SNP Loci Research Articles

Genetic diversity analysis of different geographic populations of black carp (Mylopharyngodon piceus) based on whole genome SNP markers

Black carp, Mylopharyngodon piceus, is one of the major farmed fish in China, generating a considerable amount of economic value annually. To investigate the genetic variation of black carp germplasm resources in China, this study was the first to use the whole genome SNPs of black carp for analysis. A total of 139 samples of nine black carp populations in the Yangtze River and Pearl River Systems of China were collected, and 53,322 high-quality SNP loci were obtained after GBS sequencing and filtering. Genetic diversity parameters were calculated for nine populations of black carp based on these genetic data. All 7 populations from the Yangtze River system and 2 populations from the Pearl River system showed high level of genetic diversity. For each population, the nucleotide diversity (π) varied from 0.283 to 0.308, the observed heterozygosity (Ho) from 0.271 to 0.317, the expected heterozygosity (He) from 0.273 to 0.292，the number of effective alleles (Ne) from 1.440 to 1.475, and the polymorphism information content (PIC) from 0.224 to 0.239. The fixation index (Fst) between populations ranged from 0.036 to 0.133, remaining at low and medium differentiation. Phylogenetic tree analysis, principal component analysis (PCA) and population genetic structure analysis revealed that the nine populations could be divided into three ancestral populations. The seven populations of the Yangtze River system comprised two primary ancestral groups, with a small amount of gene flow between populations. The internal genetic structure of populations within the Pearl River system was homogeneous, with one common ancestral source as the dominant component. In conclusion, the data and results generated from this study will provide a useful addition to the genetic resources of black carp and will provide reference information for further germplasm conservation and genetic improvement of black carp.

Large changes in detected selection signatures after a selection limit in mice bred for voluntary wheel-running behavior.

In various organisms, sequencing of selectively bred lines at apparent selection limits has demonstrated that genetic variation can remain at many loci, implying that evolution at the genetic level may continue even if the population mean phenotype remains constant. We compared selection signatures at generations 22 and 61 of the "High Runner" mouse experiment, which includes 4 replicate lines bred for voluntary wheel-running behavior (HR) and 4 non-selected control (C) lines. Previously, we reported multiple regions of differentiation between the HR and C lines, based on whole-genome sequence data for 10 mice from each line at generation 61, which was >31 generations after selection limits had been reached in all HR lines. Here, we analyzed pooled sequencing data from ~20 mice for each of the 8 lines at generation 22, around when HR lines were reaching limits. Differentiation analyses of allele frequencies at ~4.4 million SNP loci used the regularized T-test and detected 258 differentiated regions with FDR = 0.01. Comparable analyses involving pooling generation 61 individual mouse genotypes into allele frequencies by line produced only 11 such regions, with almost no overlap among the largest and most statistically significant peaks between the two generations. These results implicate a sort of "genetic churn" that continues at loci relevant for running. Simulations indicate that loss of statistical power due to random genetic drift and sampling error are insufficient to explain the differences in selection signatures. The 13 differentiated regions at generation 22 with strict culling measures include 79 genes related to a wide variety of functions. Gene ontology identified pathways related to olfaction and vomeronasal pathways as being overrepresented, consistent with generation 61 analyses, despite those specific regions differing between generations. Genes Dspp and Rbm24 are also identified as potentially explaining known bone and skeletal muscle differences, respectively, between the linetypes.

Mendelian randomization analysis reveals a causal relationship between preterm birth and myopia risk.

Preterm birth has been associated with an increased risk of myopia, but the causal relationship between these two factors remains unclear. Traditional epidemiological studies are limited by confounding factors and reverse causality. Mendelian randomization (MR) analysis, utilizing genetic variants as instrumental variables, provides a robust approach to investigate causal relationships. In this study, we aimed to explore the potential causal link between preterm birth and myopia risk using a two-sample MR analysis strategy. We conducted a Mendelian randomization study to investigate the causal relationship between preterm birth and myopia risk. Genetic variants (single nucleotide polymorphisms, SNPs) were used as instrumental variables, and summary data from genome-wide association studies (GWAS) were utilized. Four regression models, including MR-Egger regression, weighted median regression, inverse variance weighted regression, and Weighted mode regression, were employed to validate the causal relationship. Sensitivity analysis was performed using the leave-one-out method. At the same time, the funnel diagram and MR-Egger test were used to judge the stability of the research results. The MR analysis revealed a significant causal effect of preterm birth on myopia risk. Both the inverse variance weighted regression and weighted median regression models showed a p-value less than 0.05, indicating a robust association. The risk of myopia increased by approximately 30% for everyone standard deviation increase in preterm birth. Sensitivity analysis, funnel plot and MR-Egger test all confirm the stability of the research results. Our findings provide evidence supporting a causal relationship between preterm birth and myopia risk. Preterm infants are at a higher risk of developing myopia, and this association is not likely to be influenced by confounding factors or reverse causality. The SNP loci rs6699397, rs10871582, and rs2570497 should be closely monitored as they may lead to abnormal concentrations of intraocular cytokines, particularly vascular endothelial growth factor, potentially elucidating one of the pathogenic mechanisms contributing to the higher incidence of myopia in preterm infants. However the complex interconnections involved extend beyond these factors alone.

Establishment and application of a SNP molecular identification system in Grifola frondosa.

Germplasm resources of edible mushrooms are essential for the breeding of varieties with improved traits. Analysis of the genetic diversity of Grifola frondosa germplasm resources and clarification of the genetic relationships among strains can provide valuable information for the selection of breeding parents. A total of 829,488 high-quality SNP loci were screened from 2,125,382 SNPs obtained by sequencing 60 G. frondose. Phylogenetic analysis, PCA, and population structure analysis based on the high-quality SNPs showed that the 60 strains could be divided into five subgroups, and the clustering results were consistent with the geographical distributions of these strains. Based on high-quality SNP loci, a core collection containing 18 representative germplasm resources was constructed, and 1,473 Kompetitive Allele-Specific PCR markers were obtained. A total of 722 SNP markers in the exonic regions were screened using KASP-genotyping experiments, and 50 candidate SNP markers and 12 core SNP markers were obtained. Genetic fingerprints of G. frondosa germplasm resources were constructed based on the selected SNP markers; these fingerprints provide an accurate, rapid, convenient, and efficient method for the identification of G. frondosa germplasm resources. The results of this study have important implications for the preservation and utilization of G. frondosa germplasm resources and the identification of varieties.

Genome-wide association analysis of fleece traits in Northwest Xizang white cashmere goat.

Northwest Xizang White Cashmere Goat (NXWCG) is the first new breed of cashmere goat in the Xizang Autonomous Region. It has significant characteristics of extremely high fineness, gloss, and softness. Genome-wide association analysis is an effective biological method used to measure the consistency and correlation of genotype changes between two molecular markers in the genome. In addition, it can screen out the key genes affecting the complex traits of biological individuals. The aim of this study was to analyze the genetic mechanism of cashmere trait variation in NXWCG and to discover SNP locus and key genes closely related to traits such as superfine cashmere. Additionally, the key genes near the obtained significant SNPs were analyzed by gene function annotation and biological function mining. In this study, the phenotype data of the four traits (cashmere length, fiber length, cashmere diameter, and cashmere production) were collected. GGP_Goat_70K SNP chip was used for genotyping the ear tissue DNA of the experimental group. Subsequently, the association of phenotype data and genotype data was performed using Gemma-0.98.1 software. A linear mixed model was used for the association study. The results showed that four fleece traits were associated with 18 significant SNPs at the genome level and 232 SNPs at the chromosome level, through gene annotated from Capra hircus genome using assembly ARS1. A total of 107 candidate genes related to fleece traits were obtained. Combined with Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis, we can find that CLNS1A, CCSER1, RPS6KC1, PRLR, KCNRG, KCNK9, and CLYBL can be used as important candidate genes for fleece traits of NXWCG. We used Sanger sequencing and suitability chi-square test to further verify the significant loci and candidate genes screened by GWAS, and the results show that the base mutations loci on the five candidate genes, CCSER1 (snp12579, 34,449,796, A → G), RPS6KC1 (snp41503, 69,173,527, A → G), KCNRG (snp41082, 67,134,820, G → A), KCNK9 (14:78472665, 78,472,665, G → A), and CLYBL (12: 9705753, 9,705,753, C → T), significantly affect the fleece traits of NXWCG. The results provide a valuable basis for future research and contribute to a better understanding of the genetic structure variation of the goat.

Genome-Wide Association Analysis of Reproductive Traits in Chinese Holstein Cattle.

This study was to explore potential SNP loci for reproductive traits in Chinese Holstein cattle and identify candidate genes. Genome-wide Association Study based on mixed linear model was performed on 643 Holstein cattle using GeneSeek Bovine 50 K SNP chip. Our results detected forty significant SNP loci after Bonferroni correction. We identified five genes (VWC2L, STAT1, PPP3CA, LDB3, and CTNNA3) as being associated with pregnancy ratio of young cows, five genes (PAEP, ACOXL, EPAS1, GLRB, and MARVELD1) as being associated with pregnancy ratio of adult cows, and nine genes (PDE1B, SLCO1A2, ARHGAP26, ADAM10, APBB1, MON1B, COQ9, CDC42BPB, MARVELD1, and HPSE2) as being associated with daughter pregnancy rate. Our study may provide valuable insights into identifying genes related to reproductive traits and help promote the application of molecular breeding in dairy cows.

Ridge regression and deep learning models for genome-wide selection of complex traits in New Mexican Chile peppers

BackgroundGenomewide prediction estimates the genomic breeding values of selection candidates which can be utilized for population improvement and cultivar development. Ridge regression and deep learning-based selection models were implemented for yield and agronomic traits of 204 chile pepper genotypes evaluated in multi-environment trials in New Mexico, USA.ResultsAccuracy of prediction differed across different models under ten-fold cross-validations, where high prediction accuracy was observed for highly heritable traits such as plant height and plant width. No model was superior across traits using 14,922 SNP markers for genomewide selection. Bayesian ridge regression had the highest average accuracy for first pod date (0.77) and total yield per plant (0.33). Multilayer perceptron (MLP) was the most superior for flowering time (0.76) and plant height (0.73), whereas the genomic BLUP model had the highest accuracy for plant width (0.62). Using a subset of 7,690 SNP loci resulting from grouping markers based on linkage disequilibrium coefficients resulted in improved accuracy for first pod date, ten pod weight, and total yield per plant, even under a relatively small training population size for MLP and random forest models. Genomic and ridge regression BLUP models were sufficient for optimal prediction accuracies for small training population size. Combining phenotypic selection and genomewide selection resulted in improved selection response for yield-related traits, indicating that integrated approaches can result in improved gains achieved through selection.ConclusionsAccuracy values for ridge regression and deep learning prediction models demonstrate the potential of implementing genomewide selection for genetic improvement in chile pepper breeding programs. Ultimately, a large training data is relevant for improved genomic selection accuracy for the deep learning models.

Optimization of In Vitro Embryo Rescue and Development of a Kompetitive Allele-Specific PCR (KASP) Marker Related to Stenospermocarpic Seedlessness in Grape (Vitis vinifera L.).

Seedlessness is one of the highest valued agronomic traits in grapes. Embryo rescue in combination with marker-assisted selection have been widely applied in seedless grape breeding due to the advantages of increasing the ratio of seedless progenies and shortening the breeding cycle. However, the large number of deformed seedlings produced during embryo rescue and the lack of fast, efficient, and low-cost markers severely inhibit the process of seedless grape breeding. In this study, a total of eighty-three grape cultivars (51 seedless and 32 seeded) with diverse genetic backgrounds and two populations derived from embryo rescue, including 113 F1 hybrid individuals (60 seedless and 53 seeded), were utilized. We screened suitable media for converting malformed seedlings into normal seedlings, analyzed the association between the SNP in VviAGL11 and seeded/seedless phenotype, and developed a KASP marker related to stenospermocarpic seedlessness. Our results indicated that the transformation rate of 37.8% was obtained with MS medium supplemented with 2.0 mg·L-1 of 6-BA and 0.5 mg·L-1 of IBA. The presence of an A nucleotide allele at position chr18:26889437 was further confirmed to be fully associated with the stenospermocarpic seedlessness phenotype. The developed KASP marker, based on the verified SNP locus in VviAGL11, successfully distinguished the seedless and seeded genotypes with high precision and throughput. The results will contribute to enhancing the efficiency of embryo rescue and facilitate parent selection and early selection of seedless offspring with molecular markers, thereby accelerating the breeding process in seedless table grapes.

Patterns of admixture and introgression in a mosaic Mytilus galloprovincialis and Mytilus edulis hybrid zone in SW England.

The study of hybrid zones offers important insights into speciation. Earlier studies on hybrid populations of the marine mussel species Mytilus edulis and Mytilus galloprovincialis in SW England provided evidence of admixture but were constrained by the limited number of molecular markers available. We use 57 ancestry-informative SNPs, most of which have been mapped genetically, to provide evidence of distinctive differences between admixed populations in SW England and asymmetrical introgression from M. edulis to M. galloprovincialis. We combine the genetic study with analysis of phenotypic traits of potential ecological and adaptive significance. We demonstrate that hybrid individuals have brown mantle edges unlike the white or purple in the parental species, suggesting allelic or non-allelic genomic interactions. We report differences in gonad development stage between the species consistent with a prezygotic barrier between the species. By incorporating results from publications dating back to 1980, we confirm the long-term stability of the hybrid zone despite higher viability of M. galloprovincialis. This stability coincides with a dramatic change in temperature of UK coastal waters and suggests that these hybrid populations might be resisting the effects of global warming. However, a single SNP locus associated with the Notch transmembrane signalling protein shows a markedly different pattern of variation to the others and might be associated with adaptation of M. galloprovincialis to colder northern temperatures.

Genetic study on heritability and novel SNP loci of temperament in Chinese Kunming Dog

Chinese Kunming dog (CKD) is a working breed widely used by army, customs and police across the country. To better evaluate a breeding population's potential working performance and implement selective breeding for future offspring, a temperament test with five subsets, including following to trainer (FO), reaction to stranger (RS), tease by towel (TT), chase and fetch (CF) and tug of war (TW), was annually operated by the Kunming Police Dog Base since 2019. To fully utilize this behavioral data, 92 breeding animals of CKDs were genotyped by a 50K SNP chip, and a GWAS method supporting repeated measurement was adopted to estimate heritabilities and explore genetic variants associated with the five subsets. The heritabilities estimated for the five subsets ranged from 0,03 to 0.14, which showed a possibility for genetic improvement. Meanwhile, in total seven novel SNPs were identified associated with subsets FO, TT, CF and TW. In addition to that five of the seven loci are separately located within ACOT11, PRDM16, SAMD12, CPA1 and ENSCAFG00000023173 genes. Nevertheless, genetic effects of these novel loci on dog temperament should be further validated by a larger dataset in the future.

Safety tests and clinical research on buccal and nasal microneedle swabs for genomic analysis.

Conventional swabs have been used as a non-invasive method to obtain samples for DNA analysis from the buccal and the nasal mucosa. However, swabs may not always collect pure enough genetic material. In this study, buccal and nasal microneedle swab is developed to improve the accuracy and reliability of genomic analysis. A cytotoxicity test, a skin sensitivity test, and a skin irritation test are conducted with microneedle swabs. Polymer microneedle swabs meet the safety requirements for clinical research and commercial use. When buccal and nasal microneedle swabs are used, the amount of genetic material obtained is greater than that from commercially available swabs, and DNA purity is also high. The comparatively short microneedle swab (250μm long) cause almost no pain to all 25 participants. All participants also report that the microneedle swabs are very easy to use. When genotypes are compared at five SNP loci from blood of a participant and from that person's buccal or nasal microneedle swab, the buccal and nasal microneedle swabs show 100% concordance for all five SNP genotypes. Microneedle swabs can be effectively used for genomic analysis and prevention through genomic analysis, so the utilization of microneedle swabs is expected to be high.

Candidate Gene Analysis of Genetic Resistance to Gastrointestinal Nematodes in Sheep Through Association of Single Nucleotide Polymorphism with Phenotypic Traits

Background: A study was executed to analyze the genetic resistance to gastrointestinal nematodes through the association of single nucleotide polymorphism markers in Toll-like receptor genes with phenotypic indicator traits in Kilakarsal and Vembur sheep breeds. Methods: The phenotypic traits for analyzing the gastrointestinal nematode infection namely FEC, change in PCV and change in body weight were recorded. The SNP markers in TLR3, TLR5, TLR6, TLR9 and TLR10 genes were employed for genotyping. Competitive allele-specific PCR-based endpoint genotyping was used to type the SNPs. The gene and genotype frequencies were estimated by using the PEAS software program. A complete fixed effects model was utilized for analysis of the association of various genotypes at each SNP with phenotypic indicator traits. Result: The global minor allele frequency of different polymorphic SNP loci ranged from 0.06 to 0.48 with a mean of 0.23, signifying their fitness for the association study. The effect of the farm had no significant influence on FEC and change in body weight, however, had a significant effect on change in PCV (P less than 0.05). No significant difference was detected between the sexes with FEC, change in PCV and change in body weight. The TT genotype in the TLR9_1769_CT locus showed the lowest least-squares mean FEC. The remaining 22 SNP loci showed no significant difference (P greater than 0.05) with mean FEC. Association of 23 TLR SNP genotypes with change in PCV and change in body weight revealed no significant effect (P greater than 0.05).

The male and female genomes of golden pompano (Trachinotus ovatus) provide insights into the sex chromosome evolution and rapid growth

IntroductionGolden pompano (Trachinotus ovatus) is economically significant important for offshore cage aquaculture in China and Southeast Asian countries. Lack of high-quality genomic data and accurate gene annotations greatly restricts its genetic breeding progress. ObjectivesTo decode the mechanisms of sex determination and rapid growth in golden pompano and facilitate the sex- and growth-aimed genetic breeding. MethodsGenome assemblies of male and female golden pompano were generated using Illumina, PacBio, BioNano, genetic maps and Hi-C sequencing data. Genomic comparisons, whole genome re-sequencing of 202 F1 individuals, QTL mapping and gonadal transcriptomes were used to analyze the sex determining region, sex chromosome evolution, SNP loci, and growth candidate genes. Zebrafish model was used to investigate the functions of growth candidate gene. ResultsFemale (644.45 Mb) and male (652.12 Mb) genomes of golden pompano were assembled and annotated at the chromosome level. Both genomes are highly conserved and no new or highly differentiated sex chromosomes occur. A 3.5 Mb sex determining region on LG15 was identified, where Hsd17b1, Micall2 and Lmx1a were putative candidates for sex determination. Three SNP loci significantly linked to growth were pinpointed, and a growth-linked gene gpsstr1 was identified by locus BSNP1369 (G → C, 17489695, Chr23). Loss of sstr1a (homologue of gpsstr1) in zebrafish caused growth retardation. ConclusionThis study provides insights into sex chromosome evolution, sex determination and rapid growth of golden pompano.

SNP Loci and Favorable Haplotype Mining for Alkalinity Tolerance in the Rice Bud Stage

The mining of favorable SNP loci and haplotypes is of great significance for the further cloning and molecular-assisted breeding of alkalinity-tolerance genes in rice. To improve the utilization rate of saline–alkaline lands and the yield of rice, we used the 1,322,884 SNPs obtained from the sequencing 173 of rice accessions in this study. Alkalinity-tolerance-related traits, including the germination energy (GE), germination rate (GR), seedling length (SL), root length (RL), relative alkaline damage rate (RADR) of the GERADR of the GR, RADR of the SL and RADR of the RL, were evaluated in 2019 and 2020 and revealed abundant phenotypes in the studied population. A genome-wide association analysis detected 10 quantitative trait loci (QTLs) related to alkalinity tolerance. In addition, a transcriptome sequencing analysis of the alkalinity-tolerant rice variety ‘Yuedao 9’ and the alkali-sensitive rice variety ‘Tijin’ under alkalinity stress and control conditions was performed. Three candidate genes that were predicted to be related to alkalinity tolerance in rice, namely LOC_Os06g06600, LOC_Os011g44680 and LOC_Os011g44600, were screened based on gene annotation, coding sequences and haplotype analysis. The results of this study provide important genetic information for the molecular improvement of rice.

Three systems of molecular markers reveal genetic differences between varieties sabina and balkanensis in the Juniperus sabina L. range

Key messageJ. sabina var. balkanensis, that is of hybrid origin, and its maternal progenitor J. sabina var. sabina are genetically distinct with respect to cpDNA, SNP, and SilicoDArT loci. Mostly non-overlapping distributions of the sabina and balkanensis varieties are the result of their different climatic requirements.ContextJuniperus sabina L. is present in the Eurasian mountains, but its range is severely fragmented. In Europe, two varieties of J. sabina occur: var. sabina and var. balkanensis, the latter being an allotetraploid hybrid between the diploid var. sabina and a tetraploid ancestor of Juniperus thurifera L. The distribution of the two varieties is mostly disjunct.AimsAssess the taxonomic affiliation and genetic differentiation of the populations of var. sabina and var. balkanensis in Europe and Asia using cpDNA, SilicoDArT, and SNP markers. Identify climatic niches of both juniper varieties in Europe.MethodsAltogether, 21,134 SilicoDArT, 8,579 SNP, and four cpDNA loci were used. Seven climatic variables were compared in sites inhabited by var. balkanensis and the two parental species.ResultsThe SilicoDArTs and SNPs revealed a pattern of population differentiation that was congruent with the cpDNA analysis. The hybrid var. balkanensis occupies habitats with higher temperatures and intermediate levels of precipitation compared to both parental taxa.ConclusionThe low genetic variation and significant genetic differentiation among J. sabina populations likely result from the restriction of gene flow imposed by the mountain ranges. The balkanensis variety is able to cope with hot and dry climates probably thanks to the admixture of J. thurifera genes.

A missense mutation in Lama3 causes androgen alopecia

Hair loss disorders such as androgenetic alopecia have caused serious disturbances to normal human life. Animal models play an important role in exploring pathogenesis of disease and evaluating new therapies. NIH hairless mice are a spontaneous hairless mouse discovered and bred in our laboratory. In this study, we resequenced the genomes of NIH normal mice and NIH hairless mice and obtained 3,575,560 high-quality, plausible SNP loci and 995,475 InDels. The Euclidean distance algorithm was used to assess the association of SNP loci with the hairless phenotype, at a threshold of 0.62. Two regions of chromosome 18 having the highest association with the phenotype contained 345 genes with a total length of 13.98 Mb. The same algorithm was used to assess the association of InDels with the hairless phenotype at a threshold of 0.54 and revealed a region of 25.45 Mb in length, containing 518 genes. The mutation candidate gene Lama3 (NM_010680.2: c.652C>T; NP_034810.1: p. Arg217Cys) was selected based on the results of functional gene analysis and mutation prediction screening. Lama3 (R217C) mutant mice were further constructed using CRISPR/Cas9 technology, and the relationship between Lama3 point mutations and the hairless phenotype were clarified by phenotypic observation. The results showed that male Lama3 point mutation mice started to lose hair on the 80th day after birth, and the hair loss area gradually expanded over time. H&E staining of skin sections showed that the point mutation mice had increased sebaceous glands in the dermis and missing hair follicle structure (i.e., typical symptoms of androgenetic alopecia). This study is a good extension of the current body of knowledge about the function of Lama3, and the constructed Lama3 (R217C) mutant mice may be a good animal model for studying androgenetic alopecia.

Targeted sequencing of high-density SNPs provides an enhanced tool for forensic applications and genetic landscape exploration in Chinese Korean ethnic group

BackgroundIn this study, we present a NGS-based panel designed for sequencing 1993 SNP loci for forensic DNA investigation. This panel addresses unique challenges encountered in forensic practice and allows for a comprehensive population genetic study of the Chinese Korean ethnic group. To achieve this, we combine our results with datasets from the 1000 Genomes Project and the Human Genome Diversity Panel.ResultsWe demonstrate that this panel is a reliable tool for individual identification and parentage testing, even when dealing with degraded DNA samples featuring exceedingly low SNP detection rates. The performance of this panel for complex kinship determinations, such as half-sibling and grandparent-grandchild scenarios, is also validated by various kinship simulations. Population genetic studies indicate that this panel can uncover population substructures on both global and regional scales. Notably, the Han population can be distinguished from the ethnic minorities in the northern and southern regions of East Asia, suggesting its potential for regional ancestry inference. Furthermore, we highlight that the Chinese Korean ethnic group, along with various Han populations from different regional areas and certain northern ethnic minorities (Daur, Tujia, Japanese, Mongolian, Xibo), exhibit a higher degree of genetic affinities when examined from a genomic perspective.ConclusionThis study provides convincing evidence that the NGS-based panel can serve as a reliable tool for various forensic applications. Moreover, it has helped to enhance our knowledge about the genetic landscape of the Chinese Korean ethnic group.

Genome-Wide Association Study Reveals Novel Loci Associated with Body Conformation Traits in Qinchuan Cattle

A genome-wide association study (GWAS) is an effective tool for identifying the dominant genes of complex economic traits in livestock by statistical analysis of genotype data and measured phenotype data. In this study, we rigorously measured 14 body conformation traits in 254 Qinchuan cattle, comprising body weight (BW), body height (BOH), back height (BAH), buttock height (BUH), chest depth (CD), chest width (CW), hip cross height (HCH), body length (BL), hip width (HW), rump length (RL), pin bone width (PBW), chest girth (CG), abdomen circumference (AG), and calf circumference (CC). After quality control, 281,889 SNPs were generated for GWAS with different traits. A total of 250 suggestive SNPs (p < 3.54 × 10−6) were screened and 37 candidate genes were annotated. Furthermore, we performed a linkage disequilibrium analysis of SNP loci and considered published studies, identifying the eight genes (ADAMTS17, ALDH1A3, CHSY1, MAGEL2, MEF2A, SYNM, CNTNAP5, and CTNNA3) most likely to be involved in growth traits. This study provides new insights into the regulatory mechanisms of bovine body size development, which can be very useful in the development of management and breeding strategies.

Genome-wide association analysis identifies a candidate gene controlling seed size and yield in Xanthoceras sorbifolium Bunge.

Yellow horn (Xanthoceras sorbifolium Bunge) is a woody oilseed tree species whose seed oil is rich in unsaturated fatty acids and rare neuronic acids, and can be used as a high-grade edible oil or as a feedstock for biodiesel production. However, the genetic mechanisms related to seed yield in yellow horn are not well elucidated. This study identified 2 164 863 SNP loci based on 222 genome-wide resequencing data of yellow horn germplasm. We conducted genome-wide association study (GWAS) analysis on three core traits (hundred-grain weight, single-fruit seed mass, and single-fruit seed number) that influence seed yield for the years 2022 and 2020, and identified 399 significant SNP loci. Among these loci, the Chr10_24013014 and Chr10_24012613 loci caught our attention due to their consistent associations across multiple analyses. Through Sanger sequencing, we validated the genotypes of these two loci across 16 germplasms, confirming their consistency with the GWAS analysis results. Downstream of these two significant loci, we identified a candidate gene encoding an AP2 transcription factor protein, which we named XsAP2. RT-qPCR analysis revealed high expression of the XsAP2 gene in seeds, and a significant negative correlation between its expression levels and seed hundred-grain weight, as well as single-fruit seed mass, suggesting its potential role in the normal seed development process. Transgenic Arabidopsis lines with the overexpressed XsAP2 gene exhibited varying degrees of reduction in seed size, number of seeds per silique, and number of siliques per plant compared with wild-type Arabidopsis. Combining these results, we hypothesize that the XsAP2 gene may have a negative regulatory effect on seed yield of yellow horn. These results provide a reference for the molecular breeding of high-yielding yellow horn.

Identification of QTLs for resistance to 10 pathotypes of Plasmodiophora brassicae in Brassica oleracea cultivar ECD11 through genotyping-by-sequencing

Key messageTwo major quantitative trait loci (QTLs) and five minor QTLs for 10 pathotypes were identified on chromosomes C01, C03, C04 and C08 through genotyping-by-sequencing from Brassica oleracea.Clubroot caused by Plasmodiophora brassicae is an important disease in brassica crops. Managing clubroot disease of canola on the Canadian prairie is challenging due to the continuous emergence of new pathotypes. Brassica oleracea is considered a major source of quantitative resistance to clubroot. Genotyping-by-sequencing (GBS) was performed in the parental lines; T010000DH3 (susceptible), ECD11 (resistant) and 124 BC1 plants. A total of 4769 high-quality polymorphic SNP loci were obtained and distributed on 9 chromosomes of B. oleracea. Evaluation of 124 BC1S1 lines for resistance to 10 pathotypes: 3A, 2B, 5C, 3D, 5G, 3H, 8J, 5K, 5L and 3O of P. brassicae, was carried out. Seven QTLs, 5 originating from ECD11 and 2 from T010000DH3, were detected. One major QTL designated as Rcr_C03-1 on C03 contributed 16.0–65.6% of phenotypic variation explained (PVE) for 8 pathotypes: 2B, 5C, 5G, 3H, 8J, 5K, 5L and 3O. Another major QTL designated as Rcr_C08-1 on C08 contributed 8.3 and 23.5% PVE for resistance to 8J and 5K, respectively. Five minor QTLs designated as Rcr_C01-1, Rcr_C03-2, Rcr_C03-3, Rcr_C04-1 and Rcr_C08-2 were detected on chromosomes C01, C03, C04 and C08 that contributed 8.3–23.5% PVE for 5 pathotypes each of 3A, 2B, 3D, 8J and 5K. There were 1, 10 and 4 genes encoding TIR-NBS-LRR/CC-NBS-LRR class disease resistance proteins in the Rcr_C01-1, Rcr_C03-1 and Rcr_C08-1 flanking regions. The syntenic regions of the two major QTLs Rcr_C03-1 and Rcr_C08-1 in the B. rapa genome ‘Chiifu’ were searched.