Genome-Wide Patterns of Population Structure and Linkage Disequilibrium in Farmed Nile Tilapia (Oreochromis niloticus)

Abstract

Nile tilapia (Oreochromis niloticus) is one of the most produced farmed fish in the world and represents an important source of protein for human consumption. Farmed Nile tilapia populations are increasingly based on genetically improved stocks, which have been established from admixed populations. To date, there is scarce information about the population genomics of farmed Nile tilapia, assessed by dense single nucleotide polymorphism (SNP) panels. The patterns of linkage disequilibrium (LD) may affect the success of genome-wide association studies (GWAS) and genomic selection (GS), and also provide key information about demographic history of farmed Nile tilapia populations. The objectives of this study were to provide further knowledge about the population structure and LD patterns, as well as, estimate the effective population size (N e) for three farmed Nile tilapia populations, one from Brazil (POP A) and two from Costa Rica (POP B and POP C). A total of 55 individuals from each population, were genotyped using a 50K SNP panel selected from a whole-genome sequencing (WGS) experiment. The first two principal components explained about 20% of the total variation and clearly differentiated between the three populations. Population genetic structure analysis showed evidence of admixture, especially for POP C. The contemporary N e estimated, based on LD values, ranged from 78 to 159. No differences were observed in the LD decay among populations, with a rapid decrease of r 2 with increasing inter-marker distance. Average r 2 between adjacent SNP pairs ranged from 0.19 to 0.03 for both POP A and C, and 0.20 to 0.03 f or POP B. Based on the number of independent chromosome segments in the Nile tilapia genome, at least 9.4, 7.6, and 4.6K SNPs for POP A, POP B, and POP C respectively, are required for the implementation of GS in the present farmed Nile tilapia populations.

Development and Validation of an Open Access SNP Array for Nile Tilapia (Oreochromis niloticus)

“…For all the evaluated Nile tilapia populations (GIFT, GIFT-derived and non-GIFT), overall relatively low levels of LD (r 2 0.2) were accompanied by a moderate to slow decay with increasing distance. Despite the small number of animals used to assess LD decay (15 individuals per strain / population), a similar pattern was found to that reported by Yoshida et al (2019b) for GIFT and GIFT-derived commercial populations in South America. The weak correlation found between SNPs is consistent with previous findings in GIFT strains (Xia et al 2015;Yoshida et al 2019b) and is comparatively lower than estimates obtained from other farmed fish species such as Atlantic salmon (Barria et al 2018;Kijas et al 2017).…”

“…Despite the small number of animals used to assess LD decay (15 individuals per strain / population), a similar pattern was found to that reported by Yoshida et al (2019b) for GIFT and GIFT-derived commercial populations in South America. The weak correlation found between SNPs is consistent with previous findings in GIFT strains (Xia et al 2015;Yoshida et al 2019b) and is comparatively lower than estimates obtained from other farmed fish species such as Atlantic salmon (Barria et al 2018;Kijas et al 2017). Nevertheless, it is worth noting that despite the relatively low levels of LD, the SNP density of the array is in excess of requirements to obtain maximal genomic prediction accuracy in the context of a typical sibling testing breeding program in tilapia (Yoshida et al 2019a), and indeed for the majority of aquaculture species tested to date (Houston et al 2020).…”

Whole genome re-sequencing reveals recent signatures of selection in three strains of farmed Nile tilapia (Oreochromis niloticus)

“…Our results account for a similar rapid LD decay between these strains. Previous studies in this species revealed similar low values of LD; which may have been influenced by recombination rates, effective populations sizes, genetic background and breeding history, including admixture events 34,37 . The results described above are in accordance with those values of N e reported by Yoshida et al (2019) (159, 128, 78 for strains A, B and C, respectively).…”

“…These values are somewhat higher than expected, as domesticated animals typically have values of N e < 100 38 . Even though these values of N e are relatively small, they are enough to maintain inbreeding at acceptable rates of accumulation per generation and the necessary levels of diversity in the long-term for these breeding populations 34,39 . www.nature.com/scientificreports/ Regarding the genetic structure, the PCA identified three clusters consistent with the three strains of Nile tilapia analyzed here ( Fig.…”

Multi-trait GWAS using high-density genotypes identifies genes associated with body traits in Nile tilapia

“…We used a total of 1,309 phenotyped animals from 72 families (mean = 18, minimum = 7, and maximum = 25 animals per family) belonging to a breeding nucleus owned by Aquacorporación International group (ACI), Costa Rica. More details about the breeding program and the origin of the Nile tilapia population is described in detail [17,19,75].…”