scholarly journals Construction of an SNP-based high-density genetic map for Japanese plum in a Chinese population using specific length fragment sequencing

2020 ◽  
Vol 16 (1) ◽  
Author(s):  
Qiu-ping Zhang ◽  
Xiao Wei ◽  
Ning Liu ◽  
Yu-ping Zhang ◽  
Ming Xu ◽  
...  
Keyword(s):  
Genetic Map ◽  
Large Scale ◽  
Prunus Persica ◽  
Reference Genome ◽  
Average Distance ◽  
High Density ◽  
Linkage Maps ◽  
Japanese Plum ◽  
Peach Genome ◽  
Map Construction

AbstractThe Japanese plum (Prunus salicina Lindl.) is one of the most important stone fruit crops in China. High-density linkage map is valuable resources which enhance functional genomics and genetic breeding studies. So far several Japanese plum linkage maps have been reported using different kinds of molecular markers; however, the marker numbers and chromosome coverage are limited. Recently, a newly developed strategy which genome sequencing towards specific-locus amplified fragments (SLAF) markers, has been proven to be powerful for rapid genotyping of genome-wide markers and for high-density genetic map construction. In this study, SLAF was used to genotype markers with 114 F1 seedlings from the ‘09–16’ × ‘Fortune’ cross. Suitable SLAF markers (160,344 out of 343,436,902 pair-end reads) were chosen to conduct genetic map construction, 16.31% of which were polymorphic. The overall integrated map contained 3,341 high quality SLAFs and 720 loci that were grouped in eight genetic linkage groups with a total length of 869.9 cM and an average distance of 1.21 cM, and only five gaps with a genetic distance > 5 cM between adjacent markers occurred in linkage group (LG) 3 and LG6. The number of markers with each LG ranged from 82.3 cM (LG3) to 138.3 cM (LG1). Aligning the map against the peach reference genome sequence (Prunus persica L.) indicated a strictly co-linear relationship between the LGs and peach genome, demonstrating the markers on ours LGs were well ordered. Overall, our studies identified large-scale of genetic markers and constructed high-density linkage maps for Japanese plum, which will obviously provide a solid foundation for marker-assisted selection and sequence assembly of the Japanese plum reference genome.

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

2017 ◽  
Vol 7 (1) ◽  
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

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

scholarly journals Preliminary Genetic Map of a New Recombinant Inbred Line Population for Narrow-leafed Lupin (Lupinus angustifolius L.)

Agronomy ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 653 ◽  
Author(s):  
Bartosz Kozak ◽  
Renata Galek ◽  
Dariusz Zalewski ◽  
Ewa Sawicka-Sienkiewicz
Keyword(s):  
Genetic Map ◽  
Genome Wide Association Study ◽  
Reference Genome ◽  
High Density ◽  
Genetic Maps ◽  
New Variety ◽  
Model Legume ◽  
Speed Up ◽  
Trait Locus ◽  
Next Generation Sequencing Ngs

Genetic maps are an essential tool for investigating molecular markers’ linkage with traits of agronomic importance. Breeders put a lot of emphasis on this type of markers, which are used in breeding programs implementation and speed up the process of a new variety development. In this paper, we construct a new, high-density linkage genetic map for Polish material on narrow-leafed lupin. The mapping population originated from crossing the Polish variety ‘Emir’ and the Belarusian breeding line ‘LAE-1’. A new map was constructed based on DArTseq markers—a new type of marker generated with the next-generation sequencing (NGS) technique. The map was built with 4602 markers, which are divided into 20 linkage groups, corresponding with the number of gametic chromosomes in narrow-leafed lupin. On the new map there are 1174 unique loci. The total length of all linkage group is 3042 cM. This map was compared to the reference genome of narrow-leafed lupin and the CDS sequence for model legume species: emphMedicago truncatula, emphLotus japonicus and Glycine max. Analysis revealed the presence of the DArTseq marker common for all investigated species. We were able to map 38 new, unplaced scaffolds on the new genetic map of narrow-leafed lupin. The high-density genetic map we received can be used for quantitative trait locus (QTL) mapping, genome-wide association study analysis and assembly of the reference genome for the whole genome sequencing (WGS) method

A peach linkage map integrating RFLPs, SSRs, RAPDs, and morphological markers

Genome ◽  
2001 ◽  
Vol 44 (5) ◽  
pp. 783-790 ◽  
Author(s):  
Maria Teresa Dettori ◽  
Roberta Quarta ◽  
Ignazio Verde
Keyword(s):  
Molecular Markers ◽  
Comparative Analysis ◽  
Linkage Map ◽  
Morphological Traits ◽  
Prunus Persica ◽  
Average Distance ◽  
Morphological Markers ◽  
Linkage Groups ◽  
Peach Genome ◽  
The Common

A linkage map was obtained using a BC1 progeny (Prunus persica × (P. persica × P. ferganensis)). The map is composed of 109 loci (74 RFLPs, 17 SSRs, 16 RAPDs, and two morphological traits) distributed in 10 linkage groups. Loci, segregating in five different ratios, were integrated in the map with JoinMap 2.0 software. The map covers 521 cM of the peach genome. The average distance between adjacent loci is 4.8 cM. Two monogenic traits, flesh adhesion (F/f) and leaf glands (E/e), were placed on the map. Thirty-two loci in common with a saturated linkage map of Prunus allowed a comparative analysis to be made between the two maps. Homologies were found among the respective linkage groups. No relevant differences were observed in the linear order of the common loci.Key words: peach, linkage map, Prunus persica, Prunus ferganensis, molecular markers.

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