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...
