High-density genetic map of the yellow drum (Nibea albiflora)

We have built a full-sib F₁ family consisting 200 individuals of the yellow drum. We sequenced the whole genomes of the parents and the F₁ offspring applying Illumina HiSeq X TEN platform. The raw reads were filtered by removing low quality reads and adapters by using Trimmomatic (v0.36) ⁴¹. An average of 9.8 Gb data was obtained for each individual. The clean reads were mapped to the reference assembly using “BWA-MEM” in BWA (v0.7.10-r78) ⁴². Genomic alignments showed that the average sequence depth of the parents and the F1 individuals was 45.9× and 15.54×, respectively.For SNP calling, the high-quality mapped reads of the 202 individuals were analyzed in GATK (v 3.3-0) ⁴³. A number of 3.36 million raw SNPs were called for subsequent filtering: 1) only bi-allele SNPs were retained in all individuals. 2) genotype depth of SNPs of parents and offspring were between 10-30 and 5-20, respectively. 3) genotype quality of all variants &gt; 10. 4) all SNPs in the parents should not be missing and at least one of the parents should be heterozygous. 5) missing rate of each SNP should be &lt; 15%. Then filtered SNPs were obtained and transmitted into JoinMap4.1 ⁴⁴ for Chi-squared test (<i>P</i> &lt;0.05). Finally, 6,219 SNPs were used for constructing linkage map by Joinmap4.1. Twenty-four linkage groups were clustered using 6,219 SNP markers across the yellow drum genome, with the number of SNPs on each chromosome ranging from 179 to 359. Each linkage group contained an average of 260 SNP markers. The maximum likelihood method was used to sort the markers on each linkage group and estimate the genetic distances between markers. The consensus map spanned 4,300.2 cM and covered nearly the whole genome with a resolution of 0.69 cM. Compared to the previous linkage map constructed by Qiu <i>et al</i>. ⁵, we have used more individuals with more genetic markers and produced a genetic linkage map with higher resolution. This high-density linkage map will facilitate the ongoing marker-assisted selection and genomic study of the yellow drum.