scholarly journals Construction of Three High-Density Genetic Linkage Maps and Dynamic QTL Mapping of Growth Traits in Yellow River Carp (Cyprinus carpio haematopterus)

2021 ◽  
Vol 43 (3) ◽  
pp. 2276-2288
Author(s):  
Lei Wang ◽  
Songpeng Jia ◽  
Yuxuan Zhang ◽  
Shuhong Jiang ◽  
Yuhan Chen ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Genetic Linkage ◽  
Growth Traits ◽  
Yellow River ◽  
Linkage Maps ◽  
Genetic Linkage Maps ◽  
Dynamic Qtl ◽  
Yellow River Carp ◽  
Growth Development ◽  
Cyprinus Carpio Haematopterus

To provide the theoretical basis for researching growth, development, and molecular marker-assisted breeding of the economically important Yellow River carp (Cyprinus carpio haematopterus) using dynamic quantitative trait locus (QTL) mapping, we constructed three genetic linkage maps from 207 progeny using a new modified genotyping-by-sequencing method. The three maps contained 16,886, 16,548, and 7482 single nucleotide polymorphism markers, respectively, with an average interval of 0.36 cM, 0.45 cM, and 1.00 cM. We identified 148 QTLs related to four growth traits that were located on 25 chromosomes from three growth stages of Yellow River carp. A total of 32, 36, 43, and 37 QTLs were associated with body length, height, width, and weight, respectively. Among them, 47 QTLs were detected for only one growth trait in one stage, but all of the other QTLs were co-localized. Of the 14 main QTLs, 13 were located on chromosome 12, which suggests the presence of growth-related genes on this chromosome. We then detected 17 candidate genes within 50 K upstream and downstream of the 14 main QTLs. This is the first report of the dynamic QTL mapping of growth traits of Yellow River carp, and the results can be used in future studies of growth, development, and molecular-assisted breeding of this species.

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

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 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.

Integrating Genetic Linkage Maps With Pachytene Chromosome Structure in Maize

Genetics ◽  
2004 ◽  
Vol 166 (4) ◽  
pp. 1923-1933 ◽  
Author(s):  
Lorinda K Anderson ◽  
Naser Salameh ◽  
Hank W Bass ◽  
Lisa C Harper ◽  
W Z Cande ◽  
...  
Keyword(s):  
Genetic Linkage ◽  
Chromosome Structure ◽  
Single Copy ◽  
Chromosome 9 ◽  
Linkage Maps ◽  
Cytogenetic Map ◽  
Recombination Nodules ◽  
Novel Approach ◽  
Genetic Linkage Maps ◽  
High Degree

Abstract Genetic linkage maps reveal the order of markers based on the frequency of recombination between markers during meiosis. Because the rate of recombination varies along chromosomes, it has been difficult to relate linkage maps to chromosome structure. Here we use cytological maps of crossing over based on recombination nodules (RNs) to predict the physical position of genetic markers on each of the 10 chromosomes of maize. This is possible because (1) all 10 maize chromosomes can be individually identified from spreads of synaptonemal complexes, (2) each RN corresponds to one crossover, and (3) the frequency of RNs on defined chromosomal segments can be converted to centimorgan values. We tested our predictions for chromosome 9 using seven genetically mapped, single-copy markers that were independently mapped on pachytene chromosomes using in situ hybridization. The correlation between predicted and observed locations was very strong (r2 = 0.996), indicating a virtual 1:1 correspondence. Thus, this new, high-resolution, cytogenetic map enables one to predict the chromosomal location of any genetically mapped marker in maize with a high degree of accuracy. This novel approach can be applied to other organisms as well.

Constructing dense genetic linkage maps

2001 ◽  
Vol 102 (6-7) ◽  
pp. 1113-1122 ◽  
Author(s):  
J. Jansen ◽  
A. G. de Jong ◽  
J. W. van Ooijen
Keyword(s):  
Genetic Linkage ◽  
Linkage Maps ◽  
Genetic Linkage Maps

MAPMAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations

Genomics ◽  
1987 ◽  
Vol 1 (2) ◽  
pp. 174-181 ◽  
Author(s):  
Eric S. Lander ◽  
Philip Green ◽  
Jeff Abrahamson ◽  
Aaron Barlow ◽  
Mark J. Daly ◽  
...  
Keyword(s):  
Genetic Linkage ◽  
Natural Populations ◽  
Linkage Maps ◽  
Genetic Linkage Maps ◽  
Computer Package

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
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