Search Results (105)

Soybean (Glycine max (L.) Merr.) is a globally important legume valued for the high protein, oil, and carbohydrate content of its seeds. However, it is difficult to simultaneously optimize the content of these three macronutrients due to their negatively correlated metabolic pathways and complex quantitative inheritance patterns. In this study, a genome-wide association study (GWAS) was conducted to elucidate the genetic architecture underlying the seed protein, oil, and carbohydrate content in 328 soybean accessions evaluated over two years using near-infrared spectroscopy. Significant negative correlations (r = −0.323 to −0.656, p < 0.001) were observed between the three traits, confirming the trade-off in carbon partitioning during seed development. The GWAS identified nine significant loci distributed across chromosomes 4, 6, 8, 9, 10, 16, and 18 as stable quantitative trait loci (QTLs) regulating the three traits. Of these, three pleiotropic loci (qProOil.4, qProOil.16, and qOilCarb.6) were found to be associated with multiple seed compositional traits. Haplotype analysis revealed seven haplotype blocks with distinct phenotypic variation, indicating that they have the potential for use as trait-specific markers in marker-assisted selection. Functional annotation of the stable QTL regions identified 22 putative genes, among which five candidate genes, Glyma.06g201700, Glyma.08g281900, Glyma.09g164900, Glyma.13g155600, and Glyma.16g209800 were likely to be involved in carbon allocation, protein biosynthesis, lipid metabolism, and carbohydrate modification pathways based on their relative expression levels. Overall, this study enhances the understanding of the genetic and molecular mechanism controlling the composition of soybean seed and identifies promising genomic targets for precision breeding programs aimed at improving nutritional quality. Full article

Butidae is a family of teleost fishes with diverse morphological and ecological adaptations, including the marbled goby (Oxyeleotris marmorata), a large species of high economic value in Southeast and East Asia. The previous mitogenomic studies on cultured populations of O. marmorata from non-native habitats have provided limited insights into genetic divergence, structural variation, and evolutionary relationships. Hence, this study presented the complete mitochondrial genome of O. marmorata from its native habitat in Indonesia, providing structural characterization, assessment of genetic diversity, and matrilineal phylogenetic analysis. The circular mitogenome was 16,525 bp, comprising 37 genes and a non-coding control region (CR). The gene organization and strand distribution were conserved among Oxyeleotris species, with 28 genes on the heavy strand and nine on the light strand, and a pronounced A+T compositional bias. The comparative analyses of O. marmorata (from both native and cultured habitats) and Oxyeleotris lineolata mitogenomes revealed minor variations in intergenic spacers, gene overlaps, protein-coding gene (PCGs) lengths, and codon usage patterns. Conversely, the nonsynonymous and synonymous substitution ratios observed in species of the family Butidae and its closest related family (Eleotridae) indicate strong purifying selection in the present dataset. Notably, the ATG was the predominant start codon, whereas the COI gene utilized GTG, and amino acid composition analysis demonstrated high frequencies of arginine, leucine, and serine. Most transfer RNAs retained the canonical cloverleaf secondary structure except for trnS1, which lacked a functional dihydrouridine arm, whereas the CR contained four conserved sequence blocks with variable nucleotide motifs and no detectable tandem repeats. The haplotype analysis of native (Indonesia) and introduced populations (China) highlighted three haplotypes with high diversity (Hd = 1.0000) and substantial nucleotide variation (π = 0.6667). The genetic divergence across 13 PCGs was gene-specific, with COI and ND5 showing the highest variation, while ND4L and ATP8 were highly conserved. The phylogenetic analyses based on concatenated 13 PCGs using both Bayesian Inference and Maximum Likelihood methods revealed that Oxyeleotris forms a monophyletic clade and is closely related to Bostrychus sinensis. In addition, the broader phylogenetic framework inferred the matrilineal relationships within the family Butidae and its closest related family, Eleotridae. This study also recommends expanding analyses to include the mitogenomes of the remaining 17 Oxyeleotris species, together with comprehensive genomic data, to further elucidate their genetic architecture, evolutionary history, and ecological adaptability across diverse aquatic ecosystems. Full article

(1) Background: Backcross (BC) breeding is a key technology of crop improvement, yet its efficiency largely depends on the precise assessment of the genetic background recovery. Conventional molecular marker-assisted techniques suffer from inadequate genomic coverage or an inability to resolve true chromosomal structure. (2) Methods: To address major issues in maize BC breeding, we devised a G2H block-scanning strategy. This approach converts high-density point markers into haplotype blocks, enabling precise evaluation of the genetic background in backcross progenies. A key innovation is the CFDI, which quantifies the distribution of unrecovered fragments, allowing for visual tracking of chromosomal recombination and identification of ideal individuals with both a high genetic background recovery rate and few small fragments retention. (3) Results: We validated the accuracy and effectiveness of the G2H strategy across multiple backcross generations. Through enabling a precise “point-to-line-to-area” panoramic assessment of genetic background, G2H provides a powerful tool for developing ideal breeding materials with pure genetic background and minimized linkage drag. (4) Conclusions: Notably, this strategy significantly shortens the breeding cycle by 2–3 generations compared to conventional background assessment methods, thereby accelerating precision molecular design breeding in crops. Full article

Background: Human chromosome 3p21.31 variants introgressed from Neanderthals have been associated with a higher risk of developing a severe form of COVID-19. These Neanderthal DNA variants would regulate the expression of several genes, including LZTFL1 (implicated in the epithelial–mesenchymal transition) and proinflammatory chemokine receptors. Methods: We studied three introgressed haplotypes in patients who developed critical COVID-19 (N = 446; 82 deaths), less severe non-critical COVID-19 (N = 552), and population controls (N = 500) from the region of Asturias, Northern Spain. All the participants were genotyped for six single nucleotide polymorphisms that defined the three 3p21.31 haplotypes. Results: For the haplotype in the LZTFL1 gene, the total patients were significantly higher frequency carriers of the Neanderthal variant compared to controls (24% vs. 17%; p < 0.05, OR = 1.53, 95% CI = 1.16–2.01). Multiple logistic regression showed that critical COVID-19 was independently associated with male sex, hypertension, dyslipaemia, and the introgressed LZTFL1 haplotype (p = 0.006). The frequency of these introgressed genotypes did not differ between normotensives and normolipaemics in the two patient groups but was significantly increased among hypertensives (p = 0.003) and dyslipaemics (p = 0.001). Conclusions: In our population, the 3p21.31 haplotypes introgressed from Neanderthals were associated with increased risk of critical COVID-19, and the risk effect was higher among patients with hypertension and dyslipaemia. Full article

Chengkou mountain chicken, a Chinese indigenous breed, exhibits unique flavor characteristics. However, the genetic basis of its flavor precursor substances remains unexplored. We performed a genome-wide association study (GWAS) using low-coverage whole-genome sequencing (lcWGS) and genotype imputation to explore genetic markers linked to flavor precursors (nucleotides, amino acids, etc.) in Chengkou mountain chicken breast muscle. We identified 44 SNPs potentially or significantly associated with flavor precursor traits and localized 18 genes. Functional analysis revealed eight important candidate genes, including ZBTB20, RFX4, MAMLD1, SYN3, ABTB3, PRPF39, LRFN5, and DGCR14, which may play key roles in influencing flavor precursor substances. Moreover, two SNPs residing in the haplotype block (53,448,483 bp to 53,450,834 bp) on chromosome 1 were significantly associated with a di-unsaturated acyl chain (C20:2) residue and mapped to the ABTB3 gene. This study analyzes the composition of flavor precursor substances in the pectoralis major muscle of Chengkou mountain chicken. Moreover, the SNPs, haplotypes, and candidate genes identified in this study can be used to improve the accuracy of the marker-assisted selection of traits related to flavor precursor substances in the breast muscle of chicken. In addition, the candidate genes that are significantly associated with these traits will potentially lay the foundation for future genetic selection aimed at improving the flavor traits of chicken meat. Full article

In our previous studies on the liver proteome of Holstein cows, the acyl-CoA oxidase 2 (ACOX2) gene was identified as a promising candidate for milk traits, being involved in the processes of fatty acid metabolism and bile acid formation. Herein, we evaluated its genetic effects on milk production traits in 922 Chinese Holstein cows. By sequencing the entire coding region and 2000 bp of the 5′ and 3′ flanking sequences of the ACOX2 gene, we identified a total of five SNPs, including one SNP in the 5′ UTR, one in intron 5, and three in the 3′ flanking region. Using an animal model, we found that the SNPs rs109066086, rs109665171, and rs454339362 were significantly associated with at least one of the milk production traits, including 305-day milk yield, milk fat yield, milk protein yield, milk fat percentage, and milk protein percentage in the first lactation (p ≤ 4.03 × 10⁻²). And in the second lactation, all five SNPs were significantly associated with at least three of the milk production traits (p ≤ 1.17 × 10⁻²). We also found that in the second lactation, the SNP rs209677248 had a high phenotypic variance rate for milk protein percentage, with a value of 4.90%. With Haploview 4.2, it was observed that the four SNPs formed two haplotype blocks, which were significantly associated with the 305-day milk, fat, and protein yields (p ≤ 1.03 × 10⁻²; p ≤ 8.60 × 10⁻³; p ≤ 3.20 × 10⁻³). In addition, it was predicted that the T allele in the SNP rs109066086 created TFBSs for transcription factors NC2R2 and TFAP4, thereby potentially affecting ACOX2 expression. Overall, our results provide the first confirmation of the genetic effects of the ACOX2 gene on milk yield and composition traits in dairy cattle and revealed the referable molecular markers for genomic selection. Full article

In our previous study, we found that changes in plasma prolactin (PRL) concentration were significantly associated with heat stress in dairy cows, and that PRL plays an important role in milk performance. Microarray sequencing revealed that thyrotropin releasing hormone (TRH) and prolactin receptor (PRLR), two genes important for PRL expression or function, may affect milk performance, reproduction, and heat stress response in dairy cattle. In this study, we further validated the genetic effects of the three genes in Chinese Holsteins. The potential variants within the three genes were first detected in 70 Chinese Holstein bulls and then screened in 1152 Chinese Holstein cows using the KASP (Kompetitive allele-specific PCR) method. In total, 42 variants were identified. Further, 13 SNPs were retained for KASP genotyping, including 8 in TRH, 3 in PRL, and 2 in PRLR. Using SNP-based association analyses, the multiple significant (p < 0.05) associations of these 13 SNPs with milk performance, reproduction, and heat stress response traits were found in the Holstein population. Furthermore, linkage disequilibrium analysis found a haplotype block in each of the TRH and PRL genes. Haplotype-based association analyses showed that haplotype blocks were also significantly (p < 0.05) associated with milk performance, reproduction, and heat stress response traits. Collectively, our results identified the genetic associations of TRH, PRL, and PRLR with milk performance, reproduction, and heat stress response traits in dairy cows, and found the important roles of SNP g.55888602A/C and g.55885455A/G in TRH in all traits, providing important molecular markers for genetic selection of high-yielding dairy cows. Full article

The Inner Mongolia cashmere goat is a local breed valued for both its cashmere and meat production. Early growth traits include birth weight and weaning weight. Generally, cashmere goats with higher birth and weaning weights tend to exhibit a higher carcass weight at slaughter. Consequently, exploring the genetic variation associated with these early growth traits is crucial in enhancing the meat production performance of Inner Mongolia cashmere goats. For this study, we performed genome-wide association analysis and haplotype analysis on the early growth traits of 212 Inner Mongolia cashmere goats (72 rams, 140 ewes) to identify molecular markers and haplotypes significantly associated with birth and weaning weights. Through genome-wide association analysis and gene annotation, we identified 21 SNPs and 117 candidate genes linked to early growth traits. Notably, genes such as RUNX1T1, ERBIN, MYO15B, NT5C, GRB2, ITGB4, and GALK emerged as significant factors influencing the early growth of Inner Mongolia cashmere goats. Additionally, nine haplotype blocks related to early growth traits were constructed, resulting in eight haplotype combinations. In conclusion, the haplotype combinations A1A1, C1C1, and D1D1 were found to be beneficial for the genetic improvement of early growth traits in Inner Mongolia cashmere goats. Full article

Phytophthora sojae (Kauffman and Gerdemann) is an oomycete pathogen that threatens soybean (Glycine max L.) production worldwide. The development of soybean cultivars with resistance to this pathogen is of paramount importance for the sustainable management of the disease. The objective of this study was to identify genomic regions associated with resistance to P. sojae isolate 40468 through genome-wide association analyses of 983 soybean germplasms. To elucidate the genetic basis of resistance, three statistical models were employed: the compressed mixed linear model (CMLM), Bayesian-information and linkage disequilibrium iteratively nested keyway (BLINK), and fixed and random model circulating probability unification (FarmCPU). The three models consistently identified a genomic region (3.8–5.3 Mbp) on chromosome 3, which has been previously identified as an Rps cluster. A total of 18 single nucleotide polymorphisms demonstrated high statistical significance across all three models, which were distributed in eight linkage disequilibrium (LD) blocks within the aforementioned interval. Of the eight, LD3-2 exhibited the discernible segregation of phenotypic reactions by haplotype. Specifically, over 93% of accessions with haplotypes LD3-2-F or LD3-2-G displayed resistance, whereas over 91% with LD3-2-A, LD3-2-C, or LD3-2-D exhibited susceptibility. Furthermore, the BLINK and FarmCPU models identified new genomic variations significantly associated with the resistance on several other chromosomes, indicating that the resistance observed in this panel was due to the presence of different alleles of multiple Rps genes. These findings underscore the necessity for robust statistical models to accurately detect true marker–trait associations and provide valuable insights into soybean genetics and breeding. Full article

Background: Type 2 diabetes (T2D) is one of the leading causes of mortality and is a public health challenge worldwide. Metformin is the first-choice treatment for T2D; its pharmacokinetics (PK) is facilitated by members of the solute carrier (SLC) superfamily of transporters, it is not metabolized, and it is excreted by the kidney. Although interindividual variability in metformin pharmacokinetics is documented in the Mexican population, its pharmacogenomics is still underexplored. We aimed to identify variants in metformin SLC transporter genes associated with metformin PK and response in Mexican patients. Methods: Using exome data from 2217 Mexican adults, we identified 86 biallelic SNVs in the eight known genes encoding SLC transporters, with a minor allele frequency ≥ 1%, which were analyzed in an inadequate glycemic control (IGC) association study in T2D metformin treated patients. Metformin PK was evaluated in a pediatric cohort and the effect of associated SNVs was correlated. Results: Functional annotation classified two SNVs as pathogenic. The association study revealed two blocks associated with IGC. These haplotypes comprise rs622591, rs4646272, rs4646273, and rs4646276 in SLC22A1; and rs1810126 and rs668871 in SLC22A3. PK profiles revealed that homozygotes of the SLC22A1 haplotype reached lower plasma metformin concentrations 2 h post administration than the other groups. Conclusions: Our findings highlight the potential of pharmacogenomics studies to enhance precision medicine, which may involve dosage adjustments or the exploration of alternative therapeutic options. These hold significant implications for public health, particularly in populations with a high susceptibility to develop metabolic diseases, such as Latin Americans. Full article

Traditional expression quantitative trait locus (eQTL) mapping associates single nucleotide polymorphisms (SNPs) with gene expression, where the SNPs are derived from large-scale whole-genome sequencing (WGS) data or transcriptome data. While WGS provides a high SNP density, it also incurs substantial sequencing costs. In contrast, RNA-seq data, which are more accessible and less expensive, can simultaneously yield gene expressions and SNPs. Thus, eQTL analysis based on RNA-seq offers significant potential applications. Two primary strategies were employed for eQTL in this study. The first involved analyzing expression levels in relation to variant sites detected between populations from RNA-seq data. The second approach utilized kmers, which are sequences of length k derived from RNA-seq reads, to represent variant sites and associated these kmer genotypes with gene expression. We discovered 87 significant association signals involving eGene on the basis of the SNP-based eQTL analysis. These genes include DYNLT1, NMNAT1, and MRLC2, which are closely related to neurological functions such as motor coordination and homeostasis, play a role in cellular energy metabolism, and function in regulating calcium-dependent signaling in muscle contraction, respectively. This study compared the results obtained from eQTL mapping using RNA-seq identified SNPs and gene expression with those derived from kmers. We found that the vast majority (23/30) of the association signals overlapping the two methods could be verified by haplotype block analysis. This comparison elucidates the strengths and limitations of each method, providing insights into their relative efficacy for eQTL identification. Full article

In the context of crop breeding, plant height (PH) plays a pivotal role in determining straw and grain yield. Although extensive research has explored the genetic control of PH in wheat, there remains an opportunity for further advancements by integrating genomics with growth-related phenomics. Our study utilizes the latest genome-wide association scan (GWAS) techniques to unravel the genetic basis of temporal variation in PH across 179 Bulgarian bread wheat accessions, including landraces, tall historical, and semi-dwarf modern varieties. A GWAS was performed with phenotypic data from three growing seasons, the calculated best linear unbiased estimators, and the leveraging genotypic information from the 25K Infinium iSelect array, using three statistical methods (MLM, FarmCPU, and BLINK). Twenty-five quantitative trait loci (QTL) associated with PH were identified across fourteen chromosomes, encompassing 21 environmentally stable quantitative trait nucleotides (QTNs), and four haplotype blocks. Certain loci (17) on chromosomes 1A, 1B, 1D, 2A, 2D, 3A, 3B, 4A, 5B, 5D, and 6A remain unlinked to any known Rht (Reduced height) genes, QTL, or GWAS loci associated with PH, and represent novel regions of potential breeding significance. Notably, these loci exhibit varying effects on PH, contribute significantly to natural variance, and are expressed during seedling to reproductive stages. The haplotype block on chromosome 6A contains five QTN loci associated with reduced height and two loci promoting height. This configuration suggests a substantial impact on natural variation and holds promise for accurate marker-assisted selection. The potentially novel genomic regions harbor putative candidate gene coding for glutamine synthetase, gibberellin 2-oxidase, auxin response factor, ethylene-responsive transcription factor, and nitric oxide synthase; cell cycle-related genes, encoding cyclin, regulator of chromosome condensation (RCC1) protein, katanin p60 ATPase-containing subunit, and expansins; genes implicated in stem mechanical strength and defense mechanisms, as well as gene regulators such as transcription factors and protein kinases. These findings enrich the pool of semi-dwarfing gene resources, providing the potential to further optimize PH, improve lodging resistance, and achieve higher grain yields in bread wheat. Full article

Previous study revealed that isocitrate dehydrogenase (NADP (+)) 2, mitochondrial (IDH2), lactate dehydrogenase A (LDHA), and lactate dehydrogenase B (LDHB) genes were significantly differentially expressed in liver tissues of Holstein cows among different lactation periods and associated with lipid and protein metabolism; hence, they were considered as candidates for milk production traits. Herein, the genetic effects of the three genes on milk yield, fat, and protein traits were studied by association analysis using 926 Chinese Holstein cows from 45 sire families. As a result, five single nucleotide polymorphisms (SNPs) in IDH2, one in LDHA, and three in LDHB were identified by re-sequencing, and subsequently, they were genotyped in 926 Chinese Holstein cows by genotyping by target sequencing (GBTS). With the animal model, single-locus association analysis revealed that four SNPs in IDH2 and one SNP in LDHA were significantly associated with milk, fat, and protein yields (p ≤ 0.0491), and three SNPs in LDHB were associated with milk yield, milk fat yield, and fat percentage (p ≤ 0.0285). Further, four IDH2 SNPs were found to form a haplotype block significantly associated with milk yield, fat yield, protein yield, and protein percentage (p ≤ 0.0249). In addition, functional predictions indicated that one SNP in LDHA, g.26304153G>A, may affect transcription factor binding and two SNPs, g.88544541A>G and g.88556310T>C could alter LDHB mRNA secondary structure. In summary, this study profiled the significant genetic effects of IDH2, LDHA, and LDHB on milk yield and composition traits and provided referable genetic markers for genomic selection programs in dairy cattle. Full article

Genome-wide association studies have identified a locus on chromosome 10q22, where many co-inherited single nucleotide polymorphisms (SNPs) are associated with atrial fibrillation (AF). This study seeks to identify the impact of this locus on gene expression at the transcript isoform level in human left atria and to gain insight into potential causal variants. Bulk RNA sequencing was analyzed to identify myozenin 1 (MYOZ1) and synaptopodin 2-like (SYNPO2L) transcript isoforms and the association of common SNPs in this region with transcript isoform expression levels. Chromatin marks were used to suggest candidate regulatory SNPs in this region. Protein amino acid changes were examined for predicted functional consequences. Transfection of MYOZ1 and two SYNPO2L isoforms were performed to localize their encoded proteins in cardiomyocytes derived from stem cells. We identified one MYOZ1 transcript isoform and four SYNPO2L transcript isoforms, two of which encode proteins, while the other two encode long noncoding RNAs (lncRNAs). The risk allele of the strongest AF susceptibility SNP on chromosome 10q22 is associated with decreased MYOZ1 expression and increased expression of the two SNYPO2L lncRNA isoforms. There are many SNPs co-inherited with the top AF-associated SNP due to linkage disequilibrium (LD), including rs11000728, which we propose as the MYOZ1 regulatory SNP, confirmed by reporter gene transfection. In addition, this LD block includes three missense SNPs in the SYNPO2L gene, with the minor protective haplotype predicted to be detrimental to protein function. MYOZ1 and both protein isoforms of SYNPO2L were localized to the sarcomere. This is a complex locus with the potential for several SNPs in a haplotype to alter AF susceptibility by opposing effects on MYOZ1 and SYNPO2L lncRNA expression, along with effects on SYNPO2L protein function. Full article

Plants are an important source for the discovery of novel natural growth regulators. We used activity screening to demonstrate that treatment of Nipponbare seeds with 25 μg/mL isopimaric acid significantly increased the resulting shoot length, root length, and shoot weight of rice seedlings by 11.37 ± 5.05%, 12.96 ± 7.63%, and 27.98 ± 10.88% and that it has a higher activity than Gibberellin A3 (GA₃) at the same concentration. A total of 213 inbred lines of different rice lineages were screened, and we found that isopimaric acid had different growth promotional activities on rice seedlings of different varieties. After induction with 25 μg/mL isopimaric acid, 15.02% of the rice varieties tested showed increased growth, while 15.96% of the varieties showed decreased growth; the growth of the remaining 69.02% did not show any significant change from the control. In the rice varieties showing an increase in growth, the shoot length and shoot weight significantly increased, accounting for 21.88% and 31.25%. The root length and weight significantly increased, accounting for 6.25% and 3.13%. Using genome-wide association studies (GWASs), linkage disequilibrium block, and gene haplotype significance analysis, we identified single nucleotide polymorphism (SNP) signals that were significantly associated with the length and weight of shoots on chromosomes 2 and 8, respectively. After that, we obtained 17 candidate genes related to the length of shoots and 4 candidate genes related to the weight of shoots. Finally, from the gene annotation data and gene tissue-specific expression; two genes related to this isopimaric acid regulation phenotype were identified as OsASC1 (LOC_Os02g37080) on chromosome 2 and OsBUD13 (LOC_Os08g08080) on chromosome 8. Subcellular localization analysis indicated that OsASC1 was expressed in the plasma membrane and the nuclear membrane, while OsBUD13 was expressed in the nucleus. Further RT-qPCR analysis showed that the relative expression levels of the resistance gene OsASC1 and the antibody protein gene OsBUD13 decreased significantly following treatment with 25 μg/mL isopimaric acid. These results suggest that isopimaric acid may inhibit defense pathways in order to promote the growth of rice seedlings. Full article