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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 and 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 adult largemouth bass, including two parents and 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, single-nucleotide polymorphisms SNPs located in 24 linkage groups LGs. The total genetic length of the linkage map was 1, However, one notable QTL, which accounted for 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 bass. The largemouth bass, Micropterus salmoidesis a large carnivorous fish inhabiting freshwater rivers and lakes in North America Bai et al. This species is now widely cultivated in China because of characteristics such as strong temperature resistance, adaptability to new environments, and attractiveness as sex food source.

Inthe largemouth bass was first introduced into mainland China. At present, it plays an indispensable role as a freshwater aquaculture species in China Sex et al. However, the lack of artificial selection and directional breeding in previous decades has resulted in a decline in the growth rate of pond-cultured fish Dongmei et and. In summary, a largemouth bass species program needs to be established to improve its economic traits and sustain the development of the largemouth bass industry.

One of the most common phenomena in biology is the strikingly different patterns of morphology, reproductive strategies, and behaviors exhibited by male and female individuals within a species Songlin et al.

Teleosts are the most widely distributed and diverse group of vertebrates. Unlike mammals and birds, which exhibit highly conserved master sex-determination genes that control a conserved genetic network responsible for gonad differentiation, teleosts exhibit a wide range of sex-determination patterns, which may be regulated by genetic and environmental factors and their interactions Fowler and Buonaccorsi, ; Sun et al.

From the perspective of evolution, how the transition between temperature and genetic determination takes place and why such a shift occurs remain a mystery, but they are a very interesting phenomenon And and Wang, Generally, fish species show obvious sex determination. In some fish, significant differences in body size and growth rate exist between males and females, and these disparities can have a significant influence on their commercial value, such as the half-smooth tongue sole Cynoglossus semilaevis Song et al.

The males of largemouth bass also have a better growth rate than the females. Therefore, identification of sex-associated markers can reveal the mechanisms underlying the genomic evolution and help determine and for the generation of single-sex groups Liao et al. Linkage maps provide a framework for marker-assisted selection programs and have been widely used for quantitative trait locus QTL mapping of many important traits on chromosomes Yue, ; Yu et al.

Quantitative trait locus localization based on a high-density genetic linkage map can play an important role in promoting marker-assisted selection bass breeding of aquaculture varieties Liu and Cordes, ; Wang et al.

In the process of constructing a high-density genetic linkage map Salem et al. The advent of bass new generation of sequencing, including restriction site—related DNA sequencing RAD-Seqhas revolutionized the genomic approach and allowed the discovery of thousands of SNPs throughout the genome Davey et al. Using the methods mentioned above, QTL maps have been drawn to identify genetic structures associated with complex quantitative traits in many fish species Palaiokostas et al.

When constructed successfully by RAD-Seq, a genetic map for a nonmodel species provides high efficiency at a low cost Brown et al. Thus, the main purpose of this study is to construct the first high-density linkage map of largemouth bass as well as to fine-mapping bass sex determination and growth in this species using RAD-Seq technology Feng et al.

Our study will contribute to the identification of potential genes for economic traits in largemouth bass; these genes can be used for sex determination and selective breeding. Our results will also support a new genome sequence assembly and comparative genome research in largemouth bass in the future.

The largemouth bass F1 full-sib family was produced from the parental fish. Artificial injection of oxytocin was used to promote egg laying, and the collected fertilized eggs were placed in indoor incubators for incubation. Small zooplankton and fairy shrimp were fed as an open bait, and then red worms were fed. When the largemouth bass was 3 months old, all the fish were put into one m 2 breeding pond.

At the age of sex months, experimental fish were randomly collected from the progeny of the family for measurement of body weight BWand length BLbody height BHand head length HL with an average BW of g and BL of Then, anatomical method was carried out to determine the gender of each sample. To construct a RAD library, genomic DNA from samples offspring and two parents was extracted according to a previously published protocol Baird et al. Six pools containing all sex DNA samples were assembled.

Fragments with a size range from to bp were chosen to build the libraries. The six libraries were independently sequenced on different lanes of an Illumina HiSeq Illumina with bp paired-end reads. Unconstrained reads without sample-specific barcodes and enzyme motifs were discarded as well. Then, the high-quality reads were used for the subsequent analyses. A minimum depth of two sequencing reads was allowed for Stacks assembling.

The modules Stacks and Genotypes were operated mapping each progeny data to the catalog for SNP calling and genotyping, respectively. Markers were initially grouped in JoinMap v4. After this initial grouping to individual linkage groups LGsmarkers were divided into 24 groups. Utilizing parallelized computing, this step was repeated several times to assess consistency of marker order between replicates.

Meanwhile, error rates were calculated. And for LOD scores were determined by implementing a method of permutation iterations with the P value less than 0. Thus, the linkage genome-wide LOD threshold was determined to 3. After the low-quality reads had been filtered out, Gigabytes Gb of clean data were obtained from the two parents and their progeny Supplemental Table 1. The average clean data of each progeny accounted for 2. These refined SNP markers were used to construct the linkage map.

After the distorted segregation markers bass been eliminated, 7, markers were improved and successfully assigned to 24 LGs, which was consistent with the reported karyotype analysis of largemouth bass. The linkage map of the total genomic length was 1, Figure 1 Genetic lengths and SNP distribution of 24 linkage groups of largemouth bass. The high-density, high-resolution genetic linkage map consisted of 6, SNPs, approximately fold more markers than the previous linkage map.

This linkage map will be applied widely to mapping and positional cloning of important traits, thereby providing a new chromosome framework for the assembly and map integration of genome sequences. It is located in the 1. In addition, an adjacent QTL accounts for Figure 2 The sex determination in sex bass, where chromosome-wide LOD 3.

Among these, the bass LOD value for sexual determination is 4. In addition, QTL5 is located at 0 to 1. The large distribution and low phenotypic variation of these QTLs indicate that they are controlled by complex genetic regulation during growth.

The most prominent region had the highest LOD value at 4. Although the QTL profiles of sex four growth-related traits showed significant differences, a few overlaps were present. Additionally, the BW7, the smallest region, ranged from Figure 3 The body weight in largemouth bass, where chromosome-wide LOD 3. Figure 4 The body length in largemouth bass, where chromosome-wide LOD 3. Figure 5 The head length in largemouth bass, where chromosome-wide LOD 3. Figure 6 The body height in largemouth bass, where chromosome-wide LOD 3.

Comparing with other genetic sex, SNP markers are the most abundant type of marker in the genome with high polymorphism. However, in a nonmodel aquaculture species with a relatively large mapping population, developing a sufficient number of SNPs and performing cost-effective genotyping are difficult Palaiokostas et al.

With advances of the NGS technologies, various sex SNP genotyping technologies have been developed providing rapid and cost-effective high-throughput SNP genotyping platforms for linkage mapping.

In many species, such as the common carp Jian et al. If a reference genome is unavailable, the de novo method is one of the best approaches sex use with the available analytical tools Baxter et al. Therefore, most researchers can perform RAD-Seq in dozens of individuals from an F1 hybrid population as well as their parents Yue,such as catfish Yun et al.

As one of the important applications of genetic mapping, QTL mapping provides a bridge from structural genome research to functional genome research and has important applications in production. By providing a framework for QTL mapping, high-quality genetic linkage maps can facilitate genetic breeding of economically important aquaculture varieties Chen et al.

In salmon Reid et al. A number of linkage maps of common carp have been constructed, and immediately afterward, different QTLs for body shape, swimming ability, meat quality, and so on were successfully mapped Zhang et al.

In this study, with the help of RAD-seq method, we were able to take advantage of our novel genotyping array, which contained 6, SNPs and provided new insights into sex-related traits. As the first high-density genetic map and largemouth bass, this map provides an essential tool for QTL fine-mapping of sex determination.

One major QTL LG05 associated with sex determination was supported by two markers, which clustered in a narrow linkage span 2.

From the details of genotype bass SNPs and the number of male and female fish of QTL2-SD in largemouth bass, we found that these two markers suggested that this species may have monogenic sex determination of ZW female and ZZ male kind.

Normally, heterogametic sex chromosomes have evolved independently in various lineages of vertebrates, with one of the chromosomes harboring master sex-determining genes or major loci. Such phenomena are sometimes found in fish sex determination studies. They also discovered that two other species of Takifugu are conserved with the association and the Amhr2 SNP with phenotypic sex.

Bass undifferentiated sex chromosomes may be more common in vertebrates than previously thought Takashi et al. We also found similar phenomena in the mandarin fish; one major QTL LG23 related to sex determination was supported by five markers that were found to cluster at a narrow linkage span In Atlantic halibut, four and sex-determination markers were located in the 3.

The above research results indicate that single or multiple LGs or chromosomes are involved in sex determination in different species, providing support for monogenic or polygenic sex determination. Therefore, the mechanisms of sex determination of teleosts are extremely complicated and remain to be further elucidated. However, in this study, the high LOD values and phenotypic variations in the major sex-related QTLs in this study suggest that a single LG may be involved in sex determination in largemouth bass and that one sex-determining gene may be located in this LG.

For years, researchers have tried to unravel the genetic basis of growth-related measurements, not only because of their high biological value but bass owing to their economic importance.

The markers on LG04 were identical, and both significantly correlated with BW and HL, as well as the markers on LG15; this result demonstrated the similarity of these two traits, in agreement with the result of the phenotypic comparison, which showed that higher HL was correlated with higher BW. Similar studies have been reported in the Songpu mirror carp, Yellow River carp, and related hybrids, with few molecular markers Yunjing et al.

HL has been reported to be important in determining the BW of rounded fish Neto et al. This phenomenon, where a single QTL is associated with two or more growth traits in some chromosome regions, is common. Similar phenomena have been observed in some fish, suggesting that genes in that particular region have significant pleiotropic effects, controlling a series of related traits. Moreover, the identification of QTLs influencing many traits could enhance genetic progress and molecular marker—assisted breeding and imply that a genetic interaction underlies these traits in aquaculture Niu et al.

Herein, we performed high-throughput SNP genotyping on a mapping family of largemouth bass and constructed a high-density genetic linkage map. This map provides an important tool for QTL fine-mapping of economically important traits.

We were able to take advantage of a high-throughput SNP genotyping array to provide new insights into sex- and growth-related traits and determine the number and position of QTLs for these traits, although candidate gene identification was difficult because of the absence of a reference genome. Therefore, further molecular cloning to examine the locations of the QTLs in this study or whole-genome sequencing and gene annotation of largemouth bass is the ideal solution for identifying the candidate genes, and these strategies should be employed in the future.

All methods were carried out in accordance with the approved guidelines. SL conceived the project and designed the scientific objectives. CD and JZ conducted bioinformatics analysis. CD and SL prepared the manuscript.

All authors have read and approved the final manuscript. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

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