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Soil microbes are crucial in shaping the root-associated microbial communities. In this study, we analyzed the effect of the soil–root niche gradient on the diversity, composition, and assembly of the bacterial community and co-occurrence network of two cotton varieties. The results revealed that the bacterial communities in cotton soil–root compartment niches exhibited a skewed species abundance distribution, dominated by abundant taxa showing a strong spatial specificity. The assembly processes of the rhizosphere bacterial communities were mainly driven by stochastic processes, dominated by the enrichment pattern and supplemented by the depletion pattern to recruit bacteria from the bulk soil, resulting in a more stable bacterial community. The assembly processes of the endosphere bacterial communities were determined by processes dominated by the depletion pattern and supplemented by the enrichment pattern to recruit species from the rhizosphere, resulting in a decrease in the stability and complexity of the community co-occurrence network. The compartment niche shaped the diversity of the bacterial communities, and the cotton variety genotype was an important source of diversity in bacterial communities within the compartment niche. We suggest that the moderate taxa contribute to significantly more changes in the diversity of the bacterial community than the rare and abundant taxa during the succession of bacterial communities in the cotton root–soil continuum.

Grain size is a key trait associated with bread wheat yield. It is also the most frequently selected trait during domestication. After the phenotypic characterization of 768 bread wheat accessions in three plots for at least two years, the present study shows that the improved variety showed significantly higher grain size but lower grain protein content than the landrace. Using 55K SNP assay genotyping and large-scale phenotyping population and GWAS data, we identified 5, 6, 6, and 6 QTLs associated with grain length, grain weight, grain area, and thousand grain weight, respectively. Seven of the 23 QTLs showed common association within different locations or years. Most significantly, the key locus associated with grain length, qGL-2D, showed the highest association after years of multi-plot testing. Haplotype and evolution analysis indicated that the superior allele of qGL-2D was mainly hidden in the improved variety rather than in landrace, which may contribute to the significant difference in grain length. A comprehensive analysis of transcriptome and homolog showed that TraesCS2D02G414800 could be the most likely candidate gene for qGL-2D. Overall, this study presents several reliable grain size QTLs and candidate gene for grain length associated with bread wheat yield.

Abstract Background Phosphorus (P) is an important in ensuring plant morphogenesis and grain quality, therefore an efficient root system is crucial for P-uptake. Identification of useful loci for root morphological and P uptake related traits at seedling stage is important for wheat breeding. The aims of this study were to evaluate phenotypic diversity of Yangmai 16/Zhongmai 895 derived doubled haploid (DH) population for root system architecture (RSA) and biomass related traits (BRT) in different P treatments at seedling stage using hydroponic culture, and to identify QTL using 660 K SNP array based high-density genetic map. Results All traits showed significant variations among the DH lines with high heritabilities (0.76 to 0.91) and high correlations (r = 0.59 to 0.98) among all traits. Inclusive composite interval mapping (ICIM) identified 34 QTL with 4.64–20.41% of the phenotypic variances individually, and the log of odds (LOD) values ranging from 2.59 to 10.43. Seven QTL clusters (C1 to C7) were mapped on chromosomes 3DL, 4BS, 4DS, 6BL, 7AS, 7AL and 7BL, cluster C5 on chromosome 7AS (AX-109955164 - AX-109445593) with pleiotropic effect played key role in modulating root length (RL), root tips number (RTN) and root surface area (ROSA) under low P condition, with the favorable allele from Zhongmai 895. Conclusions This study carried out an imaging pipeline-based rapid phenotyping of RSA and BRT traits in hydroponic culture. It is an efficient approach for screening of large populations under different nutrient conditions. Four QTL on chromosomes 6BL (2) and 7AL (2) identified in low P treatment showed positive additive effects contributed by Zhongmai 895, indicating that Zhongmai 895 could be used as parent for P-deficient breeding. The most stable QTL QRRS.caas-4DS for ratio of root to shoot dry weight (RRS) harbored the stable genetic region with high phenotypic effect, and QTL clusters on 7A might be used for speedy selection of genotypes for P-uptake. SNPs closely linked to QTLs and clusters could be used to improve nutrient-use efficiency.

Abstract Silicon plays a vital role in plant growth. However, molecular mechanisms in response to silicon have not previously been studied in wheat. In this study, we used RNA-seq technology to identify differentially expressed genes (DEGs) in wheat seedlings treated with silicon. Results showed that many wheat genes responded to silicon treatment, including 3057 DEGs, of which 6.25% (191/3057) were predicted transcription factors (TFs). Approximately 14.67% (28 out of 191) of the differentially expressed TFs belonged to the MYB TF family. Gene ontology (GO) enrichment showed that the highly enriched DEGs were responsible for secondary biosynthetic processes. According to KEGG pathway analysis, the DEGs were related to chaperones and folding catalysts, phenylpropanoid biosynthesis, and protein processing in the endoplasmic reticulum. Moreover, 411 R2R3-MYB TFs were identified in the wheat genome, all of which were classified into 15 groups and accordingly named S1–S15. Among them, 28 were down-regulated under silicon treatment. This study revealed the essential role of MYB TFs in the silicon response mechanism of plants, and provides important genetic resources for breeding silicon-tolerant wheat.

Background YABBY is a plant-specific transcription factor (TF) that belongs to the zinc finger protein superfamily and is composed of a C2–C2 domain at the N-terminus and a YABBY domain at the C-terminus. It plays a role in plant development and growth. Methods In this study, 20 YABBY TFs were identified in the wheat genome. Phylogenetic relationships, collinearity relationships, gene structures, conserved motifs, and expression patterns were analyzed. Results Twenty TaYABBY TFs were distributed unevenly on 15 chromosomes. Collinearity analysis showed that these genes have a close relationship with monocot plants. The phylogenetic tree of wheat YABBYs classified these TaYABBYs into FIL, YAB2, INO, and CRC clades. Gene structure and conserved motif analyses showed that they share similar components in the same clades. Expression profile analysis showed that many TaYABBY genes have high expression levels in leaf tissues and are regulated by abiotic stresses, especially salt stress. Our results provide a basis for further functional characterization of the YABBY gene family.

The Ethylene-Response Factor (ERF) subfamily transcription factors (TFs) belong to the APETALA2/Ethylene-Responsive Factor (AP2/ERF) superfamily and play a vital role in plant growth and development. However, identification and analysis of the ERF subfamily genes in maize have not yet been performed at genome-wide level. In this study, a total of 76 ERF subfamily TFs were identified and were found to be unevenly distributed on the maize chromosomes. These maize ERF (ZmERF) TFs were classified into six groups, namely groups B1 to B6, based on phylogenetic analysis. Synteny analysis showed that 50, 54, and 58 of the ZmERF genes were orthologous to those in rice, Brachypodium, and Sorghum, respectively. Cis-element analysis showed that elements related to plant growth and development, hormones, and abiotic stress were identified in the promoter region of ZmERF genes. Expression profiles suggested that ZmERF genes might participate in plant development and in response to salinity and drought stresses. Our findings lay a foundation and provide clues for understanding the biological functions of ERF TFs in maize.