^{Eukaryotic genomes are hierarchically packaged into cell nucleus, affecting gene regulation.  The genome is organized into multiscale structural units, including chromosome territories, compartments, topologically associating domains (TADs), and DNA loops.  The identification of these hierarchical structures has benefited from the development of experimental approaches, such as 3C-based methods (Hi-C, ChIA-PET, etc.), imaging tools (2D-FISH, 3D-FISH, Cryo-FISH, etc.) and ligation-free methods (GAM, SPRITE, etc.).  In recent two decades, numerous studies have shown that the 3D organization of genome plays essential roles in multiple cellular processes via various mechanisms, such as regulating enhancer activity and promoter-enhancer interactions.  However, there are relatively few studies about the 3D genome in livestock species.  Therefore, studies for exploring the function of 3D genomes in livestock are urgently needed to provide a more comprehensive understanding of potential relationships between the genome and production traits.  In this review, we summarize the recent advances of 3D genomics and its biological functions in human and mouse studies, drawing inspiration to explore the 3D genomics of livestock species.  We then mainly focus on the biological functions of 3D genome organization in muscle development and its implications in animal breeding.}

In the postharvest processing of tea leaves, withering is the first indispensable manufacturing process which produces the mellow, umami and sweet taste of white tea.  In this study, we aimed to determine the dynamic changes of the main metabolites and clarify the key differentially expressed genes (DEGs) involved in forming the characteristic taste of white tea during withering.  Phytochemical analyses revealed that the contents of total catechins and starch decreased continuously, whereas the contents of theaflavin, γ-aminobutyric acid (GABA), maltose, and soluble sugars increased significantly during withering (from 0–48 h).  Meanwhile, the elevation of α-amylase (AMY), β-amylase (BAM), total amylase, and glutamate decarboxylase (GAD) activities may be correlated with the accumulation of GABA and maltose.  By transcriptome sequencing, we detected 9 707, 15 921, 17 353, and 17 538 DEGs at 12, 24, 36, and 48 h of the withering process, respectively, compared with 0 h sample (fresh leaves).  The transcript levels of most of the DEGs involved in catechin biosynthesis were significantly inhibited, whereas those involved in catechin oxidation were significantly up-regulated, which could be correlated to a decrease in catechin content and an increase in theaflavin content.  The DEGs involved in GABA biosynthesis were considerably up-regulated, and the down-regulation of SPMS could reduce the competition for converting spermidine to GABA.  The up-regulation of the AMY and BAM genes could trigger starch degradation, resulting in the increase of soluble sugar content.  These results provide new insights into the importance of the withering process to the characteristic taste of white tea.

CCCH (C3H) Zinc finger (Znf) transcription factors (TFs), as a novel type of Znf gene, regulate the expression of genes by binding to their mRNAs and play important roles in plant growth and development and abiotic stress resistance.  Longan (Dimocarpous longan) is a tropical/subtropical fruit tree of great economic importance in Southeast Asia.  However, genomic information on C3H and their functions in longan are still unknown.  In this study, a comprehensive analysis of the longan C3H (DlC3H) gene family was carried out.  A total of 49 DlC3H genes in three clades were identified from the longan genome database.  Characteristics of the genes were analyzed with respect to gene structure, motif composition, phylogenetic tree and potential functions.  The analysis of alternative splicing (AS) events suggested that AS events in DlC3H genes were related to the transformation from longan non-embryonic to embryonic cultures.  Promoter analysis indicated that most of the DlC3H genes included cis-acting elements associated with hormones and stresses responses.  Quantitative real-time PCR (qRT-PCR) analysis indicated that 26 of the 49 DlC3Hs, which possess methyl jasmonate (MeJA) and abscisic acid (ABA) responsive cis-acting elements, showed differential expression patterns under treatment with ABA, MeJA and their endogenous inhibitors, suggesting that DlC3Hs might be involved in the ABA and MeJA signaling pathways.  The expression profiles of 17 of the 49 DlC3Hs in non-embryonic callus and three tissues of embryonic cultures showed that only five of the 17 DlC3Hs had the same expression trends as the FPKM trends in transcriptome data; the expression levels of DlC3H07/14/16/36/49 in embryogenic callus and DlC3H04/38 in globular embryos were high, suggesting that they have different functions in embryonic development.  Further, we verified that DlC3H01/03/05/11/19/39 were regulated by sRNAs by a modified 5´ RLM-RACE method.  This study provides the first systematic analysis of C3H genes in longan, and found that C3H genes may be involved in hormone and stress responses, and somatic embryogenesis.  Our preliminary investigation may provide clues to further studies on the characteristics and functions of this family in longan.

Synthetic hexaploid wheat (SHW), possesses numerous genes for drought that can help breeding for drought-tolerant wheat varieties.  We evaluated 10 root traits at seedling stage in 111 F₉ recombinant inbred lines derived from a F₂ population of a SHW line (SHW-L1) and a common wheat line, under normal (NC) and polyethylene glycol-simulated drought stress conditions (DC).  We mapped quantitative trait loci (QTLs) for root traits using an enriched high-density genetic map containing 120 370 single nucleotide polymorphisms (SNPs), 733 diversity arrays technology markers (DArT) and 119 simple sequence repeats (SSRs).  With four replicates per treatment, we identified 19 QTLs for root traits under NC and DC, and 12 of them could be consistently detected with three or four replicates.  Two novel QTLs for root fresh weight and root diameter under NC explained 9 and 15.7% of the phenotypic variation respectively, and six novel QTLs for root fresh weight, the ratio of root water loss, total root surface area, number of root tips, and number of root forks under DC explained 8.5–14% of the phenotypic variation.  Here seven of eight novel QTLs could be consistently detected with more than three replicates.  Results provide essential information for fine-mapping QTLs related to drought tolerance that will facilitate breeding drought-tolerant wheat cultivars.

MicroRNAs (miRNAs) are endogenous non-protein-coding small RNAs that play crucial and versatile regulatory roles in plants.  Using a computational identification method, we identified 55 conserved miRNAs in tea (Camellia sinensis) by aligning miRNA sequences of different plant species with the transcriptome library of tea strain 1005.  We then used quantitative real-time PCR (qRT-PCR) to analyze the expression of 31 identified miRNAs in tea leaves of different ages, thereby verifying the existence of these miRNAs and confirming the reliability of the computational identification method.  We predicted which miRNAs were involved in catechin synthesis using psRNAtarget Software based on conserved miRNAs and catechin synthesis pathway-related genes.  Then, we used RNA ligase-mediated rapid amplification of cDNA ends (RLM-RACE) to obtain seven miRNAs cleaving eight catechin synthesis pathway-related genes including chalcone synthase (CHS), chalcone isomerase (CHI), dihydroflavonol 4-reductase (DFR), anthocyanidin reductase (ANR), leucoanthocyanidin reductase (LAR), and flavanone 3-hydroxylase (F3H).  An expression analysis of miRNAs and target genes revealed that miR529d and miR156g-3p were negatively correlated with their targets CHI and F3H, respectively.  The expression of other miRNAs was not significantly related to their target genes in the catechin synthesis pathway.  The RLM-RACE results suggest that catechin synthesis is regulated by miRNAs that can cleave genes involved in catechin synthesis. 

The increasing atmospheric carbon dioxide concentration, caused by fossil fuel combustion and deforestation, plays an important role in plant growth and development. Wheat, as a major staple crop, adapts to climate change by tuning its inherent molecular mechanism, which is not well understood. The present study employed the RNA-Seq method to generate transcriptome profiles of the wheat Norin 10 in response to elevated CO₂ in comparison with ambient CO₂. The 10 895 787 high-quality clean reads of Norin 10 were assembled de novo using Trinity (without a reference genome) resulting in a total of 18 206 candidate transcripts with significant BLAST matches. GO enrichment analysis of Norin 10 at different CO₂ concentrations showed that some functional genes related to plastids, precursor metabolites, and energy, thylakoid and photosynthesis were apparently enriched at elevated CO₂ (550 μmol mol^–1) in contrast to that at ambient CO₂ (400 μmol mol–1); these findings were further confirmed by RT-PCR analysis. The findings demonstrated the specific effects of elevated CO₂ during long-term period in free air CO2 enrichment (FACE) on transcriptome response of the high yielding wheat variety, Norin 10, which has a large spike.