.05) chalky rice percentage, chalky area, chalky degree, and grain protein. N_MP demonstrated a better milling quality under non-shading, while N_DP demonstrated under shading. N_DP exhibited both lower chalky rice percentage, chalky area, and chalky degree under non-shading and shading, compared with N_MP and N_IP. N_DP under shading decreased amylose content and breakdown but increased grain protein content and setback, contributing to similar overall palatability to nonshading. Our results suggested severe grain yield and quality penalty of rice when subjected to shading after heading. N_DP improved NSC remobilization, harvest index, and sink-filling efficiency and alleviated yield loss under shading. Besides, N_DP would maintain rice’s milling, appearance, and cooking and eating qualities under shading. Proper N management with a decreased panicle N rate could be adopted to mitigate the negative effects of shading on rice grain yield and quality.

Denitrification-induced nitrogen (N) losses from croplands may be greatly increased by intensive fertilization.  However, the accurate quantification of these losses is still challenging due to insufficient available in situ measurements of soil dinitrogen (N₂) emissions.  We carried out two one-week experiments in a maize–wheat cropping system with calcareous soil using the ¹⁵N gas-flux (¹⁵NGF) method to measure in situ N₂ fluxes following urea application.  Applications of ¹⁵N-labeled urea (99 atom%, 130–150 kg N ha⁻¹) were followed by irrigation on the 1st, 3rd, and 5th days after fertilization (DAF 1, 3, and 5, respectively).  The detection limits of the soil N₂ fluxes were 163–1 565, 81–485, and 54–281 μg N m⁻² h⁻¹ for the two-, four-, and six-hour static chamber enclosures, respectively.  The N₂ fluxes measured in 120 cases varied between 159 and 2 943 (811 on average) μg N m⁻² h⁻¹, which were higher than the detection limits, with the exception of only two cases.  The N₂ fluxes at DAF 3 were significantly higher (by nearly 80% (P<0.01)) than those at DAF 1 and 5 in the maize experiment, while there were no significant differences among the irrigation times in the wheat experiment.  The N₂ fluxes and the ratios of nitrous oxide (N₂O) to the N₂O plus N₂ fluxes following urea application to maize were approximately 65% and 11 times larger, respectively (P<0.01), than those following urea application to wheat.  Such differences could be mainly attributed to the higher soil water contents, temperatures, and availability of soil N substrates in the maize experiment than in the wheat experiment.  This study suggests that the ¹⁵NGF method is sensitive enough to measure in situ N₂ fluxes from intensively fertilized croplands with calcareous soils.

   Understanding the morphological and physiological traits associated with improved filling efficiency in large-panicle rice varieties is critical to devise strategies for breeding programs and cultivation management practices. Information on such traits, however, remains limited. Two large-panicle varieties with high filled-grain percentage (HF) and two check large-panicle varieties with low filled-grain percentage (LF) were field-grown in 2012 and 2013. The number of spikelets per panicle of HF and LF both exceeded 300, and the filled-grain percentage (%) of HF was approximately 90, while that of LF was approximately 75 over the two years. The results showed that when the values were averaged across two years, HF yielded 12.9 t ha^–1, while LF yielded 11.0 t ha^–1. HF had a greater leaf area duration, biomass accumulation and transport of carbohydrates stored in the culm to the grains from heading to maturity compared with LF. HF exhibited a higher leaf photosynthetic rate, more green leaves on the culm, and higher root activity during filling phase, especially during the middle and late filling phases, in relative to LF. The length of HF for upper three leaves was significantly higher than that of LF, while the angle of upper three leaves on the main culm was less in both years. Meanwhile, specific leaf weight of HF was significantly higher when compared with LF. In addition, the grain filling characteristics of HF and LF were investigated in our study. Our results suggested that a higher leaf photosynthetic rate and root activity during filling phase, greater biomass accumulation and assimilate transport after heading, and longer, thicker and more erect upper three leaves were important morphological and physiological traits of HF, and these traits could be considered as selection criterion to develop large-panicle varieties with high filled-grain percentage.

Late-maturity type of Yongyou japonica/indica hybrids series (LMYS) have shown great yield potential, and are being widely planted in the lower reaches of Yangtze River, China. Knowledge about suitable growing zone and evaluation of yield advantage is of practical importance for LMYS in this region. Fifteen LMYS, two high-yielding inbred japonica check varieties (CK-J) and two high-yielding hybrid indica check varieties (CK-I) were grown at Xinghua (119.57°E, 33.05°N) of Lixiahe region, Yangzhou (119.25°E, 32.30°N) of Yanjiang region, Changshu (120.46°E, 31.41°N) of Taihu Lake region, and Ningbo (121.31°E, 29.45°N) of Ningshao Plain in 2013 and 2014. The results showed that maturity dates of the 15 were later than the secure maturity date at Xinghua and 6, 14 and 15 LMYS were mature before the secure maturity date at Yangzhou, Changshu and Ningbo, respectively. One variety was identified as high-yielding variety among LMYS (HYYS) at Yangzhou, 8 HYYS in 2013 and 9 HYYS in 2014 at Changshu, 9 HYYS at Ningbo. HYYS here referred to the variety among LMYS that was mature before the secure maturity date and had at least 8% higher grain yield than both CK-J and CK-I at each experimental site. Grain yield of HYYS at each experimental site was about 12.0 t ha–1 or higher, and was significantly higher than CK varieties. High yield of HYYS was mainly attributed to larger sink size due to more spikelets per panicle. Plant height of HYYS was about 140 cm, and was significantly higher than check varieties. Significant positive correlations were recorded between duration from heading to maturity stage and grain yield, and also between whole growth periods and grain yield. HYYS had obvious advantage over check varieties in biomass accumulation and leaf area duration from heading to maturity stage. Comprehensive consideration about safe maturity and yield performance of LMYS at each experimental site, Taihu Lake region (representative site Changshu) and Ningshao Plain (representative site Ningbo) were thought suitable growing zones for LMYS in the lower reaches of Yangtze River. The main factors underlying high yield of HYYS were larger sink size, higher plant height, longer duration from heading to maturity stage and whole growth periods, and higher biomass accumulation and leaf area duration during grain filling stage.

Synthetic hexaploid wheat (SHW) represents a valuable source of new resistances to a range of biotic and abiotic stresses. A recombinant inbred line (RIL) population with 127 recombinant inbred lines derived from a SHW-derived variety Chuanmai 42 crossing with a Chinese spring wheat variety Chuannong 16 was used to map QTLs for agronomic traits including grain yield, grains per square meter, thousand-kernel weight, spikes per square meter, grain number per spike, grains weight per spike, and biomass yield. The population was genotyped using 184 simple-sequence repeat (SSR) markers and 34 sequence-related amplified polymorphism (SRAP) markers. Of 76 QTLs (LOD>2.5) identified, 42 were found to have a positive effect from Chuanmai 42. The QTL QGy.saas-4D.2 associated with grain yield on chromosome 4D was detected in four of the six environments and the combined analysis, and the mean yield, across six environments, of individuals carrying the Chuanmai 42 allele at this locus was 8.9% higher than that of those lines carrying the Chuannong 16 allele. Seven clusters of the yield-coincident QTLs were detected on 1A, 4A, 3B, 5B, 4D, and 7D.

Geese, descendants of migratory birds, have preserved the distinct reproductive and lipid metabolism traits of their wild ancestors.  Therefore, compared to other poultry, geese have lower egg production ability and a more sensitive susceptibility to fatty liver.  Recent research underscores the impact of lipid metabolism disorders on female reproductive health.  In this context, we observed reproductive disorders (RD) and lipid metabolism anomalies in certain geese populations.  This study systematically elucidated the differences between RD and normal geese at various levels, including genomics, transcriptomics, bile acid metabolomics, and microbiomics, revealing the crucial role of microorganisms.  Our study provides a thorough examination of the ovarian anatomical, histological, and transcriptomic profiles between normal and RD geese.  Genomic analyses pinpoint mutations in genes associated with bile acid metabolism, highlighting their potential role in RD pathogenesis.  The genomic discoveries are substantiated by precise bile acid assays and ileum transcriptome analyses, which expose a significant disruption in bile acid absorption, activation of FXR, and an increase in serum chenodeoxycholic acid (CDCA) concentrations within RD geese.  Notably, 16S rRNA sequencing uncovers significantly greater beta diversity in the ileum microbiota of RD geese as compared to the normal group.  Both Wilcoxon rank sum test and LEfSe analyses highlighted a marked increase in Romboutsia abundance in RD geese. Experimental cultivation of microbiota with CDCA supplementation confirms the impact of CDCA on Romboutsia lituseburensis (R. lituseburensis) proliferation. Gavage experiments with R. lituseburensis elucidates its involvement in primary follicle reduction via immune-mediated pathways.  Collectively, our multi-faceted analysis unravels the intricate involvement of Romboutsia in goose RD, offering insights from genetic, physiological, and microbial dimensions. Our findings not only deepen our understanding of the etiology of RD in geese but also suggest potential avenues for therapeutic interventions targeting bile acid metabolism and the modulation of specific microbiota components. 

As a multifunctional crop, rapeseed provides vegetables by picking shoots.  Shoot removal reduced yield, while nitrogen (N) application results in efficiency gains.  However, the effect of N rate on pod growth, N use efficiency (NUE) and seed yield after shoot removal is unclear.  A 2-year field experiment was set with four N rates (0 [N0], 90 [N1], 180 [N2], and 270 [N3] kg ha^-1) and two shoot treatments (no shoot removal [CK], shoot removal [SR]).  Results showed the shoot removal decreased population biomass (PB) at maturity across all N levels.  Conversely, N application increased the PB after shoot removal and elevated soluble sugar and protein in shoots.  Shoot removal increased the seeds per pod (13.5-26.9%), reduced the pods per plant (33.1-45.8%) and population seed yield (19.5-38.4%).  N application effectively increased the yield related index, and led to an increase in population seed yield by 187.2 - 465.0% in the CK group, and by 185.6 - 430.7% in the SR group.  Moreover, the seed yield reached its maximum under the N3 in both groups.  The leaf N content per area (N_a) and net photosynthetic rate (P_n) were increased, but leaf photosynthetic N use efficiency (PNUE) were decreased at 20 days after shoot removal, which lead to a significant decrease in N use efficiency(NUE).  N supply increased the plant organ N content and PB, but decreased the NUE at maturity stage.  P_n of the pod wall at 25 days after flowering was elevated due to its optimized chloroplasts ultrastructure and increased rubisco and sucrose synthase activities under shoot removal and more N.  However, the greater amino acid/soluble sugar ratio (A/S) of the pod wall significantly increased the seed protein content and decreased the oil content.  Though the oil yield was reduced by 63.8-71.0% under SR×N3 treatment compared with CK×N3, it was comparable to that of CK with 90 kg N ha^-1 treatment.  The results indicated that N applying improves the carbon metabolism of the pod wall and alleviates yield reduction after shoot removal but reduces NUE and seed oil content of rapeseed.  The findings guide the balancing of rapeseed’s vegetable and oil production, and optimize N fertilization for sustainable, efficient rapeseed farming.