Genome-wide SNP identification by high-throughput sequencing and selective mapping allows sequence assembly positioning using a framework genetic linkage map

Abstract Background A high-density genetic linkage map is essential for QTL fine mapping, comparative genome analysis, identification of candidate genes and marker-assisted selection in aquaculture species. Pelteobagrus vachelli is a very popular commercial species in Asia. However, some specific characters hindered achievement of the traditional selective breeding based on phenotypes, such as lack of large-scale genomic resource and short of markers tightly associated with growth, sex determination and hypoxia tolerance related traits. Results By making use of 5059 ddRAD markers in P. vachelli, a high-resolution genetic linkage map was successfully constructed. The map’ length was 4047.01 cM by using an interval of 0.11 cm, which is an average marker standard. Comparative genome mapping revealed that a high proportion (83.2%) of markers with a one-to-one correspondence were observed between P. vachelli and P. fulvidraco. Based on the genetic map, 8 significant genome-wide QTLs for 4 weight, 1 body proportion, 2 sex determination, and 1 hypoxia tolerance related traits were detected on 4 LGs. Some SNPs from these significant genome-wide QTLs were observably associated with these phenotypic traits in other individuals by Kompetitive Allele Specific PCR. In addition, two candidate genes for weight, Sipa1 and HSD11B2, were differentially expressed between fast-, medium- and slow-growing P. vachelli. Sema7a, associated with hypoxia tolerance, was induced after hypoxia exposure and reoxygenation. Conclusions We mapped a set of suggestive and significant QTLs as well as candidate genes for 12 growth, 1 sex determination and 1 hypoxia tolerance related traits based on a high-density genetic linkage map by making use of SNP markers for P. fulvidraco. Our results have offered a valuable method about the much more efficient production of all-male, fast growth and hypoxia tolerance P. vachelli for the aquaculture industry.

Download Full-text

An SNP-Based High-Density Genetic Linkage Map for Tetraploid Potato Using Specific Length Amplified Fragment Sequencing (SLAF-Seq) Technology

Agronomy ◽

10.3390/agronomy10010114 ◽

2020 ◽

Vol 10 (1) ◽

pp. 114 ◽

Cited By ~ 2

Author(s):

Xiaoxia Yu ◽

Mingfei Zhang ◽

Zhuo Yu ◽

Dongsheng Yang ◽

Jingwei Li ◽

...

Keyword(s):

Linkage Map ◽

Genetic Linkage ◽

Large Scale ◽

High Throughput Sequencing ◽

Genetic Linkage Map ◽

De Novo ◽

Snp Markers ◽

High Density ◽

Tetraploid Potato ◽

Specific Length

Specific length amplified fragment sequencing (SLAF-seq) is a recently developed high-resolution strategy for the discovery of large-scale de novo genotyping of single nucleotide polymorphism (SNP) markers. In the present research, in order to facilitate genome-guided breeding in potato, this strategy was used to develop a large number of SNP markers and construct a high-density genetic linkage map for tetraploid potato. The genomic DNA extracted from 106 F1 individuals derived from a cross between two tetraploid potato varieties YSP-4 × MIN-021 and their parents was used for high-throughput sequencing and SLAF library construction. A total of 556.71 Gb data, which contained 2269.98 million pair-end reads, were obtained after preprocessing. According to bioinformatics analysis, a total of 838,604 SLAF labels were developed, with an average sequencing depth of 26.14-fold for parents and 15.36-fold for offspring of each SLAF, respectively. In total, 113,473 polymorphic SLAFs were obtained, from which 7638 SLAFs were successfully classified into four segregation patterns. After filtering, a total of 7329 SNP markers were detected for genetic map construction. The final integrated linkage map of tetraploid potato included 3001 SNP markers on 12 linkage groups, and covered 1415.88 cM, with an average distance of 0.47 cM between adjacent markers. To our knowledge, the integrated map described herein has the best coverage of the potato genome and the highest marker density for tetraploid potato. This work provides a foundation for further quantitative trait loci (QTL) location, map-based gene cloning of important traits and marker-assisted selection (MAS) of potato.

Download Full-text

Genome-wide identification of silique-related traits based on high-density genetic linkage map in Brassica napus

Molecular Breeding ◽

10.1007/s11032-019-0988-1 ◽

2019 ◽

Vol 39 (6) ◽

Author(s):

Weiguo Zhao ◽

Lina Zhang ◽

Hongbo Chao ◽

Hao Wang ◽

Na Ta ◽

...

Keyword(s):

Brassica Napus ◽

Linkage Map ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

High Density ◽

Genome Wide

Download Full-text

Genome-wide SNP discovery and genetic linkage map construction in sunflower (Helianthus annuus L.) using a genotyping by sequencing (GBS) approach

Molecular Breeding ◽

10.1007/s11032-016-0558-8 ◽

2016 ◽

Vol 36 (9) ◽

Cited By ~ 12

Author(s):

Ibrahim Celik ◽

Sabahattin Bodur ◽

Anne Frary ◽

Sami Doganlar

Keyword(s):

Linkage Map ◽

Helianthus Annuus ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Genotyping By Sequencing ◽

Snp Discovery ◽

Helianthus Annuus L ◽

Map Construction ◽

Genome Wide

Download Full-text

A high-density SNP-based genetic map in Pelteobagrus vachelli and mapping of growth, sex determination and hypoxia tolerance related loci

10.21203/rs.2.11007/v1 ◽

2019 ◽

Author(s):

Guosong Zhang ◽

Jie Li ◽

Jiajia Zhang ◽

Xia Liang ◽

Tao Wang ◽

...

Keyword(s):

Sex Determination ◽

Linkage Map ◽

Candidate Genes ◽

Genetic Map ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

High Density ◽

Hypoxia Tolerance ◽

Genome Wide ◽

Pelteobagrus Vachelli

Abstract Background: As is known to all, when we are doing QTL fine mapping, analyzing comparative genome, identifying candidate genes, making marker-assisted selection in aquaculture species, the high-density genetic linkage map is of great significance. Pelteobagrus vachelli is a very popular commercial species in Asia. However, some specific characters made it difficult to do traditional selective breeding based on phenotypes. For instance, potential problems include lacking in genomic resource which is in large scale and short of markers that is related tightly to growth, sex determination and hypoxia tolerance related traits. Results: By making use of 5059 ddRAD markers in P. vachelli，a high-resolution genetic linkage map was successfully constructed. The map’ length was 4047.01 cM by using an interval of 0.11 cm, which is an average marker standard. It is reflected that bu using comparative genome mapping, a large majority (83.2%) of markers with a one-to-one correspondence were observed between P. vachelli and P. fulvidraco. Based on the genetic map, 8 significant genome-wide QTLs for 4 weight, 1 body proportion, 2 sex determination, and 1 hypoxia tolerance related traits were detected on 4 LGs. Some SNPs from these significant genome-wide QTLs were observably associated with these phenotypic traits in other individuals by Kompetitive Allele Specific PCR. In addition, two candidate gene for weight, Sipa1 and HSD11B2, were diﬀerentially expressed between fast-, medium- and slow-growing P. vachelli. Sema7a, associated with hypoxia tolerance, was induced after hypoxia exposure and reoxygenation. Conclusions: We mapped a set of suggestive and significant QTLs as well as candidate genes for 12 growth, 1 sex determination and 1 hypoxia tolerance related traits based on a high-density genetic linkage map by making use of SNP markers for P. fulvidraco. Our results have offered a valuable method about the much more efficient production of all-male, fast growth and hypoxia tolerance P. vachelli for the aquaculture industry.

Download Full-text