SNP Array Research Articles

Correlation between Circle of Willis configuration and intracranial arterial dolichoectasia, and genetic contributions

ObjectivesIntracranial arterial dolichoectasia (IADE) is characterized by the dilation, elongation, and tortuosity of intracranial arteries. We aimed to investigate the association between variations of the Circle of Willis (COW) and IADE in the general population, as well as estimate the genetic correlation between COW variations and IADE. MethodsA total of 981 individuals from a population-based cohort were included. Brain magnetic resonance angiography was performed to assess COW variants and measure the diameters of intracranial arteries. IADE was defined as a total intracranial volume-adjusted diameter ≥ 2 standard deviations. Logistic regression models were used to analyze the association between COW variations and IADE. The heritability and genetic correlation were estimated using genome-wide complex trait analysis (GCTA) based on single nucleotide polymorphism (SNP) array data. ResultsThe prevalence of IADE was 6.2 %. Hypoplastic/absent A1 segments were associated with an increase in contralateral ICA diameter (β ± SE, 0.279 ± 0.049; p = 0.001) and a decrease in ipsilateral ICA diameter (β ± SE, -0.300 ± 0.050; p = 0.001). Fetal-type posterior cerebral artery (FTP) was associated with a larger ICA diameter (β ± SE, 0.326 ± 0.048; p = 0.001) and a smaller BA diameter (β ± SE, -0.662 ± 0.043; p = 0.001). FTP revealed a positive genetic correlation with ICA dilation (rG = 0.259 ± 0.175; p = 0.0009) and a negative genetic correlation with BA dilation (rG = -0.192 ± 0.153, p = 0.015). ConclusionsThere was an association between COW variations and larger intracranial arterial diameters in the general population. Genetic factors may play a role in the development of intracranial arterial dilation and the formation of COW variants.

Intrapericardial Teratoma and Associated 3q29 Deletion in a Fetus: Case Report.

Depending on its location, size, and proximity to the cardiac structures, an intrapericardial teratoma may lead to severe circulatory disturbances and even fetal demise. A 34-year-old G2P1 presented at 20w5d with a solid cystic mass in the right thorax of the fetus, originating from the right atrium or lung, with signs of non-immune fetal hydrops, soon resulting in intrauterine fetal death. Detailed post-mortem autopsy revealed signs of hydrops fetalis universalis due to a spherical tumor mass originating from the aortic root. Histologic examination of the tumor showed the characteristic morphology of a teratoma. A 1.6-Mb microdeletion at 3q29 was identified by single nucleotide polymorphism array. This is the first report presenting the diagnosis of an intrapericardial teratoma in a fetus with a microdeletion of 3q29. Intrapericardial teratoma has a poor prognosis and the fetal outcome relies on the development of hydrops. A post-mortem examination is essential in order to make a definitive diagnosis, which underlines the status of the fetal pathologist and the need for interdisciplinary cooperation.

Exposure-associated DNA methylation among people exposed to multiple industrial pollutants

BackgroundCurrent research on the epigenetic repercussions of exposure to a combination of pollutants is limited. This study aims to discern DNA methylation probes associated with exposure to multiple pollutants, serving as early effect markers, and single-nucleotide polymorphisms (SNPs) as surrogate indicators for population susceptibility. The investigation involved the analysis of urine exposure biomarkers for 11 heavy metals (vanadium, arsenic, mercury, cadmium, chromium, nickel, lead, manganese, copper, strontium, thallium), polycyclic aromatic hydrocarbon (PAHs) (1-hydroxypyrene), genome-wide DNA methylation sequencing, and SNPs array on all study participants. The data were integrated with metabolomics information and analyzed both at a community level based on proximity to home addresses relative to the complex and at an individual level based on exposure biomarker concentrations.ResultsOn a community level, 67 exposure-related CpG probes were identified, while 70 CpG probes were associated with urine arsenic concentration, 2 with mercury, and 46 with vanadium on an individual level. These probes were annotated to genes implicated in cancers and chronic kidney disease. Weighted quantile sum regression analysis revealed that vanadium, mercury, and 1-hydroxypyrene contributed the most to cg08238319 hypomethylation. cg08238319 is annotated to the aryl hydrocarbon receptor repressor (AHRR) gene, and AHRR hypomethylation was correlated with an elevated risk of lung cancer. AHRR was further linked to deregulations in phenylalanine metabolism, alanine, aspartate, and glutamate metabolism, along with heightened oxidative stress. Additionally, three SNPs (rs11085020, rs199442, and rs10947050) corresponding to exposure-related CpG probes exhibited significant interaction effects with multiple heavy metals and PAHs exposure, and have been implicated in cancer progression and respiratory diseases.ConclusionOur findings underscore the pivotal role of AHRR methylation in gene-environment interactions and highlight SNPs that could potentially serve as indicators of population susceptibility in regions exposed to multiple heavy metals and PAHs.

A genotype–phenotype approach to discriminate Central European spelt landraces from modern wheat-spelt intercrosses in the Swiss context

Marketed as a healthier alternative to bread wheat, spelt (Triticum aestivum ssp. spelta) is in increasing demand from consumers and bakers in Switzerland. The Swiss spelt landscape is currently dominated by two varieties—Ostro and Oberkulmer Rotkorn—considered as references for Swiss “typical” spelt. However, these two varieties are rather old and deliver low yields; the market therefore needs improved spelt varieties with higher agronomic potential while keeping the essential attributes of typical spelt. As spelt and winter wheat can be interbred, modern spelt varieties often result from crosses between the two. It has therefore become increasingly difficult to distinguish between typical spelt and modern wheat-spelt intercrosses. This project aims to clarify the phenotypic distinction between typical spelt and modern wheat-spelt intercrosses in the Swiss context. To do this, we performed field trials with 50 spelt varieties, including typical and modern cultivars from Switzerland and Central Europe. We measured agronomic, rheological and nutritional parameters of each variety. In addition, these cultivars were genotyped using a 25 K Illumina Wheat SNP array. This allowed us to identify which phenotypic parameters were associated with genetic proximity to typical spelt. Swiss typical spelt varieties were characterized by highly extensible doughs, later phenology, low harvest index, high thousand kernel weights, and lower Zeleny/protein ratio. By linking phenotypic characteristics, easily measurable in fields, to the underlying genetic information of each variety, these results will help to better classify spelt varieties in Switzerland and pave the way for more clarity and transparency on the Swiss spelt market.

Identification of interactions between genetic risk scores and dietary patterns for personalized prevention of kidney dysfunction in a population-based cohort

Background & AimChronic kidney disease (CKD) is a heterogeneous disorder that affects the kidney structure and function. This study investigated the effect of the interaction between genetic factors and dietary pattern on kidney dysfunction in Korean adults.MethodsBaseline data were obtained from the Ansan and Ansung Study of the Korean Genome and Epidemiology Study involving 8230 participants aged 40–69 years. Kidney dysfunction was defined as an estimated glomerular filtration rate < 90 mL/minute/1.73 m2. Genomic DNAs genotyped on the Affymetrix® Genome-Wide Human SNP array 5.0 were isolated from peripheral blood. A genome-wide association study using a generalized linear model was performed on 1,590,162 single-nucleotide polymorphisms (SNPs). To select significant SNPs, the threshold criterion was set at P-value < 5 × 10−8. Linkage disequilibrium clumping was performed based on the R2 value, and 94 SNPs had a significant effect. Participants were divided into two groups based on their generic risk score (GRS): the low-GR group had GRS > 0, while the high-GR group had GRS ≤ 0.ResultsThree distinct dietary patterns were extracted, namely, the “prudent pattern,” “flour-based and animal food pattern,” and “white rice pattern,” to analyze the effect of dietary pattern on kidney function. In the “flour-based and animal food pattern,” higher pattern scores were associated with a higher prevalence of kidney dysfunction in both the low and high GR groups (P for trend < 0.0001 in the low-, high-GR groups of model 1; 0.0050 and 0.0065 in the low-, high-GR groups of model 2, respectively).ConclusionsThe results highlight a significant association between the ‘flour-based and animal food pattern’ and higher kidney dysfunction prevalence in individuals with both low and high GR. These findings suggest that personalized nutritional interventions based on GR profiles may become the basis for presenting GR-based individual dietary patterns for kidney dysfunction.

Two dwarfing genes Rht-B1b and Rht-D1b show pleiotropic effects on grain protein content in bread wheat (Triticum aestivum L.).

Five QTL for wheat grain protein content were identified, and the effects of two dwarfing genes Rht-B1b and Rht-D1b on grain protein content were validated in multiple populations. Grain protein content (GPC) plays an important role in wheat quality. Here, a recombinant inbred line (RIL) population derived from a cross between Yangmai 12 (YM12) and Yanzhan 1 (YZ1) was used to identify quantitative trait loci (QTL) for GPC. Two hundred and five RILs and their parents were grown in three years in randomized complete blocks each with two replications, and genotyped using the wheat 55K SNP array. Five QTL were identified for GPC on chromosomes 1A, 1B, 2D, 4B, and 4D. Notably, QGpc.yaas-4B (co-located with Rht-B1) and QGpc.yaas-4D (co-located with Rht-D1) were consistently detected across all experiments and best linear unbiased estimating, accounting for 6.61-8.39% and 6.05-10.21% of the phenotypic variances, respectively. The effects of these two dwarfing alleles Rht-B1b and Rht-D1b on reducing GPC and plant height were validated in two additional RIL populations and one natural population. This study lays a foundation for further investigating the effects of dwarfing genes Rht-B1b and Rht-D1b on wheat GPC.

The molecular profile of gastric intraepithelial foveolar type neoplasia based on somatic copy number alterations and multiple mutation analysis

BackgroundGastric foveolar type neoplasia is a rare histological variant of gastric tumors. It is very difficult to differentiate between benign and malignant intraepithelial foveolar neoplasia (IFN). Although limited molecular alterations have been identified in IFNs, somatic copy number alterations (SCNAs), which are linked to tumor progression, have not been systematically evaluated in IFN.MethodsThe aim of the present study was to comprehensively examine SCNAs using a SNP array in 37 cases of IFN, compared with intestinal type dysplasia, including 39 low grade (LGD) and 32 high grade dysplasia (HGD) cases. In addition, gene mutations were evaluated using a gene panel. Finally, we attempted to determine molecular profiles using a hierarchical clustering analysis.ResultsTwo patterns could be categorized according to the SCNAs in 108 tumors examined: high (subgroup 1) and low (subgroup 2) frequencies of SCNAs. Although IFN and LGD were associated with subgroup 2, HGD was found in both subgroups. The median numbers of total SCNAs and copy number gains were higher in IFN or HGD than in LGD. In addition, the IFN genotype was characterized by altered genes located at 4p13–4q35.2, including RAP1GDS1 and LEF1, which may be associated with IFN development. Finally, no significant mutations were found in IFNs using a gene panel.ConclusionsThe current molecular profiles of IFN may help elucidate the mechanisms of IFN development.

Decoding the fish genome opens a new era in important trait research and molecular breeding in China.

Aquaculture represents the fastest-growing global food production sector, as it has become an essential component of the global food supply. China has the world's largest aquaculture industry in terms of production volume. However, the sustainable development of fish culture is hindered by several concerns, including germplasm degradation and disease outbreaks. The practice of genomic breeding, which relies heavily on genome information and genotypephenotype relationships, has significant potential for increasing the efficiency of aquaculture production. In 2014, the completion of the genome sequencing and annotation of the Chinese tongue sole signified the beginning of the fish genomics era in China. Since then, domestic researchers have made dramatic progress in functional genomic studies. To date, the genomes of more than 60 species of fish in China have been assembled and annotated. Based on these reference genomes, evolutionary, comparative, and functional genomic studies have revolutionized our understanding of a wide range of biologically and economically important traits of fishes, including growth and development, sex determination, disease resistance, metamorphosis, and pigmentation. Furthermore, genomic tools and breeding techniques such as SNP arrays, genomic selection, and genome editing have greatly accelerated genetic improvement through the incorporation of functional genomic information into breeding activities. This review aims to summarize the current status, advances, and perspectives of the genome resources, genomic study of important traits, and genomic breeding techniques of fish in China. The review will provide aquaculture researchers, fish breeders, and farmers with updated information concerning fish genomic research and breeding technology. The summary will help to promote the genetic improvement of production traits and thus will support the sustainable development of fish aquaculture.

Genomic profiles and clinical presentation of chordoma

Chordoma is a rare bone cancer with variable clinical outcomes. Here, we recruited 184 sporadic chordoma patients from the US and Canada and collected their clinical and treatment data. The average age at diagnosis was 45.5 years (Range 5–78) and the chordoma site distribution was 49.2% clivus, 26.2% spinal, and 24.0% sacral. Most patients (97.5%) received surgery as the primary treatment, among whom 85.3% also received additional treatment. Except for the most prevalent cancers like prostate, lung, breast, and skin cancer, there was no discernible enrichment for any specific cancer type among patients or their family members. Among a subset of patients (N = 70) with tumor materials, we conducted omics analyses and obtained targeted panel sequencing and SNP array genotyping data for 51 and 49 patients, respectively. The most recurrent somatic driver mutations included PIK3CA (12%), followed by chromatin remodeling genes PBRM1 and SETD2. Amplification of the 6q27 region, containing the chordoma susceptibility gene TBXT, was detected in eight patients (16.3%). Clival patients appeared to be less likely to carry driver gene mutations, chromosome arm level deletion events (e.g., 5p, 5p, and 9p), or 6q27 amplification compared to sacral patients. After adjusting for age, sex, tumor site, and additional treatment, patients with somatic deletions of 14q (OR = 13.73, 95% CI 1.96–96.02, P = 0.008) and 18p (OR = 13.68, 95% CI 1.77–105.89, P = 0.012) were more likely to have persistent chordoma. The study highlights genomic heterogeneity in chordoma, potentially linked to location and clinical progression.

Interplay between polygenic risk score and solar insolation: Implication for systemic lupus erythematosus diagnosis and pathogenesis

ObjectivesThis research elucidates the correlation between solar radiation insolation, polygenic risk score (PRS), and systemic lupus erythematosus (SLE) diagnosis, utilizing genomic, environmental, and clinical data. MethodsWe included 1,800 SLE participants and 1,800 controls from the Taiwan Precision Medicine Initiative, genotyped via the Affymetrix Genome-Wide TWB 2.0 SNP Array. The study employed a SLE-PRS tailored for individuals of Taiwanese ancestry, comprising 27 single nucleotide polymorphisms (SNPs). QGIS computed solar radiation insolation from participants' residences. We employed logistic regression to investigate the associations between SLE-PRS, solar insolation susceptibility, and SLE. Additive and multiplicative interactions were utilized to assess the interactions between solar insolation and SLE-PRS regarding the risk of SLE. ResultsSLE patients showed decreased solar insolation (p < 0.001). The highest decile of SLE-PRS exhibited a statistically significant lower solar insolation 1, 3, 6, and 12 months prior to diagnosis as compared to the lowest decile. Specifically, there were significant differences observed at 1 and 12 months (p = 0.025 and p = 0.004, respectively). It suggests that higher SLE-PRS correlated with reduced solar insolation tolerance. We observed an increase in SLE risk across ascending SLE-PRS percentiles exclusively in the high solar insolation group, not in the low solar insolation group. However, the interaction effect of SLE-PRS and solar insolation on SLE risk is not statistically significant. Compared to the lowest decile, the highest SLE-PRS decile showed a 10.98-fold increase in SLE risk (95 % CI, 3.773–31.952, p < 0.001). High SLE-PRS scores in conjunction with high solar insolation contribute to SLE incidence. ConclusionsOur study unveils the intertwined nature of UV insolation and polygenic risks in SLE. Future studies should explore the preventative potential of robust solar radiation protection for high-risk individuals before the disease onset.

Whole paternal uniparental disomy of chromosome 4 with a novel homozygous IDUA splicing variant, c.159-9T>A, in a Chinese patient with mucopolysaccharidosis type I.

Mucopolysaccharidosis type I (MPS-I) is a rare autosomal recessive genetic lysosomal storage disorder that is caused by pathogenic variants of the α-L-iduronidase (IDUA) gene. This study aimed to identify the genetic causes of MPS-I in a Chinese patient and construct a minigene of IDUA to analyze its variants upon splicing. Whole-exome sequencing (WES) and Sanger sequencing were used to confirm the potential causative variants. Single-nucleotide polymorphism (SNP) array was subsequently performed to confirm uniparental disomy (UPD). Minigene assay was performed to analyze the effect on splicing of mRNA. We meanwhile explored the conservative analysis and protein homology simulation. A novel homozygous splicing mutation of IDUA, c.159-9T>A, was identified in an individual presenting with overlapping features of MPS-I. Interestingly, only the father and sisters, but not the mother, carried the variant in a heterozygous state. WES and SNP array analyses validated paternal UPD on chromosome 4. Minigene splicing revealed two aberrant splicing events: exon 2 skipping and intron 1 retention. Moreover, the specific structure of the mutant protein obviously changed according to the results of the homologous model. This study describes a rare autosomal recessive disorder with paternal UPD of chromosome 4 leading to the homozygosity of the IDUA splicing variant in patients with MPS-I for the first time. This study expands the variant spectrum of IDUA and provides insights into the splicing system, facilitating its enhanced diagnosis and treatment.

Structural Variants in the SMC1A Gene Associated With Near-Haploidy in Undifferentiated Pleomorphic Sarcomas.

Near-haploidization, that is, loss of one copy of most chromosomes, is a relatively rare phenomenon in most tumors, but is enriched among certain soft tissue sarcomas, including undifferentiated pleomorphic sarcoma (UPS). Presumably, near-haploidization can arise through many mechanisms. This study aimed to identify gene rearrangements that could cause near-haploidization. We here present two UPS in which near-haploidization was an early event, identified through single nucleotide polymorphism (SNP) array analysis. One of the cases was studied further using whole genome and transcriptome sequencing, as well as cytogenetic and molecular cytogenetic methods. Both tumors had chromosomal rearrangements in the form of copy number shifts/structural variants affecting the SMC1A gene. These findings suggest that cohesin defects could contribute to mitotic errors resulting in massive loss of chromosomes. SMC1A encodes one of the components of the cohesin multiprotein complex, which is critical for proper alignment of the sister chromatids during S-phase and separation to opposite spindle poles. Further studies should explore the role of cohesin defects in near-haploidization in other sarcomas and to clarify its role in tumor development.

Application effectiveness of "Youxin-1" in genetic diversity and structure analysis of local chickens.

China's local chicken breeds are rich in resources, and have formed different germplasm characteristics in the process of long-term selection and evolution. Scientific assessment of population genetic diversity and identification of inter-breed genetic structure are of great value to the protection and innovative utilization of local chicken breed resource. In order to evaluate the application effectiveness of 23K SNP chip "Youxin-1" in the analysis of genetic diversity and genetic structure of local chickens, we used RADseq to identify genomic genetic variation of 21 local chicken breeds and developed 23K chip "Youxin-1". The genetic statistics of each variety were calculated based on two sets of SNP data, and correlation, fitting and phylogenetic analysis were carried out to evaluate the application effectiveness of the chip. The results showed that the observed heterozygosity (Ho), polymorphism information content (PIC), inbred coefficient (FROH) and genetic differentiation coefficient (Fst) calculated based on the two SNP data sets were basically consistent in the 21 local chicken breeds. The genetic diversity of Langya chicken (LA), Piao chicken (PJ) and Wenchang chicken (WC) was relatively rich. The genetic diversity of Bian chickens (BJ), Langshan chickens (LS), Gushi chickens (GS), Dongxiang blue-eggshell chickens (DX) and Beijing fatty chickens (BY) was relatively poor, and the correlation coefficients of Ho, PIC, FROH and average Fst in the two groups were 0.794, 0.901, 0.926 and 0.984, respectively, all reaching extremely significant levels (P<0.01) with a high degree of fit (P<0.001) and R2 were 0.644, 0.827, 0.916 and 0.927. For the two sets of SNP data, the evolutionary tree constructed by neighbor-joining (NJ) method and maximum likelihood (ML) method was reasonable, and the 21 local chicken breeds were generally divided into six categories, which was consistent with the formation history and geographical distribution of the varieties. The 23K chip also realized reasonable clustering of the five new varieties without individual deviation. There are some differences in the estimation of genetic statistics using SNP with different densities, and data standardization is needed. 23K chip has good efficacy in the analysis of genetic diversity and structure of local chickens.

To be or not to be tetraploid-the impact of marker ploidy on genomic prediction and GWAS of potato.

Cultivated potato, Solanum tuberosum L., is considered an autotetraploid with 12 chromosomes with four homologous phases. However, recent evidence found that, due to frequent large phase deletions in the genome, gene ploidy is not constant across the genome. The elite cultivar "Otava" was found to have an average gene copy number of 3.2 across all loci. Breeding programs for elite potato cultivars rely increasingly on genomic prediction tools for selection breeding and elucidation of quantitative trait loci underpinning trait genetic variance. These are typically based on anonymous single nucleotide polymorphism (SNP) markers, which are usually called from, for example, SNP array or sequencing data using a tetraploid model. In this study, we analyzed the impact of using whole genome markers genotyped as either tetraploid or observed allele frequencies from genotype-by-sequencing data on single-trait additive genomic best linear unbiased prediction (GBLUP) genomic prediction (GP) models and single-marker regression genome-wide association studies of potato to evaluate the implications of capturing varying ploidy on the statistical models employed in genomic breeding. A panel of 762 offspring of a diallel cross of 18 parents of elite breeding material was used for modeling. These were genotyped by sequencing and phenotyped for five key performance traits: chipping quality, length/width ratio, senescence, dry matter content, and yield. We also estimated the read coverage required to confidently discriminate between a heterozygous triploid and tetraploid state from simulated data. It was found that using a tetraploid model neither impaired nor improved genomic predictions compared to using the observed allele frequencies that account for true marker ploidy. In genome-wide associations studies (GWAS), very minor variations of both signal amplitude and number of SNPs supporting both minor and major quantitative trait loci (QTLs) were observed between the two data sets. However, all major QTLs were reproducible using both data sets.

Development and identification of a novel wheat-Thinopyrum ponticum disomic substitution line DS5Ag(5D) with new genes conferring resistance to powdery mildew and leaf rust

BackgroundPowdery mildew (caused by Blumeria graminis f. sp. tritici (Bgt)) and leaf rust (caused by Puccinia triticina (Pt)) are prevalent diseases in wheat (Triticum aestivum L.) production. Thinopyrum ponticum (2n = 10x = 70, EeEeEbEbExExStStStSt) contains genes that confer high levels of resistance to these diseases.ResultsAn elite wheat-Th. ponticum disomic substitution line, DS5Ag(5D), was developed in the Bainong Aikang 58 (AK58) background. The line was assessed using genomic in situ hybridization (GISH), oligo-nucleotide probe multiplex (ONPM) fluorescence in situ hybridization (FISH), and molecular markers. Twenty eight chromosome-specific molecular markers were identified for the alien chromosome, and 22 of them were co-dominant. Additionally, SNP markers from the wheat 660 K SNP chip were utilized to confirm chromosome identification and they provide molecular tools for tagging the chromosome in concern. The substitution line demonstrated high levels of resistance to powdery mildew throughout its growth period and to leaf rust at the adult stage. Based on the resistance evaluation of five F5 populations between the substitution lines and wheat genotypes with different levels of sensitivity to the two diseases. Results showed that the resistance genes located on 5Ag confered stable resistance against both diseases across different backgrounds. Resistance spectrum analysis combined with diagnostic marker detection of known resistance genes of Th. ponticum revealed that 5Ag contained two novel genes, Pm5Ag and Lr5Ag, which conferred resistance to powdery mildew and leaf rust, respectively.ConclusionsIn this study, a novel wheat-Th. ponticum disomic substitution line DS5Ag(5D) was successfully developed. The Th. ponticum chromosome 5Ag contain new resistance genes for powdery mildew and leaf rust. Chromosomic—specific molecular markers were generated and they can be used to track the 5Ag chromosome fragments. Consequently, this study provides new elite germplasm resources and molecular markers to facilitate the breeding of wheat varieties that is resistant to powdery mildew and leaf rust.

Review on camel genetic diversity: ecological and economic perspectives.

Camels, known as the "Ship of the Desert," play a vital role in the ecosystems and economies of arid and semi-arid regions. They provide meat, milk, transportation, and other essential services, and their resilience to harsh environments makes them invaluable. Despite their similarities, camel breeds exhibit notable differences in size, color, and structure, with over 40million camels worldwide. This number is projected to increase, underscoring their growing significance. Economically, camels are crucial for food production, tourism, and trade, with camel racing being particularly significant in Arab countries. Their unique physiological traits, such as low disease susceptibility and efficient water conservation, further enhance their value. Camel products, especially meat and milk, offer substantial nutritional and therapeutic benefits, contributing to their high demand. Genetic diversity studies have advanced our understanding of camels' adaptation to extreme environments. Functional genomics and whole-genome sequencing have identified genes responsible for these adaptations, aiding breeding programs and conservation efforts. High-throughput sequencing has revealed genetic markers linked to traits like milk production and disease resistance. The development of SNP chips has revolutionized genetic studies by providing a cost-effective alternative to whole-genome sequencing. These tools facilitate large-scale genotyping, essential for conserving genetic diversity and improving breeding strategies. To prevent the depletion of camel genetic diversity, it is crucial to streamline in situ and ex situ conservation efforts to maintain their ecological and economic value. A comprehensive approach to camel conservation and genetic preservation, involving advanced genomic technologies, reproductive biotechniques, and sustainable management practices, will ensure their continued contribution to human societies.

Development and validation of a 40 K liquid SNP array for the mud crab (Scylla paramamosain)

Genomic selection (GS) and genome-wide association studies (GWAS) have been widely implemented to accelerate the genetic improvement of important economic traits. Developing an efficient and reliable high-throughput genotyping tool is the premise and basis of implementing GS and GWAS on the mud crab (Scylla paramamosain). In this study, leveraging the whole-genome resequencing data of 146 mud crabs from the southeast coast of China, a total of 16,714,943 high-quality SNPs were discovered. Based on polymorphic information content and evenly distribution on 49 chromosomes, a total of 40,352 SNPs was selected to develop a 40 K liquid SNP array (named “Xiexin No. 1”) using the genotyping by target sequencing (GBTS) technology. The genotyping performance test showed that this SNP array had a high site polymorphism (over 92.70%) and individual calling rate (97.02%). Furthermore, the mean of SNP concordance, genotype concordance, non-reference sensitivity, and non-reference discrepancy between “Xiexin No. 1” SNP array and resequencing were identified to be 0.986, 0.954, 0.942, and 0.097, respectively. Using this SNP array data, the genomic heritabilities were evaluated as 0.887 ± 0.065, 0.643 ± 0.108, 0.599 ± 0.111, and 0.624 ± 0.111 for body weight (BW), carapace length (CL), carapace length (CW), and body height (BH) in a cultured population (233 crabs). Furthermore, five significant SNPs associated with growth traits were identified by GWAS. After annotation, one candidate gene (XP_027221997.1) associated with BW and one candidate gene (XP_027210446.1) associated with CW and BH were identified. Most importantly, the prediction accuracy of GBLUP for BW, BH, CL, and CW were 0.535 ± 0.064, 0.544 ± 0.101, 0.574 ± 0.087, and 0.585 ± 0.083, with the unbiasedness values of 0.988 ± 0.22, 1.015 ± 0.274, 1.011 ± 0.196 and 1.037 ± 0.235. In conclusion, the “Xiexin No. 1” SNP array provides an efficient and reliable platform for high-quality genotyping, which would greatly promote the genetic studies and thus accelerate the genetic improvement of mud crabs.

Asian Screening Array and Next-Generation Sequencing Based Panels Applied to Preimplantation Genetic Testing for Monogenic Disorders Preclinical Workup in 294 Families: A Retrospective Analysis.

Currently, the most commonly used methods for linkage analysis of pre-implantation genetic testing for monogenic disorders (PGT-M) are next generation sequencing (NGS) and SNP array. We aim to investigate whether the application efficacy of Asian screening array (ASA) in PGT-M preclinical workup for the Chinese population is superior to NGS based single nucleotide polymorphism (SNP) panels. We conducted a retrospective analysis by reviewing 294 couples from a single center over the past 4years and compared the detection results between NGS-based SNP panels and ASA. Using the numbers of informative SNPs upstream and downstream flanking of variants, we assessed the detection efficiency of both methods in monogenic diseases, chromosomal microdeletion syndrome and males with de novo variants, among other scenarios. Results indicate that ASA offers a greater number of informative SNPs compared with NGS-based SNP panels. Additionally, data analysis for ASA is generally more straightforward and may require less computational resources. While ASA can address most PGT-M challenges, we have also identified certain genes in previous tests that are not suitable for PGT-M using ASA. The application of ASA in PGT-M preclinical workup for Chinese populations has good practical value as it can perform linkage analysis for most genetic variants. However, for certain variants, NGS or other testing methods, such as mutated allele revealed by sequencing with aneuploidy and linkage analysis (MARSALA), may still be necessary for completion.

Detection and evaluation of parameters influencing the identification of heterozygous-enriched regions in Holstein cattle based on SNP chip or whole-genome sequence data

BackgroundA heterozygous-enriched region (HER) is a genomic region with high variability generated by factors such as balancing selection, introgression, and admixture processes. In this study, we evaluated the genomic background of HERs and the impact of different parameters (i.e., minimum number of SNPs in a HER, maximum distance between two consecutive SNPs, minimum length of a HER, maximum number of homozygous allowed in a HER) and scenarios [i.e., different SNP panel densities and whole-genome sequence (WGS)] on the detection of HERs. We also compared HERs characterized in Holstein cattle with those identified in Angus, Jersey, and Norwegian Red cattle using WGS data.ResultsThe parameters used for the identification of HERs significantly impact their detection. The maximum distance between two consecutive SNPs did not impact HERs detection as the same average of HERs (269.31 ± 787.00) was observed across scenarios. However, the minimum number of markers, maximum homozygous markers allowed inside a HER, and the minimum length size impacted HERs detection. For the minimum length size, the 10 Kb scenario showed the highest average number of HERs (1,364.69 ± 1,483.64). The number of HERs decreased as the minimum number of markers increased (621.31 ± 1,271.83 to 6.08 ± 21.94), and an opposite pattern was observed for the maximum homozygous markers allowed inside a HER (54.47 ± 195.51 to 494.89 ± 1,169.35). Forty-five HER islands located in 23 chromosomes with high Tajima’s D values and differential among the observed and estimated heterozygosity were detected in all evaluated scenarios, indicating their ability to potentially detect regions under balancing selection. In total, 3,440 markers and 28 genes previously related to fertility (e.g., TP63, ZSCAN23, NEK5, ARHGAP44), immunity (e.g., TP63, IGC, ARHGAP44), residual feed intake (e.g., MAYO9A), stress sensitivity (e.g., SERPINA6), and milk fat percentage (e.g., NOL4) were identified. When comparing HER islands among breeds, there were substantial overlaps between Holstein with Angus (95.3%), Jersey (94.3%), and Norwegian Red cattle (97.1%), indicating conserved HER across taurine breeds.ConclusionsThe detection of HERs varied according to the parameters used, but some HERs were consistently identified across all scenarios. Heterozygous genotypes observed across generations and breeds appear to be conserved in HERs. The results presented could serve as a guide for defining HERs detection parameters and further investigating their biological roles in future studies.

Genetic Analysis of Stripe Rust Resistance in the Chinese Wheat Cultivar Luomai 163.

Stripe or yellow rust (YR) caused by Puccinia striiformis tritici (Pst) is an important foliar disease affecting wheat production globally. Resistant varieties are the most economically and environmentally effective way to manage this disease. The common winter wheat (Triticum aestivum L.) cultivar Luomai 163 exhibited resistance to Pst races CYR32 and CYR33 at the seedling stage and showed a high level adult plant resistance in the field. To understand the genetic basis of YR resistance in this cultivar, 142 F5 recombinant inbred lines (RILs) derived from cross Apav#1 × LM163 and both parents were genotyped with the 16K SNP array and bulked segregant analysis sequencing (BSA-Seq). The analysis detected a major gene, YrLM163, at the seedling stage associated with the 1BL.1RS translocation. Additionally, three genes for resistance at the adult plant stage were detected on chromosome arms 1BL (Lr46/Yr29/Pm39/Sr58), 6BS and 6BL in Luomai 163, whereas Apav#1 contributed resistance at a QTL on 2BL. These QTL explained YR disease severity variations ranging from 6.9 to 54.8%. KASP markers KASP-2BL, KASP-6BS and KASP-6BL for three novel loci QYr.hzau-2BL, QYr.hzau-6BS and QYr.hzau-6BL were developed and validated. QYr.hzau-1BL, QYr.hzau-2BL and QYr.hzau-6BS showed varying degrees of resistance to YR when present individually or in combination based on genotype and phenotype analysis of a panel of 570 wheat accessions. Six RILs combining resistance alleles of all QTL, showing higher resistance to YR in the field than Luomai 163 with disease severities of 10.7-16.0%, are important germplasm resources for breeding programs to develop YR resistant wheat varieties with good agronomic traits.