scholarly journals Genomic Resource Development for Hydrangea (Hydrangea macrophylla (Thunb.) Ser.)—A Transcriptome Assembly and a High-Density Genetic Linkage Map

Horticulturae ◽  
2021 ◽  
Vol 7 (2) ◽  
pp. 25
Author(s):  
Xingbo Wu ◽  
Amanda M. Hulse-Kemp ◽  
Phillip A. Wadl ◽  
Zach Smith ◽  
Keithanne Mockaitis ◽  
...  
Keyword(s):  
Genetic Resources ◽  
Linkage Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Mapping Population ◽  
High Density ◽  
Linkage Maps ◽  
Map Construction ◽  
Hydrangea Macrophylla ◽  
Genetic Linkage Maps

Hydrangea (Hydrangea macrophylla) is an important ornamental crop that has been cultivated for more than 300 years. Despite the economic importance, genetic studies for hydrangea have been limited by the lack of genetic resources. Genetic linkage maps and subsequent trait mapping are essential tools to identify and make markers available for marker-assisted breeding. A transcriptomic study was performed on two important cultivars, Veitchii and Endless Summer, to discover simple sequence repeat (SSR) markers and an F1 population based on the cross ‘Veitchii’ × ‘Endless Summer’ was established for genetic linkage map construction. Genotyping by sequencing (GBS) was performed on the mapping population along with SSR genotyping. From an analysis of 42,682 putative transcripts, 8780 SSRs were identified and 1535 were validated in the mapping parents. A total of 267 polymorphic SSRs were selected for linkage map construction. The GBS yielded 3923 high quality single nucleotide polymorphisms (SNPs) in the mapping population, resulting in a total of 4190 markers that were used to generate maps for each parent and a consensus map. The consensus linkage map contained 1767 positioned markers (146 SSRs and 1621 SNPs), spanned 1383.4 centiMorgans (cM), and was comprised of 18 linkage groups, with an average mapping interval of 0.8 cM. The transcriptome information and large-scale marker development in this study greatly expanded the genetic resources that are available for hydrangea. The high-density genetic linkage maps presented here will serve as an important foundation for quantitative trait loci mapping, map-based gene cloning, and marker-assisted selection of H. macrophylla.

scholarly journals Construction of a microsatellite-based genetic linkage map for half-smooth tongue sole Cynoglossus semilaevis

2013 ◽  
Vol 59 (1) ◽  
pp. 99-108 ◽  
Author(s):  
Wentao Song ◽  
Guidong Miao ◽  
Yongwei Zhao ◽  
Yuze Niu ◽  
Renyi Pang ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Cynoglossus Semilaevis ◽  
Scar Markers ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Tongue Sole ◽  
Genetic Linkage Maps ◽  
Half Smooth Tongue Sole

Abstract The half-smooth tongue sole Cynoglossus semilaevis is an important cultured marine fish and a promising model fish for the study of sex determination. Sex-specific genetic linkage maps of half-smooth tongue sole were developed with 567 markers (565 microsatellite markers and two SCAR markers). The parents and F1 progeny (92 individuals) were used as segregating populations. The female map was composed of 480 markers in 21 linkage groups, covering a total of 1388.1 cM, with an average interval 3.06 cM between markers. The male map consisted of 417 markers in 21 linkage groups, spanning 1480.9 cM, with an average interval of 3.75 cM. The female and male maps had 474 and 416 unique positions, respectively. The genome length of half-smooth tongue sole was estimated to be 1522.9 cM for females and 1649.1cM for males. Based on estimations of map length, the female and male maps covered 91.1% and 89.8% of the genome, respectively. Furthermore, two female-specific SCAR markers, f-382 and f-783, were mapped on LG15f (linkage group 15 in female maps). The present study presents a mid-density genetic linkage map for half-smooth tongue sole. These improved genetic linkage maps may facilitate systematic genome searches to identify quantitative trait loci (QTL), such as disease resistance, growth and sex-related traits, and are very useful for marker-assisted selection breeding programs for economically important traits in half-smooth tongue sole.

scholarly journals The History Of Genome Mapping In Fragaria Spp.

2014 ◽  
Vol 22 (2) ◽  
pp. 93-103 ◽  
Author(s):  
Abdel-Rahman Moustafa Abdel-Wahab Mohamed ◽  
Tomasz Jęcz ◽  
Małgorzata Korbin
Keyword(s):  
Linkage Map ◽  
Genetic Linkage ◽  
Genome Mapping ◽  
Mapping Population ◽  
Physical Map ◽  
Linkage Maps ◽  
Genetic Linkage Maps ◽  
Mapping Process ◽  
History Of ◽  
Fragaria Species

AbstractThis overview summarizes the research programs devoted to mapping the genomes within Fragaria genus. A few genetic linkage maps of diploid and octoploid Fragaria species as well as impressive physical map of F. vesca were developed in the last decade and resulted in the collection of data useful for further fundamental and applied studies. The information concerning the rules for proper preparation of mapping population, the choice of markers useful for generating linkage map, the saturation of existing maps with new markers linked to economically important traits, as well as problems faced during mapping process are presented in this paper.

scholarly journals High-density genetic linkage-map construction of hawthorn and QTL mapping for important fruit traits

PLoS ONE ◽  
2020 ◽  
Vol 15 (2) ◽  
pp. e0229020
Author(s):  
Yuhui Zhao ◽  
Yidi Zhao ◽  
Yinshan Guo ◽  
Kai Su ◽  
Xiaochang Shi ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Linkage Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
High Density ◽  
Fruit Traits ◽  
Map Construction

scholarly journals High-Density Genetic Linkage Map Construction and QTL Mapping of Grain Shape and Size in the Wheat Population Yanda1817 × Beinong6

PLoS ONE ◽  
2015 ◽  
Vol 10 (2) ◽  
pp. e0118144 ◽  
Author(s):  
Qiu-Hong Wu ◽  
Yong-Xing Chen ◽  
Sheng-Hui Zhou ◽  
Lin Fu ◽  
Jiao-Jiao Chen ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Linkage Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Grain Shape ◽  
High Density ◽  
Map Construction ◽  
Wheat Population ◽  
Shape And Size

scholarly journals High-density genetic linkage map construction and identification of fruit-related QTLs in pear using SNP and SSR markers

2014 ◽  
Vol 65 (20) ◽  
pp. 5771-5781 ◽  
Author(s):  
Jun Wu ◽  
Lei-Ting Li ◽  
Meng Li ◽  
M. Awais Khan ◽  
Xiu-Gen Li ◽  
...  
Keyword(s):  
Linkage Map ◽  
Ssr Markers ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
High Density ◽  
Map Construction

scholarly journals Genotyping-by-Sequencing Derived Genetic Linkage Map and Quantitative Trait Loci for Sugar Content in Onion (Allium cepa L.)

Plants ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2267
Author(s):  
Ye-Rin Lee ◽  
Cheol Woo Kim ◽  
JiWon Han ◽  
Hyun Jin Choi ◽  
Koeun Han ◽  
...  
Keyword(s):  
Linkage Map ◽  
Quantitative Trait ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Sugar Content ◽  
Genotyping By Sequencing ◽  
Total Sugar ◽  
Linkage Maps ◽  
Total Sugar Content ◽  
Genetic Linkage Maps

Onion (2n = 2x = 16) has been a nutritional, medicinal and economically valuable vegetable crop all over the world since ancient times. To accelerate the molecular breeding in onion, genetic linkage maps are prerequisite. However, construction of genetic linkage maps of onion remains relatively rudimentary due to a large genome (about 16.3 Gbp) as well as biennial life cycle, cross-pollinated nature, and high inbreeding depression. In this study, we constructed single nucleotide polymorphism (SNP)-based genetic linkage map of onion in an F2 segregating population derived from a cross between the doubled haploid line ‘16P118′ and inbred line ‘Sweet Green’ through genotyping by sequencing (GBS). A total of 207.3 Gbp of raw sequences were generated using an Illumina HiSeq X system, and 24,341 SNPs were identified with the criteria based on three minimum depths, lower than 30% missing rate, and more than 5% minor allele frequency. As a result, an onion genetic linkage map consisting of 216 GBS-based SNPs were constructed comprising eight linkage groups spanning a genetic length of 827.0 cM. Furthermore, we identified the quantitative trait loci (QTLs) for the sucrose, glucose, fructose, and total sugar content across the onion genome. We identified a total of four QTLs associated with sucrose (qSC4.1), glucose (qGC5.1), fructose (qFC5.1), and total sugar content (qTSC5.1) explaining the phenotypic variation (R2%) ranging from 6.07–11.47%. This map and QTL information will contribute to develop the molecular markers to breed the cultivars with high sugar content in onion.

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