Supplementary material

Supplementary materia

Additional file 2 from Restriction site-associated DNA sequencing for SNP discovery and high-density genetic map construction in southern catfish (<i>Silurus meridionalis</i>)

The summary of the sequencing data production (Clean Data

Additional file 5 from Restriction site-associated DNA sequencing for SNP discovery and high-density genetic map construction in southern catfish (<i>Silurus meridionalis</i>)

The statistics of the tags, stacks, alleles and SNPs in the F1 populatio

Additional file 4 from Restriction site-associated DNA sequencing for SNP discovery and high-density genetic map construction in southern catfish (<i>Silurus meridionalis</i>)

The putative SNPs between two parent

Additional file 3 from Restriction site-associated DNA sequencing for SNP discovery and high-density genetic map construction in southern catfish (<i>Silurus meridionalis</i>)

Single-nucleotide polymorphism (SNP) markers and high-density genetic maps are important resources for marker-assisted selection, mapping of quantitative trait loci (QTLs) and genome structure analysis. Although linkage maps in certain catfish species have been obtained, high-density maps remain unavailable in the economically important southern catfish (<i>Silurus meridionalis</i>). Recently, developed restriction site-associated DNA (RAD) markers have proved to be a promising tool for SNP detection and genetic map construction. The objective of the present study was to construct a high-density linkage map using SNPs generated by next-generation RAD sequencing in <i>S. meridionalis</i> for future genetic and genomic studies. An F1 population of 100 individuals was obtained by intraspecific crossing of two wild heterozygous individuals. In total, 77 634 putative high-quality bi-allelic SNPs between the parents were discovered by mapping the parents' paired-end RAD reads onto the reference contigs from both parents, of which 54.7% were transitions and 45.3% were transversions (transition/transversion ratio of 1.2). Finally, 26 714 high-quality RAD markers were grouped into 29 linkage groups by using de novo clustering methods (Stacks). Among these markers, 4514 were linked to the female genetic map, 23 718 to the male map and 6715 effective loci were linked to the integrated map spanning 5918.31 centimorgans (cM), with an average marker interval of 0.89 cM. High-resolution genetic maps are a useful tool for both marker-assisted breeding and various genome investigations in catfish, such as sequence assembly, gene localization, QTL detection and genome structure comparison. Hence, such a high-density linkage map will serve as a valuable resource for comparative genomics and fine-scale QTL mapping in catfish species

Additional file 1 from Restriction site-associated DNA sequencing for SNP discovery and high-density genetic map construction in southern catfish (<i>Silurus meridionalis</i>)

Single-nucleotide polymorphism (SNP) markers and high-density genetic maps are important resources for marker-assisted selection, mapping of quantitative trait loci (QTLs) and genome structure analysis. Although linkage maps in certain catfish species have been obtained, high-density maps remain unavailable in the economically important southern catfish (<i>Silurus meridionalis</i>). Recently, developed restriction site-associated DNA (RAD) markers have proved to be a promising tool for SNP detection and genetic map construction. The objective of the present study was to construct a high-density linkage map using SNPs generated by next-generation RAD sequencing in <i>S. meridionalis</i> for future genetic and genomic studies. An F1 population of 100 individuals was obtained by intraspecific crossing of two wild heterozygous individuals. In total, 77 634 putative high-quality bi-allelic SNPs between the parents were discovered by mapping the parents' paired-end RAD reads onto the reference contigs from both parents, of which 54.7% were transitions and 45.3% were transversions (transition/transversion ratio of 1.2). Finally, 26 714 high-quality RAD markers were grouped into 29 linkage groups by using de novo clustering methods (Stacks). Among these markers, 4514 were linked to the female genetic map, 23 718 to the male map and 6715 effective loci were linked to the integrated map spanning 5918.31 centimorgans (cM), with an average marker interval of 0.89 cM. High-resolution genetic maps are a useful tool for both marker-assisted breeding and various genome investigations in catfish, such as sequence assembly, gene localization, QTL detection and genome structure comparison. Hence, such a high-density linkage map will serve as a valuable resource for comparative genomics and fine-scale QTL mapping in catfish species

Rapid SNP Discovery and a RAD-Based High-Density Linkage Map in Jujube (<i>Ziziphus</i> Mill.)

<div><p>Background</p><p><i>Ziziphus</i> Mill. (jujube), the most valued genus of Rhamnaceae, comprises of a number of economically and ecologically important species such as <i>Z. jujuba</i> Mill., <i>Z. acidojujuba</i> Cheng et Liu and <i>Z. mauritiana</i> Lam. Single nucleotide polymorphism (SNP) markers and a high-density genetic map are of great benefit to the improvement of the crop, mapping quantitative trait loci (QTL) and analyzing genome structure. However, such a high-density map is still absent in the genus <i>Ziziphus</i> and even the family Rhamnaceae. The recently developed restriction-site associated DNA (RAD) marker has been proven to be most powerful in genetic map construction. The objective of this study was to construct a high-density linkage map using the RAD tags generated by next generation sequencing.</p><p>Results</p><p>An interspecific F1 population and their parents (<i>Z. jujuba</i> Mill. ‘JMS2’ × <i>Z. acidojujuba</i> Cheng et Liu ‘Xing 16’) were genotyped using a mapping-by-sequencing approach, to generate RAD-based SNP markers. A total of 42,784 putative high quality SNPs were identified between the parents and 2,872 high-quality RAD markers were grouped in genetic maps. Of the 2,872 RAD markers, 1,307 were linked to the female genetic map, 1,336 to the male map, and 2,748 to the integrated map spanning 913.87 centi-morgans (cM) with an average marker interval of 0.34 cM. The integrated map contained 12 linkage groups (LGs), consistent with the haploid chromosome number of the two parents.</p><p>Conclusion</p><p>We first generated a high-density genetic linkage map with 2,748 RAD markers for jujube and a large number of SNPs were also developed. It provides a useful tool for both marker-assisted breeding and a variety of genome investigations in jujube, such as sequence assembly, gene localization, QTL detection and genome structure comparison.</p></div

RAD paired-end contig assembly of the parents.

<p>RAD paired-end contig assembly of the parents.</p

RAD tag and SNP discovery in the parents.

<p>RAD tag and SNP discovery in the parents.</p

Transitions and transversions within 42,784 biallelic single nucleotide polymorphisms (SNPs) detected among jujube parents.

<p>This figure shows all the statistics of transitions and transversions SNPs between the jujube parents.</p