Candidate Gene For Growth Traits Research Articles

Genome-wide mapping of signatures of selection using a high-density array identified candidate genes for growth traits and local adaptation in chickens

BackgroundAvailability of single nucleotide polymorphism (SNP) genotyping arrays and progress in statistical analyses have allowed the identification of genomic regions and genes under selection in chicken. In this study, SNP data from the 600 K Affymetrix chicken array were used to detect signatures of selection in 23 local Italian chicken populations. The populations were categorized into four groups for comparative analysis based on live weight (heavy vs light) and geographical area (Northern vs Southern Italy). Putative signatures of selection were investigated by combining three extended haplotype homozygosity (EHH) statistical approaches to quantify excess of haplotype homozygosity within (iHS) and between (Rsb and XP-EHH) groups. Presence of runs of homozygosity (ROH) islands was also analysed for each group.ResultsAfter editing, 541 animals and 313,508 SNPs were available for statistical analyses. In total, 15 candidate genomic regions that are potentially under selection were detected among the four groups: eight within a group by iHS and seven by combining the results of Rsb and XP-EHH, which revealed divergent selection between the groups. The largest overlap between genomic regions identified to be under selection by the three approaches was on chicken chromosome 8. Twenty-one genomic regions were identified with the ROH approach but none of these overlapped with regions identified with the three EHH-derived statistics. Some of the identified regions under selection contained candidate genes with biological functions related to environmental stress, immune responses, and disease resistance, which indicate local adaptation of these chicken populations.ConclusionsCompared to commercial lines, local populations are predominantly reared as backyard chickens, and thus, may have developed stronger resistance to environmental challenges. Our results indicate that selection can play an important role in shaping signatures of selection in local chicken populations and can be a starting point to identify gene mutations that could have a useful role with respect to climate change.

Structure and function analyses of the Mmd2 gene in pacific white shrimp Litopenaeus vannamei.

Monocyte to macrophage differentiation factor 2 gene (Mmd2) encodes a member of the progestin and adipoQ receptor (PAQR) family, and plays a key role in growth and development. Our previous studies had found Mmd2 (Monocyte to macrophage differentiation factor 2) is a new candidate gene for growth traits in Pacific white shrimp (Litopenaeus vannamei). For the purpose of understanding the underlying mechanism of LvMmd2 affecting the growth of shrimp, we analyzed the gene structure, phylogeny, expression profiles and RNA interference of this gene in L. vannamei. We found the LvMmd2 gene sequence was highly conserved in transmembrane regions, it was widely expressed in different tissues, with the highest expression level in the eye stalk. Knockdown LvMmd2 could significantly promote body length and body weight gain, suggesting it is a growth suppressor. Through transcriptome analysis we identified 422 differentially expressed genes (DEGs) between the dsMmd2 group and control group, among which 337 genes were upregulated in the dsMmd2 group, including numerous muscle-related genes and protein synthesis genes. Further bioinformatics analysis showed that growth, metabolism, and immune-related signal pathway had changed significantly. The above results greatly increase our understanding on the conservative structure and function of LvMmd2 gene, and provide potential application prospects in genetics and breeding.

Genome-Wide Association Study Reveals Additive and Non-Additive Effects on Growth Traits in Duroc Pigs.

Growth rate plays a critical role in the pig industry and is related to quantitative traits controlled by many genes. Here, we aimed to identify causative mutations and candidate genes responsible for pig growth traits. In this study, 2360 Duroc pigs were used to detect significant additive, dominance, and epistatic effects associated with growth traits. As a result, a total number of 32 significant SNPs for additive or dominance effects were found to be associated with various factors, including adjusted age at a specified weight (AGE), average daily gain (ADG), backfat thickness (BF), and loin muscle depth (LMD). In addition, the detected additive significant SNPs explained 2.49%, 3.02%, 3.18%, and 1.96% of the deregressed estimated breeding value (DEBV) variance for AGE, ADG, BF, and LMD, respectively, while significant dominance SNPs could explain 2.24%, 13.26%, and 4.08% of AGE, BF, and LMD, respectively. Meanwhile, a total of 805 significant epistatic effects SNPs were associated with one of ADG, AGE, and LMD, from which 11 sub-networks were constructed. In total, 46 potential genes involved in muscle development, fat deposition, and regulation of cell growth were considered as candidates for growth traits, including CD55 and NRIP1 for AGE and ADG, TRIP11 and MIS2 for BF, and VRTN and ZEB2 for LMD, respectively. Generally, in this study, we detected both new and reported variants and potential candidate genes for growth traits of Duroc pigs, which might to be taken into account in future molecular breeding programs to improve the growth performance of pigs.

Keragaman Gen Growth Hormone Receptor (GHR) Ekson 10 pada itik Sikumbang Janti

Growth Hormone Receptor (GHR) gene play important roles in duck performances due to their crucialfunctions in growth and has been considered as a candidate gene for growth traits. This reasearch wasaimed to indification polymorphism of Growth Hormon Receptor (GHR) gene in Sikumbang Janti duckand this study used 68 blood duck. Polymerase chain reaction (PCR) and sequencing analysis wereconducted to detect SNP existence in exon 10 of GHR gene. The result of this study showed that wasfound two SNP at g.1112 A>G and g.1304 C>T with transision mutation in exon 10 GHR gene. Genotypesfound in the g.1112 A>G were AA and GG with types of Allele A and G. Genotypes found in the g.1304T>C the were TT and CC with types of Allele T and C. Polymorphism of GHR gene were polymorphicand Population of Sikumbang Janti duck in Hardy-Weinberg equilibrium. It could be concluded thatGHR gene has potential to can be marker genetic in Sikumbang Janti ducks.

Weighted Single-Step GWAS Identified Candidate Genes Associated with Growth Traits in a Duroc Pig Population.

Growth traits are important economic traits of pigs that are controlled by several major genes and multiple minor genes. To better understand the genetic architecture of growth traits, we performed a weighted single-step genome-wide association study (wssGWAS) to identify genomic regions and candidate genes that are associated with days to 100 kg (AGE), average daily gain (ADG), backfat thickness (BF) and lean meat percentage (LMP) in a Duroc pig population. In this study, 3945 individuals with phenotypic and genealogical information, of which 2084 pigs were genotyped with a 50 K single-nucleotide polymorphism (SNP) array, were used for association analyses. We found that the most significant regions explained 2.56–3.07% of genetic variance for four traits, and the detected significant regions (>1%) explained 17.07%, 18.59%, 23.87% and 21.94% for four traits. Finally, 21 genes that have been reported to be associated with metabolism, bone growth, and fat deposition were treated as candidate genes for growth traits in pigs. Moreover, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses implied that the identified genes took part in bone formation, the immune system, and digestion. In conclusion, such full use of phenotypic, genotypic, and genealogical information will accelerate the genetic improvement of growth traits in pigs.

Association of the thyroid hormone responsive spot 14 alpha gene with growth-related traits in Korean native chicken.

ObjectiveThyroid hormone responsive spot 14 alpha (THRSP) has been used to investigate the regulation of de novo lipogenesis because the variation of THRSP mRNA content in the tissue affects directly the ability of that tissue to synthetize lipids. Also, this gene responds to thyroid hormone stimulation and high level of carbohydrate feeding or insulin-injection. This study was carried out to investigate variations within THRSP and their effects on body and carcass weights in Korean native chicken (KNC).MethodsA total of 585 chickens which represent the five lines of KNC (Black, Gray-Brown, Red-Brown, White, and Yellow-Brown) were reared and body weight data were recorded every two weeks from hatch until 20 weeks of age. Polymerase chain reaction-restriction fragment length polymorphism, DNA chips for Agilent 2100 Bioanalyzer, and Fluidigm Genotyping Technology, were applied to genotype selected markers. A linear mixed-effect model was used to access association between these single nucleotide polymorphism (SNP) markers and growth-related traits.ResultsA total of 30 polymorphisms were investigated in THRSP. Of these, nine SNPs for loci were selected to perform association analyses. Significant associations were detected between g.-49G>T SNP with body weight at 20 weeks of age (BW20), g.451T>C SNP with growth at 10 to 12 weeks of age (GR10-12), and g.1432A>C SNP with growth at 14 to 16 weeks trait (GR14-16) and body weight at 18 weeks of age (BW18). Moreover, diplotype of the THRSP gene significantly affected body weight at 12 weeks of age (BW12) and GR10-12 traits. Diplotype of ht1/ht2 was favorable for BW12 and GR10-12 traits.ConclusionThese results suggest that THRSP can be regarded as a candidate gene for growth traits in KNC.

Melanocortin-4 Receptor (MC4R) Gene as the Main Gene for Rapid Growth Selection in Beef Cattle

Genetic improvement for economic traits such as growth is important in beef cattle selection program. This paper discusses melanocortin-4 receptor (MC4R) gene as a candidate gene for rapid growth based on its function, location and pathway, as well as its polymorphism and identified genotypes associated with economic traits, and its application as a marker-assisted selection. MC4R is a prominent gene encoding growth traits and has a critical role in mediating the effect of leptin in regulating food consumption and energy balance. Many identified MC4R gene polymorphisms are associated with growth traits. The MC4R gene, therefore, is considered as a functional candidate gene for growth traits and can be used as a marker in selection program based on molecular genetics. The use of molecular markers such as MC4R gene, therefore, can be applied in genetic improvement program for growth traits in cattle. By using MC4R gene, the efforts to build breeding system in small populations can be proposed. For instance, with an effective population size (Ne) of about 40 heads, the first generation (G1) will be obtained with a composition of GG 61.1%, CG 33.3% and CC 5.6% and male and female ratio of 178:11 and generates ideal Ne of 41 heads. In the third generation, therefore, GG composition will be 100%. The results of molecular analysis can be further used as a guideline in the development and genetic improvement strategies of beef cattle.

Identification of GH Gene Polymorphisms and Their Association with Body Weight in Bayang Duck, Local Duck from West Sumatra, Indonesia

Polymorphisms in the growth hormone (GH) gene that is associated with the growth rate of duck have been the target of many breeding programmes. Molecular market selection has been an acceptable tool in the acceleration of the genetic response of desired to improve production performance in livestock. Growth hormone (GH) has been considered as a candidate gene for growth traits. In this study, polymorphisms of the GH gene were evaluated for associations with body weight in 210 Bayang duck. The objective of this study was to assess the association of polymorphisms in Growth Hormone (GH) genes with growth in Bayang ducks. The polymorphism of the ducks GH gene from promoter region into exon 3 was researched by polymerase chain reaction and DNA sequencing methods. Fifty duck were genotyped by sequencing twenty mutations were detected in the Bayang duck GH gene. Mutation G→A were detected at position -142, 1155, 1117, 1423, and 1786. Mutation C→T were detected at position -62, 506, and 308. Mutation A→G were detected at position 160, 264, 293, 1245, and 2542. Mutation T→G detected at position 250 and mutation TT→AA detected at position 350. Mutation G→T detected at position 775 and mutation T→C were detected at position 1353, 1424, and 2973. All polymorphism were polymorphics except polymorphism T→G at position 250 was monomorphics. Mutation G→A in position 1117 and 1786 were restriction with enzyme Eco721 and TscaI. In the case GH-Eco721 three genotypes were observed, GG, GA, and AA with frequency 0.041, 0.59 and 0.369 respectively. For GH-TscaI locus the frequency were 0.034, 0.782, and 0.184 respectively. The effect of GH-TscaI polymorphism were observed on body weight in 4 to 8 week of Bayang duck.

Two Novel SNPs of PPARγ Significantly Affect Weaning Growth Traits of Nanyang Cattle

ABSTRACTPeroxisome-proliferator-activated receptor gamma (PPARγ) is a key transcription factor that controls adipocyte differentiation and energy in mammals. Therefore, PPARγ is a potential factor influencing animal growth traits. This study primarily evaluates PPARγ as candidate gene for growth traits of cattle and identifies potential molecular marker for cattle breeding. Per previous studies, PPARγ mRNA was mainly expressed at extremely high levels in adipose tissues as shown by quantitative real-time polymerase chain reaction analysis. Three novel SNPs of the bovine PPARγ gene were identified in 514 individuals from six Chinese cattle breeds: SNP1 (AC_000179.1 g.57386668 C > G) in intron 2 and SNP2 (AC_000179.1 g.57431964 C > T) and SNP3 (AC_000179.1 g.57431994 T > C) in exon 7. The present study also investigated genetic characteristics of these SNP loci in six populations. Association analysis showed that SNP1 and SNP3 loci significantly affect weaning growth traits, especially body weight of Nanyang cattle. These results revealed that SNP1 and SNP3 are potential molecular markers for cattle breeding.

Association of a Cac8I polymorphism in the IGF1 gene with growth traits in Indian goats.

The Insulin-like Growth Factor 1 (IGF1) gene is a member of somatotropic axis and plays a key role in proliferation of cells, mitosis, myogenesis, meiosis, differentiation in foetal development and post natal growth. The objectives of this study were to verify the single nucleotide polymorphisms (SNPs) in IGF1 gene and their association with growth traits in two indigenous native goat genetic groups of Kerala, viz., Malabari and Attappady Black. A total of 277 goats were genotyped using a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) using the restriction enzyme Cac8I. One SNP, A224G was detected in the 5′ non-coding region of the IGF1 gene, and accordingly two genotypes were revealed, GG and AG. This SNP was significantly associated with growth traits in Attappady Black goats, which is maintained as meat breed in Kerala. Results from this study demonstrated higher performance of GG animals for growth traits. The association of IGF1 gene with these traits emphasizes the importance of caprine IGF1 as a candidate gene for growth traits in goat breeding.

Detection of Growth-Related Quantitative Trait Loci and High-Resolution Genetic Linkage Maps Using Simple Sequence Repeat Markers in the Kelp Grouper (Epinephelus bruneus).

To initiate breeding programs for kelp grouper (Epinephelus bruneus), the establishment of genetic linkage maps becomes essential accompanied by the search for quantitative trait loci (QTLs) that may be utilized in selection programs. We constructed a high-resolution genetic linkage map using 1055 simple sequence repeat (SSR) markers in an F1 family. Genome-wide and chromosome-wide significances of growth-related QTLs (body weight: BW and total length: TL) were detected using non-parametric mapping, Kruskal-Wallis analysis, simple interval mapping (IM), and a permutation test (PT). Two stages and two families of fish were used to confirm the QTL regions. Ultimately, 714 SSR markers were matched that evenly covered the 24 linkage groups. In total, 509 and 512 markers were localized to the female and male maps, respectively. The genome lengths were approximately 1475.95 and 1370.39cM and covered 84.68 and 83.21% of the genome, with an average interval of 4.1 and 4.0cM, in females and males, respectively. One major QTL affecting BW and TL was found on linkage group EBR 17F that identified for 1% of the genome-wide significance and accounted for 14.6-18.9% and 14.7-18.5% of the phenotypic variance, and several putative QTL with 5% chromosome-wide significance were detected on eight linkage groups. Furthermore, the confirmed results of the regions harboring the major and putative QTLs showed consistent significant experiment-wide values of 1 and 5% as well as a chromosome-wide value of 5%. We identified growth-related QTLs that could be applied to find candidate genes for growth traits in further studies and potentially useful in marker assisted selection (MAS) breeding.

Polymorphism in Growth Hormone Gene and its Association with Growth Traits in Siniperca chuatsi

Growth hormone (GH) is a candidate gene for growth traits in fish. In this study, we assessed associations between single nucleotide polymorphisms (SNPs) in GH gene with growth traits in 357 Siniperca chuatsi individuals using high-resolution melting. Two SNPs were identified in GH gene, with one mutation in exon 5 (g.5045T>C), and one mutation in intron 5 (g.5234T>G). The corrections analysis of SNPs with the four growth traits was carried out using General Linear Model (GLM) estimation. Results showed that both of them were significantly associated with growth performance in S. chuatsi. For g.5234T>G, it was significantly associated with body weight (P＜0.01), body length (P＜0.05), body depth (P＜0.01), and body width (P＜0.01), and the individuals of genotype GG grew faster than those of genotypes TT and TG (P＜0.05). A further diplotype-trait association analysis confirmed that in fish with H3H2 (TC-GG) diplotype body weight, body length, and body width was greater than in those with other diplotypes (P＜0.05). These results demonstrated GH gene SNPs could be used as potential genetic markers in future marker assisted selection of S. chuatsi.

Detection of Growth-Related Quantitative Trait Loci and High-Resolution Genetic Linkage Maps Using Simple Sequence Repeat Markers in the Kelp Grouper (Epinephelus bruneus).

To initiate breeding programs for kelp grouper (Epinephelus bruneus), the establishment of genetic linkage maps becomes essential accompanied by the search for quantitative trait loci that may be utilized in selection programs. We constructed a high-resolution genetic linkage map using 1055 simple sequence repeat (SSR) markers in an F1 family. Genome-wide and chromosome-wide significances of growth-related quantitative trait loci (QTLs) (body weight (BW) and total length (TL)) were detected using non-parametric mapping, Kruskal-Wallis (K-W) analysis, simple interval mapping (IM) and a permutation test (PT). Two stages and two families of fish were used to confirm the QTL regions. Ultimately, 714 SSR markers were matched that evenly covered the 24 linkage groups. In total, 509 and 512 markers were localized to the female and male maps, respectively. The genome lengths were approximately 1475.95 and 1370.39 cM and covered 84.68 and 83.21 % of the genome, with an average interval of 4.1 and 4.0 cM, in females and males, respectively. One major QTL affecting BW and TL was found on linkage group EBR 17F that identified for 1 % of the genome-wide significance and accounted for 14.6–18.9 and 14.7–18.5 % of the phenotypic variance, and several putative QTL with 5 % chromosome-wide significance were detected on eight linkage groups. Furthermore, the confirmed results of the regions harboring the major and putative QTLs showed consistent significant experiment-wide values of 1 and 5 % as well as a chromosome-wide value of 5 %. We identified growth-related QTLs that could be applied to find candidate genes for growth traits in further studies, and potentially useful in MAS breeding.Electronic supplementary materialThe online version of this article (doi:10.1007/s10126-015-9673-5) contains supplementary material, which is available to authorized users.

Molecular characterization and expression patterns of insulin-like growth factor-binding protein genes in postnatal Nanjiang brown goats.

Insulin-like growth factor-binding proteins (IGFBPs) play a key role in modulating insulin-like growth factors (IGFs), and are considered candidate genes for growth traits in livestock. In this study, we identified the complete coding sequences of IGFBP-1 to -6 in the Nanjiang brown goat, and assessed gene tissue expression patterns by quantitative polymerase chain reaction. Expression of mRNA for the six gene targets was detectable in liver, heart, and longissimus dorsi (LD) muscle. Expression levels of IGFBP-1, -2 and -5 mRNA were higher in liver than in heart and LD muscle (P < 0.01), while IGFBP-6 expression was highest in LD muscle, and IGFBP-3 and -4 were predominantly expressed in LD muscle and liver. Higher IGFBP-2, -3, -4, and -6 mRNA levels were observed in LD, compared to triceps brachii muscle (P < 0.01). Additionally, the target genes had different temporal expression profiles during postnatal development. Histological assessment of muscle sections revealed a constant increase in muscle fiber diameter with aging. These results suggest that IGFBPs may be important for liver and skeletal muscle development, and may contribute to the biological function of these tissues in goats.

Single nucleotide polymorphisms in growth hormone gene and their association with growth traits in Siniperca chuatsi (Basilewsky).

Growth hormone (GH) has been considered as a candidate gene for growth traits in fish. In this study, polymorphisms of the GH gene were evaluated for associations with growth traits in 282 Siniperca chuatsi individuals. Using directly sequencing, four single nucleotide polymorphisms (SNPs) were identified in GH gene, with two mutations in intron 4 (g.4940A>C, g.4948A>T), one mutation in exon 5 (g.5045T>C) and one in intron 5 (g.5234T>G). Notably, three of them were significantly associated with growth performance, particularly for g.4940A>C which was highly correlated with all the four growth traits. In conclusion, our results demonstrated that these SNPs in GH gene could influence growth performance of S.chuatsi and could be used for marker-assisted selection (MAS) in this species.

Single nucleotide polymorphism scanning and expression of the FRZB gene in pig populations.

Secreted frizzled-related protein 3 (sFRP3), encoded by the gene FRZB, is a member of the sFRP family with important roles in inhibition of the Wnt signalling pathway through competitive binding of the Wnt receptor. Here, we investigated pig FRZB as a candidate gene for growth traits and identified three polymorphic sites, an insertion (A-532B) and two SNPs (G636A and C650T) in its 5'-UTR. The genotype distributions of G636A and C650T were significantly different among mini-type indigenous (Diannan Small-ear and Tibetan), normal indigenous (Laiwu and Huai), and introduced (Large Yorkshire and Landrace) breeds. In semi-quantitative PCR expression analysis, expression of FRZB mRNA was abundant in tissues of hypophysis, longissimus dorsi muscle, and adipose tissues, and low in the heart, hypothalamus, and brain. Quantitative determination of mRNA level and protein expression analysis were corresponding. The results demonstrated that FRZB gene expression in longissimus dorsi muscle and liver tissue was significantly higher in Diannan Small-ear and Tibetan pigs than in the Large Yorkshire breed (P<0.05); however, in back fat tissue, the expression was significantly higher in Diannan Small-ear pig than in Tibetan or Large Yorkshire breeds (P<0.05). Given the known growth and fat characteristics of the breeds, these results indicate that FRZB expression has a negative association with muscle growth and a positive association with fat deposition. In conclusion, FRZB may be a major candidate gene for growth traits in pigs.

Polymorphism and sequence analysis of growth hormone gene and its relationship with body weight in meat type of chicken

The growth hormone gene is a candidate gene controlling the metabolic and physiologic actions. Blood and feather samples were collected from 200 individuals of birds and genomic DNA was extracted using salting out technique. DNA fragment with 776 bp at growth hormone gene was amplified using polymerase chin reaction (PCR).The products from each strain (New Genotype, Punjabi Broiler-2, Indian Curnish-3 and University Male Line) were digested with MspI. In total, 4 RFLP pattern were observed. The genotypic frequencies obtained for different strains were tested using chi-square test. The differences among genotypes for all the 4 strains were significant. The overall allele frequency for A, B and C alleles were 0.495, 0.110 and 0.395 respectively. Correlation of cGH/MspI patterns with sixth week body weight was estimated. There were significant differences among 4 strains for body weight. Nucleotide sequencing of the amplified fragment of GH gene of 4 strains were done and submitted to the NCBI Genbank (accession nos JN403372 and JN403373). The nucleotide sequence analysis indicated that the per cent similarity of GH gene fragment of 4 strains were more than 99. In this study result also showed that there is a scope for using growth hormone gene as a candidate gene for growth traits.

Haplotype combinations of AdPLA gene polymorphisms associate with growth traits in Chinese cattle

Ablation of AdPLA in mice could prevent obesity, which implicated AdPLA was a new candidate gene for growth traits. In this study, we screened the polymorphisms of AdPLA gene and revealed three novel SNPs (NC_007330.4:g.43638506 C>T, 43658457 T>C and 43661404 T>C) by DNA sequencing and forced PCR-RFLP methods in 1340 individuals from six breeds. A preliminary single SNP-traits association analysis demonstrated that CC genotype was significantly higher than TT genotype at two growth traits in P6-EcoRII locus (P < 0.05). Moreover, the P8-FbaI locus had a significant association with some growth traits, individuals with TT genotype were higher than CC genotype (P < 0.05). A further analysis confirmed that these two SNPs were in linkage disequilibrium, and haplotype H2, both advantage allelic in P6-EcoRII and P8-FbaI loci, was better than the others for bovine growth traits, which was consistent with single SNP-traits association results. Therefore, this study not only proved that these SNPs were in association with bovine growth traits, but also contributed to evaluate them as genetic markers in bovine genetics and breeding and had potential application in breeding programs.

Genotypes, haplotypes and diplotypes of IGF-II SNPs and their association with growth traits in largemouth bass (Micropterus salmoides)

Insulin-like growth factor II (IGF-II) is involved in the regulation of somatic growth and metabolism in many fishes. IGF-II is an important candidate gene for growth traits in fishes and its polymorphisms were associated with the growth traits. The aim of this study is to screen single nucleotide polymorphisms (SNPs) of the largemouth bass (Micropterus salmoides) IGF-II gene and to analyze potential association between IGF-II gene polymorphisms and growth traits in largemouth bass. Four SNPs (C127T, T1012G, C1836T and C1861T) were detected and verified by DNA sequencing in the largemouth bass IGF-II gene. These SNPs were found to organize into seven haplotypes, which formed 13 diplotypes (haplotype pairs). Association analysis showed that four individual SNPs were not significantly associated with growth traits. Significant associations were, however, noted between diplotypes and growth traits (P<0.05). The fish with H1H3 (CTCC/CGCC) and H1H5 (CTCC/TTTT) had greater body weight than those with H1H1 (CTCC/CTCC), H1H2 (CTCC/TGTT) and H4H4 (TGCT/TGCT/) did. Our data suggest a significant association between genetic variations in the largemouth bass IGF-II gene and growth traits. IGF-II SNPs could be used as potential genetic markers in future breeding programs of largemouth bass.

A high-resolution linkage map for comparative genome analysis and QTL fine mapping in Asian seabass, Lates calcarifer

BackgroundHigh density linkage maps are essential for comparative analysis of synteny, fine mapping of quantitative trait loci (QTL), searching for candidate genes and facilitating genome sequence assembly. However, in most foodfish species, marker density is still low. We previously reported a first generation linkage map with 240 DNA markers and its application to preliminarily map QTL for growth traits in Asian seabass (Lates calcarifer). Here, we report a high-resolution linkage map with 790 microsatellites and SNPs, comparative analysis of synteny, fine-mapping of QTL and the identification of potential candidate genes for growth traits.ResultsA second generation linkage map of Asian seabass was developed with 790 microsatellite and SNP markers. The map spanned a genetic length of 2411.5 cM, with an average intermarker distance of 3.4 cM or 1.1 Mb. This high density map allowed for comparison of the map with Tetraodon nigroviridis genome, which revealed 16 synteny regions between the two species. Moreover, by employing this map we refined QTL to regions of 1.4 and 0.2 cM (or 400 and 50 kb) in linkage groups 2 and 3 in a population containing 380 progeny; potential candidate genes for growth traits in QTL regions were further identified using comparative genome analysis, whose effects on growth traits were investigated. Interestingly, a QTL cluster at Lca371 underlying growth traits of Asian seabass showed similarity to the cathepsin D gene of human, which is related to cancer and Alzheimer's disease.ConclusionsWe constructed a high resolution linkage map, carried out comparative mapping, refined the positions of QTL, identified candidate genes for growth traits and analyzed their effects on growth. Our study developed a framework that will be indispensable for further identification of genes and analysis of molecular variation within the refined QTL to enhance understanding of the molecular basis of growth and speed up genetic improvement of growth performance, and it also provides critical resource for future genome sequence assembly and comparative genomics studies on the evolution of fish genomes.