Genomic organization of the molt-inhibiting hormone gene in the red swamp crayfish Procambarus clarkii and characterization of single-nucleotide polymorphisms associated with growth

Integration of transcriptome and whole-genome re-sequencing analyses reveal growth-related candidate genes in Procambarus clarkii

Growth is a crucial economic trait of all aquaculture species. It is important to explore the molecular regulation on growth, which could help improve the growth rate of species. Mining the growth-related genes is the foundation for revealing its molecular regulation on growth. Presently, the molecular regulation of growth in Procambarus clarkii is not clear, and the study on exploring growth-related genes is limited. In this study, RNA-Seq was used to compare gene expression profiles of the individuals with different growth rates involved in four groups including Big Male (BM), Big Female (BF), Small male (SM), and Small Female (SF) from one P. clarkii family, and the analyses were performed in combination with sex. Meanwhile, whole-genome resequencing data was used to get growth-specific SNP (Single Nucleotide Polymorphism)/InDel (Insertion/Deletion) sites information. Totally, we identified 16,127 genes, of which 9065 were successfully annotated in the GO database. Among these, 1328 DEGs were identified in BM vs. SM, with 357 up-regulated and 971 down-regulated. Additionally, 3507 DEGs were identified in BF vs. SF, with 241 up-regulated and 3266 down-regulated. 96 DEGs were up-regulated and 820 DEGs were down-regulated in Growth-related Group. The expression levels of nine DEGs were validated by RT-qPCR to verify the analysis results of sequencing. 684,040 growth-related SNPs and 182,050 growth-related InDels were obtained after screened. These findings provide candidate growth-related genes and growth-specific SNP/InDel sites for regulation of growth traits in P. clarkii, and new insight into the molecular regulation of P. clarkii growth.

Influence of Garlic (Allium sativum) Clove-Based Selenium Nanoparticles on Status of Nutritional, Biochemical, Enzymological, and Gene Expressions in the Freshwater Prawn Macrobrachium rosenbergii (De Man, 1879)

Selenium (Se) is one of the essential micronutrients for performing vital body functions. This study aims at examining the influence of dietary supplementation of garlic clove-based green-synthesized selenium nanoparticles (GBGS-SeNPs, 48-87 nm) on carcass minerals and trace elements, and growth, biochemical, enzymological, and gene expression analyses in the freshwater prawn, Macrobrachium rosenbergii post larvae (PL). The 96 h LC₅₀ of this GBGS-SeNPs to M. rosenbergii PL was 52.23 mg L^-1. Five different artificial diets without supplementation of GBGS-SeNPs (control, 0.0 mg kg^-1) and with supplementations of GBGS-SeNPs starting from 100 times lower than the LC₅₀ value (0.5, 1.0, 1.5, and 2.0 mg kg^-1) were prepared and fed to M. rosenbergii PL for 90 days. A dose-dependent accumulation of Se was observed in the carcass of experimental prawns. GBGS-SeNPs, up to 1.5 mg kg^-1 significantly influenced the absorption of other trace elements (Ca, Cu, and Fe) and mineral salts (K, Mg, Na, and Zn). GBGS-SeNPs-supplemented diets showed efficient food conversion ratio (FCR) of 1.32 g against 2.71 g, and therefore enhanced the survival rate (85.6% against 78.8% in control) and weight gain (WG) of 1.41 g against 0.46 g of control prawn. GBGS-SeNPs significantly elevated the activities of protease, amylase, and lipase, and the contents of total protein, essential amino acids (EAA), total carbohydrate, total lipid, monounsaturated fatty acids (MUFA), polyunsaturated fatty acids (PUFA), and ash. These indicate the growth promoting potential of GBGS-SeNPs in prawn. The insignificantly altered activities of glutamic oxaloacetate transaminase (GOT), glutamic pyruvate transaminase (GPT), superoxide dismutase (SOD), and catalase, and the content of malondialdehyde (MDA) up to 1.5 mg kg^-1 suggest its acceptability in prawn. Moreover, a respective down- and upregulated myostatin (MSTN) and crustacean hyperglycemic hormone (CHH) genes confirmed the influence of GBGS-SeNPs on the growth of prawn. In contrast, 2.0 mg kg^-1 GBGS-SeNPs supplementation starts to produce negative effects on prawn (FCR, 1.76 g; survival rate, 82.2%; WG, 0.84 g against respective values of 1.32 g, 85.6%; and 1.41 g observed in 1.5 mg kg^-1 of GBGS-SeNPs-supplemented diet fed prawn). This study recommends a maximum of 1.5 mg kg^-1 GBGS-SeNPs as dietary supplement to attain sustainable growth of M. rosenbergii. This was confirmed through polynomial and linear regression analyses.

A High-Density Genetic Map and QTL Fine Mapping for Growth- and Sex-Related Traits in Red Swamp Crayfish (Procambarus clarkii)

Red swamp crayfish (Procambarus clarkii) is a commercially important species in global aquaculture and most successfully invasive freshwater shrimp in China. In order to determine the genetic basis of growth- and sex-related traits, a high-density genetic linkage map was constructed using 2b-RAD sequencing technology in a full-sib family. The consensus map contains 4,878 SNP markers assigned to 94 linkage groups (LGs) and spanned 6,157.737 cM with an average marker interval of 1.26 cM and 96.93% genome coverage. The quantitative trait locus (QTL) mapping for growth and sex traits was performed for the first time. QTL mapping uncovers 28 QTLs for growth-related traits in nine LGs, explaining 7.9-14.4% of the phenotypic variation, and identifies some potential candidate growth-related genes such as mih, lamr, golgb1, nurf301, and tbcd1 within the QTL intervals. A single major locus for sex determination was revealed in LG20 that explains 59.3-63.7% of the phenotypic variations. Some candidate sex-related genes, such as vps4bl, ssrf, and acot1, were identified in the QTL intervals and found to be differentially expressed in the muscle tissues between the females and the males. Furthermore, the identified SNPs were revealed to be female heterozygotes, suggesting that red swamp crayfish might have the female heterogametic ZZ/ZW sex determination system. The present study provides a valuable resource for marker-assisted selection and genetic improvement and for further genetic and genomic research in red swamp crayfish.

Identification of a Growth-Associated Single Nucleotide Polymorphism (SNP) in Cyclin C of the Giant Tiger Shrimp Penaeus monodon

The full-length cDNA of cyclin C of the giant tiger shrimp Penaeus monodon (PmCyC) was isolated by RACE-PCR. It was 1443 bp in length containing an open reading frame (ORF) of 804 bp and 267 deduced amino acids. Tissue distribution analysis indicated that PmCyC was more abundantly expressed in ovaries and testes than other tissues of female and male juveniles (P < 0.05). A pair of primers was designed, and an amplification product of 403 bp containing an intron of 123 bp was obtained. Polymorphism of amplified PmCyC gene segments of the 5th (3-month-old G5, N = 30) and 7th (5-month-old G7, N = 18) generations of domesticated juveniles was analyzed. Four conserved SNPs (T>C₁₃₄, T>C₁₈₈, G>A₃₇₉, and T>C₃₈₂) were found within the examined sequences. A TaqMan genotyping assay was developed for detection of a T>C₁₃₄ SNP. Association analysis indicated that this SNP displayed significant association with body weight (P < 4.2e-10) and total length (P < 2e-09) of the examined G7 P. monodon (N = 419) with an allele substitution effect of 5.02 ± 0.78 g and 1.41 ± 0.19 cm, respectively. Juveniles with C/C₁₃₄ (22.80 ± 2.51 g and 12.97 ± 0.53 cm, N = 19) and T/C₁₃₄ (20.41 ± 0.93 g and 12.77 ± 0.21 cm, N = 129) genotypes exhibited a significantly greater average body weight and total length than those with a T/T₁₃₄ genotype (14.72 ± 0.53 g and 11.37 ± 0.13 cm, N = 271) (P < 0.05).