Integrated Analysis of CRY1 Gene Expression and InDel Polymorphism Reveals Associations with Ovarian Morphological Traits in Chinese Holstein Dairy Cattle
Aug 2026· Biomolecules· Vol 16· 0 citations· 64 references
Medicine
TL;DR
The preliminary findings suggest that CRY1 is associated with specific ovarian morphological traits and may serve as a basis for further investigation of its potential role in bovine reproductive function.
Abstract
Clock genes, such as cryptochrome 1 (CRY1), exhibit rhythmic expression in the reproductive organs. This gene is a key component of the circadian clock and is involved in various physiological processes, including reproduction, suggesting that it may be linked to ovarian activity via neuroendocrine pathways. However, the association between CRY1 variants and ovarian traits in dairy cows is unclear. In this study we used qRT-PCR to assay the mRNA expression of this gene, and found that CRY1 expression was highest in oocytes in several tissues; subsequently, we found that CRY1 expression was highest in the ovary in Chinese Holstein dairy cattle, followed by muscle and spleen tissues (p < 0.01). Next, we identified a six bp insertion/deletion (indel) locus within the CRY1 gene in Chinese Holstein dairy cattle. Only two genotypes were detected: II (n = 854, 83.7%) and ID (n = 166, 16.3%). Association analysis revealed that the identified indel was significantly associated with dominant follicle and corpus albicans diameters (p < 0.05) during metestrus. Specifically, individuals with the ID genotype exhibited smaller dominant follicles and corpus albicans than those with the II genotype. Our preliminary findings suggest that CRY1 is associated with specific ovarian morphological traits and may serve as a basis for further investigation of its potential role in bovine reproductive function.
This narrative review synthesizes major advances in sheep genetic mapping, functional genomics, and GS relevant to economically important traits to provide researchers, breeders, and students with a balanced, evidence-based resource to guide future genomic improvements in sustainable sheep production.
Mostafa Ghaderi-Zefrehei, Effat Nasre Esfahani, Hassan Amini Pozveh et al.· Frontiers in Genetics· 0 citations
The genetic and physiological variations among individuals of Holstein dairy cattle contribute to variations in milk yield. Selecting high-yield cows is critical for improving lactation performance. The present study aimed to identify functional genetic variants of the 3′ untranslated region (3′ UTR) in the ELF5 gene associated with milk production traits and to elucidate their underlying molecular mechanisms. A total of 1314 Chinese Holstein cows were genotyped, and a novel single nucleotide polymorphism (SNP), ELF5 g.32793 G>T, was identified in the 3′ UTR of ELF5. This SNP was significantly associated with milk production, such as milk yield, milk fat percentage, milk protein percentage, and somatic cell score. Bioinformatic prediction and dual-luciferase reporter assays demonstrated that the ELF5 g.32793 G>T affects the interaction between bta-miR-487a and the ELF5 3′ UTR. Functional analyses in bovine mammary epithelial (MAC-T) cells showed that bta-miR-487a suppressed cell proliferation by inducing G0/G1 phase arrest and reduced the expression of proliferation-related proteins. Collectively, these findings suggested that bta-miR-487a participates in the regulation of MAC-T cell growth and that the ELF5 g.32793 G>T polymorphism may influence lactation performance through an miRNA-associated mechanism. Therefore, the variant can be used as a functional marker for marker-assisted selection in dairy cattle breeding.
Lin Ma, Li Sun, Haotian Zhang et al.· Biomolecules· 0 citations
Abstract In dairy farming, reproductive efficiency is vital to both profitability and sustainability. However, years of selective breeding for increased milk yield have adversely affected reproductive potential. This study aimed to pinpoint genomic regions and identify potential candidate genes associated with reproductive traits in Chinese Holstein cattle. In this study, a single-step genome-wide association study (ssGWAS) was conducted using 33,202 phenotypic records from 16,379 animals, 55,244 pedigree records, and genomic data from 1,698 cows. These data were integrated into the ssGWAS analysis, resulting in a total pedigree structure of 21,635 animals. A total of 12 significant markers were identified for calving interval (IC), days open (DO), number of services per conception (NS), and conception rate (CR). Among these significant SNPs, three SNPs were for IC, two SNPs were for DO, three SNPs were for NS, and four SNPs were for CR. Several promising candidate genes located near these SNPs have been identified, including SFXN4, B3GAT2, GRK5, PRDX3, and MTHFD1L, highlighting their potential involvement in fertility-related biological processes. Furthermore, functional enrichment analysis identified significant enrichment of pathways associated with cell adhesion and embryonic development, suggesting a potential mechanistic role for DSG family members (DSG1, DSG2, DSG3, and DSG4) in fertility regulation. Collectively, our findings enhance understanding of the complex genetic basis of reproductive traits in dairy cattle and may offer a valuable set of genomic targets for precision breeding of Chinese Holsteins. Integrating these markers into genomic selection programs may contribute to genetic improvements in reproductive efficiency and support the long-term sustainability of dairy production.
W. A. Lombebo, Ming-Xin Du, G. Tarekegn et al.· Journal of Animal Science· 0 citations
Hu sheep are a well-known Chinese dual-purpose breed valued for meat production, early sexual maturity, high prolificacy, and adaptability to hot, humid environments. In this study, we combined whole-genome sequencing, GWAS, and eQTL analyses to investigate the genetic basis of growth and slaughter traits in 420 eight-month-old Hu sheep. Using a discovery cohort (
N
= 112) and a validation cohort (
N
= 308), we integrated high-throughput SNP genotyping and RNA sequencing, identifying 559,996 high-quality SNPs and multiple significant loci associated with traits such as live weight and carcass weight. Among the 2,368 cis-eQTLs detected, the most significant was linked to
ZNF280B
expression in the longissimus lumborum muscle. Functional validation showed that
ZNF280B
downregulation significantly inhibited skeletal muscle satellite cell proliferation and induced apoptosis, highlighting its critical role in muscle development and fat metabolism. The novelty of this study lies in its large sample size, comprehensive multi-trait analysis, and the integration of functional validation, providing reliable genetic markers for marker-assisted selection in Hu sheep. These findings deepen our understanding of the genetic mechanisms underlying growth and slaughter performance and offer valuable insights for improving production efficiency and promoting sustainable livestock development.
Qiang Wang, Jie Xu, Meng-Huan Bao et al.· BMC Genomics· 0 citations
Simple Summary Morphometric traits are important in beef cattle breeding because they directly affect meat production and economic value. Differences in these traits among cattle breeds are partly influenced by genetic variation. In this study, we examined copy number variation (CNV) in the MYC-associated factor X gene in 572 Chinese cattle from five breeds, including Qinchuan, Ji’an, Jinnan, Nanyang, and Xianan cattle. CNVs are defined as differences in the number of copies of genomic DNA segments among individuals within a population. The copy number variation in this gene showed different distribution patterns among the five breeds. Based on raw p values, MAX CNVs showed nominal associations with chest girth in Jinnan cattle and with chest girth and hucklebone width in Nanyang cattle. Animals with the medium copy type, defined as two copies, showed higher values for the nominally associated traits than those with the loss type (<2 copies) or gain type (>2 copies). These findings suggest that copy number variation in the MYC-associated factor X gene may represent a potential candidate locus related to morphometric traits in Chinese cattle. Further validation in larger cattle populations is still needed before it can be used in breeding programs.
Shi-Yi Lv, Boyu Li, Suyun Fan et al.· Animals· 0 citations
Differential coloration of potato tuber skin is an important agronomic trait. However, its genetic regulatory mechanism remains unclear. In this study, an F₁ segregation population was constructed, and segregation in tuber skin coloration was observed. Using bulked segregant analysis by sequencing (BSA-seq) combined with fine mapping, a major quantitative trait locus (QTL) was mapped to a 52.24–53.08 Mb interval on Chr10. Within this region, StMYBA1, an R2R3-MYB transcription factor, emerged as the key candidate gene. Notably, a 6-bp (CTCCTC) deletion in the exon of StMYBA1 caused the loss of two proline residues, which was strongly associated with the absence of differential skin coloration. Further investigations demonstrated that overexpression of StMYBA1 markedly enhanced anthocyanin accumulation in both leaves and tubers. In transgenic lines, delphinidin content in leaves increased by 216.6%–297.4%, and after five days of light exposure, tuber eyes and heels exhibited a pronounced purple pigmentation. Consistently, key anthocyanin biosynthetic genes, including StANS and StF3′H, were significantly upregulated. Dual-luciferase assays further confirmed that StMYBA1 promotes anthocyanin biosynthesis by activating the MYB transcription factor StAN2 and its downstream targets. Importantly, the 6-bp deletion partially attenuated StMYBA1 regulatory activity, as reflected by reduced activation of several anthocyanin-related promoters and moderately lower anthocyanin accumulation in transient assays, while DNA-binding activity was retained. Collectively, these findings provide new insights into the regulatory role of StMYBA1 in potato anthocyanin biosynthesis and identify a potentially useful genetic target for potato quality improvement.
Xi-Juan Zhao, Chen-Xi Li, Sheng-Xuan Liu et al.· Horticulture Research· 0 citations
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