Per- and polyfluoroalkyl substances in waterbird feathers around Poyang Lake, China: Compound and species-specific bioaccumulation.

As a nondestructive means of environmental monitoring, bird feathers have been used to analyze levels of per- and polyfluoroalkyl substances (PFASs) in specific environments. In this study, feather samples from 10 waterbird species around Poyang Lake were collected, and a pretreatment method for PFASs in feathers was optimized. The results showed that a combined cleaning method using ultrapure water and n-hexane effectively removed external PFASs. Twenty-three legacy and emerging PFASs were identified in the feathers of waterbirds, of which hexafluoropropylene oxides (HFPOs), chlorinated polyfluoroalkyl ether sulfonates (Cl-PFESAs), and sodium p-perfluorinated noneoxybenzene sulfonate (OBS) were reported for the first time, with their concentrations ranging from 0.060-2.4 ng·g-1 dw, 0.046-30 ng·g-1 dw, and lower than the method detection limit to 30 ng·g-1 dw, respectively. Compound- and species-specific bioaccumulation of PFASs was observed in the feathers of different waterbird species, suggesting that different PFAS types can be monitored through the selection of different species. Moreover, the concentrations of most PFCAs (except perfluorobutyric acid), perfluorooctane sulfonate (PFOS), and perfluorooctane sulfonamide (FOSA) were significantly positively correlated with δ15N (p < 0.05), while the concentrations of HFPOs, Cl-PFESAs, and OBS had significant positive correlations with δ13C. This indicates that the bioaccumulation of legacy and emerging PFASs in waterbird feathers is affected by their trophic level, feeding habits, and foraging area.

Response of Siberian Cranes (Grus leucogeranus) to Hydrological Changes and the Availability of Foraging Habitat at Various Water Levels in Poyang Lake.

To assess the Siberian crane (Grus leucogeranus)'s response to changing water levels and habitat quality at Poyang Lake, we analyzed the lake's hydrological trends over the past two decades with the Mann-Kendall and Sen slope methods. Additionally, we explored the link between the crane population size and hydrological conditions at the lake from 2011 to 2019. Meanwhile, five environmental factors, including habitat type, distance from shallow lakes, human footprint index, elevation and normalized vegetation index were selected, and the distribution patterns of suitable habitats for the Siberian crane under 10 water level gradients with intervals of about 1 m (5.3-14.2 m) were simulated by using an improved habitat suitability index model that determines the weights of evaluating factors based on the MaxEnt model. The results showed that the overall trend of the inundated area in Poyang Lake was shrinking in the last 20 years, with a significant increase in the area of exposed floodland during the early wintering period (Z = -2.26). The prolonged drought resulting from this will force vegetation succession, thereby diminishing the food resources for cranes in their natural habitat. The mean inundated area in June demonstrated a significant negative correlation with the population of Siberian cranes in natural habitats (r = -0.75, p = 0.02). Shortage of the Siberian crane-preferred Vallisneria tuber due to June flooding was the primary driver of the crane's altered foraging strategy and habitat shift. In years with relatively normal June inundation, indicating abundant Vallisneria resources, the relationship between the inundated area during the dry season and the crane population fit well, with a quadratic curve (R2 = 0.92, p = 0.02). The dry season's inundated area primarily affected the crane population and distribution pattern by influencing the availability of food resources, and both excessive and insufficient inundation areas were unfavorable for crane survival. The modeling results for habitat suitability indicated that as the water level decreased, the trend of the area of good habitat for the Siberian crane showed an inverted bell shape, peaking at a water level of 8.8 m, with optimal conditions occurring between 8 and 10 m. The combined effects of climate and human activities have made the shortage of food resources in Poyang Lake the new normal. The degradation of natural habitats has led to a decline in the quality of Siberian crane habitats, and artificial habitats can only be used as refuges to a certain extent. Thus, formulating strategies to restore natural habitats and enhance the management of artificial habitats is crucial for the conservation efforts of Siberian cranes.

Suitable overwintering habitat simulation and the drivers of their population expansion for Siberian cranes (Grus leucogeranus) in China.

To gain a more comprehensive understanding of habitat preferences, potential wintering area distribution and drivers of population expansion of Grus leucogeranus, we selected 70 geographical distribution points and 11 environmental variables in its wintering period from 2015-2022. We modeled suitable habitat patterns for G. leucogeranus in China using MaxEnt model, and analyzed the relationship between suitable habitat distribution and environmental factors. The results showed that the dominant factors affecting the overwintering distribution of G. leucogeranus were distance to mudflats, elevation, average precipitation in February, distance to water sources, minimum temperature in December, and land use type, with a cumulative contribution rate of 94.6%. The wintering ground of G. leucogeranus in China was mainly distributed in the middle and lower reaches of the Yangtze Plain and the Yellow River Delta of the North China Plain. In these regions, the area of high-, medium- and low-suitability habitat were 17685, 60787 and 60747 km2, respectively. A total of 40 protected areas had been established in the high-suitability wintering range of G. leucogeranus in China, whereas 12 high-suitability wetlands such as Qili Lake in Anhui, Liangzi Lake in Hubei and Chenjia Lake in Jiangxi were still unprotected. The wintering grounds had shown a trend of expansion to the northeast and southeast since 2015. Considering the large-scale habitat shifts of G. leucogeranus in recent years and the frequent new wintering records in various places, we suggested that the shortage of food resources in natural habitats was the main factor driving the expansion of G. leucogeranus' wintering range. To protect G. leucogeranus more effectively, we should strengthen the restoration of natural habitats and the management of farmland habitats.

PHYTOCHROME C regulation of photoperiodic flowering via PHOTOPERIOD1 is mediated by EARLY FLOWERING 3 in Brachypodium distachyon.

Daylength sensing in many plants is critical for coordinating the timing of flowering with the appropriate season. Temperate climate-adapted grasses such as Brachypodium distachyon flower during the spring when days are becoming longer. The photoreceptor PHYTOCHROME C is essential for long-day (LD) flowering in B. distachyon. PHYC is required for the LD activation of a suite of genes in the photoperiod pathway including PHOTOPERIOD1 (PPD1) that, in turn, result in the activation of FLOWERING LOCUS T (FT1)/FLORIGEN, which causes flowering. Thus, B. distachyon phyC mutants are extremely delayed in flowering. Here we show that PHYC-mediated activation of PPD1 occurs via EARLY FLOWERING 3 (ELF3), a component of the evening complex in the circadian clock. The extreme delay of flowering of the phyC mutant disappears when combined with an elf3 loss-of-function mutation. Moreover, the dampened PPD1 expression in phyC mutant plants is elevated in phyC/elf3 mutant plants consistent with the rapid flowering of the double mutant. We show that loss of PPD1 function also results in reduced FT1 expression and extremely delayed flowering consistent with results from wheat and barley. Additionally, elf3 mutant plants have elevated expression levels of PPD1, and we show that overexpression of ELF3 results in delayed flowering associated with a reduction of PPD1 and FT1 expression, indicating that ELF3 represses PPD1 transcription consistent with previous studies showing that ELF3 binds to the PPD1 promoter. Indeed, PPD1 is the main target of ELF3-mediated flowering as elf3/ppd1 double mutant plants are delayed flowering. Our results indicate that ELF3 operates downstream from PHYC and acts as a repressor of PPD1 in the photoperiod flowering pathway of B. distachyon.

Mixed-Linkage Glucan Is the Main Carbohydrate Source and Starch Is an Alternative Source during Brachypodium Grain Germination.

Seeds of the model grass Brachypodium distachyon are unusual because they contain very little starch and high levels of mixed-linkage glucan (MLG) accumulated in thick cell walls. It was suggested that MLG might supplement starch as a storage carbohydrate and may be mobilised during germination. In this work, we observed massive degradation of MLG during germination in both endosperm and nucellar epidermis. The enzymes responsible for the MLG degradation were identified in germinated grains and characterized using heterologous expression. By using mutants targeting MLG biosynthesis genes, we showed that the expression level of genes coding for MLG and starch-degrading enzymes was modified in the germinated grains of knocked-out cslf6 mutants depleted in MLG but with higher starch content. Our results suggest a substrate-dependent regulation of the storage sugars during germination. These overall results demonstrated the function of MLG as the main carbohydrate source during germination of Brachypodium grain. More astonishingly, cslf6 Brachypodium mutants are able to adapt their metabolism to the lack of MLG by modifying the energy source for germination and the expression of genes dedicated for its use.

Chronic social defeat alters behaviors and neuronal activation in the brain of female Mongolian gerbils.

Chronic social defeat has been found to be stressful and to affect many aspects of the brain and behaviors in males. However, relatively little is known about its effects on females. In the present study, we examined the effects of repeated social defeat on social approach and anxiety-like behaviors as well as the neuronal activation in the brain of sexually naïve female Mongolian gerbils (Meriones unguiculatus). Our data indicate that repeated social defeats for 20 days reduced social approach and social investigation, but increased risk assessment or vigilance to an unfamiliar conspecific. Such social defeat experience also increased anxiety-like behavior and reduced locomotor activity. Using ΔFosB-immunoreactive (ΔFosB-ir) staining as a marker of neuronal activation in the brain, we found significant elevations by social defeat experience in the density of ΔFosB-ir stained neurons in several brain regions, including the prelimbic (PL) and infralimbic (IL) subnuclei of the prefrontal cortex (PFC), CA1 subfields (CA1) of the hippocampus, central subnuclei of the amygdala (CeA), the paraventricular nucleus (PVN), dorsomedial nucleus (DMH), and ventrolateral subdivision of the ventromedial nucleus (VMHvl) of the hypothalamus. As these brain regions have been implicated in social behaviors and stress responses, our data suggest that the specific patterns of neuronal activation in the brain may relate to the altered social and anxiety-like behaviors following chronic social defeat in female Mongolian gerbils.

Multiple origins, one evolutionary trajectory: gradual evolution characterizes distinct lineages of allotetraploid Brachypodium.

The "genomic shock" hypothesis posits that unusual challenges to genome integrity such as whole genome duplication may induce chaotic genome restructuring. Decades of research on polyploid genomes have revealed that this is often, but not always the case. While some polyploids show major chromosomal rearrangements and derepression of transposable elements in the immediate aftermath of whole genome duplication, others do not. Nonetheless, all polyploids show gradual diploidization over evolutionary time. To evaluate these hypotheses, we produced a chromosome-scale reference genome for the natural allotetraploid grass Brachypodium hybridum, accession "Bhyb26." We compared 2 independently derived accessions of B. hybridum and their deeply diverged diploid progenitor species Brachypodium stacei and Brachypodium distachyon. The 2 B. hybridum lineages provide a natural timecourse in genome evolution because one formed 1.4 million years ago, and the other formed 140 thousand years ago. The genome of the older lineage reveals signs of gradual post-whole genome duplication genome evolution including minor gene loss and genome rearrangement that are missing from the younger lineage. In neither B. hybridum lineage do we find signs of homeologous recombination or pronounced transposable element activation, though we find evidence supporting steady post-whole genome duplication transposable element activity in the older lineage. Gene loss in the older lineage was slightly biased toward 1 subgenome, but genome dominance was not observed at the transcriptomic level. We propose that relaxed selection, rather than an abrupt genomic shock, drives evolutionary novelty in B. hybridum, and that the progenitor species' similarity in transposable element load may account for the subtlety of the observed genome dominance.

Whole-genome assembly and annotation of northern wild rice, Zizania palustris L., supports a whole-genome duplication in the Zizania genus.

Zizania palustris L. (northern wild rice, NWR) is an aquatic grass native to North America that is notable for its nutritious grain. This is an important species with ecological, cultural and agricultural significance, specifically in the Great Lakes region of the USA. Using flow cytometry, we first estimated the NWR genome size to be 1.8 Gb. Using long- and short-range sequencing, Hi-C scaffolding and RNA-seq data from eight tissues, we generated an annotated whole-genome de novo assembly of NWR. The assembly was 1.29 Gb in length, highly repetitive (approx. 76.0%) and contained 46 421 putative protein-coding genes. The expansion of retrotransposons within the genome and a whole-genome duplication (WGD) after the Zizania-Oryza speciation event have both led to an increase in the genome size of NWR in comparison with Oryza sativa L. and Zizania latifolia. Both events depict a genome rapidly undergoing change over a short evolutionary time. Comparative analyses revealed the conservation of large syntenic blocks between NWR and O. sativa, which were used to identify putative seed-shattering genes. Estimates of divergence times revealed that the Zizania genus diverged from Oryza approximately 26-30 million years ago (26-30 MYA), whereas NWR and Z. latifolia diverged from one another approximately 6-8 MYA. Comparative genomics confirmed evidence of a WGD in the Zizania genus and provided support that the event occurred prior to the NWR-Z. latifolia speciation event. This genome assembly and annotation provides a valuable resource for comparative genomics in the Oryzeae tribe and provides an important resource for future conservation and breeding efforts of NWR.

QTL mapping of pre-harvest sprouting resistance in a white wheat cultivar Danby.

KEY MESSAGE: One major and three minor QTLs for resistance to pre-harvest sprouting (PHS) were identified from a white wheat variety "Danby." The major QTL on chromosome 3A is TaPHS1, and the sequence variation in its promoter region was responsible for the PHS resistance. Additive × additive effects were detected between two minor QTLs on chromosomes 3B and 5A, which can greatly enhance the PHS resistance. Pre-harvest sprouting (PHS) causes significant losses in yield and quality in wheat. White wheat is usually more susceptible to PHS than red wheat. Therefore, the use of none grain color-related PHS resistance quantitative trait loci (QTLs) is essential for the improvement in PHS resistance in white wheat. To identify PHS resistance QTLs in the white wheat cultivar "Danby" and determine their effects, a doubled haploid population derived from a cross of Danby × "Tiger" was genotyped using genotyping-by-sequencing markers and phenotyped for PHS resistance in two greenhouse and one field experiments. One major QTL corresponding to a previously cloned gene, TaPHS1, was consistently detected on the chromosome arm 3AS in all three experiments and explained 21.6-41.0% of the phenotypic variations. A SNP (SNP-222) in the promoter of TaPHS1 co-segregated with PHS in this mapping population and was also significantly associated with PHS in an association panel. Gene sequence comparison and gene expression analysis further confirmed that SNP-222 is most likely the causal mutation in TaPHS1 for PHS resistance in Danby in this study. In addition, two stable minor QTLs on chromosome arms 3BS and 5AL were detected in two experiments with allele effects consistently contributed by Danby, while one minor QTL on 2AS was detected in two environments with contradicted allelic effects. The two stable minor QTLs showed significant additive × additive effects. The results demonstrated that pyramiding those three QTLs using breeder-friendly KASP markers developed in this study could greatly improve PHS resistance in white wheat.

Population sizes and group characteristics of Siberian Crane (Leuco-geranus leucogeranus) and Hooded Crane (Grus monacha) in Poyang Lake Wetland.

Both the Siberian Crane (Leucogeranus leucogeranus) and Hooded Crane (Grus monacha) have limited population sizes and are considered endangered by domestic Chinese and international agencies. To document the current size of their respective populations and characterize their groups, between October 2012 and April 2013 we undertook fieldwork at four nature reserve areas within the Poyang Lake wetlands. We divided Poyanghu National Nature Reserve (PYH) into the Wucheng (PWC) and Hengfeng areas (PHF), because each are each located in different counties. Our fieldwork showed that the Siberian Crane occurred mainly in PYH (364 in the PHF, 158 in the PWC) and the Nanjishan Wetland National Nature Reserve (NJS, with 200 individuals). The Hooded Crane was mainly distributed in PYH (302 in the PHF and 154 in the PWC). Family groups accounted for more than 50% of the total number of groups among both species, with Hooded Cranes forming more family groups than Siberian Cranes. Typically, these groups were formed of two adults with one offspring (Siberian Crane), and two adults with two offspring (Hooded Crane), with the mean family group size of the Siberian Crane and Hooded Crane being respectively 2.65 ± 0.53 (n=43) and 3.09 ± 0.86 (n=47) individuals per group. The mean collective group size of the Siberian Crane and Hooded Crane included 28.09 ± 24.94 (n=23) and 28.94 ± 27.97 (n=16) individuals per group, respectively, with the proportion of juveniles among Hooded Cranes being more than double that seen among the Siberian Cranes.

Epigenetic QTL mapping in Brassica napus.

There is increasing evidence that epigenetic marks such as DNA methylation contribute to phenotypic variation by regulating gene transcription, developmental plasticity, and interactions with the environment. However, relatively little is known about the relationship between the stability and distribution of DNA methylation within chromosomes and the ability to detect trait loci. Plant genomes have a distinct range of target sites and more extensive DNA methylation than animals. We analyzed the stability and distribution of epialleles within the complex genome of the oilseed crop plant Brassica napus. For methylation sensitive AFLP (MSAP) and retrotransposon (RT) epimarkers, we found a high degree of stability, with 90% of mapped markers retaining their allelic pattern in contrasting environments and developmental stages. Moreover, for two distinct parental lines 97% of epialleles were transmitted through five meioses and segregated in a mapping population. For the first time we have established the genetic position for 17 of the 19 centromeres within this amphidiploid species. Epiloci and genetic loci were distributed within distinct clusters, indicating differential detection of recombination events. This enabled us to identify additional significant QTL associated with seven important agronomic traits in the centromeric regions of five linkage groups.