scholarly journals Genome-wide SNP detection in Darjeeling tea: unravelling genetic structure, functional impact and trait associations

2020 ◽  
Author(s):  
Anjan Hazra ◽  
Rakesh Kumar ◽  
Chandan Sengupta ◽  
Sauren Das
Keyword(s):  
Genetic Relatedness ◽  
Sequence Data ◽  
Snp Markers ◽  
High Impact ◽  
Phenotypic Traits ◽  
Nucleotide Polymorphisms ◽  
Association Analyses ◽  
Genome Wide ◽  
Darjeeling Tea ◽  
Trait Associations

AbstractGenotyping by sequencing and identification of functionally relevant nucleotide variations in crop accessions are the key steps to unravel genetic control of desirable traits. In the scope of present work, elite cultivars of Darjeeling tea were undergone SNP genotyping by double-digest restriction site associated DNA sequencing method. This study reports a set of 54,206 high-quality SNP markers discovered from ∼10.4 GB sequence data, encompassing 15 chromosomes of reference tea genome. Genetic relatedness among the accessions conforms to the analyses of Bayesian clustering, UPGMA, and PCoA methods. High percent of heterozygous loci in the majority of the cultivars reflect their ‘hybrid’ ancestry as reported earlier. Genomic positions of the discovered SNPs and their putative effect on annotated genes designated a thoughtful understanding of their functional aspects in tea system biology. A group of 95 genes was identified to be affected by high impact variants, most of them are involved in signal transduction, biosynthesis of secondary metabolite, transcriptional and translational regulation. Genome-wide association analyses of 21 agronomic and biochemical phenotypes resulted in trait-linked polymorphic loci with strong confidence (p < 0.05 and 0.001). The selection of significant marker-trait associations with the Bonferroni correction threshold retained a set of 57 SNPs distributed across 14 chromosomes to be linked with eight phenotypic traits. High impact and trait-associated nucleotide polymorphisms perceived in this study can be exploited in worldwide germplasm of contrasting origin to depict their heritability and to unlock their potentiality in marker-assisted breeding.

scholarly journals Genome-Wide SNP Markers for Genotypic and Phenotypic Differentiation of Melon (Cucumis melo L.) Varieties Using Genotyping-by-Sequencing

2021 ◽  
Vol 22 (13) ◽  
pp. 6722
Author(s):  
Do Yoon Hyun ◽  
Raveendar Sebastin ◽  
Gi-An Lee ◽  
Kyung Jun Lee ◽  
Seong-Hoon Kim ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Cucumis Melo ◽  
Systematic Approach ◽  
Genome Wide Association Study ◽  
Genotyping By Sequencing ◽  
Snp Markers ◽  
Phenotypic Traits ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
Cucumis Melo L

Melon (Cucumis melo L.) is an economically important horticultural crop with abundant morphological and genetic variability. Complex genetic variations exist even among melon varieties and remain unclear to date. Therefore, unraveling the genetic variability among the three different melon varieties, muskmelon (C. melo subsp. melo), makuwa (C. melo L. var. makuwa), and cantaloupes (C. melo subsp. melo var. cantalupensis), could provide a basis for evolutionary research. In this study, we attempted a systematic approach with genotyping-by-sequencing (GBS)-derived single nucleotide polymorphisms (SNPs) to reveal the genetic structure and diversity, haplotype differences, and marker-based varieties differentiation. A total of 6406 GBS-derived SNPs were selected for the diversity analysis, in which the muskmelon varieties showed higher heterozygote SNPs. Linkage disequilibrium (LD) decay varied significantly among the three melon varieties, in which more rapid LD decay was observed in muskmelon (r2 = 0.25) varieties. The Bayesian phylogenetic tree provided the intraspecific relationships among the three melon varieties that formed, as expected, individual clusters exhibiting the greatest genetic distance based on the posterior probability. The haplotype analysis also supported the phylogeny result by generating three major networks for 48 haplotypes. Further investigation for varieties discrimination allowed us to detect a total of 52 SNP markers that discriminated muskmelon from makuwa varieties, of which two SNPs were converted into cleaved amplified polymorphic sequence markers for practical use. In addition to these markers, the genome-wide association study identified two SNPs located in the genes on chromosome 6, which were significantly associated with the phenotypic traits of melon seed. This study demonstrated that a systematic approach using GBS-derived SNPs could serve to efficiently classify and manage the melon varieties in the genebank.

scholarly journals Genome-Wide Analysis of Sex Disparities in the Genetic Architecture of Lung and Colorectal Cancers

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 686
Author(s):  
Alireza Nazarian ◽  
Alexander M. Kulminski
Keyword(s):  
Nucleotide Polymorphisms ◽  
Genetic Associations ◽  
Significance Level ◽  
Association Analyses ◽  
Complex Disorders ◽  
Specific Effects ◽  
Genome Wide ◽  
Genetic Mechanisms ◽  
Sex Disparities ◽  
Almost All

Almost all complex disorders have manifested epidemiological and clinical sex disparities which might partially arise from sex-specific genetic mechanisms. Addressing such differences can be important from a precision medicine perspective which aims to make medical interventions more personalized and effective. We investigated sex-specific genetic associations with colorectal (CRCa) and lung (LCa) cancers using genome-wide single-nucleotide polymorphisms (SNPs) data from three independent datasets. The genome-wide association analyses revealed that 33 SNPs were associated with CRCa/LCa at P < 5.0 × 10−6 neither males or females. Of these, 26 SNPs had sex-specific effects as their effect sizes were statistically different between the two sexes at a Bonferroni-adjusted significance level of 0.0015. None had proxy SNPs within their ±1 Mb regions and the closest genes to 32 SNPs were not previously associated with the corresponding cancers. The pathway enrichment analyses demonstrated the associations of 35 pathways with CRCa or LCa which were mostly implicated in immune system responses, cell cycle, and chromosome stability. The significant pathways were mostly enriched in either males or females. Our findings provided novel insights into the potential sex-specific genetic heterogeneity of CRCa and LCa at SNP and pathway levels.

scholarly journals Genome-Wide Patterns of Homozygosity Reveal the Conservation Status in Five Italian Goat Populations

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1510
Author(s):  
Salvatore Mastrangelo ◽  
Rosalia Di Gerlando ◽  
Maria Teresa Sardina ◽  
Anna Maria Sutera ◽  
Angelo Moscarelli ◽  
...  
Keyword(s):  
Conservation Status ◽  
Phenotypic Traits ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Local Populations ◽  
Genomic Technologies ◽  
Fitness Traits ◽  
Genome Wide ◽  
Breeding Schemes ◽  
Genomic Inbreeding

The application of genomic technologies has facilitated the assessment of genomic inbreeding based on single nucleotide polymorphisms (SNPs). In this study, we computed several runs of homozygosity (ROH) parameters to investigate the patterns of homozygosity using Illumina Goat SNP50 in five Italian local populations: Argentata dell’Etna (N = 48), Derivata di Siria (N = 32), Girgentana (N = 59), Maltese (N = 16) and Messinese (N = 22). The ROH results showed well-defined differences among the populations. A total of 3687 ROH segments >2 Mb were detected in the whole sample. The Argentata dell’Etna and Messinese were the populations with the lowest mean number of ROH and inbreeding coefficient values, which reflect admixture and gene flow. In the Girgentana, we identified an ROH pattern related with recent inbreeding that can endanger the viability of the breed due to reduced population size. The genomes of Derivata di Siria and Maltese breeds showed the presence of long ROH (>16 Mb) that could seriously impact the overall biological fitness of these breeds. Moreover, the results confirmed that ROH parameters are in agreement with the known demography of these populations and highlighted the different selection histories and breeding schemes of these goat populations. In the analysis of ROH islands, we detected harbored genes involved with important traits, such as for milk yield, reproduction, and immune response, and are consistent with the phenotypic traits of the studied goat populations. Finally, the results of this study can be used for implementing conservation programs for these local populations in order to avoid further loss of genetic diversity and to preserve the production and fitness traits. In view of this, the availability of genomic data is a fundamental resource.

scholarly journals Genotyping-by-Sequencing of Gossypium hirsutum Races and Cultivars Uncovers Novel Patterns of Genetic Relationships and Domestication Footprints

2019 ◽  
Vol 15 ◽  
pp. 117693431988994
Author(s):  
Shulin Zhang ◽  
Yaling Cai ◽  
Jinggong Guo ◽  
Kun Li ◽  
Renhai Peng ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Genetic Relationships ◽  
Phylogenetic Analyses ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Association Analyses ◽  
Genome Wide ◽  
Candidate Gene Locus

Determining the genetic rearrangement and domestication footprints in Gossypium hirsutum cultivars and primitive race genotypes are essential for effective gene conservation efforts and the development of advanced breeding molecular markers for marker-assisted breeding. In this study, 94 accessions representing the 7 primitive races of G hirsutum, along with 9 G hirsutum and 12 Gossypium barbadense cultivated accessions were evaluated. The genotyping-by-sequencing (GBS) approach was employed and 146 558 single nucleotide polymorphisms (SNP) were generated. Distinct SNP signatures were identified through the combination of selection scans and association analyses. Phylogenetic analyses were also conducted, and we concluded that the Latifolium, Richmondi, and Marie-Galante race accessions were more genetically related to the G hirsutum cultivars and tend to cluster together. Fifty-four outlier SNP loci were identified by selection-scan analysis, and 3 SNPs were located in genes related to the processes of plant responding to stress conditions and confirmed through further genome-wide signals of marker-phenotype association analysis, which indicate a clear selection signature for such trait. These results identified useful candidate gene locus for cotton breeding programs.

scholarly journals EVOLUTION OF DNA SEQUENCING METHODS AND PROSPECTS FOR THEIR USE IN FORENSIC DNA EXAMINATION

2020 ◽  
Vol 11 (87) ◽  
Author(s):  
Zhanna Bazyliuk ◽  
Keyword(s):  
Dna Sequencing ◽  
Molecular Genetic ◽  
Genetic Research ◽  
Snp Markers ◽  
Degraded Dna ◽  
Phenotypic Traits ◽  
Nucleotide Polymorphisms ◽  
Biological Origin ◽  
Genetic Traits ◽  
Str Loci

The study of the human genome makes it possible to use genetic information to identify individual traits, diagnosis of diseases and forecasting and prevention of their development, promotes a personal approach when choosing treatment methods; population research, ethnogenesis and evolutionary processes. Introduction of DNA sequencing methods in domestic genetic fingerprinting will contribute to a more informative establishment of human genetic traits. The main purpose of molecular genetic research is to establish the genetic features of missing people, their relatives, to conduct paternity, to identify traces of biological origin and their identification. This article talks about the gradual development of DNA sequencing technology, which is conventionally divided into three types. The first type includes sequencing using capillary electrophoresis and pyrosequencing. The second type is high-throughput pyrosequencing, semiconductor, cyclic ligase, and the use of fluorescently labeled precursors, based on the sequencing of millions of DNA fragments simultaneously. The third stage includes methods that do not require prior sample preparation. These are methods of nanoporous sequencing, sequencing of one molecule, one-molecular sequencing. Today, each of the sequencing methods is aimed at performing different tasks. A number of methods are promising in the field of molecular-genetic examination. In world jurisprudence, sequencing is implemented mainly with the help of devices - Illumina’s, MiSeq FGx, Ion Torrent PGM from ThermoFisher and Ion S5. Research in forensic expertise of single nucleotide polymorphisms (SNP), sequencing of STR-loci and mitochondrial DNA, STR-loci and SNP-markers of the Y chromosome, will provide a high level of information, determination of human phenotypic traits, the possibility of establishing genetic traits from significantly degraded DNA. This article deals with modern problems of identification of human genetic traits and the prospect of introduction of the newest methods of sequencing for their qualitative and complete establishment.

scholarly journals Progressive effects of single-nucleotide polymorphisms on 16 phenotypic traits based on longitudinal data

2020 ◽  
Vol 42 (4) ◽  
pp. 393-403
Author(s):  
Donghe Li ◽  
Hahn Kang ◽  
Sanghun Lee ◽  
Sungho Won
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Longitudinal Data ◽  
Density Lipoprotein ◽  
Phenotypic Traits ◽  
Chromosome 2 ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Longitudinal Changes ◽  
Genome Wide ◽  
A Genome

Abstract Background There are many research studies have estimated the heritability of phenotypic traits, but few have considered longitudinal changes in several phenotypic traits together. Objective To evaluate the progressive effect of single nucleotide polymorphisms (SNPs) on prominent health-related phenotypic traits by determining SNP-based heritability ($$h_{snp}^{2}$$hsnp2) using longitudinal data. Methods Sixteen phenotypic traits associated with major health indices were observed biennially for 6843 individuals with 10-year follow-up in a Korean community-based cohort. Average SNP heritability and longitudinal changes in the total period were estimated using a two-stage model. Average and periodic differences for each subject were considered responses to estimate SNP heritability. Furthermore, a genome-wide association study (GWAS) was performed for significant SNPs. Results Each SNP heritability for the phenotypic mean of all sixteen traits through 6 periods (baseline and five follow-ups) were significant. Gradually, the forced vital capacity in one second (FEV1) reflected the only significant SNP heritability among longitudinal changes at a false discovery rate (FDR)-adjusted 0.05 significance level ($$h_{snp}^{2} = 0.171$$hsnp2=0.171, FDR = 0.0012). On estimating chromosomal heritability, chromosome 2 displayed the highest heritability upon periodic changes in FEV1. SNPs including rs2272402 and rs7209788 displayed a genome-wide significant association with longitudinal changes in FEV1 (P = 1.22 × 10−8 for rs2272402 and P = 3.36 × 10−7 for rs7209788). De novo variants including rs4922117 (near LPL, P = 2.13 × 10−15) of log-transformed high-density lipoprotein (HDL) ratios and rs2335418 (near HMGCR, P = 3.2 $$\times$$× 10−9) of low-density lipoprotein were detected on GWAS. Conclusion Significant genetic effects on longitudinal changes in FEV1 among the middle-aged general population and chromosome 2 account for most of the genetic variance.

scholarly journals Genotyping-by-sequencing enables linkage mapping in three octoploid cultivated strawberry families

2017 ◽  
Author(s):  
Kelly J Vining ◽  
Natalia Salinas ◽  
Jacob A Tennessen ◽  
Jason D Zurn ◽  
Daniel James Sargent ◽  
...  
Keyword(s):  
Reference Genome ◽  
Sequence Data ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
Linkage Groups ◽  
Single Nucleotide ◽  
Ancestral Species ◽  
Polymorphic Snps ◽  
Genome Wide ◽  
Diploid Ancestor

With the goal of evaluating genotyping-by-sequencing (GBS) in a species with a complex octoploid genome, GBS was used to survey genome-wide single-nucleotide polymorphisms (SNPs) in three biparental strawberry (Fragaria ×ananassa) populations. GBS sequence data were aligned to the F. vesca ‘Fvb’ reference genome in order to call SNPs. Numbers of polymorphic SNPs per population ranged from 1,163 to 3,190. Linkage maps consisting of 30-65 linkage groups were produced from the SNP sets derived from each parent. The linkage groups covered 99% of the Fvb reference genome, with three to seven linkage groups from a given parent aligned to any particular chromosome. A phylogenetic analysis performed using the POLiMAPS pipeline revealed linkage groups that were most similar to ancestral species F. vesca for each chromosome. Linkage groups that were most similar to a second ancestral species, F. iinumae, were only resolved for Fvb 4. The quantity of missing data and heterogeneity in genome coverage inherent in GBS complicated the analysis, but POLiMAPS resolved F. ×ananassa chromosomal regions derived from diploid ancestor F. vesca.

scholarly journals Genetic Dissection Uncovers Genome Wide Marker-Trait Associations for Plant Growth, Yield and Yield Related Traits Under Varying Nitrogen Levels in Nested Synthetic Wheat Introgression Libraries

2021 ◽  
Author(s):  
NITIKA SANDHU ◽  
Amandeep Kaur ◽  
Mehak Sethi ◽  
Satinder Kaur ◽  
Varinderpal Singh ◽  
...  
Keyword(s):  
Plant Growth ◽  
Grain Yield ◽  
Field Experiments ◽  
Agronomic Traits ◽  
Growth Yield ◽  
Snp Markers ◽  
Synthetic Wheat ◽  
Wheat Varieties ◽  
Genome Wide ◽  
Trait Associations

Abstract Nitrogen is one of the most important macronutrients for crop growth and metabolism. To identify marker-trait associations for complex NUE-related agronomic traits, field experiments were conducted on nested synthetic wheat introgression libraries at three nitrogen input levels across two seasons. The introgression libraries were genotyped using the 35K Axiom® Wheat Breeder’s Array and genetic diversity and population structure were examined. Significant phenotypic variation was observed across genotypes, treatments and their interactions across seasons for all the 22 traits measured. Significant positive correlations were observed among grain yield and yield attributing traits and root traits. Across seasons, a total of 233 marker-trait associations (MTAs) associated with fifteen traits of interest at differential levels of nitrogen (N0, N60 and N120) were detected using 9,474 genome-wide single nucleotide polymorphism (SNP) markers. Of these, 45 MTAs for 10 traits in the N0 treatment, 100 MTAs for 11 traits in the N60 treatment and 88 MTAs for 11 traits in the N120 treatment were detected. We identified putative candidate genes underlying the significant MTAs which were associated directly or indirectly with various biological processes, cellular component organization and molecular functions involving improved plant growth and grain yield. In addition, the top 10 lines based on N response and grain yield across seasons and treatments were identified. The identification and introgression of superior alleles/donors improving NUE while maintaining grain yield may open new avenues in designing next-generation nitrogen efficient high yielding wheat varieties.

scholarly journals High-density linkage map and QTLs for growth in snapper (Chrysophrys auratus)

2018 ◽  
Author(s):  
David T. Ashton ◽  
Peter A. Ritchie ◽  
Maren Wellenreuther
Keyword(s):  
Linkage Map ◽  
Genome Structure ◽  
Snp Markers ◽  
Biological Research ◽  
Phenotypic Traits ◽  
Strongly Correlated ◽  
Fish Family ◽  
Significant Qtls ◽  
Snp Data ◽  
Genome Wide

ABSTRACTCharacterizing the genetic variation underlying phenotypic traits is a central objective in biological research. This research has been hampered in the past by the limited genomic resources available for most non-model species. However, recent advances in sequencing technology and related genotyping methods are rapidly changing this. Here we report the use of genome-wide SNP data from the ecologically and commercially important marine fish species Chrysophrys auratus (snapper) to 1) construct the first linkage map for this species, 2) scan for growth QTLs, and 3) search for candidate genes in the surrounding QTL regions. The newly constructed linkage map contained ~11K SNP markers and is the densest map to date in the fish family Sparidae. Comparisons with available genome scaffolds indicated that overall marker placement was strongly correlated between the scaffolds and linkage map (R = 0.7), but at fine scales (< 5 cM) there were some precision limitations. Of the 24 linkage groups, which reflect the 24 chromosomes of this species, three were found to contain QTLs with genome-wide significance for growth-related traits. A scan for 13 known candidate growth genes located the genes for growth hormone, parvalbumin, and myogenin within 13.2, 2.6, and 5.0 cM of these genome-wide significant QTLs, respectively. The linkage map and QTLs found in this study will advance the investigation of genome structure and selective breeding in snapper.

scholarly journals Genome-wide association analysis of anthracnose resistance in sorghum [Sorghum bicolor (L.) Moench]

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0261461
Author(s):  
Girma Mengistu ◽  
Hussein Shimelis ◽  
Ermias Assefa ◽  
Dagnachew Lule
Keyword(s):  
Sorghum Bicolor ◽  
Resistance Breeding ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Breeding Programs ◽  
Anthracnose Resistance ◽  
Progress Curve ◽  
Genome Wide ◽  
Population Structure Analysis

In warm-humid ago-ecologies of the world, sorghum [Sorghum bicolor (L.) Moench] production is severely affected by anthracnose disease caused by Colletotrichum sublineolum Henn. New sources of anthracnose resistance should be identified to introgress novel genes into susceptible varieties in resistance breeding programs. The objective of this study was to determine genome-wide association of Diversity Arrays Technology Sequencing (DArTseq) based single nucleotide polymorphisms (SNP) markers and anthracnose resistance genes in diverse sorghum populations for resistance breeding. Three hundred sixty-six sorghum populations were assessed for anthracnose resistance in three seasons in western Ethiopia using artificial inoculation. Data on anthracnose severity and the relative area under the disease progress curve were computed. Furthermore, the test populations were genotyped using SNP markers with DArTseq protocol. Population structure analysis and genome-wide association mapping were undertaken based on 11,643 SNPs with <10% missing data. The evaluated population was grouped into eight distinct genetic clusters. A total of eight significant (P < 0.001) marker-trait associations (MTAs) were detected, explaining 4.86–15.9% of the phenotypic variation for anthracnose resistance. Out of which the four markers were above the cutoff point. The significant MTAs in the assessed sorghum population are useful for marker-assisted selection (MAS) in anthracnose resistance breeding programs and for gene and quantitative trait loci (QTL) mapping.

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