Whole-Genome Characteristics and Polymorphic Analysis of Vietnamese Rice Landraces as a Comprehensive Information Resource for Marker-Assisted Selection

Next generation sequencing technologies have provided numerous opportunities for application in the study of whole plant genomes. In this study, we present the sequencing and bioinformatic analyses of five typical rice landraces including threeindicaand twojaponicawith potential blast resistance. A total of 688.4 million 100 bp paired-end reads have yielded approximately 30-fold coverage to compare with the Nipponbare reference genome. Among them, a small number of reads were mapped to both chromosomes and organellar genomes. Over two million and eight hundred thousand single nucleotide polymorphisms (SNPs) and insertions and deletions (InDels) inindicaandjaponicalines have been determined, which potentially have significant impacts on multiple transcripts of genes. SNP deserts, contiguous SNP-low regions, were found on chromosomes 1, 4, and 5 of all genomes of rice examined. Based on the distribution of SNPs per 100 kilobase pairs, the phylogenetic relationships among the landraces have been constructed. This is the first step towards revealing several salient features of rice genomes in Vietnam and providing significant information resources to further marker-assisted selection (MAS) in rice breeding programs.

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Accuracy of marker-assisted selection with single markers and marker haplotypes in cattle

Genetics Research ◽

10.1017/s0016672307008865 ◽

2007 ◽

Vol 89 (4) ◽

pp. 215-220 ◽

Cited By ~ 49

Author(s):

B. J. HAYES ◽

A. J. CHAMBERLAIN ◽

H. McPARTLAN ◽

I. MACLEOD ◽

L. SETHURAMAN ◽

...

Keyword(s):

Linkage Disequilibrium ◽

Quantitative Trait Loci ◽

Single Nucleotide Polymorphisms ◽

Quantitative Trait ◽

Marker Assisted Selection ◽

Nucleotide Polymorphisms ◽

Data Set ◽

Single Nucleotide ◽

Angus Cattle ◽

Genome Wide

SummaryA key question for the implementation of marker-assisted selection (MAS) using markers in linkage disequilibrium with quantitative trait loci (QTLs) is how many markers surrounding each QTL should be used to ensure the marker or marker haplotypes are in sufficient linkage disequilibrium (LD) with the QTL. In this paper we compare the accuracy of MAS using either single markers or marker haplotypes in an Angus cattle data set consisting of 9323 genome-wide single nucleotide polymorphisms (SNPs) genotyped in 379 Angus cattle. The extent of LD in the data set was such that the average marker–marker r2 was 0·2 at 200 kb. The accuracy of MAS increased as the number of markers in the haplotype surrounding the QTL increased, although only when the number of markers in the haplotype was 4 or greater did the accuracy exceed that achieved when the SNP in the highest LD with the QTL was used. A large number of phenotypic records (>1000) were required to accurately estimate the effects of the haplotypes.

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Recent advances in understanding genetic variants associated with growth, carcass and meat productivity traits in sheep (<i>Ovis aries</i>): an update

Archives Animal Breeding ◽

10.5194/aab-62-579-2019 ◽

2019 ◽

Vol 62 (2) ◽

pp. 579-583

Author(s):

Alexander S. Zlobin ◽

Natalia A. Volkova ◽

Pavel M. Borodin ◽

Tatiana I. Aksenovich ◽

Yakov A. Tsepilov

Keyword(s):

Marker Assisted Selection ◽

Association Studies ◽

Ovis Aries ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Essential Information ◽

Manual Curation ◽

Comprehensive Search ◽

Meat Productivity ◽

Selection Of

Abstract. Identification of quantitative trait loci (QTLs) and candidate genes that affect growth intensity is a prerequisite for the marker-assisted selection of economically important traits. The number of QTL studies on sheep is relatively small in comparison to those on cattle and pigs. The current QTL sheep database – Sheep QTLdb – contains information on 1658 QTLs for 225 different traits. A few genes and markers associated with growth, carcass and meat productivity traits have been reported. The information about QTLs from the Sheep QTLdb cannot be directly used in marker-assisted selection due to the lack of essential information such as effective and reference alleles, the effect direction etc., and it requires manual curation and validation. In this study we performed a comprehensive search for QTLs focusing on single nucleotide polymorphisms (SNPs) associated with growth and meat traits in sheep. The database contains information about 156 SNP–trait associations (123 unique SNPs) and a list of 165 associated genes. The updated information is freely available at https://github.com/Defrag1236/Ovines_2018 (last access: 18 September 2019). This information can be useful for further association studies and preliminary estimation of genetic variability for economically important traits in different breeds.

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Single Nucleotide Polymorphisms: A Modern Tool to Screen Plants for Desirable Traits

10.5772/intechopen.94935 ◽

2021 ◽

Author(s):

Lovina I. Udoh ◽

Willie Peggy Obaseojei ◽

Chiebuka Uzoebo

Keyword(s):

Marker Assisted Selection ◽

Target Genes ◽

Snp Markers ◽

Nucleotide Polymorphisms ◽

Coding Region ◽

Single Nucleotide ◽

Allele Specific ◽

Sequencing Platforms ◽

Generation Sequencing ◽

Modern Tool

Single nucleotide polymorphism (SNP) represent a change in a single nucleotide within the genome. This can alter the phenotype of an individual within the same species if it occurs in a coding region of the gene. The change in nucleotide can produce desirable characteristic in plants and can become an object for selection. New SNPs have been discovered and subsequently converted to molecular markers using various non-gel based and next generation sequencing platforms. Considering that SNP markers are based on target genes, its abundance in the genome, high automation and multiplexability, has made it a marker of choice and an effective tool for screening plant germplasm for desirable traits. This chapter considers SNP as molecular marker, their discovery and different SNP genotyping methods was documented. A few case studies of SNP as allele specific markers and their association with traits of interest was considered. Thus, highlighting their efficacy as useful tool for marker assisted selection and plant germplasms screening.

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Haplotype characterization and markers at the barley Mlo powdery mildew resistance locus as tools for marker-assisted selection

Genome ◽

10.1139/g06-044 ◽

2006 ◽

Vol 49 (8) ◽

pp. 864-872 ◽

Cited By ~ 9

Author(s):

G Tacconi ◽

V Baldassarre ◽

N C Collins ◽

D Bulgarelli ◽

A M Stanca ◽

...

Keyword(s):

Powdery Mildew ◽

Marker Assisted Selection ◽

Powdery Mildew Resistance ◽

Resistance Locus ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Mildew Resistance ◽

Barley Cultivars ◽

Barley Powdery Mildew ◽

Almost All

Recessive mlo alleles of the barley Mlo gene confer resistance to almost all known isolates of the powdery mildew fungal pathogen targeting barley (Hordeum vulgare). To characterize haplotypes present in the Mlo chromosomal region of cultivated Mlo and mlo barley genotypes, weconducted a polymorphism search in 3 predicted low-copy sequence regions adjacent to the Mlo gene by examining a sample of 4 Mlo and 3 mlo cultivars. Eight single-nucleotide polymorphisms (SNPs) and 1 insertiondeletion (indel) were detected, and easy to use PCR-based markers were developed for typing the SNPs. The PCR markers were used to characterize a collection of 46 Mlo and 25 mlo barley cultivars, identifying 3 distinct mlo-11 haplotypes, 1 mlo-9 haplotype, and 4 Mlo haplotypes. We summarized the haplotype and marker information obtained here and in a previous study to help breeders identify strategies for mlo marker-assisted selection. The ability of the markers to identify mlo-resistant genotypes in segregating populations was demonstrated using 2 resistance-characterized F2 populations derived by 3-way crosses.Key words: barley, powdery mildew resistance, mlo, SNPs, marker-assisted selection.

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Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations

Aquatic Living Resources ◽

10.1051/alr/2017043 ◽

2017 ◽

Vol 31 ◽

pp. 2 ◽

Cited By ~ 8

Author(s):

Roman Wenne

Keyword(s):

Marker Assisted Selection ◽

New Technologies ◽

Association Studies ◽

Natural Populations ◽

Food Product ◽

Aquatic Animal ◽

Genome Wide Association Studies ◽

Nucleotide Polymorphisms ◽

Low Oxygen ◽

Single Nucleotide

An increase in aquatic animal production can be achieved by extending aquaculture areas geographically, utilizing new species for culture, and using new technologies. Among new technologies useful for the increase of aquaculture production is the application of genetics and genomics. New molecular tools that benefit aquaculture have been developed. There has been a large number of experimental and review papers published concerning molecular markers and the range of their applications, including aquaculture and food product analyses. Analysis of single nucleotide polymorphisms (SNPs) has emerged as genotyping technology with wide and significant applications in aquaculture. SNPs can be used for construction of genetic linkage maps, finding quantitative trait loci (QTL) for useful traits like growth, body weight, grilsing, thermal and low oxygen tolerance, resistance to stress and diseases, mapping sex determination loci and identification of progeny in selection and chromosome manipulation experiments, assessment of genomic selectionand marker assisted selection in aquaculture. Genome-wide association studies (GWAS) facilitate the finding associations between SNPs and a trait in related or unrelated specimens. However, many traits are complex and can be controlled by number of QTL. Genotyping by genome reduction complexity sequencing emerged as an efficient and applicable technology in genomic selection. Identification of genes, sequences and nucleotides (substitutions) directly influencing phenotypic variations opens the possibility of marker-assisted selection for desirable characters in culture. SNP and QTL associations can be enhanced using genome editing technology. Examples of successful applications of SNPs in aquaculture of fish, crustacean and mollusk species, representing most geographic areas, and ecological risks assessment are reviewed.

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Functional markers for selection of potyvirus resistance alleles at the pvr2-eIF4E locus in pepper using tetra-primer ARMS–PCR

Genome ◽

10.1139/g08-056 ◽

2008 ◽

Vol 51 (9) ◽

pp. 767-771 ◽

Cited By ~ 18

Author(s):

Manuel Rubio ◽

Carole Caranta ◽

Alain Palloix

Keyword(s):

Single Nucleotide Polymorphisms ◽

Phenotypic Variation ◽

Marker Assisted Selection ◽

Functional Markers ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Arms Pcr ◽

Codominant Markers ◽

The World ◽

Selection Of

Functional markers targeted on single nucleotide polymorphisms (SNPs) responsible for phenotypic variation constitute optimal tools for marker-assisted selection (MAS) of resistance alleles with different specificities. Here, we used the tetra-primer ARMS–PCR procedure to assay SNP signatures of four distinct alleles at the pvr2-eIF4E locus, which controls pepper resistance to several potyviruses. These simple, economical, and codominant markers open the way for MAS of pepper genotypes resistant to the potyviral strains and species that are prevalent in distinct cultivation areas across the world.

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A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes

10.1101/022616 ◽

2015 ◽

Author(s):

Nicole E. Wheeler ◽

Lars Barquist ◽

Robert A. Kingsley ◽

Paul P. Gardner

Keyword(s):

Protein Function ◽

Large Scale ◽

Functional Divergence ◽

Supplementary Information ◽

Nucleotide Polymorphisms ◽

Amino Acid Sequence Level ◽

Single Nucleotide ◽

Genetic Changes ◽

Sequencing Technologies ◽

Bacterial Genomics

AbstractMotivationNext generation sequencing technologies have provided us with a wealth of information on genetic variation, but predicting the functional significance of this variation is a difficult task. While many comparative genomics studies have focused on gene flux and large scale changes, relatively little attention has been paid to quantifying the effects of single nucleotide polymorphisms and indels on protein function, particularly in bacterial genomics.ResultsWe present a hidden Markov model based approach we call delta-bitscore (DBS) for identifying orthologous proteins that have diverged at the amino acid sequence level in a way that is likely to impact biological function. We benchmark this approach with several widely used datasets and apply it to a proof-of-concept study of orthologous proteomes in an investigation of host adaptation in Salmonella enterica. We highlight the value of the method in identifying functional divergence of genes, and suggest that this tool may be a better approach than the commonly used dN/dS metric for identifying functionally significant genetic changes occurring in recently diverged organisms.AvailabilityA program implementing DBS for pairwise genome comparisons is freely available at: https://github.com/UCanCompBio/[email protected], [email protected] informationSupplementary data are available at BioRxiv online.

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Tandem repeats structure of gel-forming mucin domains could be revealed by SMRT sequencing data

10.21203/rs.3.rs-112828/v1 ◽

2020 ◽

Author(s):

Tiange Lang

Keyword(s):

Single Molecule ◽

Tandem Repeats ◽

Nucleotide Polymorphisms ◽

Sequencing Data ◽

Coding Region ◽

Smrt Sequencing ◽

Single Nucleotide ◽

Sequencing Technologies ◽

Long Reads ◽

Great Complexity

Abstract Background. Gel-forming mucin domains of mucin genes show great complexity with tandem repeats (TRs), thus make it difficult to study the sequences. Methods. With the coming of single molecule real-time (SMRT) sequencing technologies, we manage to present sequence structure of mucin domains via SMRT long reads for MUC2, MUC5AC, MUC5B and MUC6. Results. Our study shows that for different individuals, single nucleotide polymorphisms (SNPs) could be found in mucin domains of MUC2, MUC5AC, MUC5B and MUC6, while different number of tandem repeats could be found in mucin domains of MUC2 and MUC6. Conclusions. This information will provided new insights on getting the sequence for Tandem Repeat parts which locate in coding region.

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Evaluation of linkage disequilibrium measures between multi-allelic markers as predictors of linkage disequilibrium between single nucleotide polymorphisms

Genetics Research ◽

10.1017/s0016672307008634 ◽

2007 ◽

Vol 89 (1) ◽

pp. 1-6 ◽

Cited By ~ 52

Author(s):

H. ZHAO ◽

D. NETTLETON ◽

J. C. M. DEKKERS

Keyword(s):

Linkage Disequilibrium ◽

Single Nucleotide Polymorphisms ◽

Qtl Mapping ◽

Marker Assisted Selection ◽

Nucleotide Polymorphisms ◽

Chi Square ◽

Single Nucleotide ◽

Standardized Measures ◽

Trait Locus ◽

Standardized Measure

Effectiveness of marker-assisted selection (MAS) and quantitative trait locus (QTL) mapping using population-wide linkage disequilibrium (LD) between markers and QTLs depends on the extent of LD and how it declines with distance between markers and QTLs in a population. Marker–QTL LD can be predicted from LD between markers. Our previous work evaluated LD measures between multi-allelic markers as predictors of usable LD of multi-allelic markers with QTLs. Since single nucleotide polymorphisms (SNPs) are the current marker of choice for high-density genotyping and LD-mapping of QTLs, the objective of this study was to use LD between multi-allelic markers to predict LD among biallelic SNPs or between SNPs and QTLs. Observable LD between multi-allelic markers was evaluated using nine measures. These included two pooled and standardized measures of LD between pairs of alleles at two markers based on Lewontin's LD measure, two pooled measures of squared correlations between alleles, one standardized measure using Hardy–Weinberg heterozygosities, and four measures based on the chi-square statistic for testing for association between alleles at two loci. The standardized chi-square measure that best predicted usable LD between multi-allelic markers and QTLs, based on our previous work, overestimated usable SNP–SNP or SNP–QTL LD. Instead, three other measures were found to be good predictors of usable SNP–SNP or SNP–QTL LD when LD is generated by drift. Therefore, the LD measure between multi-allelic markers that is best for predicting usable LD in a population depends on the type of markers (i.e. multi-allelic or biallelic) that will eventually be used for QTL mapping or MAS.

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Exploring the Effect of Climate Factors on SNPs within FHA Domain Genes in Eurasian Arabidopsis Ecotypes

Agriculture ◽

10.3390/agriculture11020166 ◽

2021 ◽

Vol 11 (2) ◽

pp. 166

Author(s):

Tamer Aldwairi ◽

David J. Chevalier ◽

Andy D. Perkins

Keyword(s):

High Throughput Sequencing ◽

Genomic Sequence ◽

Geographical Area ◽

Nucleotide Polymorphisms ◽

Climate Factors ◽

Fha Domain ◽

Single Nucleotide ◽

Sequencing Technologies ◽

Full Genomic Sequence ◽

The Impact

The rapid developments in high-throughput sequencing technologies have allowed researchers to analyze the full genomic sequence of organisms faster and cheaper than ever before. An important application of such advancements is to identify the impact of single nucleotide polymorphisms (SNPs) on the phenotypes and genotypes of the same species by discovering the factors that affect the occurrence of SNPs. The focus of this study is to determine whether climate factors such as the main climate, the precipitation, and the temperature affecting a certain geographical area might be associated with specific variations in certain ecotypes of the plant Arabidopsis thaliana. To test our hypothesis we analyzed 18 genes that encode Forkhead-Associated domain-containing proteins. They were extracted from 80 genomic sequences gathered from within 8 Eurasian regions. We used k-means clustering to separate the plants into distinct groups and evaluated the clusters using an innovative scoring system based upon the Köppen-Geiger climate classification system. The methods we used allow the selection of candidate clusters most likely to contain samples with similar polymorphisms. These clusters show that there is a correlation between genomic variations and the geographic distribution of those ecotypes.

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