High-Density Linkage Map and Mapping for Sex and Growth-Related Traits of Largemouth Bass (Micropterus salmoides)

Abstract

The largemouth bass is an important species, and its culture has risen sharply with the surge in fish aquaculture in China. Due to the lack of selective breeding technology for the largemouth bass, the growth rate and disease resistance are low, its sexual maturation is slow, and other serious problems are contributing to a sharp decline in the safety and quality of largemouth bass products in recent decades. Therefore, comprehensive breeding programs to improve the economic performance and promote the modern industrial development of largemouth bass must be considered a priority. Here, a total of 152 adult largemouth bass, including two parents and 150 progenies, were selected to produce the genetic mapping family. Then, a high-density linkage map was constructed based on restriction site–associated DNA sequencing using 6,917 single-nucleotide polymorphisms (SNPs) located in 24 linkage groups (LGs). The total genetic length of the linkage map was 1,261.96 cM, and the length of each LG varied from 24.72 cM for LG02 to 117.53 cM for LG16, with an average length of 52.58 cM and an average SNP number of 286. Thirteen significant quantitative trait loci (QTLs) for sex determination were located on LG04, LG05, LG08, LG12, LG15, LG21, and LG23. An informative QTL cluster that included six QTLs was detected on LG12. However, one notable QTL, which accounted for 71.48% of the total phenotypic variation, was located in the region of 1.85 cM on LG05. In addition, 32 identified QTLs were related to growth, including body weight, body length, body height, and head length. The QTLs for these growth-related traits are located in 13 LG regions and have little effect on phenotypic variation. This high-density genetic linkage map will enable the fine-mapping of economic traits and support the future genome assembly of the largemouth bass. Additionally, our study will be useful for future selective culture of largemouth bass and could potentially be used in molecular-assisted breeding of largemouth bass for aquaculture.

Prediction of the Sex-Associated Genomic Region in Tunas (Thunnus Fishes)

“…In particular, when the region contains recently duplicated sequences, the traditional SNV-based approach may not only miss structural variants but also produce artifacts due to cross-mapping to unassociated regions. In other fish species, sex-associated SNVs have often been observed in multiple scaffolds [49][50][51], some of which might be cases of cross-mapping of short reads, unless the sexes are polygenically determined. We believe that a combination of traditional SNV-and CNV-based approaches is useful for the identification of sex-associated genes in fish species with a genetic sex determination system.…”

Prediction of the sex-determination gene in tunas (Thunnus fishes)

“…In particular, when the region contains recently duplicated sequences, the traditional SNV-based approach may not only miss structural variants but also produce artifacts due to cross-mapping to unassociated regions. In other fish species, sex-associated SNVs have often been observed in multiple scaffolds (Fowler and Buonaccorsi, 2016; Star et al, 2016; Dong et al, 2019), some of which might be cases of cross-mapping of short reads, unless the sexes are polygenically determined. We believe that a combination of traditional SNV- and CNV-based approaches is useful for the identification of sex-associated genes in fish species with a genetic sex-determination system.…”

A Novel Sandwich ELASA Based on Aptamer for Detection of Largemouth Bass Virus (LMBV)

“…Largemouth bass ( Micropterus salmoides ) is an important economic freshwater fish, which is widely farmed because of its fast growth, strong adaptability and delicious taste [ 1 , 2 ]. The production of largemouth bass has reached 0.4778 million tons in China in 2019 [ 3 ].…”