Batsch douglas gary bielenberg, bradley rauh, shenghua fan, ksenija gasic, albert glenn abbott. The objective of this study was to establish a highdensity single nucleotide polymorphism snpbased genetic map for cultivated peanut by analyzing. A highresolution linkage map facilitates fine mapping of quantitative trait loci qtls and can be produced because of the abundance of snps within the genome. The steps to estimate the linkage map are the same as for tetraploidmap for windows.
Highdensity snp genetic linkage map construction and. Here we report a genomewide linkage study of sex determination in zebrafish using a novel snp genetic map. Construction of genetic linkage maps for agropyron based on the wheat 660k snp array in this study, we constructed a genetic linkage map based on the wheat 660k snp array to determine the highest coverage density and degree reflected by gap. A genebased snp resource and linkage map for the copepod tigriopus californicus brad r foley, 1 colin g rose, 1, 2 daniel e rundle, 1, 3 wai leong, 1 gary w moy, 4. Dna from each progeny was added to a single well of a 96well plate, while the parents were analyzed in triplicate, to increase sequencing depth and provide the information necessary for linkage mapping based on the inheritance of snp alleles.
A major qtl for resistance to fusarium oxysporum f. Construction of the first snpbased linkage map using genotyping. The faba bean inbred lines used in this study either for transcriptome resequencing or snp validation and their sources are listed in table 3, as well as all mapping population parents. This led to a 2943 snp consensus genetic map with 975 unique positions. In the age of highthroughput sequencing, if the sequence depth is low, parental sequence information provides little useful information that can be used as references of. A snpbased genetic linkage map of soybean using the.
However, the male map contained more numbers of snp 2,939 and unique locations 2,005. Wei q, wang w, hu t, hu h, wang j and bao c 2020 construction of a snpbased genetic map using slafseq and qtl analysis of morphological traits in eggplant. We established a firstgeneration linkage map using a mapping panel containing two backcross populations. Frontiers construction of the first snpbased linkage. The combination of snp maps and high density snp arrays allows snps to be used as markers for genetic diseases that have complex traits. Linkage map with snp dosage data in tetraploid urochloa decumbens rebecca caroline ulbricht ferreira university of campinas unicamp, brazil. The genetic map was constructed using lepmap software 28. It is one of the most important aquacultural species in china. However, such approaches usually generate lowcoverage and errorprone sequences for each line in a population. Predicted effect of snps on protein sequence of the 190 snps used to construct the linkage map, 125 66% are predicted to be translated, and of these 125, 101 79. The final genetic map included 4,145 snp markers on 15 linkage groups and was 2,632.
Genotyping by sequencing for snpbased linkage map construction and qtl analysis of chilling requirement and bloom date in peach prunus persica l. The other five maps were more fragmented with between 12 and 20 linkage groups and less well populated with between 109 and. Construction of the first snpbased linkage map using. E cient genetic linkage map construction and diagnosis julian taylor university of adelaide david butler queensland government abstract although various forms of linkage map construction software are widely available, there is a distinct lack of packages for use in the r statistical computing environment r core team2015. Fusarium wilt, a fungal disease caused by fusarium oxysporum f. Construction of an snpbased highdensity linkage map for. Construction of a snpbased genetic linkage map for. Snpbased linkage mapping for validation of adult plant stripe rust. A newly developed sequencebased marker technology, restriction site. The qtl on 3bs with its linked kasp markers can be used in markerassisted selection to improve stripe rust resistance in breeding programs. Douches walks through map generation procedures for diploids. On the basis of the highdensity rad genetic map, qtl mapping of the 16.
Through composite interval mapping, 29 qtls were identified on chromosomes, with lod values ranging from 2. To construct a genetic linkage map, a 102 f1 line mapping population of actinidia chinensis 2n 58 was derived by combining parents that had contrasting phenotypic traits. Kantartzi2, khalid meksem2, qijian song3, dechun wang4, zixiang wen5, david a. Identification of qtls for blast, bacterial blight, and. Markers are shown on right side of the lgs, while map distances are shown on the left side. Goals objectives the overall objective of this research is the creation of a single nucleotide polymorphism snpbased genetic map of the soybean. Frontiers construction of a snpbased genetic map using. Linkage maps were also constructed using antmap software iwata and. Pdf construction of a snpbased genetic linkage map in.
The first snpbased linkage map of chicory through gbs. This study reports a high density genetic linkage map based on the maryland 965722 by spencer recombinant inbred line ril population of soybean glycine max l. Here, we report a genomewide snp based genetic map of kiwifruit by analysing nextgeneration restrictionsiteassociated dna sequencing radseq reads. The framework for the consensus map was provided by the nv648. The snpbased genetic linkage map for cultivated peanut using the zhonghua 5. Of the,974 polymorphic snp markers,273 including 5694 snps mapped to unique genetic locations were mapped to 24 highdensity linkage groups of tobacco. Construction of highdensity genetic linkage maps for. A first generation microsatellite and snpbased linkage map of jatropha chun ming wang, 1 peng liu, 1 chengxin yi, 2 keyu gu, 3 fei sun, 1 lei li, 1 loong chueng lo, 1, 2 xiaokun liu, 4 felicia feng, 1 grace lin, 1 suying cao, 1 yan hong, 2, 4 zhongchao yin, 3 and gen hua yue 1. A snp based linkage map of the turkey genome reveals. A linkage map is an essential framework for mapping traits of interest and a basic tool needed in many fields of genetic studies. Snpbased linkage mapping for validation of adult plant. The left bar represents a linkage map of tomatoexpen 2000, which is an interspecific map constructed in our previous study.
Barcoded multiplexed sequencing approaches based on newgeneration sequencing technologies provide capacity to sequence a mapping population in a single sequencing run. Snpbased genetic linkage analysis can be used to map disease loci, and determine disease susceptibility genes in individuals. The highmap software was used to construct a highdensity genetic. A 55 k snp arraybased genetic map and its utilization in qtl mapping for productive tiller number in common wheat. A highdensity linkage map of chickpea using 3430 snps was constructed and used to identify qtls and candidate genes for ascochyta blight resistance in chickpea. The illumina infinium soysnp6k beadchip genotyping array produced 5,376 snps in the mapping population, with a 96. Qtl mapping based on six agronomic traits, namely fruit transverse diameter. To our knowledge, the integrated map described herein has the best coverage of the potato genome and the highest marker density for tetraploid potato. Due to the narrow genetic base in cucumber, it has been difficult to construct highdensity genetic maps from intravarietal crosses to facilitate genetic mapping and qtl analysis. Cultivation of resistant cultivars in combination with fungicide application within an informed disease management package is the most. Dna molecular markers, especially simple sequence repeats ssrs and singlenucleotide polymorphisms snps, are used widely for the construction of linkage maps, mapping of quantitative trait loci qtl, mapbased gene cloning, markerassisted selection, exploration of population diversity, etc.
A snpbased genetic linkage map of soybean using the soysnp6k illumina infinium beadchip genotyping array masum akond1, shiming liu2, lauren schoener1, james a. High density linkage map construction and qtl mapping for runner. To our knowledge, this map is the densest snpbased genetic map for flax. A webbased tool that allows researchers to browse between various snp chips and types of information in many species, such as list snps that are contained in commercial snp chips, chromosome and physical position of your snps, make commercial snpprobe names linked to a rsssids, access to sender original information, including. A gbssnpbased linkage map and quantitative trait loci. The final integrated linkage map of tetraploid potato included 3001 snp markers on 12 linkage groups, and covered 1415.
The identity of three linkage groups without microsatellite markers ac25, ac30, and ac31 was determined based on. Here, we report a gbsbased highdensity consensus linkage map constructed for. To improve the productivity, genetic improvement through breeding is essential. Gbs typically provides a large number of snp markers per mapping population.
Construction of a single nucleotide polymorphism linkage. A highdensity linkage map is a valuable tool for functional genomics and breeding. Ldlink an interactive web tool for exploring linkage. We identified loci on zebrafish chromosomes 5 lod score 7. A dense singlenucleotide polymorphismbased genetic linkage map of grapevine vitis vinifera l. Qtl controlling fifteen traits were detected by winqtl software.
The new recessive dwarfing gene btwd1 in huaai 11 was mapped onto the high density linkage maps. A genomewide snpbased genetic map and qtl mapping for. To construct a genetic linkage map, it is essential to know the parental genotypes. A first generation microsatellite and snpbased linkage. Genetic linkage mapping was conducted using six biparental populations, further details of which are presented in table 4. Snp assay development for linkage map construction.
Several races, which are differentiated by host range, of the. Snp markers could be placed in just six linkage groups. An snpbased genetic map and qtl mapping for growth. Main intention to introduce snp software technology will be delivering correct and useful solution to customer for their business read more. Genotypingbysequencing facilitates a highdensity consensus. Each included application is specialized for querying and displaying unique aspects of linkage disequilibrium. A genetic linkage map of the sea cucumber apostichopus. A major qtl for downy mildew resistance was detected on chromosome 18 rpv27 in vitis aestivalisderived norton based on a highresolution linkage map with snp and ssr markers as well as 2 years of field and laboratory phenotyping data. Snpbased genetic linkage maps for potato 4 of 6 youtube. There were 2,516 snps on the female map, and the number of unique locus was 1,902. Ldlink is a suite of webbased applications designed to easily and efficiently interrogate linkage disequilibrium in population groups.
Since each of the snp markers is directly linked to a specific genomic bac clone and to wholegenome sequence data, and some of them are also linked to est data, the snp linkage map will be a powerful tool for investigating silkworm genome properties, mutation mapping, and mapbased cloning of genes of industrial and agricultural interest. Pdf an snpbased genetic map and qtl mapping for growth. Snpbased high density genetic map and mapping of btwd1. Jatropha curcas is a potential plant species for biodiesel production.
Genomewide snp discovery for development of highdensity. The heterozygous or failure calling allele is white. However, its seed yield is too low for profitable production of biodiesel. Chickpea cultivation in temperate conditions is highly vulnerable to ascochyta blight infection.
The same snp as the chakwal 86 allele is blue, while the same snp as the mingxian 169 allele is red. Free single nucleotide polymorphism snp analysis tools. High density linkage mapping of genomic and transcriptomic. The specific objective of this research is the analysis of snp dna marker data using joinmap or similar genetic mapping software for the purpose of integrating new snp dna markers with the existing genetic linkage map of the soybean. Thus, it is a significant challenge to genotype individual lines in a population for linkage map. The saturated snpbased genetic linkage map in cucumber in the present study, we report an snpbased genetic linkage map in cucumber using slaf sequencing technology. After filtering, 4,638 snps were found suitable for genetic map construction.
The name and genetic location of each 35k snp marker was based on the genetic linkage map. Common markers between two maps are connected with black lines. Snp discovery and linkage map construction in cultivated. An improved consensus linkage map of barley based on flow. Dna molecular markers, especially simple sequence repeats ssrs and singlenucleotide polymorphisms snps, are used widely for the construction of linkage maps, mapping of quantitative trait loci qtl, map based gene cloning, markerassisted selection, exploration of population diversity, etc. A genebased snp resource and linkage map for the copepod. Our results contribute to the available molecular marker resources and to the assembly of a reference genome sequence for the peanut. The genotyping data according to the 35k snp array. Of 39 linkage groups, 36 contained one or more microsatellite markers, allowing the new snpbased linkage groups to be aligned with the microsatellitebased linkage maps woram et al. In this study, we constructed a consensus genetic map of apostichopus japonicus exclusively based on microsatellites and snp markers using two f 1 families. Highdensity genetic linkagemap construction of hawthorn and qtl. A linkage map is an important component in molecular breeding. Slaf sequencing, snp markers, eggplant, genetic linkage map, qtl analysis.
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