ddRADseq-assisted construction of a high-density SNP genetic map and QTL fine mapping for growth-related traits in the spotted scat (Scatophagus argus)

Abstract

Background: Scatophagus argus is a popular farmed fish in several countries of Southeast Asia, including China. Although S. argus has a highly promising economic value, a significant lag of breeding research severely obstructs the sustainable development of aquaculture industry. As one of the most important economic traits, growth traits are controlled by multiple gene loci called quantitative trait loci (QTLs). It is urgently needed to launch a marker assisted selection (MAS) breeding program to improve growth and other pivotal traits. Thus a high-density genetic linkage map is necessary for the fine mapping of QTLs associated with target traits. Results: Using restriction site-associated DNA sequencing, 6196 single nucleotide polymorphism (SNP) markers were developed from a full-sib mapping population for genetic map construction. A total of 6193 SNPs were grouped into 24 linkage groups (LGs), and the total length reached 2191.65 cM with an average marker interval of 0.35 cM. Comparative genome mapping revealed 23 one-to-one and 1 one-to-two syntenic relationships between S. argus LGs and Larimichthys crocea chromosomes. Based on the high-quality linkage map, a total of 44 QTLs associated with growth-related traits were identified on 11 LGs. Of which, 19 significant QTLs for body weight were detected on 9 LGs, explaining 8.8-19.6% of phenotypic variances. Within genomic regions flanking the SNP markers in QTL intervals, we predicted 15 candidate genes showing potential relationships with growth, such as Hbp1, Vgll4 and Pim3, which merit further functional exploration. Conclusions: The first SNP genetic map with a fine resolution of 0.35 cM for S. argus has been developed, which shows a high level of syntenic relationship with L. crocea genomes. This map can provide valuable information for future genetic, genomic and evolutionary studies. The QTLs and SNP markers significantly associated with growthrelated traits will act as useful tools in gene mapping, map-based cloning and MAS breeding to speed up the genetic improvement in important traits of S. argus. The interesting candidate genes are promising for further investigations and have the potential to provide deeper insights into growth regulation in the future.

A Chromosome—Level Genome Assembly of the Spotted Scat (Scatophagus argus)

“…There are only two genera and three species in the family Scatophagidae: Spotted scat, banded scat ( Scatophagus tetracanthus ), and spot-banded scat ( Selenotoca multifasciata ) ( Froese and Pauly 1995 ). Scatophagus argus is an economically important aquaculture species in East and Southeast Asia due to its easy cultivation, low feeding cost, and high market price ( Cai et al 2010 ; Yang et al 2020 ). It also is a popular food, with a low fat and high-protein content ( Shao et al 2004 ; Gupta 2016 ) and is a popular aquarium species due to its colorful appearance and calm behavior ( Amarasinghe et al 2002 ).…”

“…It also is a popular food, with a low fat and high-protein content ( Shao et al 2004 ; Gupta 2016 ) and is a popular aquarium species due to its colorful appearance and calm behavior ( Amarasinghe et al 2002 ). Considering its importance, S. argus has been intensively studied on its reproductive biology ( Mandal et al 2020 ; Mustapha et al 2018 ; He et al 2019 ), population genetics ( Liu et al 2013 ; Yan et al 2020 ; Yang et al 2020 ), and osmoregulation ( Mu et al 2015 ; Su et al 2020 ). With advances in genomics, the genetic basis of significant traits, molecular markers for important economic traits, and genome-assisted breeding in this species are being investigated.…”

A High-Density SNP Genetic Map Construction Using ddRAD-Seq and Mapping of Capsule Shattering Trait in Sesame

“…Discarded linkage groups and fewer segregation distortion markers in mapping analysis might also be reasons for a shorter map (Wu et al, 2014). Changing the types of restriction enzyme in the library construction or increasing the size of the mapping population might be alternatives to improve this genetic map using the ddRAD-Seq approach (Yang et al, 2020). The mutant sesame line (PI 599466) had a non-shattering capsule and phenotypically differs from Muganli-57 (shattered capsule cultivar), with curling leaves and oval and smaller capsules at the vegetative stage (Figure 1).…”

Golden pompano genome resource enables discovery of valuable gene determining growth traits

“…The filtered SNP markers were divided into linkage groups (LGs) based on their locations in the reference genome, and the linkage relationships between markers on each chromosome were tested by two-points analysis. The missing genotyping imputation and the genotyping errors were corrected by SMOOTH 15,93 .…”