Effectiveness of SNPs for parentage and sibship assessment in polygamous yellowtail kingfish Seriola lalandi

Parentage Analysis in Giant Grouper (Epinephelus lanceolatus) Using Microsatellite and SNP Markers from Genotyping-by-Sequencing Data

“…Nevertheless, the number of loci may have a more significant effect on the power of parentage analysis than expected. Premachandra et al [ 3 ], similarly, found the number of SNPs had a clear and major impact on the accuracy of sibship assignment, as the increase of number of SNPs led to a bigger raise in accuracy measures than that of the average MAF values. Baruch and Weller [ 69 ] conducted a series of simulations and found that non-exclusion probability decreased with increasing number of SNPs at the same level of MAF cut-off.…”

“…Since mixed breeding system is often adopted in aquaculture breeding programs, accurate pedigree information is the basis of sustainable genetic selection and hatchery management [ 1 ]. Although tagging of individuals with physical tags is difficult in most fish species due to their mass spawning and tiny larvae [ 2 , 3 ], the introduce of molecular tools makes it feasible for fish pedigree traceability. Microsatellites, i.e., simple sequence repeats, have been classic molecular tools in parentage analysis and pedigree reconstruction in a considerably range of aquaculture fish species since its discovery in 1990s [ 4 , 5 , 6 , 7 ], due to their relatively small locus size, inheritance in a Mendelian fashion, codominance and high polymorphism based on the variable size of repeat units by alleles [ 6 ].…”

“…However, parentage analysis using microsatellites has suffered from genotyping errors that may cause multiple peaks, allelic dropout, null alleles or other issues, which is due in large part to the manual operation and subjective scoring process [ 8 , 9 , 10 ], and could lead to the mistakenly assignment of candidate parents. In addition, microsatellites are limited in the application in terms of genome wide trait associations or breeding value estimation, due to their relatively low density over the genome [ 3 ]. Furthermore, although Next-generation sequencing (NGS) has facilitated the mining process of molecular markers [ 11 ], genotyping of microsatellite loci can be still costly, laborious and time-consuming [ 12 ], especially when handling with a large number of individuals derived from mass spawning fish.…”

“…A recent rising molecular tool for parentage analysis is single nucleotide polymorphisms (SNPs), since the availability of genomic resources and multiplexed detecting methods have been greatly enhanced by NGS and bioinformatic techniques [ 13 ]. Over the last decade, SNPs have been used in parentage assignment [ 14 ], relatedness analysis [ 15 ], sibship assessment [ 3 ], population structure [ 16 ] or mating system research [ 17 ] in about 20 fish species [ 13 ]. Compared to microsatellites, SNPs are superior in their abundance over genomes [ 12 ], lower mutation rates [ 18 ], higher automation and easier standardization across laboratories [ 19 ], which effectively reduce the cost of time and genotyping errors caused by human factors.…”

Pedigree reconstruction and distant pairwise relatedness estimation from genome sequence data: A demonstration in a population of rhesus macaques (Macaca mulatta)

“…More recently, researchers have begun to use single nucleotide polymorphisms (SNPs) for parentage and kinship analyses in long‐lived mammals such as yellow baboons ( Papio cynocephalus : Snyder‐Mackler et al, 2016), dolphins ( Tursiops aduncus : Foroughirad et al, 2019), and pilot whales ( Globicephala macrorhynchus : Van Cise et al, 2017). In some cases these studies have used thousands of SNPs from across the genome (Andrews et al, 2018; Premachandra et al, 2019; Snyder‐Mackler et al, 2016; Strucken et al, 2016; Zhang et al, 2018). The methods employed in these studies can accurately infer very close pairwise relationships and some can cluster closely related individuals together into a family group with assigned parentage (as in COLONY: Wang, 2013) and grandparentage (as in SEQUOIA: Huisman, 2017).…”