Regions Of Linkage Disequilibrium Research Articles

Identification of Candidate Genes for Soybean Storability via GWAS and WGCNA Approaches

Soybean (Glycine max (L.) Merr.) is an important crop for both food and feed, playing a significant role in agricultural production and the human diet. During long-term storage, soybean seeds often exhibit reduced quality, decreased germination, and lower seedling vigor, ultimately leading to significant yield reductions in soybean crops. Seed storage tolerance is a complex quantitative trait controlled by multiple genes and is also influenced by environmental factors during seed formation, harvest, and storage. This study aimed to evaluate soybean germplasms for their storage tolerance, identify quantitative trait nucleotides (QTNs) associated with seed storage tolerance traits, and screen for candidate genes. The storage tolerance of 168 soybean germplasms was evaluated, and 23,156 high-quality single nucleotide polymorphism (SNP) markers were screened and analyzed through a genome-wide association study (GWAS). Ultimately, 14 QTNs were identified as being associated with seed storage tolerance and were distributed across the eight chromosomes of soybean, with five QTNs (rs25887810, rs27941858, rs33981296, rs44713950, and rs18610980) being newly reported loci in this study. In the linkage disequilibrium regions of these SNPs, 256 genes were identified. By combining GWAS and weighted gene co-expression network analysis (WGCNA), eight hub genes (Glyma.03G058300, Glyma.04G1921100, Glyma.04G192600, Glyma.04G192900, Glyma.07G002000, Glyma.08G329400, Glyma.16G074600, Glyma.16G091400) were jointly identified. Through the analysis of expression patterns, two candidate genes (Glyma.03G058300, Glyma.16G074600) potentially involved in seed storage tolerance were ultimately identified. Additionally, haplotype analysis revealed that natural variations in Glyma.03G058300 could affect seed storage tolerance. The findings of this research provide a theoretical foundation for understanding the regulatory mechanism underlying soybean storage.

Abstract 74: The rs1173771 Haplotype Associated with Blood Pressure Influences Chromatin Interactions Involving the Natriuretic Peptide Receptor 3 Gene Promoter

Determining the mechanisms of action for human blood pressure (BP) variants in the noncoding regions of genome, particularly large haplotypes containing multiple variants, is both critical and challenging. Human BP-associated rs1173771 locus includes a haplotype containing 11 single nucleotide polymorphisms (SNPs) spanning 17.4 kbp. The Linkage Disequilibrium (LD) region is approximately 126 kbp from the transcription start site of the closest protein-coding gene NPR3 (natriuretic peptide receptor 3). We used genome editing and region-capture Micro-C to examine the effect of the rs1173771 haplotype on the expression of neighboring genes and the chromatin mechanisms involved. The BP-elevating and -lowering haplotypes of rs1173771 locus were precisely reconstituted in human induced pluripotent stem cells (iPSCs) using an efficient, two-step genome editing technique. We then differentiated the edited iPSCs to endothelial (iEC) and vascular smooth muscle cells (iVSMC). The BP-elevating haplotype significantly (p ≤ 0.05) decreased NPR3 expression in iEC and iVSMC. Using region capture Micro-C targeting the rs1173771 haplotype region and the promoter regions of neighboring genes, we found in both iECs and iVSMCs, the BP-elevating rs1173771 haplotype increased chromatin contacts between the rs1173771 haplotype region and NPR3 promoter region, compared to the BP-lowering haplotype. Statistical comparison of chromatin interaction using HiCCompare showed the interactions of a genomic segment overlapping the 5’ end of the rs1173771 haplotype region with the NPR3 promoter region and a region just upstream of the promoter were 10 and 6 fold stronger (p.adj ≤ 0.001) in iECs with homozygous BP-elevating haplotype compared to BP-lowering haplotype. Similarly, in iVSMCs, the interaction of a genomic segment overlapping the rs1173771 haplotype region with a region just upstream of the NPR3 promoter was 4 fold stronger (p.adj = 0.02) for homozygous BP-elevating haplotype compared to BP-lowering haplotype. These results suggest that the BP-elevating rs1173771 haplotype interacts with the NPR3 promoter more strongly to suppress NPR3 expression, possibly through the recruitment of inhibitory protein complexes.

Spinocerebellar ataxia type 27B (SCA27B) in India: insights from a large cohort study suggest ancient origin.

The ethnic diversity of India provides a unique opportunity to study the history of the origin of mutations of genetic disorders. Spinocerebellar ataxia type 27B (SCA27B), a recently identified dominantly inherited cerebellar disorder is caused by GAA-repeat expansions in intron 1 of Fibroblast Growth Factor 14 (FGF14). Predominantly reported in the European population, we aimed to screen this mutation and study the founder haplotype of SCA27B in Indian ataxia patients. We have undertaken screening of GAA repeats in a large Indian cohort of ~ 1400 uncharacterised ataxia patients and kindreds and long-read sequencing-based GAA repeat length assessment. High throughput genotyping-based haplotype analysis was also performed. We utilized ~ 1000 Indian genomes to study the GAA at-risk expansion alleles. We report a high frequency of 1.83% (n = 23) of SCA27B in the uncharacterized Indian ataxia cohort. We observed several biallelic GAA expansion mutations (n = 5) with younger disease onset. We observed a risk haplotype (AATCCGTGG) flanking the FGF14-GAA locus over a 74kb region in linkage disequilibrium. We further studied the frequency of this risk haplotype across diverse geographical population groups. The highest prevalence of the risk haplotype was observed in the European population (29.9%) followed by Indians (21.5%). The observed risk haplotype has existed through ~ 1100 generations (~ 22,000 years), assuming a correlated genealogy. This study provides valuable insights into SCA27B and its Upper Paleolithic origin in the Indian subcontinent. The high occurrence of biallelic expansion is probably relevant to the endogamous nature of the Indian population.

Analyzing genetic diversity in luffa and developing a Fusarium wilt-susceptible linked SNP marker through a single plant genome-wide association (sp-GWAS) study

BackgroundLuffa (Luffa spp.) is an economically important crop of the Cucurbitaceae family, commonly known as sponge gourd or vegetable gourd. It is an annual cross-pollinated crop primarily found in the subtropical and tropical regions of Asia, Australia, Africa, and the Americas. Luffa serves not only as a vegetable but also exhibits medicinal properties, including anti-inflammatory, antidiabetic, and anticancer effects. Moreover, the fiber derived from luffa finds extensive applications in various fields such as biotechnology and construction. However, luffa Fusarium wilt poses a severe threat to its production, and existing control methods have proven ineffective in terms of cost-effectiveness and environmental considerations. Therefore, there is an urgent need to develop luffa varieties resistant to Fusarium wilt. Single-plant GWAS (sp-GWAS) has been demonstrated as a promising tool for the rapid and efficient identification of quantitative trait loci (QTLs) associated with target traits, as well as closely linked molecular markers.ResultsIn this study, a collection of 97 individuals from 73 luffa accessions including two major luffa species underwent single-plant GWAS to investigate luffa Fusarium wilt resistance. Utilizing the double digest restriction site associated DNA (ddRAD) method, a total of 8,919 high-quality single nucleotide polymorphisms (SNPs) were identified. The analysis revealed the potential for Fusarium wilt resistance in accessions from both luffa species. There are 6 QTLs identified from 3 traits, including the area under the disease progress curve (AUDPC), a putative disease-resistant QTL, was identified on the second chromosome of luffa. Within the region of linkage disequilibrium, a candidate gene homologous to LOC111009722, which encodes peroxidase 40 and is associated with disease resistance in Cucumis melo, was identified. Furthermore, to validate the applicability of the marker associated with resistance from sp-GWAS, an additional set of 21 individual luffa plants were tested, exhibiting 93.75% accuracy in detecting susceptible of luffa species L. aegyptiaca Mill.ConclusionIn summary, these findings give a hint of genome position that may contribute to luffa wild resistance to Fusarium and can be utilized in the future luffa wilt resistant breeding programs aimed at developing wilt-resistant varieties by using the susceptible-linked SNP marker.

Genetic parameter estimation and molecular foundation of chicken beak shape

The bird beak is mainly functioned as feeding and attacking, and its shape has extremely important significance for survival and reproduction. In chickens, since beak shape could lead to some disadvantages including pecking and waste of feed, it is important to understand the inheritance of chicken beak shape. In the present study, we firstly established 4 indicators to describe the chicken beak shapes, including upper beak length (UL), lower beak length (LL), distance between upper and lower beak tips (DB) and upper beak curvature (BC). And then, we measured the 4 beak shape indicators as well as some production traits including body weight (BW), shank length (SL), egg weight (EW), eggshell strength (ES) of a layer breed, Rhode Island Red (RIR), in order to estimate genetic parameters of chicken beak shape. The heritabilities of UL and LL were 0.41 and 0.37, and the heritabilities of DB and BC were 0.22 and 0.21, indicating that beak shape was a highly or mediumly heritable. There were significant positive genetic and phenotypic correlations among UL, LL, and DB. And UL was positively correlated with body weight (BW18) and shank length (SL18) at 18 weeks of age in genetics, and DB was positively correlated with BC in terms of genetics and phenotype. We also found that layers of chicken cages played a role on beak shape, which could be attributed to the difference of lightness in different cage layers. By a genome-wide association study (GWAS) for the chicken UL, we identified 9 significant candidate genes associated with UL in RIR. For the variants with low minor allele frequencies (MAF <0.01) and outside of high linkage disequilibrium (LD) regions, we also conducted rare variant association studies (RVA) and GWAS to find the association between genotype and phenotype. We also analyzed transcriptomic data from multiple tissues of chicken embryos and revealed that all of the 9 genes were highly expressed in beak of chicken embryos, indicating their potential function for beak development. Our results provided the genetic foundation of chicken beak shape, which could help chicken breeding on beak related traits.

QTL Detection and Candidate Gene Identification for Eating and Cooking Quality Traits in Rice (Oryza sativa L.) via a Genome-Wide Association Study.

The eating and cooking quality (ECQ) directly affects the taste of rice, being closely related to factors such as gelatinization temperature (GT), gel consistency (GC) and amylose content (AC). Mining the quantitative trait loci (QTLs), and gene loci controlling ECQ-related traits is vital. A genome-wide association study on ECQ-related traits was conducted, combining 1.2 million single nucleotide polymorphisms (SNPs) with the phenotypic data of 173 rice accessions. Two QTLs for GT, one for GC and five for AC were identified, of which two were found in previously reported genes, and six were newly found. There were 28 positional candidate genes in the region of qAC11. Based on a linkage disequilibrium (LD) analysis, three candidate genes were screened within the LD region associated with AC. There were significant differences between the haplotypes of LOC_Os11g10170, but no significant differences were found for the other two genes. The qRT-PCR results showed that the gene expression levels in the accessions with high ACs were significantly larger than those in the accessions with low ACs at 35d and 42d after flowering. Hap 2 and Hap 3 of LOC_Os11g10170 reduced the AC by 13.09% and 10.77%, respectively. These results provide a theoretical and material basis for improving the ECQ of rice.

A genome-wide association study reveals fetal genetic factor for gestation length on chromosome 21 in Japanese Black cattle.

Gestation length (GL) in cattle is associated with neonatal health and the subsequent reproductive performance of dams. We performed a genome-wide association study (GWAS) using 25,144 single nucleotide polymorphisms (SNPs) in 4373 animals to detect genetic variants associated with GL as a fetal trait in Japanese Black cattle in Gifu Prefecture. We identified four significant SNPs on chromosome 21 in moderate linkage disequilibrium (LD). The minor allele of the most significant SNP has the effect on -2.47 days GL with a 0.019 allele frequency. Of the 4373 animals, 140 heterozygotes and one homozygote with the minor allele were traced back to a heterozygous sire. The 7.2Mb LD region harbors three genes: gamma-aminobutyric acid type A receptor subunit beta3 (GABRB3), arrestin domain containing 4 (ARRDC4), and nuclear receptor subfamily 2 group F member 2 (NR2F2, also known as COUP-TFII). RNA expression analysis and its functions suggest that GABRB3, ARRDC4, and NR2F2 (COUP-TFII) are involved in glucose production via the hypothalamic-pituitary-adrenal axis during the fetal stress response at gestation period termination. These results suggest that an increase in the allele frequency of the associated SNPs has an impact on genetic improvement by shortening the GL in the population.

MAPT Locus in Parkinson's Disease Patients of Ashkenazi Origin: A Stratified Analysis.

Introduction: MAPT locus is associated with Parkinson's disease (PD), which is located within a large inversion region of high linkage disequilibrium (LD). We aimed to determine whether the H2-haplotype protective effect and its effect size depends on the GBA1 or LRRK2 risk allele carrier status, and to further characterize genetic alterations that might contribute to its effect. Methods: LD analysis was performed using whole-genome sequencing data of 202 unrelated Ashkenazi Jewish (AJ) PDs. A haplotype-divergent variant was genotyped in a cohort of 1200 consecutively recruited AJ-PDs. The odd ratios were calculated using AJ-non-neuro cases from the gnomAD database as the controls in an un-stratified and a stratified manner according to the mutation carrier status, and the effect on the Age at Motor Symptom Onset (AMSO) was examined. Expression and splicing quantitative trait locus (eQTL and sQTL) analyses were carried out using brain tissues from a database. Results: The H2 haplotype exhibited significant association with PD protection, with a similar effect size in GBA1 carriers, LRRK2-G2019S carriers, and non-carriers (OR = 0.77, 0.69, and 0.82, respectively), and there was no effect on AMSO. The LD interval was narrowed to approximately 1.2 Mb. The H2 haplotype carried potential variants in candidate genes (MAPT and SPPL2C); structural deletions and segmental duplication (KANSL1); and variants affecting gene expression and intron excision ratio in brain tissues (LRRC37A/2). Conclusions: Our results demonstrate that H2 is associated with PD and its protective effect is not influenced by the GBA1/LRRK2 risk allele carrier status. This effect may be genetically complex, resulting from different levels of variations such as missense mutations in relevant genes, structural variations, epigenetic modifications, and RNA expression changes, which may operate independently or in synergy.

Pan-cancer analysis of promoter activity quantitative trait loci.

Altered promoter activity has been generally observed in diverse biological processes, including tumorigenesis. Accumulating evidence suggests that employing a quantitative trait locus mapping approach is effective in comprehending the genetic basis of promoter activity. By utilizing genotype data from The Cancer Genome Atlas and calculating corresponding promoter activity values using proActiv, we systematically evaluated the impact of genetic variants on promoter activity and identified >1.0 million promoter activity quantitative trait loci (paQTLs) as both cis- and trans-acting. Additionally, leveraging data from the genome-wide association study (GWAS) catalog, we discovered >1.3 million paQTLs that overlap with known GWAS linkage disequilibrium regions. Remarkably, ∼9324 paQTLs exhibited significant associations with patient prognosis. Moreover, investigating the impact of promoter activity on >1000 imputed antitumor therapy responses among pan-cancer patients revealed >43000 million significant associations. Furthermore, ∼25000 significant associations were identified between promoter activity and immune cell abundance. Finally, a user-friendly data portal, Pancan-paQTL (https://www.hbpding.com/PancanPaQTL/), was constructed for users to browse, search and download data of interest. Pancan-paQTL serves as a comprehensive multidimensional database, enabling functional and clinical investigations into genetic variants associated with promoter activity, drug responses and immune infiltration across multiple cancer types.

Abstract 135: The Noncoding Haplotype Region Of Blood Pressure-associated Single Nucleotide Polymorphism Rs1173771 Regulates The Expression Of Natriuretic Peptide Receptor C

Genome-wide association studies have identified 1,071 loci containing 26,585 single nucleotide polymorphisms (SNPs) as associated with blood pressure (BP). These loci together explain more than 25% of BP heritability. The BP-associated SNP rs1173771 has been associated with NPR3 expression in human tissues. NPR3 encodes natriuretic peptide receptor C (NPR-C). The haplotype in linkage disequilibrium (LD) with rs1173771 contains 11 SNPs spanning a noncoding genomic region of more than 17 kbp. The haplotype region is located 126 kbp from the transcription start site of NPR3 . We used genome editing to examine the effect of the noncoding haplotype region in LD with rs1173771 on gene expression. We employed a CRISPR/Cas9 mediated genetic engineering approach to delete the 17 kbp haplotype region in a human induced pluripotent stem cell (iPSC) line. Two clones of iPSCs with homozygous deletion of the 17 kbp region were obtained after screening 50 single cell clones. The genomic modification was confirmed by PCR, Sanger sequencing, and whole genome sequencing. Immunofluorescence staining for pluripotency markers indicated that pluripotency was retained following the genome editing procedures. Each edited iPSC clone and the unedited iPSC line were differentiated into endothelial cells (iECs) in 3 independent rounds of differentiation. Real-time PCR analysis showed a 1.59±0.17-fold upregulation of NPR3 mRNA in iECs with the haplotype region deletion compared to unedited iECs (n=11 and 7, p&lt;0.05). The expression of other neighboring genes ( SUB1 and TARS ) and a distal gene ( MRPS30 ) was not significantly affected by the deletion. The results provide definitive evidence that the noncoding haplotype region in LD with BP-associated SNP rs1173771 regulates the expression of natriuretic peptide receptor C in iECs.

Abstract 070: Deletion Of A Non-coding Genomic Segment Orthologous To The Human Rs1173771 Haplotype Region Attenuates Hypertension In Dahl Salt-sensitive Rats

Most SNPs associated by GWAS with blood pressure (BP) phenotypes are located in noncoding regions of DNA. Investigating the physiological effects of these SNPs and their underlying mechanisms will advance our understanding of how genetic and epigenetic mechanisms regulate BP. The BP-associated SNP rs1173771 is in linkage disequilibrium (LD) with 10 other SNPs (r 2 &gt;0.80) forming a haplotype spanning 17.5 kb of noncoding DNA. We explored the effects of the rs1173771 LD orthologous region on BP on the genetic background of Dahl salt-sensitive (SS) rats and the physiological and molecular mechanisms involved. A ~29.5 kb noncoding segment on rat chromosome 5 orthologous to the human rs1173771 LD region was identified using LiftOver. The model SS-rs1173771LD -/- was generated using CRISPR-Cas9 to delete this region in SS rats. BP was not significantly different between SS-rs1173771LD -/- rats and wildtype (WT) littermates on a 0.4% NaCl diet. After 14 days of a 4% NaCl diet, 24-hour mean arterial pressure (MAP) and systolic blood pressure (SBP) of SS-rs1173771LD -/- male rats were significantly lower compared with WT (149.1 ± 2.7 vs 155.9 ± 2.5 mmHg for MAP and 169.6 ± 4.3 vs 179.0 ± 3.0 mmHg for SBP). No difference in diastolic blood pressure was observed. No significant difference of BP was observed between genotypes in females. The transcription start sites of human natriuretic peptide receptor 3 (NPR3) and rat Npr3 are located ~129-kbp and ~80-kbp from the human rs1173771 LD region and the rat orthologous region, respectively. RNA-seq indicated that Npr3 expression was upregulated in the mesenteric artery in SS-rs1173771LD -/- rats. Vasodilation of mesenteric arteries in response to C-type natriuretic peptide was significantly enhanced in SS-rs1173771LD -/- male rats compared with WT littermates. A selective NPR-C antagonist abolished vasodilation in both groups, suggesting the vasorelaxation was NPR-C dependent. In conclusion, deletion of the rs1173771 LD orthologous region increased mesenteric artery vasorelaxation and attenuated salt-induced hypertension in male SS rats. Our findings provided evidence that evolutionarily conserved noncoding DNA regions located far from protein-coding genes can influence BP in vivo.

Genetic Correlations Among Corneal Biophysical Parameters and Anthropometric Traits.

The genetic architecture of corneal dysfunction remains poorly understood. Epidemiological and clinical evidence suggests a relationship between corneal structural features and anthropometric measures. We used global and local genetic similarity analysis to identify genomic features that may underlie structural corneal dysfunction. We assembled genome-wide association study summary statistics for corneal features (central corneal thickness, corneal hysteresis [CH], corneal resistance factor [CRF], and the 3 mm index of keratometry) and anthropometric traits (body mass index, weight, and height) in Europeans. We calculated global genetic correlations (rg) between traits using linkage disequilibrium (LD) score regression and local genetic covariance using ρ-HESS, which partitions the genome and performs regression with LD regions. Finally, we identified genes located within regions of significant genetic covariance and analyzed patterns of tissue expression and pathway enrichment. Global LD score regression revealed significant negative correlations between height and both CH (rg = -0.12; P = 2.0 × 10-7) and CRF (rg = -0.11; P = 6.9 × 10-7). Local analysis revealed 68 genomic regions exhibiting significant local genetic covariance between CRF and height, containing 2874 unique genes. Pathway analysis of genes in regions with significant local rg revealed enrichment among signaling pathways with known keratoconus associations, including cadherin and Wnt signaling, as well as enrichment of genes modulated by copper and zinc ions. Corneal biophysical parameters and height share a common genomic architecture, which may facilitate identification of disease-associated genes and therapies for corneal ectasias. Local genetic covariance analysis enables the identification of associated genes and therapeutic targets for corneal ectatic disease.

Genetic architecture and key regulatory genes of fatty acid composition in Gushi chicken breast muscle determined by GWAS and WGCNA

BackgroundFatty acids composition in poultry muscle is directly related to its tenderness, flavour, and juiciness, whereas its genetic mechanisms have not been elucidated. In this study, the genetic structure and key regulatory genes of the breast muscle fatty acid composition of local Chinese chicken, Gushi-Anka F2 resource population by integrating genome-wide association study (GWAS) and weighted gene co-expression network analysis (WGCNA) strategies. GWAS was performed based on 323,306 single nucleotide polymorphisms (SNPs) obtained by genotyping by sequencing (GBS) method and 721 chickens from the Gushi-Anka F2 resource population with highly variable fatty acid composition traits in the breast muscle. And then, according to the transcriptome data of the candidate genes that were obtained and phenotypic data of fatty acid composition traits in breast muscle of Gushi chickens at 14, 22, and 30 weeks of age, we conducted a WGCNA.ResultsA total of 128 suggestive significantly associated SNPs for 11 fatty acid composition traits were identified and mapped on chromosomes (Chr) 2, 3, 4, 5, 13, 17, 21, and 27. Of these, the two most significant SNPs were Chr13:5,100,140 (P = 4.56423e-10) and Chr13:5,100,173 (P = 4.56423e-10), which explained 5.6% of the phenotypic variation in polyunsaturated fatty acids (PUFA). In addition, six fatty acid composition traits, including C20:1, C22:6, saturated fatty acid (SFA), unsaturated fatty acids (UFA), PUFA, and average chain length (ACL), were located in the same QTL intervals on Chr13. We obtained 505 genes by scanning the linkage disequilibrium (LD) regions of all significant SNPs and performed a WGCNA based on the transcriptome data of the above 505 genes. Combining two strategies, 9 hub genes (ENO1, ADH1, ASAH1, ADH1C, PIK3CD, WISP1, AKT1, PANK3, and C1QTNF2) were finally identified, which could be the potential candidate genes regulating fatty acid composition traits in chicken breast muscle.ConclusionThe results of this study deepen our understanding of the genetic mechanisms underlying the regulation of fatty acid composition traits, which is helpful in the design of breeding strategies for the subsequent improvement of fatty acid composition in poultry muscle.

X-Chromosome Association Study in Latin American Cohorts Identifies New Loci in Parkinson's Disease.

Sex differences in Parkinson's disease (PD) risk are well-known. However, the role of sex chromosomes in the development and progression of PD is still unclear. The objective of this study was to perform the first X-chromosome-wide association study for PD risk in a Latin American cohort. We used data from three admixed cohorts: (1) Latin American Research consortium on the Genetics of Parkinson's Disease (n = 1504) as discover cohort, and (2) Latino cohort from International Parkinson Disease Genomics Consortium (n = 155) and (3) Bambui Aging cohort (n = 1442) as replication cohorts. We also developed an X-chromosome framework specifically designed for admixed populations. We identified eight linkage disequilibrium regions associated with PD. We replicated one of these regions (top variant rs525496; discovery odds ratio [95% confidence interval]: 0.60 [0.478-0.77], P = 3.13 × 10-5 replication odds ratio: 0.60 [0.37-0.98], P = 0.04). rs5525496 is associated with multiple expression quantitative trait loci in brain and non-brain tissues, including RAB9B, H2BFM, TSMB15B, and GLRA4, but colocalization analysis suggests that rs5525496 may not mediate risk by expression of these genes. We also replicated a previous X-chromosome-wide association study finding (rs28602900), showing that this variant is associated with PD in non-European populations. Our results reinforce the importance of including X-chromosome and diverse populations in genetic studies. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

Population genomic analysis reveals key genetic variations and the driving force for embryonic callus induction capability in maize

Genetic transformation has been an effective technology for improving the agronomic traits of maize. However, it is highly reliant on the use of embryonic callus (EC) and shows a serious genotype dependence. In this study, we performed genomic sequencing for 80 core maize germplasms and constructed a high-density genomic variation map using our newly developed pipeline (MQ2Gpipe). Based on the induction rate of EC (REC), these inbred lines were categorized into three subpopulations. The low-REC germplasms displayed more abundant genetic diversity than the high-REC germplasms. By integrating a genome-wide selective signature screen and region-based association analysis, we revealed 95.23 Mb of selective regions and 43 REC-associated variants. These variants had phenotypic variance explained values ranging between 21.46 and 49.46%. In total, 103 candidate genes were identified within the linkage disequilibrium regions of these REC-associated loci. These genes mainly participate in regulation of the cell cycle, regulation of cytokinesis, and other functions, among which MYB15 and EMB2745 were located within the previously reported QTL for EC induction. Numerous leaf area-associated variants with large effects were closely linked to several REC-related loci, implying a potential synergistic selection of REC and leaf size during modern maize breeding.

SNP-Based Heritability of Osteochondrosis Dissecans in Hanoverian Warmblood Horses.

Before the genomics era, heritability estimates were performed using pedigree data. Data collection for pedigree analysis is time consuming and holds the risk of incorrect or incomplete data. With the availability of SNP-based arrays, heritability can now be estimated based on genotyping data. We used SNP array and 1.6 million imputed genotype data with different minor allele frequency restrictions to estimate heritabilities for osteochondrosis dissecans in the fetlock, hock and stifle joints of 446 Hanoverian warmblood horses. SNP-based heritabilities were estimated using a genomic restricted maximum likelihood (GREML) method and accounting for patterns of regional linkage disequilibrium in the equine genome. In addition, we employed GREML for family data to account for different degrees of relatedness in the study population. Our results indicate that we were able to capture a larger proportion of additive genetic variance compared to pedigree-based estimates in the same population of Hanoverian horses. Heritability estimates on the linear scale for fetlock-, hock- and stifle-osteochondrosis dissecans were 0.41-0.43, 0.62-0.63, and 0.23-0.25, respectively, with standard errors of 0.11-0.14. Accounting for linkage disequilibrium patterns had an upward effect on the imputed data and a downward impact on the SNP array genotype data. GREML for family data resulted in higher heritability estimates for fetlock-osteochondrosis dissecans and slightly higher estimates for hock-osteochondrosis dissecans, but had no effect on stifle-osteochondrosis dissecans. The largest and most consistent heritability estimates were obtained when we employed GREML for family data with genomic relationship matrices weighted through patterns of regional linkage disequilibrium. Estimation of SNP-based heritability should be recommended for traits that can only be phenotyped in smaller samples or are cost-effective.

The GCKR-P446L gene variant predisposes to raised blood cholesterol and lower blood glucose in the P446L mouse-a model for GCKR rs1260326

ObjectivesThe Glucokinase Regulatory Protein GKRP, encoded by GCKR, enables acute regulation of liver glucokinase to support metabolic demand. The common human GCKR rs1260326:Pro446 > Leu variant within a large linkage disequilibrium region associates with pleiotropic traits including lower Type 2 diabetes risk and raised blood triglycerides and cholesterol. Whether the GCKR-P446 > L substitution is causal to the raised lipids is unknown. We determined whether mouse GKRP phenocopies the human GKRP:P446 > L substitution and studied a GKRP:P446L knockin mouse to identify physiological consequences to P446 > L. MethodsGKRP-deficient hepatocytes were transfected with adenoviral vectors for human or mouse GKRP:446 P or 446 L for cellular comprehensive analysis including transcriptomics consequent to P446 > L. Physiological traits in the diet-challenged P446L mouse were compared with pleiotropic associations at the human rs1260326 locus. Transcriptomics was compared in P446L mouse liver with hepatocytes overexpressing glucokinase or GKRP:446 P/L. Results1. P446 > L substitution in mouse or human GKRP similarly compromises protein expressivity of GKRP:446 L, nuclear sequestration of glucokinase and counter-regulation of gene expression. 2. The P446L knockin mouse has lower liver glucokinase and GKRP protein similar to human liver homozygous for rs1260326-446 L. 3. The diet-challenged P446L mouse has lower blood glucose, raised blood cholesterol and altered hepatic cholesterol homeostasis consistent with relative glucokinase-to-GKRP excess, but not raised blood triglycerides. ConclusionsMouse GKRP phenocopies the human GKRP:P446 > L substitution despite the higher affinity for glucokinase of human GKRP. The diet-challenged P446L mouse replicates several traits found in association with the rs1260326 locus on chromosome 2 including raised blood cholesterol, lower blood glucose and lower liver glucokinase and GKRP protein but not raised blood triglycerides.

Evidence of epistasis in regions of long-range linkage disequilibrium across five complex diseases in the UK Biobank and eMERGE datasets

Leveraging linkage disequilibrium (LD) patterns as representative of population substructure enables the discovery of additive association signals in genome-wide association studies (GWASs). Standard GWASs are well-powered to interrogate additive models; however, new approaches are required for invesigating other modes of inheritance such as dominance and epistasis. Epistasis, or non-additive interaction between genes, exists across the genome but often goes undetected because of a lack of statistical power. Furthermore, the adoption of LD pruning as customary in standard GWASs excludes detection of sites that are in LD but might underlie the genetic architecture of complex traits. We hypothesize that uncovering long-range interactions between loci with strong LD due to epistatic selection can elucidate genetic mechanisms underlying common diseases. To investigate this hypothesis, we tested for associations between 23 common diseases and 5,625,845 epistatic SNP-SNP pairs (determined by Ohta's D statistics) in long-range LD (>0.25 cM). Across five disease phenotypes, we identified one significant and four near-significant associations that replicated in two large genotype-phenotype datasets (UK Biobank and eMERGE). The genes that were most likely involved in the replicated associations were (1) members of highly conserved gene families with complex roles in multiple pathways, (2) essential genes, and/or (3) genes that were associated in the literature with complex traits that display variable expressivity. These results support the highly pleiotropic and conserved nature of variants in long-range LD under epistatic selection. Our work supports the hypothesis that epistatic interactions regulate diverse clinical mechanisms and might especially be driving factors in conditions with a wide range of phenotypic outcomes.

Development of a new AgriSeq 4K mid-density SNP genotyping panel and its utility in pearl millet breeding.

Pearl millet is a crucial nutrient-rich staple food in Asia and Africa and adapted to the climate of semi-arid topics. Since the genomic resources in pearl millet are very limited, we have developed a brand-new mid-density 4K SNP panel and demonstrated its utility in genetic studies. A set of 4K SNPs were mined from 925 whole-genome sequences through a comprehensive in-silico pipeline. Three hundred and seventy-three genetically diverse pearl millet inbreds were genotyped using the newly-developed 4K SNPs through the AgriSeq Targeted Genotyping by Sequencing technology. The 4K SNPs were uniformly distributed across the pearl millet genome and showed considerable polymorphism information content (0.23), genetic diversity (0.29), expected heterozygosity (0.29), and observed heterozygosity (0.03). The SNP panel successfully differentiated the accessions into two major groups, namely B and R lines, through genetic diversity, PCA, and structure models as per their pedigree. The linkage disequilibrium (LD) analysis showed Chr3 had higher LD regions while Chr1 and Chr2 had more low LD regions. The genetic divergence between the B- and R-line populations was 13%, and within the sub-population variability was 87%. In this experiment, we have mined 4K SNPs and optimized the genotyping protocol through AgriSeq technology for routine use, which is cost-effective, fast, and highly reproducible. The newly developed 4K mid-density SNP panel will be useful in genomics and molecular breeding experiments such as assessing the genetic diversity, trait mapping, backcross breeding, and genomic selection in pearl millet.

Combined linkage mapping and association analysis uncovers candidate genes for 25 leaf-related traits across three environments in maize.

Combined linkage and association analysis revealed five co-localized genetic loci across multiple environments. The key gene Zm00001d026491 was further verified to influence leaf length by candidate gene association analysis. Leaf morphology and number determine the canopy structure and thus affect crop yield. Herein, the genetic basis and key genes for 25 leaf-related traits, including leaf lengths (LL), leaf widths (LW), and leaf areas (LA) of eight continuous leaves under the tassel, and the number of leaves above the primary ear (LAE), were dissected by using an association panel and a biparental population. Using an intermated B73 × Mo17 (IBM) Syn10 doubled haploid (DH) population, 290 quantitative trait loci (QTL) controlling these traits were detected across different locations, among which 115 QTL were individually repeatedly identified in at least two environments. Using the association panel, 165 unique significant single-nucleotide polymorphisms (SNPs) were associated with target traits (P < 2.15E-06), of which 35 were separately detected across multiple environments. In total, 42 pleiotropic QTL/SNPs (pQTL/SNPs) were responsible for at least two of the LL, LW, LA, and LAE traits across multiple environments. Combining the QTL mapping and association study, five unique SNPs were located within the confidence intervals of seven QTL, and 77 genes were identified based on the linkage disequilibrium regions of co-localized SNP loci. Gene-based association studies verified that the intragenic variants in the candidate gene Zm00001d026491 influenced LL of the third leaf counted from the top node. These findings will provide vital information to understanding the genetic basis of leaf-related traits and help to cultivate maize varieties with ideal plant architecture.