Genetic Diversity ofCoffea arabicaL.: A Genomic Approach

Coffea arabica L. produces a high-quality beverage, with pleasant aroma and flavor, but diseases, pests and abiotic stresses often affect its yield. Therefore, improving important agronomic traits of this commercial specie remains a target for most coffee improvement programs. With advances in genomic and sequencing technology, it is feasible to understand the coffee genome and the molecular inheritance underlying coffee traits, thereby helping improve the efficiency of breeding programs. Thanks to the rapid development of genomic resources and the publication of the C. canephora reference genome, third-generation markers based on single-nucleotide polymorphisms (SNPs) have gradually been identified and assayed in Coffea, particularly in C. arabica. However, high-throughput genotyping assays are still needed in order to rapidly characterize the coffee genetic diversity and to evaluate the introgression of different cultivars in a cost-effective way. The DArTseq™ platform, developed by Diversity Arrays Technology, is one of these approaches that has experienced an increasing interest worldwide since it is able to generate thousands of high quality SNPs in a timely and cost-effective manner. These validated SNP markers will be useful to molecular genetics and for innovative approaches in coffee breeding.

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Genetic diversity and population structure of sheep (Ovis aries) in Sichuan, China

PLoS ONE ◽

10.1371/journal.pone.0257974 ◽

2021 ◽

Vol 16 (9) ◽

pp. e0257974

Author(s):

Mingliang Zhou ◽

Gaofu Wang ◽

Minghua Chen ◽

Qian Pang ◽

Shihai Jiang ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ovis Aries ◽

Fixation Index ◽

Nucleotide Polymorphisms ◽

High Quality ◽

Genome Wide ◽

High Quality Snps ◽

Exotic Breed ◽

Population Structures

Sichuan, China, has abundant genetic resources of sheep (Ovis aries). However, their genetic diversity and population structure have been less studied, especially at the genome-wide level. In the present study, we employed the specific-locus amplified fragment sequencing for identifying genome-wide single nucleotide polymorphisms (SNPs) among five breeds of sheep distributed in Sichuan, including three local pure breeds, one composite breed, and one exotic breed of White Suffolk. From 494 million clean paired-end reads, we obtained a total of 327,845 high-quality SNPs that were evenly distributed among all 27 chromosomes, with a transition/transversion ratio of 2.56. Based on this SNP panel, we found that the overall nucleotide diversity was 0.2284 for all five breeds, with the highest and lowest diversity observed in Mage sheep (0.2125) and Butuo Black (0.1963) sheep, respectively. Both Wright’s fixation index and Identity-by-State distance revealed that all individuals of Liangshan Semifine-wool, White Suffolk, and Butuo Black sheep were respectively clustered together, and the breeds could be separated from each other, whereas Jialuo and Mage sheep had the closest genetic relationship and could not be distinguished from each other. In conclusion, we provide a reference panel of genome-wide and high-quality SNPs in five sheep breeds in Sichuan, by which their genetic diversity and population structures were investigated.

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De Novo SNP Discovery and Genotyping of Iranian Pimpinella Species Using ddRAD Sequencing

Agronomy ◽

10.3390/agronomy11071342 ◽

2021 ◽

Vol 11 (7) ◽

pp. 1342

Author(s):

Shaghayegh Mehravi ◽

Gholam Ali Ranjbar ◽

Ghader Mirzaghaderi ◽

Anita Alice Severn-Ellis ◽

Armin Scheben ◽

...

Keyword(s):

De Novo ◽

Genetic Relationships ◽

Nucleotide Polymorphisms ◽

High Quality ◽

Genomic Resources ◽

High Quality Snps ◽

The Family ◽

Double Digestion ◽

Flanking Sequences ◽

Downstream Analysis

The species of Pimpinella, one of the largest genera of the family Apiaceae, are traditionally cultivated for medicinal purposes. In this study, high-throughput double digest restriction-site associated DNA sequencing technology (ddRAD-seq) was used to identify single nucleotide polymorphisms (SNPs) in eight Pimpinella species from Iran. After double-digestion with the enzymes HpyCH4IV and HinfI, a total of 334,702,966 paired-end reads were de novo assembled into 1,270,791 loci with an average of 28.8 reads per locus. After stringent filtering, 2440 high-quality SNPs were identified for downstream analysis. Analysis of genetic relationships and population structure, based on these retained SNPs, indicated the presence of three major groups. Gene ontology and pathway analysis were determined by using comparison SNP-associated flanking sequences with a public non-redundant database. Due to the lack of genomic resources in this genus, our present study is the first report to provide high-quality SNPs in Pimpinella based on a de novo analysis pipeline using ddRAD-seq. This data will enhance the molecular knowledge of the genus Pimpinella and will provide an important source of information for breeders and the research community to enhance breeding programs and support the management of Pimpinella genomic resources.

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Genetic Diversity Analysis of 53 Indonesian Rice Genotypes using 6K Single Nucleotide Polymorphism Markers

Jurnal AgroBiogen ◽

10.21082/jbio.v14n1.2018.p1-10 ◽

2018 ◽

Vol 14 (1) ◽

pp. 1

Author(s):

Joko Prasetiyono ◽

Nurul Hidayatun ◽

Tasliah Tasliah

Keyword(s):

Genetic Diversity ◽

Morphological Characters ◽

Snp Markers ◽

Japonica Rice ◽

Rice Varieties ◽

Tropical Japonica ◽

Rice Chromosomes ◽

Improvement Programs ◽

Rice Genotypes ◽

Genotypic Mixtures

<p>Indonesia is rich in rice genetic resources, however, only a small number has been used in variety improvement programs. This study aimed to determine the genetic diversity of Indonesian rice varieties using 6K SNP markers. The study was conducted at ICABIOGRAD for DNA isolation and IRRI for SNP marker analysis. Genetic materials were 53 rice genotypes consisting of 49 varieties and 4 check genotypes. SNP markers used were 6K loci. Results showed that among the markers analyzed, only 4,606 SNPs (76.77%) were successfully read. The SNP markers covered all twelve rice chromosomes of 945,178.27 bp. The most common allele observed was GG, whereas the least allele was TG. Dendrograms of the 53 rice varieties analyzed with 4,606 SNPs demonstrated several small groups containing genotypic mixtures between indica and japonica rice, and no groups were found to contain firmly indica or japonica type. Structure analysis (K = 2) with value of 0.8 showed that the 53 rice varieties were divided into several groups and each group consisted of 4 japonica, 2 tropical japonica, 46 indica, and 1 aus rice type, respectively. IR64 and Ciherang proved to have an indica genome, while Rojolele has japonica one. Dupa and Hawara Bunar, usually grouped into tropical japonica rice, were classified as indica type, and Hawara Bunar has perfectly 100% indica type. The results of this study indicated that rice classification (indica-japonica) which is usually classified based only on morphological characters, e.g. grain and leaf shapes, is not enough and classification based on SNP markers should be considered for that purpose.</p>

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Genotyping Single-Nucleotide Polymorphisms by the Invader Assay with Dual-Color Fluorescence Polarization Detection

Clinical Chemistry ◽

10.1093/clinchem/47.8.1373 ◽

2001 ◽

Vol 47 (8) ◽

pp. 1373-1377 ◽

Cited By ~ 60

Author(s):

Tony M Hsu ◽

Scott M Law ◽

Shenghui Duan ◽

Bruce P Neri ◽

Pui-Yan Kwok

Keyword(s):

Fluorescence Polarization ◽

Cost Effective ◽

Snp Markers ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Clear Cut ◽

Pcr Product ◽

Invader Assay ◽

Pcr Products ◽

Incorporation Assay

Abstract Background: The PCR-Invader® assay is a robust, homogeneous assay that has been shown to be highly sensitive and specific in genotyping single-nucleotide polymorphism (SNP) markers. In this study, we introduce two changes to improve the assay: (a) we streamline the PCR-Invader method by assaying both alleles for each SNP in one reaction; and (b) we reduce the cost of the method by adopting fluorescence polarization (FP) as the detection method. Methods: PCR product was incubated with Invader oligonucleotide and two primary probes at 93 °C for 5 min. Signal probes corresponding to the cleaved flaps of the primary probes [labeled with fluorescein and 6-carboxytetramethylrhodamine (TAMRA) dye] and Cleavase® VIII enzyme (a flap endonuclease) were then added to the mixture. This reaction mixture was incubated at 63 °C for 5 min. FP measurements were made with a fluorescence plate reader. Results: Eighty-eight individuals were genotyped across a panel of 10 SNPs, using PCR product as template, for a total of 880 genotypes. An average “no call” rate of 3.2% was observed after first round of experiments. PCR products were remade in those samples that failed to produce any genotype in the first round, and all gave clear-cut genotypes. When the genotypes determined by the PCR-Invader assay and template-directed dye-terminator incorporation assay with FP were compared, they were in 100% concordance for all SNP markers and experiments. Conclusions: The improvements introduced in this study make PCR-Invader assay simpler and more cost-effective, and therefore more suitable for high-throughput genotyping.

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Population Structure and Genetic Diversity in Korean Cowpea Germplasm Based on SNP Markers

Plants ◽

10.3390/plants9091190 ◽

2020 ◽

Vol 9 (9) ◽

pp. 1190 ◽

Cited By ~ 1

Author(s):

Eunju Seo ◽

Kipoong Kim ◽

Tae-Hwan Jun ◽

Jinsil Choi ◽

Seong-Hoon Kim ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Principal Component ◽

Snp Markers ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Useful Knowledge ◽

Population Structure Analysis ◽

Group 3 ◽

Genetic Diversity Study

Cowpea is one of the most essential legume crops providing inexpensive dietary protein and nutrients. The aim of this study was to understand the genetic diversity and population structure of global and Korean cowpea germplasms. A total of 384 cowpea accessions from 21 countries were genotyped with the Cowpea iSelect Consortium Array containing 51,128 single-nucleotide polymorphisms (SNPs). After SNP filtering, a genetic diversity study was carried out using 35,116 SNPs within 376 cowpea accessions, including 229 Korean accessions. Based on structure and principal component analysis, a total of 376 global accessions were divided into four major populations. Accessions in group 1 were from Asia and Europe, those in groups 2 and 4 were from Korea, and those in group 3 were from West Africa. In addition, 229 Korean accessions were divided into three major populations (Q1, Jeonra province; Q2, Gangwon province; Q3, a mixture of provinces). Additionally, the neighbor-joining tree indicated similar results. Further genetic diversity analysis within the global and Korean population groups indicated low heterozygosity, a low polymorphism information content, and a high inbreeding coefficient in the Korean cowpea accessions. The population structure analysis will provide useful knowledge to support the genetic potential of the cowpea breeding program, especially in Korea.

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Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa

BMC Genomics ◽

10.1186/s12864-019-6160-9 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 1

Author(s):

Fernando P. Guerra ◽

Haktan Suren ◽

Jason Holliday ◽

James H. Richards ◽

Oliver Fiehn ◽

...

Keyword(s):

Biomass Production ◽

Complex Traits ◽

Association Studies ◽

Populus Trichocarpa ◽

Significant Snps ◽

Snp Markers ◽

Exome Capture ◽

Genome Wide Association Studies ◽

Nucleotide Polymorphisms ◽

Improvement Programs

Abstract Background Populus trichocarpa is an important forest tree species for the generation of lignocellulosic ethanol. Understanding the genomic basis of biomass production and chemical composition of wood is fundamental in supporting genetic improvement programs. Considerable variation has been observed in this species for complex traits related to growth, phenology, ecophysiology and wood chemistry. Those traits are influenced by both polygenic control and environmental effects, and their genome architecture and regulation are only partially understood. Genome wide association studies (GWAS) represent an approach to advance that aim using thousands of single nucleotide polymorphisms (SNPs). Genotyping using exome capture methodologies represent an efficient approach to identify specific functional regions of genomes underlying phenotypic variation. Results We identified 813 K SNPs, which were utilized for genotyping 461 P. trichocarpa clones, representing 101 provenances collected from Oregon and Washington, and established in California. A GWAS performed on 20 traits, considering single SNP-marker tests identified a variable number of significant SNPs (p-value < 6.1479E-8) in association with diameter, height, leaf carbon and nitrogen contents, and δ15N. The number of significant SNPs ranged from 2 to 220 per trait. Additionally, multiple-marker analyses by sliding-windows tests detected between 6 and 192 significant windows for the analyzed traits. The significant SNPs resided within genes that encode proteins belonging to different functional classes as such protein synthesis, energy/metabolism and DNA/RNA metabolism, among others. Conclusions SNP-markers within genes associated with traits of importance for biomass production were detected. They contribute to characterize the genomic architecture of P. trichocarpa biomass required to support the development and application of marker breeding technologies.

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Measuring Costs and Outcomes of Tele-Intervention When Serving Families of Children who are Deaf/Hard-of-Hearing

International Journal of Telerehabilitation ◽

10.5195/ijt.2013.6129 ◽

2013 ◽

Vol 5 (2) ◽

pp. 3-10 ◽

Cited By ~ 21

Author(s):

Kristina M. Blaiser ◽

Diane Behl ◽

Catherine Callow-Heusser ◽

Karl R. White

Keyword(s):

Early Intervention ◽

Hard Of Hearing ◽

Home Visit ◽

Rating Scales ◽

Child Outcomes ◽

Cost Effective ◽

High Quality ◽

Early Intervention Services ◽

Effective Manner ◽

Intervention Services

Background: Optimal outcomes for children who are deaf/hard-of-hearing (DHH) depend on access to high quality, specialized early intervention services. Tele-intervention – the delivery of early intervention services via telehealth technology - has the potential to meet this need in a cost-effective manner. Method: Twenty-seven families of infants and toddlers with varying degrees of hearing loss participated in a randomized study, receiving their services primarily through TI or via traditional in-person home visits. Pre- and post-test measures of child outcomes, family and provider statisfaction, and costs were collected. Results: The TI group scored statistically significantly higher on the expressive language measure than the in-person group (p =.03). A measure of home visit quality revealed that the TI group scored statistically significantly better on the Parent Engagement subscale of the Home Visit Rating Scales-Adapted & Extended (HOVRS-A+; Roggman, et al., 2012). Cost savings associate with providing services via TI increased as the intensity of service delivery increased. Although most providers and families were positive about TI, there was great variability in their perceptions. Conclusions: Tele-intervention is a promising cost-effective method for delivering high quality early intervention services to families of children who are DHH.

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Whole genome sequence and genome-wide distributed single nucleotide polymorphisms (SNPs) of the Black Bengal goat

F1000Research ◽

10.12688/f1000research.18316.1 ◽

2019 ◽

Vol 8 ◽

pp. 318

Author(s):

Md. Bazlur Rahman Mollah ◽

Md. Shamsul Alam Bhuiyan ◽

M.A.M. Yahia Khandoker ◽

Md. Abdul Jalil ◽

Gautam Kumar Deb ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Whole Genome Sequence ◽

Whole Genome ◽

Nucleotide Polymorphisms ◽

High Quality ◽

Single Nucleotide ◽

Genome Wide ◽

High Quality Snps ◽

Black Goat ◽

Black Bengal Goat

The Black Bengal goat (BBG) is a dwarf sized heritage goat (Capra hircus) breed from Bangladesh, and is well known for its high fertility, excellent meat and skin quality. Here we present the first whole genome sequence and genome-wide distributed single nucleotide polymorphisms (SNPs) of the BBG. A total of 833,469,900 raw reads consisting of 125,020,485,000 bases were obtained by sequencing one male BBG sample. The reads were aligned to the San Clemente and the Yunnan black goat genome which resulted in 98.65% (properly paired, 94.81%) and 98.50% (properly paired, 97.10%) of the reads aligning, respectively. Notably, the estimated sequencing coverages were 48.22X and 44.28X compared to published San Clemente and the Yunnan black goat genomes respectively. On the other hand, a total of 9,497,875 high quality SNPs (Q ≥ 20) along with 1,023,359 indels, and 8,746,849 high quality SNPs along with 842,706 indels were identified in BBG against the San Clemente and Yunnan black goat genomes respectively. The dataset is publicly available from NCBI BioSample (SAMN10391846), Sequence Read Archive (SRR8182317, SRR8549413 and SRR8549904), with BioProject ID PRJNA504436. These data might be useful genomic resources in conducting genome wide association studies, identification of quantitative trait loci (QTLs) and functional genomic analysis of the Black Bengal goat.

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Development and Characterization of PCR Markers in Cucumber

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.127.4.545 ◽

2002 ◽

Vol 127 (4) ◽

pp. 545-557 ◽

Cited By ~ 51

Author(s):

Gennaro Fazio ◽

Jack E. Staub ◽

Sang Min Chung

Keyword(s):

Large Scale ◽

Cost Effective ◽

Snp Markers ◽

Yield Component ◽

Nucleotide Polymorphisms ◽

Pcr Markers ◽

Dinucleotide Repeats ◽

Sequence Characterized Amplified Region ◽

Tetranucleotide Repeats ◽

Multiple Lateral Branching

Highly polymorphic microsatellites or simple sequence repeat (SSR), along with sequence characterized amplified region (SCAR) and single nucleotide polymorphisms (SNP), markers are reliable, cost-effective, and amenable for large scale analyses. Molecular polymorhisms are relatively rare in cucumber (Cucumis sativus L.) (3% to 8%). Therefore, experiments were designed to develop SSR, SCAR and SNP markers, and optimize reaction conditions for PCR. A set of 110 SSR markers was constructed using a unique, strategically applied methodology that included the GeneTrapper (Life Technologies, Gaithersburg, Md.) kit to select plasmids harboring microsatellites. Of these markers, 58 (52%) contained dinucleotide repeats (CT, CA, TA), 21 (19%) possessed trinucleotide repeats (CTT, ATT, ACC, GCA), 3 (2.7%) contained tetranucleotide repeats (TGCG, TTAA, TAAA), 4 (3.6%) enclosed pentanucleotide repeat (ATTTT, GTTTT, GGGTC, AGCCC), 3 (2.7%) contained hexanucleotide repeats (CCCAAA, TAAAAA, GCTGGC) and 21 possessed composite repeats. Four SCARs (L18-3 SCAR, AT1-2 SCAR, N6-A SCAR, and N6-B SCAR) and two PCR markers based on SNPs (L18-2H19 A and B) that are tightly linked to multiple lateral branching (i.e., a yield component) were also developed. The SNP markers were developed from otherwise monomorphic SCAR markers, producing genetically variable amplicons. The markers L18-3 SCAR and AT1-2 SCAR were codominant. A three-primer strategy was devised to develop a codominant SCAR from a sequence containing a transposable element, and a new codominant SCAR product was detected by annealing temperature gradient (ATG) PCR. The use of a marker among laboratories can be enhanced by methodological optimization of the PCR. The utility of the primers developed was optimized by ATG-PCR to increase reliability and facilitate technology transfer. This array of markers substantially increases the pool of genetic markers available for genetic investigation in Cucumis.

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Methicillin-resistant Staphylococcus aureus genotyping using a small set of polymorphisms

Journal of Medical Microbiology ◽

10.1099/jmm.0.46157-0 ◽

2006 ◽

Vol 55 (1) ◽

pp. 43-51 ◽

Cited By ~ 47

Author(s):

Alex J. Stephens ◽

Flavia Huygens ◽

John Inman-Bamber ◽

Erin P. Price ◽

Graeme R. Nimmo ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Population Structure ◽

Real Time ◽

Real Time Pcr ◽

Cost Effective ◽

Resolving Power ◽

Nucleotide Polymorphisms ◽

Methicillin Resistant ◽

Effective Manner ◽

Mrsa Strains

The aim of this study was to identify a set of genetic polymorphisms that efficiently divides methicillin-resistant Staphylococcus aureus (MRSA) strains into groups consistent with the population structure. The rationale was that such polymorphisms could underpin rapid real-time PCR or low-density array-based methods for monitoring MRSA dissemination in a cost-effective manner. Previously, the authors devised a computerized method for identifying sets of single nucleotide polymorphisms (SNPs) with high resolving power that are defined by multilocus sequence typing (MLST) databases, and also developed a real-time PCR method for interrogating a seven-member SNP set for genotyping S. aureus. Here, it is shown that these seven SNPs efficiently resolve the major MRSA lineages and define 27 genotypes. The SNP-based genotypes are consistent with the MRSA population structure as defined by eburst analysis. The capacity of binary markers to improve resolution was tested using 107 diverse MRSA isolates of Australian origin that encompass nine SNP-based genotypes. The addition of the virulence-associated genes cna, pvl and bbp/sdrE, and the integrated plasmids pT181, pI258 and pUB110, resolved the nine SNP-based genotypes into 21 combinatorial genotypes. Subtyping of the SCCmec locus revealed new SCCmec types and increased the number of combinatorial genotypes to 24. It was concluded that these polymorphisms provide a facile means of assigning MRSA isolates into well-recognized lineages.

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