Construction of a highdensity genetic linkage map and qtl mapping for growth traits in. The highthroughput and cost effective marker techniques have changed the entire scenario of marker applications. Gangadhara rao and tusar kanti behera and ambika b gaikwad and a. Rad sequencing discovery and genotyping using next gen dna sequencing. Furthermore, lep map is faster on large data sets, requires no manual input, and. Genotyping by sequencinggbsrestriction site associated dna. Genotyping with rad and ddrad sequencing scigenom labs. The allelic effects of the qtl associated with leaf area in the mapping population were estimated by linear regression using ordinary least squares method.
Highresolution genetic maps are essential for fine mapping of complex. Sbg ddrad sequencing discovery and genotyping using next gen dna sequencing. Pdf highdensity snp linkage map construction and qtl. Frontiers a high density genetic map derived from rad. Construction and application for qtl analysis of a restriction site. In this method, genomic dna is first digested with restriction enzymes, next barcoded adapters are added, dna sheared, amplified and sequenced. Jul 25, 2011 rad markers were initially used in conjunction with low. Cropss 23, restriction siteassociated dna sequencing radseq 24,25. Restriction site associated dna rad markers are a type of genetic marker which are useful for association mapping, qtl mapping, population genetics, ecological genetics and evolution. After data filtering, 768,592,488 raw reads, consisting of 69.
Qtl mapping and genomewide prediction of heat tolerance. Highdensity snp linkage map construction and qtl mapping for. May 14, 2019 a higher density map would hence benefit b. Apr 26, 2011 restrictionsite associated dna rad sequencing is a powerful new method for targeted sequencing across the genomes of many individuals. Dec 22, 2018 however, to our knowledge, the average distance between markers is still more than 1. This approach has broad potential for genetic analysis of nonmodel organisms including genotypephenotype association mapping, phylogeography, population genetics and scaffolding genome assemblies through linkage mapping. The difference between rad and other techniques you might have heard of such as crops, msg or gbs is that rad has a shearing step in the protocol to improve mapping and coveragedistribution of your fragments. Construction of highresolution radseq based linkage map, anchoring reference genome, and qtl mapping of the sex chromosome in the marine medaka. While the cost of sequencing is plummeting, sampling a defined, restricted portion of a genome is always going to be cheaper than sequencing the whole genome. We constructed a highdensity linkage map using single nucleotide polymorphism snp markers generated by restrictionsite associated dna sequencing radseq.
Traditional rad seq uses one restriction enzyme and random shearing to generate fragments from genomic dna. Pdf a high density genetic map derived from rad sequencing. The snp haplotyping was done by ddradseq using a mapping population containing 45 resistant and 45 susceptible f 2 genotypes and 3 resistant and 3 susceptible parents. A method for population genomics john davey illumina sequencing seminar edinburgh 1 july 2010 institute of evolutionary biology university of edinburgh john. The highly reduced 2brad libraries require much less sequencing to achieve accurate genotyping, further increasing the suitability of 2brad for highthroughput genotyping tasks with a. Mapping of a novel clubroot resistance qtl using ddradseq in. After the rad seq approach was developed 34,35, it was initially adopted in a population genomic study 36. Mapping the sex determination locus in the atlantic halibut. Mar 01, 2016 here, we built the first linkage map for common pandora and present the first application of radsequencing in the sparidae family. Highresolution linkage and quantitative trait locus mapping. Highdensity snp linkage map construction and qtl mapping for flavonoidrelated traits in a tea plant camellia sinensis using 2brad sequencing. Research article open access characterisation of qtllinked. The huge genotypic data obtained with next generation sequencing ngs also demands analytical tools, statistical advances, and comprehensive.
Qtl mapping and genomewide prediction of heat tolerance in. The assembled radonly map consists of 445 markers with an. A high density genetic map derived from rad sequencing and its. Additionally, several growthassociated qtl were isolated to other linkage groups. Mapping the sex determination locus in the atlantic halibut hippoglossus hippoglossus using rad sequencing christos palaiokostas1, michael bekaert1, andrew davie1, mairi e cowan1, munevver oral1, john b taggart1, karim gharbi2, brendan j mcandrew1, david j penman1 and herve migaud1 abstract. Using radseq to develop snp markers and construct a high density genetic linkage map to increase resolution of qtl mapping and reduce. Qtlseq and sequence assembly rapidly mapped the gene. Genomewide snp identification for the construction of a high. Aug 20, 20 restriction associated dna rad sequencing is a powerful technique for generation of highdensity linkage maps and conducting quantitative trait locus qtl analysis 22,23 including the mapping of sexdetermining loci in fish. Sbg ddradseq floragenex your partner from dna to data. Qtl mapping and genomewide prediction of heat tolerance in multiple connected populations of temperate maize. Traditional radseq uses one restriction enzyme and random shearing to generate fragments from genomic dna. Rad qtl mapping reveals both genomelevel parallelism and different genetic architecture underlying the evolution of body shape in lake whitefish coregonus clupeaformis species pairs. A highdensity genetic map and qtl mapping of leaf traits and.
A total of 170 rad seq libraries from two parents and 168 offspring were constructed and sequenced on an illumina hiseq2000 platform. Rad in the realm of nextgeneration sequencing technologies. Restriction site associated dna sequencing rad seq is a method to identify and score rad markers, a type of polymorphic genetic marker that are used for population genetic studies, particularly for species with limited existing sequence data. Jan 22, 2011 the gc bias issue makes it difficult to separate heterozygotes, homozygotes, repeats and paralogues by read count alone.
One of the strengths of rad sequencing for genomescale research projects is its generality, as, beyond the practicalities of experimental design and nucleic acid extraction, many approaches are equally applicable to organisms ranging from barley to salmon. This linkage map should provide the basis for future markerassisted selection and qtl mapping of important traits on the species, boosting its aquaculture production through genetic selection programs. Using genotypingby sequencing gbs technology, authorp. Radqtl mapping reveals both genomelevel parallelism and. Molecular mapping of restrictionsite associated dna markers. The complexity of the genome is reduced by digesng the dna with opmized enzymes. Mar 20, 2018 the allelic effects of the qtl associated with leaf area in the mapping population were estimated by linear regression using ordinary least squares method.
Characterisation of qtllinked and genomewide restriction. Bioinformatics tools for radseq analysis omicx omictools. Radpairedend radseqddradseq illumina sequencing and. Sequence based genotyping sbg, also known as double digest rad sequencing ddradseq, is a fractional genome sequencing strategy, designed to efficiently identify and score genetic variants across any genome. By combining snp discovery and genotyping into parallel sequencing events, rad. Recent development of whole genome sequencing has accelerated the analysis of qtls in yeast, a model organism with a relatively small genome size 12. Construction of a highdensity genetic linkage map and qtl. In this study, by application of restriction siteassociated dna sequencing radseq strategies and expansion of the mapping population to 255 individuals, a new highdensity linkage map with 1545 snp markers was constructed. We identified and mapped a novel clubroot resistance qtl using the same mapping population that included susceptible chinese cabbage and resistant turnip lines. Qtl mapping was done using windows qtl cartographer with permutations and a significance level of 0.
As third generation sequencing technologies come on line, it is likely to become possible to sequence rad tags kilobases in length. Mapping phenotypic, expression and transmission ratio. Recent applications of radseq have included linkage and qtl mapping with a particular focus on nonmodel species. May 20, 2012 the highly reduced 2b rad libraries require much less sequencing to achieve accurate genotyping, further increasing the suitability of 2b rad for highthroughput genotyping tasks with a fixed. Construction of highresolution radseq based linkage map. Thus, we attempted to construct a denser genetic map by using large snp markers based on 2brad sequencing to improve the precision of qtl analysis and reduce the difficulty of fine qtl mapping. Pdf mapping and qtl analysis of gynoecy and earliness in. A method for population genomics 20 million reads per lane 8 lanes per run 32 gb per run 100 base pairs per read 4 gb per lane illumina gaiix. Restrictionsite associated dna rad sequencing is a powerful new method for targeted sequencing across the genomes of many individuals. Our results demonstrate that snp discovery based on rad sequencing is efficient in the intraspecific g.
Highdensity linkage map construction and mapping qtl for. The use of rad markers for genetic mapping is often called rad mapping. Restriction site associated dna sequencing rad seq is a fractional genome sequencing strategy, designed to interrogate anywhere from 0. Thus, we attempted to construct a denser genetic map by using large snp markers based on 2brad sequencing to improve the precision of qtl. A high density genetic map derived from rad sequencing and its application in qtl analysis of yieldrelated traits in vigna unguiculata. Qtl mapping for bacterial wilt resistance in peanut arachis. As qtl were genotyped by rad sequencing, we were able to map these sequenced regions onto a draft lake whitefish genome pavey et al. Mapping qtl for leaf area in oil palm using genotyping by. For the parents, standard libraries were constructed and sequenced to a sufficient depth 7080. For these populations with multiple genes contributing large effects to a trait, a strategy of low depth re sequencing of f2 individuals followed by qtl seq analysis with the free combination of. Linkage mapping and comparative genomics using next. Restriction siteassociated dna sequencing radseq is a genome complexity reduction technique that facilitates largescale marker discovery and genotyping by sequencing. Pdf quantitative trait locus qtl mapping in plants dates to the 1980s stuber.
A candidate gene, arc5, within the narrow interval of qtl on chr 9 was identified. Rad seqbased snp, highresolution linkage map, qtl mapping. Keywords qtl analysis bacterial wilt snp ssr rad sequencing bsa resistance gene homolog peanut introduction bacterial wilt bw, caused by ralstonia solanacearum, is a disease of considerable global importance. Fortyfive resistant and 45 susceptible f2 lines along with their parental lines were used for double digest restriction siteassociated dna sequencing ddradseq. This method reduces the complexity of the genome and detect sequence variations in coding and noncoding regions across the genome. A qtl is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually, it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci. Highdensity linkage map construction and mapping qtl for yield. With the continuously decreasing cost of nextgeneration sequencing ngs, rad seq has. Quantitative trait locus an overview sciencedirect topics.
Exploring a nonmodel teleost genome through rad sequencing. Based on the calculations above, rr libraries were constructed for a c. Jan 10, 2016 recent advances in sequencing technology have brought several novel platforms for marker development and subsequent genotyping. Original article detection and mapping of qtl for temperature. Developing genomewide snps and constructing an ultrahigh. Restriction site associated dna sequencing data analysis software tools.
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