Construction of genetic linkage maps and QTL mapping for X-disease resistance in tetraploid chokecherry (Prunus virginiana L.) using SSR and AFLP markers

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.

Download Full-text

Genetic Linkage Maps of Betula platyphylla Suk Based on ISSR and AFLP Markers

Plant Molecular Biology Reporter ◽

10.1007/s11105-009-0138-8 ◽

2009 ◽

Vol 28 (1) ◽

pp. 169-175 ◽

Cited By ~ 18

Author(s):

Zhigang Wei ◽

Kaixuan Zhang ◽

Chuanping Yang ◽

Guifeng Liu ◽

Guanjun Liu ◽

...

Keyword(s):

Genetic Linkage ◽

Aflp Markers ◽

Betula Platyphylla ◽

Linkage Maps ◽

Genetic Linkage Maps ◽

Betula Platyphylla Suk

Download Full-text

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

10.21203/rs.2.17615/v1 ◽

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.

Download Full-text