Molecular Breeding Research Articles

The transcription factor REM16a promotes flowering time in soybean by activating flowering-related genes.

The flowering time of soybean [Glycine max (L.) Merr.] is extremely sensitive to photoperiod, which importantly influences its yield potential and restricts the geographical range of soybean cultivars to specific latitudes. Molecular breeding to modulate flowering time and reduce sensitivity to day length is an effective approach to enhance the adaptability and productivity of soybean. Here, we characterized reproductive meristem 16a (GmREM16a), a member of the AP2/B3-like transcription factor family. The GmREM16a protein contains 2 B3 domains, and the expression of its encoding gene is responsive to photoperiod and circadian rhythm. The overexpression of GmREM16a in soybean accelerated flowering by regulating the expression of flowering-related genes. The GmREM16a protein was able to directly bind to the promoters of GmSOC1, GmFT2a, and GmFT5a and upregulate their expression. Yeast two-hybrid screening revealed that GmCSN5 interacts with GmREM16a. GmCSN5 is the fifth subunit of the COP9 signalosome (constitutively photomorphogenic signalosome, CSN) that regulates the activity of CULLIN-RING E3 ubiquitin ligases and regulates protein degradation. Protein degradation assays in vivo and in vitro showed that GmCSN5 promotes the degradation of GmREM16a protein via the ubiquitin-proteasome pathway. Taken together, these findings indicate that the transcription factor GmREM16a promotes flowering by regulating the expression of flowering-related genes. Additionally, GmCSN5 interacts with GmREM16a to regulate its stability in soybean. The GmREM16a-GmSCN5 module may represent a pathway involved in the regulation of flowering time in soybean and is a useful genetic resource for improving the adaptability of soybean through molecular breeding approaches.

The horizontally transferred gene, CsMTAN, rewired purine traffic to build caffeine factories in tea leaves.

Purine-related metabolites are central to primary metabolic pathways in plants and serve as precursors for purine alkaloid biosynthesis in caffeinated species such as tea plants (Camellia sinensis). In this study, metabolite profiling of two tissues (young and mature leaves) was performed across 183 genetically diverse tea accessions, identifying and quantifying 10 purine alkaloid-related metabolites. Metabolite genome-wide association studies revealed 17 significant loci associated with these metabolites, including both known loci such as caffeine synthase and 16 novel loci (P < 1.05 × 10-5). Through functional annotation and in vitro enzymatic assay, we characterized 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (CsMTAN) as the causal gene underlying natural variation in adenosine and adenine content. CsMTAN can catalyze the degradation of both 5'-methylthioadenosineand S-adenosylhomocysteineto release adenine. The T → A nucleotide substitution at SNP55151898, which leads to a phenylalanine → tyrosine substitution at residue 179 (F179Y), resulted in a significant alteration of enzyme activity in vitro, as evidenced by an approximately 50% reduction in adenine abundance (P < 0.05). Transient overexpression of CsMTAN-A and CsMTAN-T in Nicotiana benthamiana both significantly increased adenine content and dramatically decreased adenosine content, providing direct evidence for the functional involvement of CsMTAN in plant purine metabolism. CsMTAN-T overexpression resulted in significantly lower adenosine level than CsMTAN-A (P < 0.05). Phylogenetic analysis across 115 species and protein structural modeling revealed a distinct evolutionary divergence between plant MTAN evolution and species phylogeny, strongly suggesting the occurrence of horizontal gene transfer events in the evolutionary history of plant MTANs. This study thus furthered our understanding of the genetics and molecular mechanisms regulating purine metabolism and purine alkaloid biosynthesis in tea plants and provided novel targets for molecular breeding and synthetic biology applications.

Optimizing the single-step model for predicting fumonisins resistance in maize hybrids accounting for the genotype-by-environment interaction

In Brazil, disease outbreaks in plant cultivars are common in tropical zones. For example, the fungus Fusarium verticillioides produces mycotoxins called fumonisins (FUMO) which are harmful to human and animal health. Besides the genetic component, the expression of this polygenic trait is regulated by interactions between genes and environmental factors (G × E). Genomic selection (GS) emerges as a promising approach to address the influence of multiple loci on resistance. We examined different manners to conduct the prediction of FUMO contamination using genomic and pedigree data, and combinations of these two via the single step model (B-matrix) which also offers the possibility of increasing training set sizes. This is the first study to apply the B-matrix approach for predicting FUMO in tropical maize breeding programs. Our research introduced a cross-validation approach to optimize the hyper-parameter w, which represents the fraction of total additive variance captured by the markers. We demonstrated the importance of selecting optimal w by environment in unbalanced datasets. A total of 13 predictive models considering General Combining Ability (GCA) and Specific Combining Ability (SCA) effects, resulted from five linear predictors and three different covariance structures including the single-step approach. Two cross-validation scenarios were considered to evaluate the model’s proficiency: CV1 simulated the prediction of completely untested hybrids, where the individuals in the validation set had no phenotypic records in the training set; and CV2 simulated the prediction of partially tested hybrids, where individuals had been evaluated in some environments but not in the target environment. Results showed that using the B-matrix in the five tested linear models increased the predictive ability compared to pedigree or genomic information. Under CV1, increasing training set sizes exhibit superior predictive accuracy. On the other hand, under CV2 the advantages of increasing the training set size are unclear and the improvements are due to better covariance structures. These insights can be applied to plant breeding programs where the GCA, SCA, and G × E interactions are of interest and pedigree information is accessible, but constraints related to genotyping costs for the entire population exist.

Molecular Mechanisms and Regulatory Factors Governing Feed Utilization Efficiency in Laying Hens: Insights for Sustainable Poultry Production and Breeding Optimization

Since the early 2000s, the poultry industry in our nation has steadily progressed towards a larger scale and increased intensification. However, the growing demand for animal-based protein, combined with significant increases in feed ingredient costs, presents substantial challenges to the advancement of egg production. The regulation of feed utilization efficiency in laying hens is a complex process, influenced by various factors including the farming environment, feed composition, microbial ecosystems, and hormonal dynamics. The feed conversion rate in laying hens not only serves as a critical indicator of agricultural productivity but also highlights the significant impact of molecular technologies in improving feed efficiency. These technological advancements have enhanced the precision and effectiveness of breeding practices while providing substantial support for optimizing feed management, improving production metrics, and promoting sustainable agricultural practices. This comprehensive synthesis of factors, regulatory pathways, and cutting-edge molecular methodologies establishes a biological framework for future breeding strategies. Notably, this review uniquely emphasizes the pivotal role of modern molecular biology techniques—such as genomic selection, transcriptomic profiling, and gene-editing tools—in decoding feed conversion efficiency (FCE), contributing to broader goals of agricultural sustainability by balancing productivity gains with eco-friendly and cost-effective egg production.

Whole-genome resequencing to investigate the genetic diversity and the molecular basis underlying key economic traits in indigenous sheep breeds adapted to hypoxic environments

Under the combined effects of long-term natural selection and artificial domestication, Tibetan sheep on the Qinghai-Tibet Plateau have evolved distinct ecotypes to survive extreme high-altitude conditions, including hypoxia, cold, and low oxygen levels. These ecotypic variations not only serve as an ideal model for studying plateau livestock adaptation but also harbor valuable genetic diversity. However, the lack of comprehensive genetic analyses on their adaptive and phenotypic traits has hindered the effective conservation and utilization of these resources. Using whole-genome resequencing, we systematically studied seven Tibetan sheep breeds, uncovering their genetic structure and diversity. Population analyses, including NJ and maximum likelihood trees, revealed clear genetic differentiation and migration patterns. Selective sweep analyses (Fst and θπ) identified hypoxia-related genes (DOCK8, IGF1R, JAK1, SLC47, TMTC2, and VPS13A) and wool color genes (TCF25, MITF, and MC1R). GWAS further detected candidate genes for body size traits (height, length, weight), enriched in cGMP-PKG, cAMP, and Hedgehog signaling pathways. Integrating GWAS and transcriptomics, we pinpointed key wool trait genes, including WNT16 (non-synonymous mutations), PRKCA, MAP3K8, MMP7, OVOL2 (intergenic SNPs), and COL7A1, KDM8, ZNF385D (intronic SNPs). Notably, HOX family transcription factors were found to critically regulate hair follicle development. These genetic markers offer promising targets for molecular breeding to enhance wool quality and adaptive traits. Our findings provide a genetic basis for understanding Tibetan sheep’s unique adaptations and production traits, supporting future breeding strategies and sustainable utilization of their genetic resources.

Transcriptomic exploration yields novel perspectives on the regulatory network underlying trichome initiation in Gossypium arboreum hypocotyl

Trichomes play a crucial role in plant stress tolerance and serve as an excellent model for studying epidermal cell differentiation. To elucidate the molecular mechanisms underlying trichome development in cotton stems, we investigated two Gossypium arboreum mutants that exhibit abnormal trichome patterns during hypocotyl growth. Based on morphological characteristics, we classified four developmental stages: preinitiation, initiation, elongation, and maturation. Comparative transcriptome profiling of epidermal cells across these stages identified differentially expressed genes (DEGs) through maSigPro analysis, which revealed that these DEGs were primarily associated with pathways involved in cell wall metabolism. Additionally, integrated weighted gene co-expression network analysis (WGCNA) and Cytoscape analyses identified 20 core regulatory genes from a total of 59 candidates linked to epidermal development. Utilizing three machine learning algorithms (SVM-RFE, Boruta, and LASSO), we consistently prioritized five key regulators: Ga02G1392 (TBR), Ga03G0474 (OMR1), Ga12G2860 (ACO1), Ga11G2117 (BBX19), and Ga12G2864 (CUE). RT-qPCR validation confirmed their stage-specific expression patterns, which were consistent with the RNA-Seq data. Our study establishes a comprehensive framework for research on cotton trichomes and identifies critical genetic components governing epidermal hair development, thereby providing new insights for the molecular breeding of stress-resistant cotton varieties.

Genome-Wide Identification and Abiotic Stress Response Analysis of C2H2 Zinc Finger Protein Genes in Foxtail Millet (Setaria italica)

C2H2 zinc finger proteins (C2H2-ZFPs) constitute one of the largest transcription factor families in plants, playing crucial roles in growth, development, and stress responses. Here, we performed a comprehensive genome-wide analysis of C2H2-ZFPs in foxtail millet (Setaria italica v2.0), identifying 67 members that were unevenly distributed across all nine chromosomes. Most SiC2H2 proteins were predicted to be alkaline, stable, and nuclear-localized, with the exception of SiC2H2-11 and SiC2H2-66, which were chloroplast-targeted. Phylogenetic analysis with Arabidopsis thaliana and Oryza sativa (rice) homologs classified these genes into seven distinct subfamilies, each containing the characteristic motif1 domain. Evolutionary studies revealed 14 segmental duplication events and strong syntenic conservation with Triticum aestivum (wheat, 163 orthologous pairs), suggesting conserved functions during evolution. Promoter analysis identified multiple cis-acting elements associated with light responsiveness, hormone signaling, and stress adaptation. Transcriptome profiling and qPCR validation in the YuGu 56 cultivar identified several stress-responsive candidates, including SiC2H2-35 and SiC2H2-58 (salt tolerance), as well as SiC2H2-23 (5.19-fold induction under salt stress) and SiC2H2-32 (5.47-fold induction under drought). This study provides some valuable insights into the C2H2-ZFP family in foxtail millet and highlights potential genetic markers for improving stress resilience through molecular breeding approaches.

Molecular and metabolic insights into muscle development and feed efficiency in beef cattle

As global demand for animal protein rises, improving feed efficiency in beef cattle has become a central focus for sustainable livestock production. Feed efficiency, often quantified through residual feed intake (RFI), is a complex trait influenced by genetic, physiological, and environmental factors. Among these, skeletal muscle plays a pivotal role due to its central function in growth, metabolism, and nutrient utilization. This mini-review explores the molecular and metabolic mechanisms linking muscle development to feed efficiency, highlighting recent advances in gene expression profiling, hormone signaling, and energy metabolism. Studies have identified key genes and pathways, such as those involved in the electron transport chain and insulin-like growth factor 1 (IGF1) signaling, that contribute to muscle growth and efficient energy use. Additionally, the role of the rumen microbiome in modulating nutrient absorption and its interaction with host muscle metabolism is discussed. Integrating these insights with genomic selection tools provides a promising avenue for enhancing feed efficiency while maintaining production goals. Understanding the biological foundations of muscle development offers valuable opportunities to refine genetic selection and management practices for a more profitable and environmentally sustainable beef industry.

Establishment of Agrobacterium-mediated genetic transformation and CRISPR/Cas9-guided gene editing in Elymus nutans.

Establishment of Agrobacterium-mediated genetic transformation and CRISPR/Cas9-guided gene editing in Elymus nutans.

Genetic parameters and haplotype-based genome-wide association study of indicator traits for gastrointestinal parasite resistance in Santa Ines sheep.

Genetic parameters and haplotype-based genome-wide association study of indicator traits for gastrointestinal parasite resistance in Santa Ines sheep.

Genetic exploration and molecular breeding of unique ready-to-eat soft rice for improvement of glycemic response

Genetic exploration and molecular breeding of unique ready-to-eat soft rice for improvement of glycemic response

Genome-Wide Identification and Evolutionary Analysis of m6A-Related Gene Family in Poplar Nanlin895

Background: N6-methyladenosine (m6A) is the most prevalent chemical modification of eukaryotic RNA, playing a crucial role in regulating plant growth and development, stress responses, and other essential biological processes. The enzymes involved in m6A modification—methyltransferases (writers), demethylases (erasers), and recognition proteins (readers)—have been identified in various plant species; however, their roles in the economically significant tree species Populus deltoides × P. euramericana (NL895) remain underexplored. Results: In this study, we identified 39 m6A-related genes in the NL895 genome, comprising 8 writers, 13 erasers, and 18 readers. Evolutionary analysis indicated that the expansion of writers and readers primarily resulted from whole-genome duplication events. Purifying selection pressures were observed on all duplicated gene pairs, suggesting their essential roles in functional differentiation. Phylogenetic analysis revealed that writers, erasers, and readers are categorized into six, four, and two groups, respectively, with these genes being more conserved among dicotyledonous plants. Gene structure, protein domains, and motifs exhibited greater conservation within the same group. Promoter analysis of m6A-related genes showed enrichment of cis-acting elements associated with responses to light, phytohormones, and stress, indicating their potential involvement in gene expression regulation. Under cadmium treatment, the expression of all writers was significantly upregulated in both the aboveground and root tissues of NL895. Conclusions: This study systematically identified m6A-related gene families in Populus deltoides × P. euramericana (NL895), elucidating their evolutionary patterns and expression regulation characteristics. These findings provide a theoretical foundation for analyzing the molecular mechanisms of m6A modification in poplar growth, development, and stress adaptation, and offered candidate genes for molecular breeding in forest trees.

Identification and characterization of PcHD8 from Pogostemon cablin related to the regulation of trichome development.

Identification and characterization of PcHD8 from Pogostemon cablin related to the regulation of trichome development.

The impact of high-light stress on the physiology and transcriptome of Pterocladiella capillacea.

The impact of high-light stress on the physiology and transcriptome of Pterocladiella capillacea.

Genome-wide identification of the HIPPs gene family and functional validation of MsHIPP12 in enhancing cadmium tolerance in Medicago sativa.

Genome-wide identification of the HIPPs gene family and functional validation of MsHIPP12 in enhancing cadmium tolerance in Medicago sativa.

Transcriptome sequence reveal the roles of MaGME777 and MabHLH770 in drought tolerance in Musa acuminata.

Transcriptome sequence reveal the roles of MaGME777 and MabHLH770 in drought tolerance in Musa acuminata.

Genetics and Molecular Breeding of Fruit Tree Species

Fruit tree species contribute to human nutrition and health security by providing important beneficial compounds (e [...]

Mango Pangenome Reveals Dramatic Impacts of Reference Bias on Genomic Analyses

Abstract Most genomics studies start by mapping sequencing data to a reference genome. The quality of reference genome assembly, genetic relatedness to the studied population, and the mapping method employed directly impact variant calling accuracy and subsequent genomic analyses, introducing reference bias and resulting in erroneous conclusions. However, the impacts of reference bias and methods to reduce it have gained limited attention. This study compared genomic analyses using four different reference genomes of mango (Mangifera indica), including the two haploid assemblies of haplotype-resolved telomere-to-telomere (T2T) genome assembly, a pangenome, and an older version of the reference genome available on NCBI. The choice of reference genome dramatically impacted the mapping efficiency and resulted in notable differences in calling the genetic variants, particularly structural variations (SVs). Phylogenetic analysis was more sensitive to the reference genome compared to genetic differentiation. Population genomic analyses of artificial selection in domestication and SV hotspot regions varied across reference genomes. Notably, the gene enrichment analyses showed significant differences in the top enriched biological processes depending on the reference genome used. Overall, the mango pangenome outperformed the other reference genomes across various metrics, followed by T2T reference genomes, as they captured greater diversity and effectively reduced reference bias. Our findings highlight the role of the mango pangenome in reducing reference bias and underscore the critical role of reference genome selection, suggesting that it is one of the most important factors in genomic studies.

Genome-wide association analyses identify single nucleotide polymorphisms associated with in vitro embryo cleavage and blastocyst rates in Holstein bulls.

Reproductive success is an essential component of profitable and sustainable dairy operations. Although selection for production traits such as milk yield has led to a decline in fertility in dairy cattle, strategies including assisted reproductive technologies such as in vitro fertilization and embryo transfer, as well as genomic selection for fertility traits, are being implemented to help mitigate this loss. Previous studies have identified genetic markers associated with fertility traits such as daughter pregnancy rate, conception rate, and interval to first conception. However, genetic markers associated with in vitro embryo development have yet to be explored. Therefore, this study aimed to identify genetic markers associated with in vitro embryo cleavage and blastocyst rates with the future goal of creating an index to select bulls with superior abilities to produce embryos in vitro. Rigorous in vitro fertilization trials identified Holstein bulls with divergent abilities to produce embryos that successfully cleave and develop into blastocysts in vitro. A total of 40 bulls with embryo cleavage and blastocyst rate phenotypes were whole-genome sequenced. Sequencing was performed on an Illumina platform with PE150 reads followed by cleaning, mapping to ARS-UCD1.2, variant calling with GATK HaplotypeCaller, and quality control following the 1000 Bulls Genomes Project best practices. Genome-wide association analyses identified 819 and 442 SNPs associated with embryo cleavage and blastocyst rates, respectively. Significant regions on chromosomes 15, 18, 21, 22, and 23 were in linkage disequilibrium with QTL previously associated with reproductive traits in cattle. Further, a region on chromosome 28 with the most significant variant associated with cleavage rate contained several synonymous variants in EGLN1, which is a critical component of the hypoxia inducible pathway. An additional region on chromosome 18 associated with cleavage rate contained a missense variant in SMG9, a gene involved in the nonsense-mediated mRNA decay pathway. A region on chromosome 21 associated with blastocyst rate also contained variants in regulatory regions downstream from AEN, a gene required for efficient DNA fragmentation during the p53-dependent apoptosis pathway. In summary, this study identified a preliminary collection of genomic regions associated with embryo cleavage and blastocyst rates in vitro that contain relevant genes and other QTL associated with reproductive traits in cattle. These regions, after validation, could contribute to a selection index for identification of bulls with genetic predispositions to produce a greater number of embryos in vitro for use in assisted reproduction techniques.

Genome-wide association mapping of scuticociliatosis resistance in a vaccinated population of olive flounder (Paralichthys olivaceus).

Genome-wide association mapping of scuticociliatosis resistance in a vaccinated population of olive flounder (Paralichthys olivaceus).