3D genome organization and its study in livestock breeding

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.

Effects of gibberellin priming on seedling emergence and transcripts involved in mesocotyl elongation in rice under deep direct-seeding conditions

Mesocotyl elongation is a key trait influencing seedling emergence and establishment in direct-seeding rice cultivation.The phytohormone gibberellin(GA)has positive effects on mesocotyl elongation in rice.However,the physiological and molecular basis underlying the regulation of mesocotyl elongation mediated by GA priming under deep-sowing conditions remains largely unclear.In the present study,we performed a physiological and comprehensive transcriptomic analysis of the function of GA priming in mesocotyl elongation and seedling emergence using a direct-seeding japonica rice cultivar ZH10 at a5-cm sowing depth.Physiological experiments indicated that GA priming significantly improved rice seedling emergence by increasing the activity of starch-metabolizing enzymes and compatible solute content to supply the energy essential for subsequent development.Transcriptomic analysis revealed 7074 differentially expressed genes(false discovery rate of<0.05,|log2(fold change)|of≥1)after GA priming.Furthermore,gene ontology(GO)and Kyoto encyclopedia of genes and genomes(KEGG)enrichment analyses revealed that genes associated with transcriptional regulation,plant hormone biosynthesis or signaling,and starch and sucrose metabolism were critical for GA-mediated promotion of rice mesocotyl elongation.Further analyses showed that the expression of the transcription factor(TF)genes(v-myb avian myeloblastosis viral oncogene homolog(MYB)alternative splicing 1(MYBAS1),phytochrome-interacting factors 1(PIF1),Oryza sativa teosinte branched 1/cycloidea/proliferating cell factor 5(Os TCP5),slender 1(SLN1),and mini zinc finger 1(MIF1)),plant hormone biosynthesis or signaling genes(brassinazole-resistant 1(BZR1),ent-kaurenoic acid oxidase-like(KAO),GRETCHEN HAGEN 3.2(GH3.2),and small auxin up RNA 36(SAUR36)),and starch and sucrose metabolism genes(α-amylases(AMY2 A and AMY1.4))was highly correlated with the mesocotyl elongation and deep-sowing tolerance response.These results enhance our understanding of how nutrient metabolism-related substances and genes regulate rice mesocotyl elongation.This may facilitate future studies on related genes and the development of novel rice varieties tolerant to deep sowing.