SNP markers for the genetic characterization of Mexican shrimp broodstocks

Abstract

16Selective breeding of shrimp has major potential to enhance production traits, including growth 17 and disease resistance. Genetic characterization of broodstock populations is a key element of 18 breeding programs, as it enables decisions on inbreeding restrictions, family structure, and the 19 potential use of genomic selection. Single Nucleotide Polymorphisms (SNPs) are suitable genetic 20 markers for this purpose. A set of SNPs was developed to characterize commercial breeding 21 stocks in Mexico. Individuals from local and imported lines were selected for sequencing using 22 the nextRAD technique, resulting in the identification of 2,619 SNPs. Genetic structure analysis 23 showed three to five genetic groups of Ecuadorian and Mexican origins. A subset of 1,231 SNPs 24 has potential for stock identification and management. Further, three SNPs were identified as 25 candidate sex-linked markers. The role of SNPs possibly associated with genes related to traits of 26 importance to shrimp farming, such as growth and immune response, should be further 27 investigated. 28 29 breeding; disease resistance 30 31 59While some shrimp farming is based on the aforementioned selected broodstock lines, selective 60 breeding programs for continuous genetic improvement of shrimp are at a formative stage in 61 Mexico. A key element for these selective breeding programs is the characterization of genetic 62 diversity and composition of stocks, as it will enable decisions on the composition of base 63 populations, inbreeding restrictions, family structure, and the potential use of genomic selection 64 (FAO, 1993). The genetic characterization will also aid in stock identification for traceability 65 purposes. 66 Single Nucleotide Polymorphisms (SNPs) have been demonstrated to be suitable markers for the 67 genetic characterization of broodstock populations, parentage assignment, and genome selection 68 in several farmed aquaculture species [see review in Robledo et al. (2017)]. In L. vannamei, 69 Perez-Enriquez and Max-Aguilar (2016) reported a SNP-based genotyping service for parentage 70 assignment but the identity of the SNPs is not known. A commercially-available Illumina SNP-71 chip has been created (Jones et al., 2017). However, the SNPs on the array were discovered in a 72 single-origin broodstock, and it might not represent the genetic diversity in broodstock 73 populations derived from different sources. Genotyping by sequencing technology enables 74 concurrent discovery and genotyping of genome-wide SNPs that are informative in the target 75 populations at moderate scale and cost, and has been widely applied in aquaculture species for 76 this purpose (Robledo et al. 2017). 77 The objective of this study was to assess the genetic diversity and constitution of the breeding 78 lines currently used in the Mexican shrimp aquaculture industry and to develop a set of 79 diagnostic SNP markers to identify those lines as a potential tool for stock management and 80 traceability. To do so, we carried out Nextera-tagmented redu...

Patterns of Geographical and Potential Adaptive Divergence in the Genome of the Common Carp (Cyprinus carpio)

“…With the fast growth of sequencing technologies, high-throughput genetic markers, such as single-nucleotide polymorphism (SNP), have been used in population genetics. Many studies have demonstrated that SNP arrays can improve the resolution of the differentiation of genetic stocks (Perez-Enriquez et al, 2018; Torati et al, 2019). SNP assays are a useful tool for studying population structure and the effects of natural and artificial selection at the genome scale.…”

Dynamic stock model for analysing semi‐intensive production of whiteleg shrimpLitopenaeus(Penaeus)vannameiaffected by the acute hepatopancreatic necrosis disease: Assessment of disease severity indicators and relationships with pond water quality parameters

“…Due to multiple import events and subsequent mixing of broodstocks, the genetic structure of the cultivated Mexican shrimp populations has not been well understood (Perez‐Enriquez, Robledo, Houston, & Llera‐Herrera, ). It should be noted that, in this study, besides the winter production cycle of 2014‐III, the lowest mortality was observed in 2016 (Figure ), when shrimp postlarvae were obtained from a hatchery other than the one providing the postlarvae during 2013–2015.…”

Effect of genotype and protein source on performance of Pacific white shrimp (Litopenaeus vannamei)

“…In northwest Mexico, approximately 20 laboratories produce 10 billion shrimp postlarvae annually through genetic improvement programmes (Mendoza-Cano et al 2014). The production laboratories of shrimp postlarvae generate fast-growth genotypes based on two-stage selection process, considering body weight and growth between 28 and 130 days of age for to increase the genetic gain for growth at harvesting age (Castillo-Ju arez et al 2010); and high-resistance genotypes with shrimp broodstock of Ecuadorian origin survivors to white spot syndrome virus to reduce mortalities caused by this virus in farmed shrimp (Perez-Enriquez et al 2018). However, genetic improvement programmes does not consider how the genotypic characterisation benefit or affect survival, growth, reproductive quality (Grijalva-Chon et al 2013) and protein requirements of the L. vannamei genotypes.…”