| Abstract: Litopenaeus vannamei, commonly known as the white shrimp, is native to the Pacific coastal waters of South America. Noted for its rapid growth rate and environmental adaptability, it was introduced to China in 1988 and has since been promoted extensively for aquaculture. In 2022, its domestic production reached 2.09 million tons, accounting for one-third of the global annual aquaculture production of shrimp. It has become a mainstay aquaculture industry of China. playing a crucial role in the economic development of coastal areas, increasing fishermen's incomes, and maintaining the stable development of the rural fisheries economy.
Growth trait is the most concerned economic trait of L. vannamei, however, with the continuous expansion of the scale culture and the deterioration of the culture environment, viral diseases are among the main causes of economic loss.and among them, White Spot Syndrome Virus (WSSV) outbreaks have had a detrimental impact in many regions oftheworld since its first appearance in 1992.shrimp infected with the virus have reduced intake, enlarged hepatopancreas, and white spots on the body,There is no effective method to prevent and control the spread of the virus, and the breeding of new varieties with both growth and WSSV resistance is an urgent need in the market.Obtaining precise genetic parameters for economic traits is the basis for developing breeding programs, and in particular, the precise assessment of heritability and genetic correlations is an important guide in the development of selection indices, retention and mating programs.
previously, genetic parameter estimation mainly uses Pedigree based Best Linear Unbiased Prediction (pBLUP). This method estimates breeding values by constructing an A matrix and correcting for different effectors, and is widely used in genetic evaluation of economic traits in aquatic animals.However, pBLUP using the A-matrix for resistance traits that are difficult to measure directly using siblings can only utilize 50% of the genetic variation, the assessment is not accurate.The use of individual typing information to construct a genomic matrix can more accurately measure the true relationship between individuals, and the calculation of breeding values is carried out taking into account the Mendelian sampling effect, which is conducive to improving the accuracy of the assessment. It plays an important role in livestock and poultry breeding such as dairy cattle, however, shrimp single-tail value is low and it is costly to carry out sequencing at the population level. The single step genomic best linear unbiased prediction (ssGBLUP) types only some of the individuals, and composite genealogical and genotypic information is used for the breeding value assessment, which reduces the cost of individual typing, and this method has been widely used in aquatic animals.Genomic breeding microarrays have become an important genotyping tool in crop and livestock breeding due to their advantages of reproducibility, high accuracy, maneuverability, and low price.
In order to assess the prospects for the application of breeding microarrays in the selection of new composite varieties for growth and WSSV resistance in the L. vannamei.In this study, 59 lines of L. vannamei, totaling 1,770 individuals, were tested for WSSV infection using an independently bred high resistance line of L. vannamei;Based on the survival time of individual resistance to WSSV within the family line, 590 individuals were uniformly selected and typed using 55K SNP liquid-phase microarrays to obtain genotypic data for some individuals. ssGBLUP model was established by combining phenotypic values, genealogical and genotypic data, and the heritability and genetic correlation were estimated for the length of the body, the survival time of individual and half-lethal survival rate(SS50) after infection with WSSV.
The results showed that the heritabilities of body length, the survival time of individual and (SS50) after infection with WSSV in L. vannamei were 0.21±0.06, 0.22±0.16, 0.16±0.06, respectively, which were medium heritability levels; the prediction accuracy of heritability of body length based on the H-matrix was increased by 18.12% compared with the A-matrix after five-fold cross validation, and the prediction bias was not significantly different; The heritability prediction accuracy of survival time against WSSV was not significantly different from the A matrix, the prediction bias was large in H-matrix;the heritability prediction accuracy of SS50 was reduced by 29.07% from the A matrix, and the prediction bias was large in H-matrix.Based on the two-trait animal model, the estimated genetic correlation between body length of L. vannamei and the survival time of individuals against WSSV and the SS50 were 0.13±0.20 and 0.30±0.22, respectively, which were not significantly different from 0 (P>0.05); the genetic correlation between the survival time of individuals against WSSV and SS50 was 0.95±0.03, which was not significantly different from 1 (P>0.05).
The study showed that the genetic assessment of the growth of L. vannamei by microarray can effectively improve the accuracy of the assessment, the evaluation of WSSV survival time traits may be affected by the selection of individuals and other factors, and the prediction accuracy is not significantly improved, and the survival time traits of individual anti-WSSV is better than SS50 trait of family anti-WSSV in terms of accuracy and prediction bias. In the case that anti-WSSV survival time is highly correlated with the SS50 trait, anti-WSSV survival time can be considered as a target trait for genomic selection.
In this study, we estimated the genetic parameters of growth and WSSV resistance in L. vannamei based on the typing information of 55K SNP liquid microarray "Yellow Sea Chip No.1", which provides a reference for the application of breeding microarrays in the selection of new multi-trait composite varieties of L. vannamei. |
