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

2017 ◽  
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]

scholarly journals High-Density Genetic Map Construction and QTL Mapping of Leaf and Needling Traits in Ziziphus jujuba Mill

2019 ◽  
Vol 10 ◽  
Author(s):  
Zhongtang Wang ◽  
Zhong Zhang ◽  
Haixia Tang ◽  
Qiong Zhang ◽  
Guangfang Zhou ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Genetic Map ◽  
High Density ◽  
Map Construction ◽  
Ziziphus Jujuba

High-Density Genetic Map Construction in Sugar Beet (Beta vulgaris L.) by High-Throughput Technology

Sugar Tech ◽  
2017 ◽  
Vol 20 (2) ◽  
pp. 212-219 ◽  
Author(s):  
Maoqian Wang ◽  
Yuhui Xu ◽  
Zedong Wu ◽  
Huazhong Wang ◽  
Hanguo Zhang
Keyword(s):  
Sugar Beet ◽  
Beta Vulgaris ◽  
Genetic Map ◽  
High Throughput ◽  
High Density ◽  
Map Construction ◽  
High Throughput Technology

scholarly journals Construction of a High-Density Genetic Map of Acca sellowiana (Berg.) Burret, an Outcrossing Species, Based on Two Connected Mapping Populations

2021 ◽  
Vol 12 ◽  
Author(s):  
Marianella Quezada ◽  
Rodrigo Rampazo Amadeu ◽  
Beatriz Vignale ◽  
Danilo Cabrera ◽  
Clara Pritsch ◽  
...  
Keyword(s):  
De Novo ◽  
Genetic Research ◽  
Diploid Species ◽  
Eucalyptus Grandis ◽  
Snp Markers ◽  
High Density ◽  
Genetic Maps ◽  
Acca Sellowiana ◽  
Marker Distance ◽  
Connected Populations

Acca sellowiana, known as feijoa or pineapple guava, is a diploid, (2n = 2x = 22) outcrossing fruit tree species native to Uruguay and Brazil. The species stands out for its highly aromatic fruits, with nutraceutical and therapeutic value. Despite its promising agronomical value, genetic studies on this species are limited. Linkage genetic maps are valuable tools for genetic and genomic studies, and constitute essential tools in breeding programs to support the development of molecular breeding strategies. A high-density composite genetic linkage map of A. sellowiana was constructed using two genetically connected populations: H5 (TCO × BR, N = 160) and H6 (TCO × DP, N = 184). Genotyping by sequencing (GBS) approach was successfully applied for developing single nucleotide polymorphism (SNP) markers. A total of 4,921 SNP markers were identified using the reference genome of the closely related species Eucalyptus grandis, whereas other 4,656 SNPs were discovered using a de novo pipeline. The individual H5 and H6 maps comprised 1,236 and 1,302 markers distributed over the expected 11 linkage groups, respectively. These two maps spanned a map length of 1,593 and 1,572 cM, with an average inter-marker distance of 1.29 and 1.21 cM, respectively. A large proportion of markers were common to both maps and showed a high degree of collinearity. The composite map consisted of 1,897 SNPs markers with a total map length of 1,314 cM and an average inter-marker distance of 0.69. A novel approach for the construction of composite maps where the meiosis information of individuals of two connected populations is captured in a single estimator is described. A high-density, accurate composite map based on a consensus ordering of markers provides a valuable contribution for future genetic research and breeding efforts in A. sellowiana. A novel mapping approach based on an estimation of multipopulation recombination fraction described here may be applied in the construction of dense composite genetic maps for any other outcrossing diploid species.

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