Ploidy variation induces butterfly effect on chromatin topology in wheat.

Polyploidy is a prominent driver of plant diversification, accompanied with dramatic chromosomal rearrangement and epigenetic changes that affect gene expression. How chromatin interactions within and between subgenomes adapt to ploidy transition remains poorly understood. We generate open chromatin interaction maps for natural hexaploid wheat (AABBDD), extracted tetraploid wheat (AABB), diploid wheat progenitor Aegilops tauschii (DD) and resynthesized hexaploid wheat (RHW, AABBDD). Thousands of intra- and interchromosomal loops are de novo established or disappeared in AB subgenomes after separation of D subgenome, in which 37-95% of novel loops are lost again in RHW after merger of D genome. Interestingly, more than half of novel loops are formed by cascade reactions that are triggered by disruption of chromatin interaction between AB and D subgenomes. The interaction repressed genes in RHW relative to DD are expression suppressed, resulting in more balanced expression of the three homoeologs in RHW. The interaction levels of cascade anchors are decreased step-by-step. Leading single nucleotide polymorphisms of yield- and plant architecture-related quantitative trait locus are significantly enriched in cascade anchors. The expression of 116 genes interacted with these anchors are significantly correlated with the corresponding traits. Our findings reveal trans-regulation of intrachromosomal loops by interchromosomal interactions during genome merger and separation in polyploid species.

Transferring a new Fusarium head blight resistance locus FhbRc1 from Roegneria ciliaris into wheat by developing alien translocation lines.

KEY MESSAGE: A new FHB resistance locus FhbRc1 was identified from the R. ciliaris chromosome 7Sc and transferred into common wheat by developing alien translocation lines. Fusarium head blight (FHB) caused by multiple Fusarium species is a globally destructive disease of common wheat. Exploring and utilization of resources with FHB resistance are the most effective and environmentally beneficial approach for the disease control. Roegneria ciliaris (Trin.) Nevski (2n = 4x = 28, ScScYcYc), a tetraploid wheat wild relative, possesses high resistance to FHB. In the previous study, a complete set of wheat-R. ciliaris disomic addition (DA) lines were evaluated for FHB resistance. DA7Sc had stable FHB resistance, which was confirmed to be derived from alien chromosome 7Sc. We tentatively designated the resistant locus as FhbRc1. For better utilization of the resistance in wheat breeding, we developed translocations by inducing chromosome structural aberrations using iron irradiation and the homologous pairing gene mutant ph1b. Totally, 26 plants having various 7Sc structural aberrations were identified. By marker analysis, a cytological map of 7Sc was constructed and 7Sc was dissected into 16 cytological bins. Seven alien chromosome aberration lines, which all had the bin 7Sc-1 on the long arm of 7Sc, showed enhanced FHB resistance. Thus, FhbRc1 was mapped to the distal region of 7ScL. A homozygous translocation line T4BS·4BL-7ScL (NAURC001) was developed. It showed improved FHB resistance, while had no obvious genetic linkage drag for the tested agronomic traits compared with the recurrent parent Alondra's. When transferring the FhbRc1 into three different wheat cultivars, the derived progenies having the translocated chromosome 4BS·4BL-7ScL all showed improved FHB resistance. This revealed the potential value of the translocation line in wheat breeding for FHB resistance.

Resistance of QYm.nau-2D to wheat yellow mosaic virus was derived from an alien introgression into common wheat.

KEY MESSAGE: The QYm.nau-2D locus conferring wheat yellow mosaic virus resistance is an exotic introgression and we developed 11 diagnostic markers tightly linked to QYm.nau-2D. Wheat yellow mosaic virus (WYMV) is a serious disease of winter wheat in China. Breeding resistant varieties is the most effective strategy for WYMV control. A WYMV resistant locus QYm.nau-2D on the chromosome arm 2DL has been repeatedly reported but the mapped region is large. In the present study, we screened recombinants using a biparental population and mapped QYm.nau-2D into an 18.8 Mb physical interval. By genome-wide association studies of 372 wheat varieties for WYMV resistance in four environments, we narrowed down QYm.nau-2D into a 16.4 Mb interval. Haplotype analysis indicated QYm.nau-2D were present as six different states due to recombination during hybridization breeding. QYm.nau-2D was finally mapped into a linkage block of 11.2 Mb. Chromosome painting using 2D specific probes and collinearity analysis among the published sequences corresponding to QYm.nau-2D region indicated the block was an exotic introgression. The Illumina-sequenced reads of four diploid Aegilops species were mapped to the sequence of Fielder, a variety having the introgression. The mapping reads were significantly increased at the putative introgression regions of Fielder. Ae. uniaristata (NN) had the highest mapping reads, suggesting that QYm.nau-2D was possibly an introgression from genome N. We investigated the agronomic performances of different haplotypes and observed no linkage drag of the alien introgression for the 15 tested traits. For marker-assisted selection of QYm.nau-2D, we developed 11 diagnostic markers tightly linked to the locus. This research provided a case study of an exotic introgression, which has been utilized in wheat improvement for WYMV resistance.

The Landscapes of Gluten Regulatory Network in Elite Wheat Cultivars Contrasting in Gluten Strength.

Yangmai-13 (YM13) is a wheat cultivar with weak gluten fractions. In contrast, Zhenmai-168 (ZM168) is an elite wheat cultivar known for its strong gluten fractions and has been widely used in a number of breeding programs. However, the genetic mechanisms underlying the gluten signatures of ZM168 remain largely unclear. To address this, we combined RNA-seq and PacBio full-length sequencing technology to unveil the potential mechanisms of ZM168 grain quality. A total of 44,709 transcripts were identified in Y13N (YM13 treated with nitrogen) and 51,942 transcripts in Z168N (ZM168 treated with nitrogen), including 28,016 and 28,626 novel isoforms in Y13N and Z168N, respectively. Five hundred and eighty-four differential alternative splicing (AS) events and 491 long noncoding RNAs (lncRNAs) were discovered. Incorporating the sodium-dodecyl-sulfate (SDS) sedimentation volume (SSV) trait, both weighted gene coexpression network analysis (WGCNA) and multiscale embedded gene coexpression network analysis (MEGENA) were employed for network construction and prediction of key drivers. Fifteen new candidates have emerged in association with SSV, including 4 transcription factors (TFs) and 11 transcripts that partake in the post-translational modification pathway. The transcriptome atlas provides new perspectives on wheat grain quality and would be beneficial for developing promising strategies for breeding programs.

Large-scale field phenotyping using backpack LiDAR and CropQuant-3D to measure structural variation in wheat.

Plant phenomics bridges the gap between traits of agricultural importance and genomic information. Limitations of current field-based phenotyping solutions include mobility, affordability, throughput, accuracy, scalability, and the ability to analyze big data collected. Here, we present a large-scale phenotyping solution that combines a commercial backpack Light Detection and Ranging (LiDAR) device and our analytic software, CropQuant-3D, which have been applied jointly to phenotype wheat (Triticum aestivum) and associated 3D trait analysis. The use of LiDAR can acquire millions of 3D points to represent spatial features of crops, and CropQuant-3D can extract meaningful traits from large, complex point clouds. In a case study examining the response of wheat varieties to three different levels of nitrogen fertilization in field experiments, the combined solution differentiated significant genotype and treatment effects on crop growth and structural variation in the canopy, with strong correlations with manual measurements. Hence, we demonstrate that this system could consistently perform 3D trait analysis at a larger scale and more quickly than heretofore possible and addresses challenges in mobility, throughput, and scalability. To ensure our work could reach non-expert users, we developed an open-source graphical user interface for CropQuant-3D. We, therefore, believe that the combined system is easy-to-use and could be used as a reliable research tool in multi-location phenotyping for both crop research and breeding. Furthermore, together with the fast maturity of LiDAR technologies, the system has the potential for further development in accuracy and affordability, contributing to the resolution of the phenotyping bottleneck and exploiting available genomic resources more effectively.

Predominant wheat-alien chromosome translocations in newly developed wheat of China.

Founder wheat lines have played key role in Chinese wheat improvement. Wheat-Dasypyrum villosum translocation T6VS·6AL has been widely used in wheat breeding in recent years due to its high level of powdery mildew resistance and other beneficial genes. Reference oligo-nucleotide multiplex probe (ONMP)-FISH karyotypes of six T6VS·6AL donor lines were developed and used for characterizing 32 derivative cultivars and lines. T6VS·6AL was present in 27 cultivar/lines with 20 from southern China. Next, ONMP-FISH was used to study chromosome constitution of randomly collected wheat cultivars and advanced breeding lines from southern and northern regions of China: 123 lines from the regional test plots of southern China and 110 from northern China. In southern China, T6VS·6AL (35.8%) was the most predominant variation, while T1RS·1BL (27.3%) was the most predominant in northern China. The pericentric inversion perInv 6B derived from its founder wheat Funo and Abbondaza was the second most predominant chromosome variant in both regions. Other chromosome variants were present in very low frequencies. Additionally, 167 polymorphic chromosome types were identified. Based on these variations, 271 cultivars and lines were clustered into three groups, including southern, northern, and mixed groups that contained wheat from both regions. Different dominant chromosome variations were seen, indicating chromosome differentiation in the three groups of wheat. The clearly identified wheat lines with T6VS·6AL in different backgrounds and oligonucleotide probe set will facilitate their utilization in wheat breeding and in identifying other beneficial traits that may be linked to this translocation. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-021-01206-3.

Fine mapping of wheat powdery mildew resistance gene Pm6 using 2B/2G homoeologous recombinants induced by the ph1b mutant.

KEY MESSAGE: Using the ph1b mutant, the recombination frequency between the homoeologous region of 2B and 2G was significantly increased. By this, we narrowed Pm6 to a 0.9 Mb physical region. The powdery mildew (Pm) resistance gene Pm6 from Triticum timopheevii (2n = 48, AAGG) was mapped to the long arm of chromosome 2G and introduced into common wheat in the form of 2B-2G introgressions. The introgression line IGV1-465 has the shortest 2G segment, which is estimated 37 Mb in size when referring to 2BL genome reference of Chinese Spring (CS). The further fine mapping of Pm6 was impeded by the inhibition of allogeneic chromosome recombination between 2B and 2G in the Pm6 region. In the present study, to overcome 2B/2G recombination suppression, a ph1b-based strategy was employed to produce introgressions with reduced 2G fragments for the fine mapping of Pm6. IGV1-465 was crossed and backcrossed to the CSph1b mutant to produce plants with increased 2B/2G chromosome pairing frequency at the Pm6 region. A total of 182 allogeneic recombinants were obtained through two-round screening, i.e., first round of screening of 820 BC1F2:3 progenies using the flanking markers CIT02g-14/CIT02g-19 and second round of screening of 642 BC1F2:4 progenies using the flanking markers CIT02g-13/CIT02g-18, respectively. Through marker analysis using 30 chromosome 2G-specific markers located in the Pm6 region, the identified recombinants were divided into 14 haplotypes. Pm resistance evaluation of these haplotypes enabled us to narrow Pm6 to a 0.9 Mb physical region of 2BL, flanked by markers CIT02g-20 and CIT02g-18. Six wheat varieties containing Pm6 were identified from a natural population, and they showed increased Pm resistance. This implied Pm6 is still effective, especially when used in combination with other Pm resistance genes.

Characterization of a common wheat (Triticum aestivum L.) high-tillering dwarf mutant.

KEY MESSAGE: A novel high-tillering dwarf mutant in common wheat Wangshuibai was characterized and mapped to facilitate breeding for plant height and tiller and the future cloning of the causal gene. Tiller number and plant height are two major agronomic traits in cereal crops affecting plant architecture and grain yield. NAUH167, a mutant of common wheat landrace Wangshuibai induced by ethylmethyl sulfide (EMS) treatment, exhibits higher tiller number and reduced plant height. Microscope observation showed that the dwarf phenotype was attributed to the decrease in the number of cells and their length. The same as the wild type, the mutant was sensitive to exogenous gibberellins. Genetic analysis showed that the high-tillering number and dwarf phenotype were related and controlled by a partial recessive gene. Using a RIL2:6 population derived from the cross NAUH167/Sumai3, a molecular marker-based genetic map was constructed. The map consisted of 283 loci, spanning a total length of 1007.98 cM with an average markers interval of 3.56 cM. By composite interval mapping, a stable major QTL designated QHt.nau-2D controlling both traits, was mapped to the short arm of chromosome 2D flanked by markers Xcfd11 and Xgpw361. To further map the QHt.nau-2D loci, another population consisted of 180 F2 progeny from a cross 2011I-78/NAUH167 was constructed. Finally, QHt.nau-2D was located within a genetic region of 0.8 cM between markers QHT239 and QHT187 covering a predicted physical distance of 6.77 Mb. This research laid the foundation for map-based cloning of QHt.nau-2D and would facilitate the characterization of plant height and tiller number in wheat.

Unveiling the Regulatory Role of LncRNA MYU in Hypoxia-Induced Angiogenesis via the miR-23a-3p Axis in Endothelial Cells.

Background: Angiogenesis is essential for various physiological and pathological processes, such as embryonic development and cancer cell proliferation, migration, and invasion. Long noncoding RNAs (lncRNAs) play pivotal roles in normal homeostasis and disease processes by regulating gene expression through various mechanisms, including competing endogenous RNAs (ceRNAs) of target microRNAs (miRNAs). The lncRNA MYU is known to promote prostate cancer proliferation via the miR-184/c-Myc regulatory axis and to be upregulated in vascular endothelial cells under hypoxic conditions, which often occurs in solid tumors. In the present study, we investigated whether MYU might affect cancer growth by regulating angiogenesis in vascular endothelial cells under hypoxia. Methods: The expression of MYU-regulated miR-23a-3p and interleukin-8 (IL-8) in HUVEC cell lines was examined using qRT-PCR. The CCK-8 assay, EdU assay, wound-healing assay, and tube-formation assay were used to assess the effects of MYU on cell proliferation, migration, and tube formation of HUVEC cells in vitro. The dual-luciferase reporter assay was performed to examine the effects of miR-23a-3p on MYU and IL-8 expression. Results: We found that the overexpression of MYU and knockdown of miR-23a-3p in human umbilical vein endothelial cells (HUVECs) under hypoxia promoted cell proliferation, migration, and tube formation. Mechanistically, MYU was shown to bind competitively to miR-23a-3p, thereby preventing miR-23a-3p binding to the 3' untranslated region of IL-8 mRNA. In turn, increased production of pro-angiogenic IL-8 promoted HUVEC proliferation, migration, and tube formation under hypoxia. Conclusion: This study identified a new role for lncRNA MYU as a ceRNA for miR-23a-3p and uncovered a novel MYU-miR-23a-3p-IL-8 regulatory axis for angiogenesis. MYU and/or miR-23a-3p may thus represent new targets for the treatment of hypoxia-related diseases by promoting angiogenesis.

Diversity and host interaction of the gut microbiota in specific pathogen-free pigs.

Pigs are widely used as animal models in various studies related to humans. The interaction between the gut microbiota and the host has significant effects on the host's health and disease status. However, although there have been many studies investigating the pig gut microbiota, the findings have been inconsistent due to variations in rearing conditions. Interactions between the gut microbiota and host have not been fully explored in pigs. Specific pathogen-free (SPF) pigs are ideal non-primate large animals to study the interactions between the gut microbiota and the host. In this study, we performed high-throughput sequencing analysis of the gut microbiota and the gut tissue transcriptome of six SPF pigs to provide a systematic understanding of the composition, function, and spatial distribution of gut microbiota in SPF pigs. We identified significant differences in microbial diversity and functionality among different gastrointestinal tract sites. Metagenomics data analysis revealed significant differences in alpha diversity and beta diversity of microbiota in different gastrointestinal sites of SPF pigs. Additionally, transcriptomic data indicated significant differences in gene expression as well as KEGG and GO functional enrichment between the small intestine and large intestine. Furthermore, by combining microbial metagenomics and host transcriptomics analyses, specific correlations were found between gut microbiota and host genes. These included a negative correlation between the TCN1 gene and Prevotella dentalis, possibly related to bacterial metabolic pathways involving vitamin B12, and a positive correlation between the BDH1 gene and Roseburia hominis, possibly because both are involved in fatty acid metabolism. These findings lay the groundwork for further exploration of the co-evolution between the microbiota and the host, specifically in relation to nutrition, metabolism, and immunity. In conclusion, we have elucidated the diversity of the gut microbiota in SPF pigs and conducted a detailed investigation into the interactions between the gut microbiota and host gene expression. These results contribute to our understanding of the intricate dynamics between the gut microbiota and the host, offering important references for advancements in life science research, bioproduct production, and sustainable development in animal husbandry.

Warm Temperature Increments Strengthen the Crosstalk between Roots and Soil in the Rhizosphere of Soybean Seedlings.

The plant rhizosphere underlies the crosstalk between plant and soil and has a crucial role in plant growth and development under various environments. We examined the effect of temperature rise on the rhizosphere environment of soybean roots to clarify the rhizosphere crosstalk between roots and soil in response to warm temperature rises in a global warming background. The in situ results of root enzyme activity revealed that soybean roots secrete ß-glucosidase, and enzyme spectrum imaging demonstrated different enzymatic activities under different temperature environments. The soil enzyme kinetics results showed that soil enzymatic activity increased with increasing temperature, and soybean rhizosphere soil enzymatic activity was higher than that of non-rhizosphere soil. Rhizosphere soil and non-rhizosphere soil showed that the dominant bacterial phylum in soybean rhizosphere soil was Acidobacteria, and the dominant bacterial genus was JG30-KF-AS9. Compared with non-rhizosphere soil, rhizosphere soil was more nutrient-rich, and root secretions provided abundant carbon sources and other nutrients for soil microorganisms in the rhizosphere. Rhizosphere microorganisms affect plant growth by influencing the decomposition of soil organic carbon. The organic carbon content of rhizosphere soil was higher than that of non-rhizosphere soil under high temperatures.

The Dissection of Nitrogen Response Traits Using Drone Phenotyping and Dynamic Phenotypic Analysis to Explore N Responsiveness and Associated Genetic Loci in Wheat.

Inefficient nitrogen (N) utilization in agricultural production has led to many negative impacts such as excessive use of N fertilizers, redundant plant growth, greenhouse gases, long-lasting toxicity in ecosystem, and even effect on human health, indicating the importance to optimize N applications in cropping systems. Here, we present a multiseasonal study that focused on measuring phenotypic changes in wheat plants when they were responding to different N treatments under field conditions. Powered by drone-based aerial phenotyping and the AirMeasurer platform, we first quantified 6 N response-related traits as targets using plot-based morphological, spectral, and textural signals collected from 54 winter wheat varieties. Then, we developed dynamic phenotypic analysis using curve fitting to establish profile curves of the traits during the season, which enabled us to compute static phenotypes at key growth stages and dynamic phenotypes (i.e., phenotypic changes) during N response. After that, we combine 12 yield production and N-utilization indices manually measured to produce N efficiency comprehensive scores (NECS), based on which we classified the varieties into 4 N responsiveness (i.e., N-dependent yield increase) groups. The NECS ranking facilitated us to establish a tailored machine learning model for N responsiveness-related varietal classification just using N-response phenotypes with high accuracies. Finally, we employed the Wheat55K SNP Array to map single-nucleotide polymorphisms using N response-related static and dynamic phenotypes, helping us explore genetic components underlying N responsiveness in wheat. In summary, we believe that our work demonstrates valuable advances in N response-related plant research, which could have major implications for improving N sustainability in wheat breeding and production.

Pleiotropic Effect of the compactum Gene and Its Combined Effects with Other Loci for Spike and Grain-Related Traits in Wheat.

Club wheat (Triticum aestivum ssp. compactum) with a distinctly compact spike morphology was conditioned by the dominant compactum (C) locus on chromosome 2D and resulted in a redistribution of spike yield components. The disclosure of the genetic basis of club wheat was a prerequisite for the development of widely adapted, agronomically competitive club wheat cultivars. In this study, we used a recombinant inbred line population derived from a cross between club wheat Hiller and modern cultivar Yangmai 158 to construct a genetic linkage map and identify quantitative trait loci associated with 15 morphological traits. The club allele acted in a semi-dominant manner and the C gene was mapped to 370.12-406.29 Mb physical region on the long arm of 2D. Apart from compact spikes, C exhibited a pleiotropic effect on ten other agronomic traits, including plant height, three spike-related traits and six grain-related traits. The compact spike phenotype was correlated with decreased grain size and weight, but with an increase in floret fertility and grain number. These pleiotropic effects make club wheat have compatible spike weight with a normal spike from common wheat. The genetic effects of various gene combinations of C with four yield-related genes, including Ppd-D1, Vrn-D3, Rht-B1b and Rht8, were evaluated. C had no epistatic interaction with any of these genes, indicating that their combinations would have an additive effect on other agronomically important traits. Our research provided a theoretical foundation for the potentially effective deployment of C gene into modern breeding varieties in combination with other favorable alleles.