Construction of High-quality Linkage Maps in Populus with RADseq Data and their Application in QTL Mapping and Genome Assembly

2019 ◽  
Author(s):  
Chunfa Tong ◽  
Dan Yao ◽  
Hainan Wu ◽  
Yuhua Chen ◽  
Wenguo Yang ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Genome Assembly ◽  
Genetic Linkage ◽  
High Density ◽  
Genetic Maps ◽  
Linkage Maps ◽  
Linkage Groups ◽  
High Quality ◽  
Populus Simonii ◽  
Genetic Linkage Maps

Abstract Background: Although great efforts have been made to construct genetic linkage maps in Populus using traditional molecular markers, these maps are typically sparse, and the number of linkage groups does not match the karyotype of Populus . With the advances in high-throughput sequencing technologies and new software packages available for extracting single nucleotide polymorphisms (SNPs) across a mapping population, it is possible to construct high-quality, high-density genetic linkage maps with thousands of SNPs in such outbred species. Results: Two parent-specific linkage maps were constructed with restriction site-associated DNA sequencing (RADseq) data from an F 1 hybrid population from Populus de l toides and Populus simonii and were applied to identify growth trait loci and facilitate genome assembly. The female Populus deltoides map contained 4,018 SNPs, which were divided into 19 linkage groups under a wide range of LOD thresholds from 7 to 55, perfectly matching the karyotype of Populus . The male Populus simonii map showed similar characteristics, consisting of 2,097 SNPs, which also belonged to 19 linkage groups under LOD thresholds of 7 to 29. The SNP genotype data for linkage analysis were confirmed to be of high quality. The SNP order of each linkage group was optimal among different ordering results from several available software platforms. Moreover, the linkage maps allowed the detection of 39 QTLs underlying tree height and 47 for diameter at breast height, some of which were strongly associated with QTLs identified in previous studies. In addition, the linkage maps enabled the anchoring of 671 contigs of a draft genome assembly of Populus simonii to chromosomes, corresponding to approximately 83.6% of the genome and showing a high level of collinearity with the genetic maps. Conclusions: The two parental genetic maps of Populus are of high quality, especially in terms of SNP data quality, the SNP order within linkage groups, and the perfect match between the number of linkage groups and the karyotype of Populus as well as performance in QTL mapping and genome assembly. The adopted approaches for both extracting and ordering SNPs could be applied to other species to construct high-density, high-quality genetic maps.

scholarly journals High-Quality SNP Linkage Maps Improved QTL Mapping and Genome Assembly in Populus

2020 ◽  
Vol 111 (6) ◽  
pp. 515-530
Author(s):  
Chunfa Tong ◽  
Dan Yao ◽  
Hainan Wu ◽  
Yuhua Chen ◽  
Wenguo Yang ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Genome Assembly ◽  
Perfect Match ◽  
Genetic Maps ◽  
Hybrid Population ◽  
Linkage Maps ◽  
Linkage Groups ◽  
High Quality ◽  
F1 Hybrid ◽  
Wide Range

Abstract With the advances in high-throughput sequencing technologies and the development of new software for extracting single nucleotide polymorphisms (SNPs) across a mapping population, it is possible to construct high-quality genetic maps with thousands of SNPs in outbred forest trees. Two parent-specific linkage maps were constructed with restriction site-associated DNA sequencing data from an F1 hybrid population derived from Populus deltoides and Populus simonii, and applied in QTL mapping and genome assembly. The female P. deltoides map contained 4018 SNPs, which were divided into 19 linkage groups under a wide range of LOD thresholds from 7 to 55. The male P. simonii map showed similar characteristics, consisting of 2097 SNPs, which also belonged to 19 linkage groups under LOD thresholds of 7 to 29. The SNP order of each linkage group was optimal among different ordering results from several available software. Moreover, the linkage maps allowed the detection of 39 QTLs underlying tree height and 47 for diameter at breast height. In addition, the linkage maps improved the anchoring of 689 contigs of P. simonii to chromosomes. The 2 parental genetic maps of Populus are of high quality, especially in terms of SNP data quality, the SNP order within linkage groups, and the perfect match between the number of linkage groups and the karyotype of Populus, as well as the excellent performances in QTL mapping and genome assembly. Both approaches for extracting and ordering SNPs could be applied to other species for constructing high-quality genetic maps.

scholarly journals Recent Advances in Molecular Genetic Linkage Maps of Cultivated Peanut

2013 ◽  
Vol 40 (2) ◽  
pp. 95-106 ◽  
Author(s):  
Baozhu Guo ◽  
Manish K. Pandey ◽  
Guohao He ◽  
Xinyou Zhang ◽  
Boshou Liao ◽  
...  
Keyword(s):  
Genetic Linkage ◽  
High Density ◽  
Genetic Maps ◽  
Linkage Maps ◽  
Consensus Map ◽  
Genetic Linkage Maps ◽  
Marker Loci ◽  
Cultivated Peanut ◽  
Peanut Genome ◽  
Mapping Populations

ABSTRACT The competitiveness of peanuts in domestic and global markets has been threatened by losses in productivity and quality that are attributed to diseases, pests, environmental stresses and allergy or food safety issues. Narrow genetic diversity and a deficiency of polymorphic DNA markers severely hindered construction of dense genetic maps and quantitative trait loci (QTL) mapping in order to deploy linked markers in marker-assisted peanut improvement. The U.S. Peanut Genome Initiative (PGI) was launched in 2004, and expanded to a global effort in 2006 to address these issues through coordination of international efforts in genome research beginning with molecular marker development and improvement of map resolution and coverage. Ultimately, a peanut genome sequencing project was launched in 2012 by the Peanut Genome Consortium (PGC). We reviewed the progress for accelerated development of peanut genomic resources in peanut, such as generation of expressed sequenced tags (ESTs) (252,832 ESTs as December 2012 in the public NCBI EST database), development of molecular markers (over 15,518 SSRs), and construction of peanut genetic linkage maps, in particular for cultivated peanut. Several consensus genetic maps have been constructed, and there are examples of recent international efforts to develop high density maps. An international reference consensus genetic map was developed recently with 897 marker loci based on 11 published mapping populations. Furthermore, a high-density integrated consensus map of cultivated peanut and wild diploid relatives also has been developed, which was enriched further with 3693 marker loci on a single map by adding information from five new genetic mapping populations to the published reference consensus map.

scholarly journals Development of High-Density Genetic Linkage Maps and Identification of Loci for Chestnut Gall Wasp Resistance in Castanea spp.

Plants ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 1048
Author(s):  
Daniela Torello Marinoni ◽  
Sogo Nishio ◽  
Nadia Valentini ◽  
Kenta Shirasawa ◽  
Alberto Acquadro ◽  
...  
Keyword(s):  
Genetic Linkage ◽  
Castanea Sativa ◽  
High Density ◽  
Genetic Maps ◽  
Phenotypic Variance ◽  
Linkage Maps ◽  
Gall Wasp ◽  
Resistance Response ◽  
Genetic Linkage Maps ◽  
Resistance Trait

Castanea sativa is an important multipurpose species in Europe for nut and timber production as well as for its role in the landscape and in the forest ecosystem. This species has low tolerance to chestnut gall wasp (Dryocosmus kuriphilus Yasumatsu), which is a pest that was accidentally introduced into Europe in early 2000 and devastated forest and orchard trees. Resistance to the gall wasp was found in the hybrid cultivar ‘Bouche de Bétizac’ (C. sativa × C. crenata) and studied by developing genetic linkage maps using a population derived from a cross between ‘Bouche de Bétizac’ and the susceptible cultivar ‘Madonna’ (C. sativa). The high-density genetic maps were constructed using double-digest restriction site-associated DNA-seq and simple sequence repeat markers. The map of ‘Bouche de Bétizac’ consisted of 1459 loci and spanned 809.6 cM; the map of ‘Madonna’ consisted of 1089 loci and spanned 753.3 cM. In both maps, 12 linkage groups were identified. A single major QTL was recognized on the ‘Bouche de Bétizac’ map, explaining up to 67–69% of the phenotypic variance of the resistance trait (Rdk1). The Rdk1 quantitative trait loci (QTL) region included 11 scaffolds and two candidate genes putatively involved in the resistance response were identified. This study will contribute to C. sativa breeding programs and to the study of Rdk1 genes.

Construction of high-density genetic linkage maps and QTL mapping in the golden pompano

Aquaculture ◽  
2018 ◽  
Vol 482 ◽  
pp. 90-95 ◽  
Author(s):  
Guoqing Zhang ◽  
Xinhui Zhang ◽  
Hengzhen Ye ◽  
Shoujia Jiang ◽  
Hui Yu ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Genetic Linkage ◽  
High Density ◽  
Linkage Maps ◽  
Golden Pompano ◽  
Genetic Linkage Maps

scholarly journals VfODB: a comprehensive database of ESTs, EST-SSRs, mtSSRs, microRNA-target markers and genetic maps in Vicia faba

AoB Plants ◽  
2020 ◽  
Vol 12 (6) ◽  
Author(s):  
Morad M Mokhtar ◽  
Ebtissam H A Hussein ◽  
Salah El-Din S El-Assal ◽  
Mohamed A M Atia
Keyword(s):  
Vicia Faba ◽  
Faba Bean ◽  
Expressed Sequence Tags ◽  
Genetic Linkage ◽  
Genetic Maps ◽  
Linkage Maps ◽  
Microrna Target ◽  
Genetic Linkage Maps ◽  
Expressed Sequence ◽  
Simple Sequence

Abstract Faba bean (Vicia faba) is an essential food and fodder legume crop worldwide due to its high content of proteins and fibres. Molecular markers tools represent an invaluable tool for faba bean breeders towards rapid crop improvement. Although there have historically been few V. faba genome resources available, several transcriptomes and mitochondrial genome sequence data have been released. These data in addition to previously developed genetic linkage maps represent a great resource for developing functional markers and maps that can accelerate the faba bean breeding programmes. Here, we present the Vicia faba Omics database (VfODB) as a comprehensive database integrating germplasm information, expressed sequence tags (ESTs), expressed sequence tags-simple sequence repeats (EST-SSRs), and mitochondrial-simple sequence repeats (mtSSRs), microRNA-target markers and genetic maps in faba bean. In addition, KEGG pathway-based markers and functional maps are integrated as a novel class of annotation-based markers/maps. Collectively, we developed 31 536 EST markers, 9071 EST-SSR markers and 3023 microRNA-target markers based on V. faba RefTrans V2 mining. By mapping 7940 EST and 2282 EST-SSR markers against the KEGG pathways database we successfully developed 107 functional maps. Also, 40 mtSSR markers were developed based on mitochondrial genome mining. On the data curation level, we retrieved 3461 markers representing 12 types of markers (CAPS, EST, EST-SSR, Gene marker, INDEL, Isozyme, ISSR, RAPD, SCAR, RGA, SNP and SSR), which mapped across 18 V. faba genetic linkage maps. VfODB provides two user-friendly tools to identify, classify SSR motifs and in silico amplify their targets. VfODB can serve as a powerful database and helpful platform for faba bean research community as well as breeders interested in Genomics-Assisted Breeding.

Genetic Linkage Maps of the Guppy ( Poecilia reticulata ): Assignment of RAPD Markers to Multipoint Linkage Groups

2003 ◽  
Vol 5 (3) ◽  
pp. 279-293 ◽  
Author(s):  
Gideon Khoo ◽  
Meng Huat Lim ◽  
Haridas Suresh ◽  
Damien K. Y. Gan ◽  
Kok Fang Lim ◽  
...  
Keyword(s):  
Genetic Linkage ◽  
Rapd Markers ◽  
Poecilia Reticulata ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Multipoint Linkage ◽  
Genetic Linkage Maps

scholarly journals Construction of high-density genetic linkage maps for orange-spotted grouper Epinephelus coioides using multiplexed shotgun genotyping

BMC Genetics ◽  
2013 ◽  
Vol 14 (1) ◽  
pp. 113 ◽  
Author(s):  
Xinxin You ◽  
Liping Shu ◽  
Shuisheng Li ◽  
Jieming Chen ◽  
Jian Luo ◽  
...  
Keyword(s):  
Genetic Linkage ◽  
High Density ◽  
Epinephelus Coioides ◽  
Linkage Maps ◽  
Genetic Linkage Maps

Two genetic linkage maps of mungbean using RFLP and RAPD markers

2000 ◽  
Vol 51 (4) ◽  
pp. 415 ◽  
Author(s):  
C. J. Lambrides ◽  
R. J. Lawn ◽  
I. D. Godwin ◽  
J. Manners ◽  
B. C. Imrie
Keyword(s):  
Linkage Map ◽  
Segregation Distortion ◽  
Recombinant Inbred ◽  
Genetic Linkage ◽  
Rapd Markers ◽  
Rflp Markers ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Genetic Linkage Maps ◽  
Map Distance

Two genetic linkage maps of mungbean derived from the cross Berken ACC 41 are reported. The F2 map constructed from 67 individuals consisted of 110 markers (52 RFLP and 56 RAPD) that grouped into 12 linkage groups. The linked markers spanned a total map distance of 758.3 cM. A recombinant inbred (RI) population derived from the 67 F2 individuals was used for the generation of an additional linkage map. The RI map, composed entirely of RAPD markers, consisted of 115 markers in 12 linkage groups. The linked markers spanned a total map distance of 691.7 cM. Using a framework set of RFLP markers, the F2 map was compared with another F2 mungbean map constructed in Minnesota. In general, the order of these markers was consistent between maps. Segregation distortion was observed for some markers. 14.5% (16/110) of mapped F2 markers and 24% (28/115) of mapped RI markers segregated with distorted ratios. Segregation distortion occurred in each successive generation after the F2 . The regions of distortion identified in the Australian maps did not coincide with regions of the Minnesota map.

scholarly journals Randomly Amplified Polymorphic DNA-based Genetic Linkage Maps of Three Apple Cultivars

1997 ◽  
Vol 122 (3) ◽  
pp. 350-359 ◽  
Author(s):  
Patrick J. Conner ◽  
Susan K. Brown ◽  
Norman F. Weeden
Keyword(s):  
Skin Color ◽  
Genetic Linkage ◽  
Average Distance ◽  
Scab Resistance ◽  
Linkage Maps ◽  
Randomly Amplified Polymorphic Dna ◽  
Linkage Groups ◽  
Single Linkage ◽  
Genetic Linkage Maps ◽  
Using Data

Genetic linkage maps were created for three apple (Malus ×domestica Borkh.) cultivars using data from two progenies (`Wijcik McIntosh' xNY 75441-67 and `Wijcik McIntosh' xNY 75441-58). The maps consist primarily of randomly amplified polymorphic DNA (RAPD) markers, but also contain six isozyme loci and four morphological markers (Rf, fruit skin color; Vf, scab resistance; Co, columnar growth habit; Ma, malic acid). Maps were constructed using a double pseudotestcross mapping format and JoinMap mapping software. An integrated `Wijcik McIntosh' map was produced by combining marker data from both progenies into a single linkage map. Homologous linkage groups from paternal maps were paired with their counterparts in the `Wijcik McIntosh' map using locus bridges composed of markers heterozygous in both parents of a progeny. The `Wijcik McIntosh' map consists of 238 markers arranged in 19 linkage groups spanning 1206 cM. The NY 75441-67 map contains 110 markers in 16 linkage groups and the NY 75441-58 map consists of 183 markers in 18 linkage groups. The average distance between markers in the maps was ≈5.0 cM.

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