High-Resolution Linkage and Quantitative Trait Locus Mapping Aided by Genome Survey Sequencing: Building Up An Integrative Genomic Framework for a Bivalve Mollusc

Abstract

Genetic linkage maps are indispensable tools in genetic and genomic studies. Recent development of genotyping-by-sequencing (GBS) methods holds great promise for constructing high-resolution linkage maps in organisms lacking extensive genomic resources. In the present study, linkage mapping was conducted for a bivalve mollusc (Chlamys farreri) using a newly developed GBS method—2b-restriction site-associated DNA (2b-RAD). Genome survey sequencing was performed to generate a preliminary reference genome that was utilized to facilitate linkage and quantitative trait locus (QTL) mapping in C. farreri. A high-resolution linkage map was constructed with a marker density (3806) that has, to our knowledge, never been achieved in any other molluscs. The linkage map covered nearly the whole genome (99.5%) with a resolution of 0.41 cM. QTL mapping and association analysis congruously revealed two growth-related QTLs and one potential sex-determination region. An important candidate QTL gene named PROP1, which functions in the regulation of growth hormone production in vertebrates, was identified from the growth-related QTL region detected on the linkage group LG3. We demonstrate that this linkage map can serve as an important platform for improving genome assembly and unifying multiple genomic resources. Our study, therefore, exemplifies how to build up an integrative genomic framework in a non-model organism.

QTL fine mapping and identification of candidate genes for growth-related traits in bighead carp ( Hypophthalmichehys nobilis )

“…As expected, these traits had similar distribution patterns of QTLs which were mainly clustered into three main regions on the genetic map, indicating the pleiotropic effect of a QTL for multiple traits. This phenomenon has also been reported in several aquaculture species, such as Atlantic salmon (Baranski et al, 2010;Tsai et al, 2015), Asian seabass (Xia et al, 2013) and Zhikong Scallop (Jiao et al, 2014).…”

High-density linkage mapping aided by transcriptomics documents ZW sex determination system in the Chinese mitten crab Eriocheir sinensis

“…Our linkage analysis successfully identified all 73 linkage groups. The linkage map provides high resolution, and the average recombination rate across all linkage groups in E. sinensis is 3.09 cM Mb − 1 , which is much higher than those reported in many other animals, such as mouse (0.5 cM Mb − 1 ), catfish (1.65 cM Mb − 1 ), zebrafish (1.35 cM Mb − 1 ), scallop (1.3 cM Mb − 1 ) and shrimp (1.9 cM Mb − 1 ) (Shimoda et al, 1999;Jensen-Seaman et al, 2004;Kucuktas et al, 2009;Huang et al, 2011;Baranski et al, 2014;Jiao et al, 2014). This suggests that QTLs, if identified, can be narrowed down to quite small genomic region in E. sinensis.…”

Genetic Mapping and QTL Analysis of Growth-Related Traits in Pinctada fucata Using Restriction-Site Associated DNA Sequencing

“…In comparisons of high resolution genetic linkage maps, those with more markers may result in a longer genome length. The consensus map of Chlamys farreri (1551.9 cM, with 3806 markers) [46] is longer than linkage maps of P. fucata , in this study, and Pinctada maxima [11]. The RAD-seq method was available for high-resolution linkage map construction of P. fucata and this research has provided foundation materials for the utility of RAD-seq in non-model animals.…”