Overexpression of GmPHR1 Promotes Soybean Yield through Global Regulation of Nutrient Acquisition and Root Development.

MYB-CC transcription factors (TFs) are essential for plant growth and development. Members of the MYB-CC subfamily with long N terminal domains, such as phosphate starvation response 1 (PHR1) or PHR1-like TFs, have well documented functions, while those with short N terminal domains remain less understood. In this study, we identified a nodule specific MYB-CC transcription factor 1 (GmPHR1) in soybean that is different from other canonical PHR family genes in that GmPHR1 harbors a short N terminal ahead of its MYB-CC domain and was highly induced by rhizobium infection. The overexpression of GmPHR1 dramatically increased the ratio of deformed root hairs, enhanced subsequent soybean nodulation, and promoted soybean growth in pot experiments. The growth promotion effects of GmPHR1 overexpression were further demonstrated in field trails in which two GmPHR1-OE lines yielded 10.78% and 8.19% more than the wild type line. Transcriptome analysis suggested that GmPHR1 overexpression led to global reprogramming, with 749 genes upregulated and 279 genes downregulated, especially for genes involved in MYB transcription factor activities, root growth, and nutrient acquisition. Taken together, we conclude that GmPHR1 is a key gene involved in the global regulation of nodulation, root growth, and nutrient acquisition in soybeans, and is thus a promising candidate gene to target for soybean yield enhancement.

Effects of pruning on mineral nutrients and untargeted metabolites in fresh leaves of Camellia sinensis cv. Shuixian.

Pruning is an important strategy for increasing tea production. However, the effects of pruning on tea quality are not well understood. In this study, tea leaves were collected from Wuyi Mountain for both ionomic and metabolomic analyses. A total of 1962 and 1188 fresh tea leaves were respectively collected from pruned and unpruned tea plants sampled across 350 tea plantations. Ionomic profiles of fresh tea leaves varied significantly between pruned and unpruned sources. For tea plants, pruning was tied to decreases in the concentrations of mobile elements, such as nitrogen (N), phosphorus (P), potassium (K) and magnesium (Mg), and dramatic increases in the concentrations of the immobile ions calcium (Ca), aluminum (Al), manganese (Mn), boron (B) and cobalt (Co). Clustering and heatmap analysis showed that pruning also affected tea leaf metabolism. Among 85 metabolites that were significantly impacted by pruning, 30 were identified through random forest analysis as characteristic differential metabolites with a prediction rate of 86.21%. Redundancy analysis showed that pruning effects on mineral nutrient concentrations accounted for 25.54% of the variation in characteristic metabolites between treatments, with the highest contributions of 6.64% and 3.69% coming from Ca and Mg, respectively. In correlation network analysis, Ca and Mg both exhibited close, though opposing correlations with six key metabolites, including key quality indicators 1,3-dicaffeoylquinic acid and 2-O-caffeoyl arbutin. In summary, large scale sampling over hundreds of tea plantations demonstrated that pruning affects tea quality, mainly through influences on leaf mineral composition, with Ca and Mg playing large roles. These results may provide a solid scientific basis for improved management of high-quality tea plantations.

Directed Accumulation of Nitrogen Metabolites through Processing Endows Wuyi Rock Tea with Singular Qualities.

The execution of specific processing protocols endows Wuyi rock tea with distinctive qualities produced through signature metabolic processes. In this work, tea leaves were collected before and after each of three processing stages for both targeted and untargeted metabolomic analysis. Metabolic profiles of processing stages through each processing stage of rotation, pan-firing and roasting were studied. Overall, 614 metabolites were significantly altered, predominantly through nitrogen- enriching (N) pathways. Roasting led to the enrichment of 342 N metabolites, including 34 lipids, 17 organic acids, 32 alkaloids and 25 amino acids, as well as secondary derivatives beneficial for tea quality. This distinctive shift towards enrichment of N metabolites strongly supports concluding that this directed accumulation of N metabolites is how each of the three processing stages endows Wuyi rock tea with singular quality.

Genomic basis of geographical adaptation to soil nitrogen in rice.

The intensive application of inorganic nitrogen underlies marked increases in crop production, but imposes detrimental effects on ecosystems1,2: it is therefore crucial for future sustainable agriculture to improve the nitrogen-use efficiency of crop plants. Here we report the genetic basis of nitrogen-use efficiency associated with adaptation to local soils in rice (Oryza sativa L.). Using a panel of diverse rice germplasm collected from different ecogeographical regions, we performed a genome-wide association study on the tillering response to nitrogen-the trait that is most closely correlated with nitrogen-use efficiency in rice-and identified OsTCP19 as a modulator of this tillering response through its transcriptional response to nitrogen and its targeting to the tiller-promoting gene DWARF AND LOW-TILLERING (DLT)3,4. A 29-bp insertion and/or deletion in the OsTCP19 promoter confers a differential transcriptional response and variation in the tillering response to nitrogen among rice varieties. The allele of OsTCP19 associated with a high tillering response to nitrogen is prevalent in wild rice populations, but has largely been lost in modern cultivars: this loss correlates with increased local soil nitrogen content, which suggests that it might have contributed to geographical adaptation in rice. Introgression of the allele associated with a high tillering response into modern rice cultivars boosts grain yield and nitrogen-use efficiency under low or moderate levels of nitrogen, which demonstrates substantial potential for rice breeding and the amelioration of negative environment effects by reducing the application of nitrogen to crops.

Genetic analysis and fine mapping of phosphorus efficiency locus 1 (PE1) in soybean.

KEY MESSAGE: PE1 is a valuable locus synergistically regulating both P acquisition and utilization efficiency. Phosphorus (P) is required for crop production, particularly for soybean, due to its high protein and oil contents, and large demands for P in biological nitrogen fixation. Therefore, enhancing P efficiency is a practical and important target for soybean-breeding programs; however, the genetic mechanisms are still unclear. Previously, we identified a phosphorus efficiency locus 1 (PE1) in soybean through field evaluation. Here, fine mapping of PE1 was conducted in field using an expanded RIL population containing 168 F9:11 families derived from the same parents, BX10 and BD2. A high-resolution genetic map covering a 67.39 cM genetic region in a ~ 20.1 M physical region was constructed using 117 bin markers from chromosome 11, and scaffolds-21 and -32. The results revealed that PE1 was comprised of 15 QTLs for 11 of 18 tested traits, all of which could be detected under both P-deficient and P-sufficient conditions. Through map-based cloning, PE1 was further delimited to a 200-kb region located on scaffold-32, where 16 candidate genes were predicted for the PE1 locus. A set of NILs were also evaluated in P-deficient field conditions, with the results that P content and grain yield were 27.9% and 74.8% higher, respectively, and 25.4% more P was allocated to reproductive tissues in #pe1 than in #PE1 plants. The results herein suggest that PE1 is a valuable locus underlying both P absorption and utilization efficiency, which may be directly applicable in breeding programs seeking to develop elite P-efficient soybean varieties.

Genetic Analysis and Mapping of QTLs for Soybean Biological Nitrogen Fixation Traits Under Varied Field Conditions.

Soybean is an important economic and green manure crop that is widely used in intercropping and rotation systems due to its high biological nitrogen fixation (BNF) capacity and the resulting reduction in N fertilization. However, the genetic mechanisms underlying soybean BNF are largely unknown. Here, two soybean parent genotypes contrasting in BNF traits and 168 F9:11 recombinant inbred lines (RILs) were evaluated under four conditions in the field. The parent FC1 always produced more big nodules, yet fewer nodules in total than the parent FC2 in the field. Furthermore, nodulation in FC1 was more responsive to environmental changes than that in FC2. Broad-sense heritability (h2 b ) for all BNF traits varied from 0.48 to 0.87, which suggests that variation in the observed BNF traits was primarily determined by genotype. Moreover, two new QTLs for BNF traits, qBNF-16 and qBNF-17, were identified in this study. The qBNF-16 locus was detected under all of the four tested conditions, where it explained 15.9-59.0% of phenotypic variation with LOD values of 6.31-32.5. Meanwhile qBNF-17 explained 12.6-18.6% of observed variation with LOD values of 4.93-7.51. Genotype group analysis indicated that the FC1 genotype of qBNF-16 primarily affected nodule size (NS), while the FC2 genotype of qBNF-16 promoted nodule number (NN). On the other hand, the FC1 genotype of qBNF-17 influenced NN and the FC2 genotype of qBNF-17 impacted NS. The results on the whole suggest that these two QTLs might be valuable markers for breeding elite soybean varieties with high BNF capacities.

Genotype and rhizobium inoculation modulate the assembly of soybean rhizobacterial communities.

Rhizosphere bacterial communities are vital for plants, yet the composition of rhizobacterial communities and the complex interactions between roots and microbiota, or between microbiota, are largely unknown. In this study, we investigated the structure and composition of rhizobacterial communities in two soybean cultivars and their recombinant inbred lines contrasting in nodulation through 16S rRNA amplicon sequencing in two years of field trials. Our results demonstrate that soybean plants are able to select microbes from bulk soils at the taxonomic and functional level. Soybean genotype significantly influenced the structure of rhizobacterial communities and resulted in dramatically different co-occurrence networks of rhizobacterial communities between different genotypes of soybean plants. Furthermore, the introduction of exogenous rhizobia through inoculation altered soybean rhizobacterial communities in genotype-dependent manner. Rhizobium inoculation not only stimulated the proliferation of potential beneficial microbes but also increased connections in rhizobacterial networks and changed the hub microbes, all of which led to the association of distinctive bacterial communities. Taken together, we demonstrated that the assembly of soybean rhizobacterial communities was determined by both genotype and the introduction of exogenous rhizobia. These findings bolster the feasibility of root microbiome engineering through inoculation of specific microbial constituents.

Rhizobium Inoculation Drives the Shifting of Rhizosphere Fungal Community in a Host Genotype Dependent Manner.

Rhizosphere microorganisms play important roles in plant health and nutrition, and interactions among plants and microorganisms are important for establishment of root microbiomes. As yet, plant-microbe and microbe-microbe interactions in the rhizosphere remain largely mysterious. In this study, rhizosphere fungal community structure was first studied in a field experiment with two soybean cultivars contrasting in nodulation grown in two rhizobium inoculation treatments. Following this, recombinant inbred lines (RILs) contrasting in markers across three QTLs for biological nitrogen fixation (BNF) were evaluated for effects of genotype and rhizobium inoculation to the rhizosphere fungal community as assessed using ITS1 amplicon sequencing. The soybean plants tested herein not only hosted rhizosphere fungal communities that were distinct from bulk soils, but also specifically recruited and enriched Cladosporium from bulk soils. The resulting rhizosphere fungal communities varied among soybean genotypes, as well as, between rhizobium inoculation treatments. Besides, Cladosporium were mostly enriched in the rhizospheres of soybean genotypes carrying two or three favorable BNF QTLs, suggesting a close association between soybean traits associated with nodulation and those affecting the rhizosphere fungal community. This inference was bolstered by the observation that introduction of exogenous rhizobia significantly altered rhizosphere fungal communities to the point that these communities could be distinguished based on the combination of soybean genotype and whether exogenous rhizobia was applied. Interestingly, grouping of host plants by BNF QTLs also distinguished fungal community responses to rhizobium inoculation. Taken together, these results reveal that complex cross-kingdom interactions exist among host plants, symbiotic N2 fixing bacteria and fungal communities in the soybean rhizosphere.

Genome-wide association study dissects yield components associated with low-phosphorus stress tolerance in maize.

KEY MESSAGE: Phosphorus deficiency in soil is a worldwide constraint threatening maize production. Through a genome-wide association study, we identified molecular markers and associated candidate genes and molecular pathways for low-phosphorus stress tolerance. Phosphorus deficiency in soils will severely affect maize (Zea mays L.) growth and development, thus decreasing the final yield. Deciphering the genetic basis of yield-related traits can benefit our understanding of maize tolerance to low-phosphorus stress. However, considering that yield-related traits should be evaluated under field condition with large populations rather than under hydroponic condition at a single-plant level, searching for appropriate field experimental sites and target traits for low-phosphorus stress tolerance is still very challenging. In this study, a genome-wide association analysis using two natural populations was performed to detect candidate genes in response to low-phosphorus stress at two experimental sites representative of different climate and soil types. In total, 259 candidate genes were identified and these candidate genes are mainly involved in four major pathways: transcriptional regulation, reactive oxygen scavenging, hormone regulation, and remodeling of cell wall. Among these candidate genes, 98 showed differential expression by transcriptome data. Based on a haplotype analysis of grain number under phosphorus deficiency condition, the positive haplotypes with favorable alleles across five loci increased grain number by 42% than those without favorable alleles. For further verifying the feasibility of genomic selection for improving maize low-phosphorus tolerance, we also validated the predictive ability of five genomic selection methods and suggested that moderate-density SNPs were sufficient to make accurate predictions for low-phosphorus tolerance traits. All these results will facilitate elucidating genetic basis of maize tolerance to low-phosphorus stress and improving marker-assisted selection efficiency in breeding process.

Large-scale evaluation of maize germplasm for low-phosphorus tolerance.

Low-phosphorus (LP) stress is a global problem for maize production and has been exacerbated by breeding activities that have reduced the genetic diversity of maize. Although LP tolerance in maize has been previously evaluated, the evaluations were generally performed with only a small number of accessions or with samples collected from a limited area. In this research, 826 maize accessions (including 580 tropical/subtropical accessions and 246 temperate accessions) were evaluated for LP tolerance under field conditions in 2011 and 2012. Plant height (PH) and leaf number were measured at three growth stages. The normalized difference vegetation index (NDVI) and fresh ear weight (FEW) were also measured. Genetic correlation analysis revealed that FEW and NDVI were strongly correlated with PH, especially at later stages. LP-tolerant and -sensitive accessions were selected based on the relative trait values of all traits using principal component analysis, and all the 14 traits of the tolerant maize accessions showed less reduction than the sensitive accessions under LP conditions. LP tolerance was strongly correlated with agronomic performance under LP stress conditions, and both criteria could be used for genetic analysis and breeding of LP tolerance. Temperate accessions showed slightly better LP tolerance than tropical/subtropical ones, although more tolerant accessions were identified from tropical/subtropical accessions, which could be contributed by their larger sample size. This large-scale evaluation provides useful information, LP-tolerant germplasm resources and evaluation protocol for genetic analysis and developing maize varieties for LP tolerance.

Root interactions in a maize/soybean intercropping system control soybean soil-borne disease, red crown rot.

BACKGROUND: Within-field multiple crop species intercropping is well documented and used for disease control, but the underlying mechanisms are still unclear. As roots are the primary organ for perceiving signals in the soil from neighboring plants, root behavior may play an important role in soil-borne disease control. PRINCIPAL FINDINGS: In two years of field experiments, maize/soybean intercropping suppressed the occurrence of soybean red crown rot, a severe soil-borne disease caused by Cylindrocladium parasiticum (C. parasiticum). The suppressive effects decreased with increasing distance between intercropped plants under both low P and high P supply, suggesting that root interactions play a significant role independent of nutrient status. Further detailed quantitative studies revealed that the diversity and intensity of root interactions altered the expression of important soybean PR genes, as well as, the activity of corresponding enzymes in both P treatments. Furthermore, 5 phenolic acids were detected in root exudates of maize/soybean intercropped plants. Among these phenolic acids, cinnamic acid was released in significantly greater concentrations when intercropped maize with soybean compared to either crop grown in monoculture, and this spike in cinnamic acid was found dramatically constrain C. parasiticum growth in vitro. CONCLUSIONS: To the best of our knowledge, this study is the first report to demonstrate that intercropping with maize can promote resistance in soybean to red crown rot in a root-dependent manner. This supports the point that intercropping may be an efficient ecological strategy to control soil-borne plant disease and should be incorporated in sustainable agricultural management practices.