Identifying a Long QTL Cluster Across chrLG18 Associated with Salt Tolerance in Tilapia Using GWAS and QTL-seq

Jiang, Dan; Gu, Xiao Hui; Li, Bi Jun; Zhu, Zong Xian; Hui, Qin; Meng, Zhijun; Lin, Haoran; Xia, Jun

doi:10.1007/s10126-019-09877-y

Cited by 39 publications

(27 citation statements)

References 59 publications

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“…ddRAD‐seq is one of the most commonly utilized member of the reduced‐representation family combining simplicity and cost efficiency during library construction (Peterson et al., 2012). Over the last years, ddRAD‐seq has been successfully utilized in a plethora of tilapia focussed studies investigating the underlying genetic structure of traits of economic value (Jiang et al., 2019; Li, Zhu, Gu, Lin, & Xia, 2019; Li et al., 2017; Palaiokostas et al., 2015; Taslima et al., 2020), for species‐specific SNPs (Syaifudin et al., 2019) and for deciphering the genetic diversity–population structure of wild and farmed populations (Kajungiro, Palaiokostas, et al, 2019; Moses et al., 2019).…”

Section: Introductionmentioning

confidence: 99%

Assessing the genetic diversity of farmed and wild Rufiji tilapia (Oreochromis urolepis urolepis) populations using ddRAD sequencing

Nyinondi

Mtolera

Mmochi

et al. 2020

Ecology and Evolution

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Rufiji tilapia (Oreochromis urolepis urolepis) is an endemic cichlid in Tanzania. In addition to its importance for biodiversity conservation, Rufiji tilapia is also attractive for farming due to its high growth rate, salinity tolerance, and the production of all‐male hybrids when crossed with Nile tilapia (Oreochromis niloticus). The aim of the current study was to assess the genetic diversity and population structure of both wild and farmed Rufiji tilapia populations in order to inform conservation and aquaculture practices. Double‐digest restriction‐site‐associated DNA (ddRAD) libraries were constructed from 195 animals originating from eight wild (Nyamisati, Utete, Mansi, Mindu, Wami, Ruaha, Kibasira, and Kilola) and two farmed (Bwawani and Chemchem) populations. The identified single nucleotide polymorphisms (SNPs; n = 2,182) were used to investigate the genetic variation within and among the studied populations. Genetic distance estimates (Fst) were low among populations from neighboring locations, with the exception of Utete and Chemchem populations (Fst = 0.34). Isolation‐by‐distance (IBD) analysis among the wild populations did not detect any significant correlation signal (r = .05; p‐value = .4) between the genetic distance and the sampling (Euclidean distance) locations. Population structure and putative ancestry were further investigated using both Bayesian (Structure) and multivariate approaches (discriminant analysis of principal components). Both analysis indicated the existence of three distinct genetic clusters. Two cross‐validation scenarios were conducted in order to test the efficiency of the SNP dataset for discriminating between farmed and wild animals or predicting the population of origin. Approximately 95% of the test dataset was correctly classified in the first scenario, while in the case of predicting for the population of origin 68% of the test dataset was correctly classified. Overall, our results provide novel insights regarding the population structure of Rufiji tilapia and a new database of informative SNP markers for both conservation management and aquaculture activities.

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Section: Introductionmentioning

confidence: 99%

Assessing the genetic diversity of farmed and wild Rufiji tilapia (Oreochromis urolepis urolepis) populations using ddRAD sequencing

Nyinondi

Mtolera

Mmochi

et al. 2020

Ecology and Evolution

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“…Compared with our previous work of growth QTL mapping (Lv et al, 2017), low salinity tolerance had fewer QTLs (12 vs. 2) and a lower PVE value (35.9 vs. 14.8%), which may be related to its lower heritability (0.53 vs. 0.18) (Baoquan et al, 2010; Zheng et al, 2015). In addition, salt tolerance are complex quantitative traits regulated by many genes (Jiang et al, 2019), its regulation mechanism may consist of multiple complex pathways when compared to growth traits. Previous research showed that 615 genes showed significant differential expression (DEG) during salinity stress, which were involved in many crucial processes including ion transport, amino acid metabolism and synthesis, proteolysis and chitin metabolic (Lv et al, 2013).…”

Section: Discussionmentioning

confidence: 99%

Quantitative Trait Loci Mapping and Marker Identification for Low Salinity Tolerance Trait in the Swimming Crab (Portunus trituberculatus)

Sun

Yan

et al. 2019

Front. Genet.

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Low salinity is one of the most important abiotic factors that directly affect the abundance of the swimming crab, Portunus trituberculatus. Quantitative trait loci (QTL) mapping could be helpful in identifying the markers and genes involved in low salinity tolerance. In this study, two QTLs of low salt tolerance were mapped on linkage group 17 (LG17, 2.6–5.2 cM) based on a high-density linkage map. Ninety-five markers related to low salinity tolerance were identified via association analysis, and seventy-nine low salt-related candidate genes (including ammonium transport, aldehyde dehydrogenase, and glucosyltransferase) were screened from draft genome of the species via these markers. This represents the first report of QTL mapping for low salinity tolerance in the swimming crab, which may be useful to elucidate salinity adaptation mechanisms.

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“…Double digest RAD (ddRAD) relying on the simultaneous usage of two enzymes is one of the most popular reduced-representation sequencing platforms. The combination of a relatively easy library construction workflow and cost-efficiency [6] makes ddRAD particularly useful for studying the genetic diversity of populations [17][18][19][20], constructing genetic maps [21][22][23][24] and quantitative trait loci mapping [25][26][27][28][29].…”

Section: Introductionmentioning

confidence: 99%

Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus)

Pappas

Palaiokostas

2021

Animals

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Incorporation of genomic technologies into fish breeding programs is a modern reality, promising substantial advances regarding the accuracy of selection, monitoring the genetic diversity and pedigree record verification. Single nucleotide polymorphism (SNP) arrays are the most commonly used genomic tool, but the investments required make them unsustainable for emerging species, such as Arctic charr (Salvelinus alpinus), where production volume is low. The requirement to genotype a large number of animals for breeding practices necessitates cost effective genotyping approaches. In the current study, we used double digest restriction site-associated DNA (ddRAD) sequencing of either high or low coverage to genotype Arctic charr from the Swedish national breeding program and performed analytical procedures to assess their utility in a range of tasks. SNPs were identified and used for deciphering the genetic structure of the studied population, estimating genomic relationships and implementing an association study for growth-related traits. Missing information and underestimation of heterozygosity in the low coverage set were limiting factors in genetic diversity and genomic relationship analyses, where high coverage performed notably better. On the other hand, the high coverage dataset proved to be valuable when it comes to identifying loci that are associated with phenotypic traits of interest. In general, both genotyping strategies offer sustainable alternatives to hybridization-based genotyping platforms and show potential for applications in aquaculture selective breeding.

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Identifying a Long QTL Cluster Across chrLG18 Associated with Salt Tolerance in Tilapia Using GWAS and QTL-seq

Cited by 39 publications

References 59 publications

Assessing the genetic diversity of farmed and wild Rufiji tilapia (Oreochromis urolepis urolepis) populations using ddRAD sequencing

Assessing the genetic diversity of farmed and wild Rufiji tilapia (Oreochromis urolepis urolepis) populations using ddRAD sequencing

Quantitative Trait Loci Mapping and Marker Identification for Low Salinity Tolerance Trait in the Swimming Crab (Portunus trituberculatus)

Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus)

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