Growth shows a moderate heritability in aquaculture animals and plays an important role in production output, therefore, making it a primary target for selective breeding15,16. Our study showed the growth traits body weight and umbrella diameter are positively correlated in R. esculentum, manifesting any trait can independently represent the growth. Excluding growth-related phenotype, molecular marker shows potential for investigating the growth of aquaculture animals in the genetic breeding industry17. SNP markers as the molecular marker were genotyped easily to construct genetic linkage maps for the genetic breeding of aquaculture animals18.
Due to the simplicity and flexibility, the 2b-RAD method was extensively used for constructing high-density linkage maps for fish5,6,18−20. Zhu et al. constructed the high-density linkage map of Pseudobagrus ussuriensis with an interval of 0.357 cM via 2b-RAD method 18. For R. esculentum, the marker interval of the linkage map is 0.58 cM at intermediate levels, higher than H. nobilis5, H. wyckioides6 and Channa argus20, less than C. auratus3, P. ussuriensis18, Larimichthys crocea21. The difference of marker interval between R. esculentum and the other aquaculture animals may attribute to the SNP numbers used for constructing linkage maps and the depth of genetic studies. For P. ussuriensis, 7435 SNPs were used for constructing the linkage map, which is 1.96-fold higher than that of R. esculentum18. In addition, the genetic studies of growth and sex-determination were widely carried out in P. ussuriensis18,22,23, deeper than that of R. esculentum. However, this is the first report of a high-density linkage map in R. esculentum.
In aquatic animals, the high-density linkage map also plays an important role in performing QTL mapping and finding genes related to the growth traits3,5,6,8. Based on the high-density linkage map, numerous QTLs about growth traits, such as body weight, body length, sex as well as disease resistance were identified3,20,21,24−28. In C. auratus at 2 months, eight QTLs in eight chromosomes were discovered associated with the body weight, explaining 10.1–13.2% of the phenotypic variations3; In Nibea albiflora, 22 and 13 QTLs were detected associated with growth (body weight, body height, body width and body length) and sex dimorphism, respectively24. For R. esculentum, three and four QTLs were separately identified concerning umbrella diameter and body weight, less than the QTL numbers found in C. auratus and N. albiflora3,24. This may be caused by the higher-level classification of C. auratus and N. albiflora, so the genomes may be more complex and genes locating on more chromosomes participated in regulating the growth. For C. auratus, eight QTLs distributing on five LGs were related to the body weight3; For N. albiflora, six QTLs distributing on six LGs were related to the body weight24. Additionally, two QTLs in similar regions are both associated with umbrella diameter and body weight in R. esculentum, further supporting the above inference and the positive correlation of the two growth traits.
QTL analysis often combines with GWAS for identifying growth-related genes in aquaculture animals29,30. For example, five QTLs were revealed associated with the body weight of catfish and the candidate genes in these regions were related to bone development and muscle growth29. In Epinephelus fuscoguttatus, 23 QTLs are detected corresponding to the growth and 19 candidate genes were detected30. Table 3 summarized the candidate genes related to growth traits of aquaculture animals by GWAS and different species showed the difference (Table 3). More than one gene about multiple functions was identified in relation to the growth of C. carpio L., L. crocea and O. mykiss while one candidate gene was identified controlling the growth in P. yessoensis, E. fuscoguttatus and L. maculatus (Table 3). In R. esculentum, RE13670 containing the EGF_CA domain showed the most possibility in controlling the growth, which is in accordance with the growth-related genes reported in C. auratus3. EGF_CA domain needs calcium for performing biological function and is present in extracellular (mostly animal) and membrane-bound31. Moreover, this domain has three main roles, including protein-protein interactions, as a spacer unit and structural stabilization32. Nevertheless, the function of EGF_CA domains has not been well understood in aquaculture animals. With the release of genomic information of R. esculentum14 and the development of biotechnology, the gene function studies of R. esculentum will be improved and more genes will be investigated for genetic breeding.
Table 3
Summary details of the candidate genes related to growth of aquaculture animals by GWAS analysis.
Species | Gene | Growth traits | Reference |
P. yessoensis | E2F transcription factor 3 | Shell length and height, body weight and adductor muscle | 33 |
C. carpio L. | BR serine/threonine-protein kinase 2 and eukaryotic translation-initiation factor 2-alpha kinase 3 | Body weight | 34 |
E. coioides | Neuropeptide Y receptor Y2 | Body weight and total length | 35 |
E. fuscoguttatus | bmp2k | Body weight, length, height and thickness | 30 |
L. crocea | fgf18, fgf1, nr3c1, cyp8b1, fabp2 and so on | Growth and body shape | 36 |
L. maculatus | fgfr4 | Body weight and length | 37 |
L. vannamei | Protein kinase C delta type and ras-related protein Rap-2a | Body weight and length | 38 |
L. vannamei | Class C scavenger receptor | Body weight | 10 |
O. mykiss | Genes involved growth factors and development of skeletal muscle, bone tissue and nutrient metabolism | Body weight | 39 |
R. esculentum | RE13670 | Body weight and umbrella diameter | This study |