A High-Density Genetic Map Enables Genome Synteny and QTL Mapping of Vegetative Growth and Leaf Traits in Gardenia

The gardenia is a traditional medicinal horticultural plant in China, but its molecular genetic research has been largely hysteretic. Here, we constructed an F1 population with 200 true hybrid individuals. Using the genotyping-by-sequencing method, a high-density sex-average genetic map was generated that contained 4,249 SNPs with a total length of 1956.28 cM and an average genetic distance of 0.46 cM. We developed 17 SNP-based Kompetitive Allele-Specific PCR markers and found that 15 SNPs were successfully genotyped, of which 13 single-nucleotide polymorphism genotypings of 96 F1 individuals showed genotypes consistent with GBS-mined genotypes. A genomic collinearity analysis between gardenia and the Rubiaceae species Coffea arabica, Coffea canephora and Ophiorrhiza pumila showed the relativity strong conservation of LG11 with NC_039,919.1, HG974438.1 and Bliw01000011.1, respectively. Lastly, a quantitative trait loci analysis at three phenotyping time points (2019, 2020, and 2021) yielded 18 QTLs for growth-related traits and 31 QTLs for leaf-related traits, of which qBSBN7-1, qCD8 and qLNP2-1 could be repeatably detected. Five QTL regions (qCD8 and qSBD8, qBSBN7 and qSI7, qCD4-1 and qLLLS4, qLNP10 and qSLWS10-2, qSBD10 and qLLLS10) with potential pleiotropic effects were also observed. This study provides novel insight into molecular genetic research and could be helpful for further gene cloning and marker-assisted selection for early growth and development traits in the gardenia.

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A high-density molecular genetic map around the weaver locus

Mammalian Genome ◽

10.1007/s003359900183 ◽

1996 ◽

Vol 7 (8) ◽

pp. 616-618 ◽

Cited By ~ 1

Author(s):

J. H. Millonig ◽

K. J. Millen ◽

M. E. Hatten

Keyword(s):

Genetic Map ◽

Molecular Genetic ◽

High Density ◽

Molecular Genetic Map

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Large-scale SNP discovery and construction of a high-density genetic map of Colossoma macropomum through genotyping-by-sequencing

Scientific Reports ◽

10.1038/srep46112 ◽

2017 ◽

Vol 7 (1) ◽

Cited By ~ 17

Author(s):

José de Ribamar da Silva Nunes ◽

Shikai Liu ◽

Fábio Pértille ◽

Caio Augusto Perazza ◽

Priscilla Marqui Schmidt Villela ◽

...

Keyword(s):

Genetic Map ◽

Large Scale ◽

Genotyping By Sequencing ◽

High Density ◽

Snp Discovery ◽

Colossoma Macropomum

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Construction of a high-density genetic map: genotyping by sequencing (GBS) to map purple seed coat color (Psc) in hulless barley

Hereditas ◽

10.1186/s41065-018-0072-6 ◽

2018 ◽

Vol 155 (1) ◽

Cited By ~ 2

Author(s):

Xiaohua Yao ◽

Kunlun Wu ◽

Youhua Yao ◽

Yixiong Bai ◽

Jingxiu Ye ◽

...

Keyword(s):

Genetic Map ◽

Seed Coat ◽

Coat Color ◽

Genotyping By Sequencing ◽

High Density ◽

Seed Coat Color ◽

Hulless Barley

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Comparison of Kompetitive Allele Specific PCR (KASP) and genotyping by sequencing (GBS) for quality control analysis in maize

BMC Genomics ◽

10.1186/s12864-015-2180-2 ◽

2015 ◽

Vol 16 (1) ◽

Cited By ~ 35

Author(s):

Berhanu Tadesse Ertiro ◽

Veronica Ogugo ◽

Mosisa Worku ◽

Biswanath Das ◽

Michael Olsen ◽

...

Keyword(s):

Quality Control ◽

Genotyping By Sequencing ◽

Control Analysis ◽

Specific Pcr ◽

Quality Control Analysis ◽

Allele Specific ◽

Allele Specific Pcr

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Construction of a high-density genetic map of Ziziphus jujuba Mill. using genotyping by sequencing technology

Tree Genetics & Genomes ◽

10.1007/s11295-016-1032-9 ◽

2016 ◽

Vol 12 (4) ◽

Cited By ~ 19

Author(s):

Zhong Zhang ◽

Tianjun Wei ◽

Ying Zhong ◽

Xingang Li ◽

Jian Huang

Keyword(s):

Genetic Map ◽

Genotyping By Sequencing ◽

High Density ◽

Sequencing Technology ◽

Ziziphus Jujuba

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A high-density molecular genetic map around the weaver locus

Mammalian Genome ◽

10.1007/s003359900277 ◽

1996 ◽

Vol 7 (12) ◽

pp. 926-926 ◽

Cited By ~ 1

Author(s):

J. H. Millonig ◽

K. J. Millen ◽

M. E. Hatten

Keyword(s):

Genetic Map ◽

Molecular Genetic ◽

High Density ◽

Molecular Genetic Map

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Construction of a high-density American cranberry (Vaccinium macrocarpon Ait.) composite map using genotyping-by-sequencing for multi-pedigree linkage mapping

10.1101/088419 ◽

2016 ◽

Author(s):

Brandon Schlautman ◽

Giovanny Covarrubias-Pazaran ◽

Luis Diaz-Garcia ◽

Massmo Iorizzo ◽

James Polashock ◽

...

Keyword(s):

Association Studies ◽

Genomic Structure ◽

Genetic Research ◽

Genotyping By Sequencing ◽

High Density ◽

Vaccinium Macrocarpon ◽

Nucleotide Polymorphisms ◽

Common Mean ◽

American Cranberry ◽

Ssr Loci

ABSTRACTThe American cranberry (Vaccinium macrocarpon Ait.) is a recently domesticated, economically important, fruit crop with limited molecular resources. New genetic resources could accelerate genetic gain in cranberry through characterization of its genomic structure and by enabling molecular-assisted breeding strategies. To increase the availability of cranberry genomic resources, genotyping-by-sequencing (GBS) was used to discover and genotype thousands of single nucleotide polymorphisms (SNPs) within three inter-related cranberry full-sib populations. Additional simple sequence repeat (SSR) loci were added to the SNP datasets and used to construct bin maps for the parents of the populations, which were then merged to create the first high-density cranberry composite map containing 6073 markers (5437 SNPs and 636 SSRs) on 12 linkage groups (LGs) spanning 1124 cM. Interestingly, higher rates of recombination were observed in maternal than paternal gametes. The large number of markers in common (mean of 57.3) and the high degree of observed collinearity (mean Pair-wise Spearman Rank Correlations > 0.99) between the LGs of the parental maps demonstrates the utility of GBS in cranberry for identifying polymorphic SNP loci that are transferable between pedigrees and populations in future trait-association studies. Furthermore, the high-density of markers anchored within the component maps allowed identification of segregation distortion regions, placement of centromeres on each of the 12 LGs, and anchoring of genomic scaffolds. Collectively, the results represent an important contribution to the current understanding of cranberry genomic structure and to the availability of molecular tools for future genetic research and breeding efforts in cranberry.

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polymapR – linkage analysis and genetic map construction from F1 populations of outcrossing polyploids

10.1101/228817 ◽

2017 ◽

Cited By ~ 1

Author(s):

Peter M. Bourke ◽

Geert van Geest ◽

Roeland E. Voorrips ◽

Johannes Jansen ◽

Twan Kranenburg ◽

...

Keyword(s):

Linkage Analysis ◽

Genetic Map ◽

Genetic Research ◽

Diploid Species ◽

R Package ◽

High Density ◽

Genetic Linkage Analysis ◽

Map Construction ◽

Preferential Chromosome Pairing ◽

Polyploid Crops

AbstractMotivationPolyploid species carry more than two copies of each chromosome, a condition found in many of the world’s most important crops. Genetic mapping in polyploids is more complex than in diploid species, resulting in a lack of available software tools. These are needed if we are to realise all the opportunities offered by modern genotyping platforms for genetic research and breeding in polyploid crops.ResultspolymapR is an R package for genetic linkage analysis and integrated genetic map construction from bi-parental populations of outcrossing autopolyploids. It can currently analyse triploid, tetraploid and hexaploid marker datasets and is applicable to various crops including potato, leek, alfalfa, blueberry, chrysanthemum, sweet potato or kiwifruit. It can detect, estimate and correct for preferential chromosome pairing, and has been tested on high-density marker datasets from potato, rose and chrysanthemum, generating high-density integrated linkage maps in all of these crops.Availability and ImplementationpolymapR is freely available under the general public license from the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/packages=polymapR.ContactChris Maliepaard [email protected] or Roeland E. Voorrips [email protected]

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The frequency of terminal deletions sY160 among men with microdeletions of AZFc region Y-chromosome

Faktori eksperimental'noi evolucii organizmiv ◽

10.7124/feeo.v21.856 ◽

1970 ◽

Vol 21 ◽

pp. 301-305

Author(s):

I. Ye. Haiboniuk ◽

M. Ya. Tyrkus ◽

H. V. Makukh

Keyword(s):

Y Chromosome ◽

Molecular Genetic ◽

Terminal Deletion ◽

Molecular Genetic Study ◽

Salting Out ◽

Azfc Region ◽

Specific Pcr ◽

Allele Specific ◽

Keywords Male Infertility ◽

Azf Region

Aim. Determine the frequency of absence marker terminal deletions sY160 among men with microdeletions of AZFc region Y-chromosome. Methods. DNA from probands blood samples was isolated using a modified salting out method. Microdeletions of Y chromosome AZF region were analyzed using two multiplex PCR. The molecular-genetic study of terminal deletions (absence of sY160) was carried out using allele-specific PCR and analysed by electrophoresis in a 2 % agarose gel. Results. Among infertile men (1500 individuals), Y chromosome microdeletions were detected in 7% males: microdeletions of AZFa subregion in 1 %, AZFb subregion – 3 %, AZF(b+c) subregions – 15 %, AZFc subregion – 67 %. The presence of heterochromatin marker sY160 was confirmed in 39 cases (84.8 %) and absence of sY160 in 7 men (15.2 %). Absence of sY160 was detected in 2 men with AZFc microdeletion and in 5 men with AZFb+AZFc microdeletions. It is important to point out that terminal AZFc deletion was confirmed in 83.3 % of cases of AZFb+c microdeletions and only in 5.1 % of isolated AZFc microdeletions. Conclusions. Thus, among 15.2 % man with different AZF microdeletions of Y-chromosome the heterochromatin marker of terminal deletion sY160 was absents. The implementation of testing of marker of terminal deletion – sY160 may help to determine if the deletion corresponds to the b2/b4 pattern and to avoid biopsy in man which most likely not benefit from the surgical procedure. Keywords: male infertility, spermatogenesis, Y chromosome, AZF region, terminal deletions.

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