Identification of genomic regions regulating sex determination in Atlantic salmon using high density SNP data

Background: A complete understanding of the genetic basis for sexual determination and differentiation is necessary in order to implement efficient breeding schemes at early stages of development. Atlantic salmon belongs to the family Salmonidae of fishes and represents a species of great commercial value. Although the species is assumed to be male heterogametic with XY sex determination, the precise genetic basis of sexual development remains unclear. The complexity is likely associated to the relatively recent salmonid specific whole genome duplication that may be responsible for certain genome instability. This instability together with the capacity of the sex-determining gene to move across the genome as reported by previous studies, may explain that sexual development genes are not circumscribed to the same chromosomes in all members of the species. In this study, we have used a 220 K SNP panel developed for Atlantic salmon to identify the chromosomes explaining the highest proportion of the genetic variance for sex as well as candidate regions and genes associated to sexual development in this species. Results: Results from regional heritability analysis showed that the chromosomes explaining the highest proportion of variance in these populations were Ssa02 (heritability = 0.42, SE = 0.12) and Ssa21 (heritability = 0.26, SE = 0.11). After pruning by linkage disequilibrium, genome-wide association analyses revealed 114 SNPs that were significantly associated with sex, being Ssa02 the chromosome containing a greatest number of regions. Close examination of the candidate regions evidenced important genes related to sex in other species of Class Actinopterygii, including SDY, genes from family SOX, RSPO1, ESR1, U2AF2A, LMO7, GNRH-R, DND and FIGLA. Conclusions: The combined results from regional heritability analysis and genome-wide association have provided new advances in the knowledge of the genetic regulation of sex determination in Atlantic salmon, supporting that Ssa02 is the candidate chromosome for sex in this species and suggesting an alternative population lineage in Spanish wild populations according to the results from Ssa21.Ministerio de Economía y Competitividad | Ref. RZ2012–00011-C02–00Ministerio de Ciencia e Innovación | Ref. JCI-2011-1089

Genomic analysis of the populations of Atlantic salmon (Salmo salar L.) of the Iberian Peninsula

After the drastic decrease of Atlantic salmon natural populations of the Iberian Peninsula in the last century, their restoration has been focused on habitat improvement and supportive breeding, with wild and captive individuals from different origins resulting in a failure of the initial enhancing aim. In order to design an efficient management of these populations, genetic studies should be taking into account because can help to maintain correct levels of variability and avoid consanguinity increase. New massive genotyping technologies, like SNP, can provide information that can be applied in conservation programs. In this thesis project, we will use the information obtained after the hybridization of salmon DNA onto an array of 200,000 SNP together with long dataset about microsatellite variability, abundances, morphological data, ages, sexes, fishing data,… in order to design a optimal conservation program from this specie in Galician rivers. The genetics status of the present populations will be evaluated, by comparing populations with other Spanish rivers, and by studying the possible introgression of foreign genomes. In addition we will try to modeling of fishing season in order to minimize the impact of this sport on populations.Tras la drástica disminución de las poblaciones naturales de salmón atlántico en el último siglo, su recuperación se ha centrado en la Península Ibérica en la mejora del hábitat y en la repoblación de los ríos, tanto con individuos salvajes como de piscifactoría, que fracasó. Para una gestión eficiente, los estudios genéticos tienen una gran importancia, tanto para mantener niveles correctos de variabilidad como evitar el incremento en consanguinidad. Con el desarrollo de nuevas tecnologías de genotipado masivo, como los SNPs, se obtiene nueva información aplicable a programas de conservación. En este proyecto se utilizará la información de un array de 220,000 SNPs de Affymetrix, datos de microsatélites de varios años desde 1990, así como datos de abundancia, información morfológica, edad, sexo, datos de capturas,… con el objetivo de diseñar un programa óptimo de conservación de esta especie en Galicia. Se evaluará el estado de las poblaciones actuales, comparando los datos poblacionales de otros ríos españoles y estudiando su posible introgresión, además de la búsqueda de genes determinantes de caracteres de interés y la modelización de temporadas de pesca.Tras a drástica diminución das poboacións naturais de salmón atlántico no último século, na Península Ibérica a súa recuperación centrouse na mellora do seu entorno e na repoboación dos ríos, con individuos salvaxes e de piscifactoría, que fracasou. Para una xestión eficiente, os estudos xenéticos teñen unha gran importancia, tanto para manter niveis correctos de variabilidade, como evitar o incremento da consanguinidade. Co desenvolvemento de novas tecnoloxías de xenotipado masivo, coma os SNPs, pódese obter nova información aplicable a programas de conservación. Neste proxecto, utilizarase a información dun array de 220,000 SNP de Affymetrix, datos de microsatélites de distintos anos dende 1990, así como datos de abundancia, información morfolóxica, idade, sexo, datos de capturas,… co obxectivo de deseñar un programa de conservación óptimo para esta especie en Galicia. Evaluarase o estado das poboacións actuais, comparando os datos poblacionais de outros ríos españois e estudando a sua posible introgresión, ademáis da pescuda de xenes determinantes de caracteres de interese e a modelización de tempadas de pesca.Xunta de Galicia | Ref. ED431C-2016-037Instituto Nacional de Investigación y Tecnología Agraria y Alimentari

Genomic analysis of the populations of Atlantic salmon (Salmo salar L.) of the Iberian Peninsula

After the drastic decrease of Atlantic salmon natural populations of the Iberian Peninsula in the last century, their restoration has been focused on habitat improvement and supportive breeding, with wild and captive individuals from different origins resulting in a failure of the initial enhancing aim. In order to design an efficient management of these populations, genetic studies should be taking into account because can help to maintain correct levels of variability and avoid consanguinity increase. New massive genotyping technologies, like SNP, can provide information that can be applied in conservation programs. In this thesis project, we will use the information obtained after the hybridization of salmon DNA onto an array of 200,000 SNP together with long dataset about microsatellite variability, abundances, morphological data, ages, sexes, fishing data,… in order to design a optimal conservation program from this specie in Galician rivers. The genetics status of the present populations will be evaluated, by comparing populations with other Spanish rivers, and by studying the possible introgression of foreign genomes. In addition we will try to modeling of fishing season in order to minimize the impact of this sport on populations.Tras la drástica disminución de las poblaciones naturales de salmón atlántico en el último siglo, su recuperación se ha centrado en la Península Ibérica en la mejora del hábitat y en la repoblación de los ríos, tanto con individuos salvajes como de piscifactoría, que fracasó. Para una gestión eficiente, los estudios genéticos tienen una gran importancia, tanto para mantener niveles correctos de variabilidad como evitar el incremento en consanguinidad. Con el desarrollo de nuevas tecnologías de genotipado masivo, como los SNPs, se obtiene nueva información aplicable a programas de conservación. En este proyecto se utilizará la información de un array de 220,000 SNPs de Affymetrix, datos de microsatélites de varios años desde 1990, así como datos de abundancia, información morfológica, edad, sexo, datos de capturas,… con el objetivo de diseñar un programa óptimo de conservación de esta especie en Galicia. Se evaluará el estado de las poblaciones actuales, comparando los datos poblacionales de otros ríos españoles y estudiando su posible introgresión, además de la búsqueda de genes determinantes de caracteres de interés y la modelización de temporadas de pesca.Tras a drástica diminución das poboacións naturais de salmón atlántico no último século, na Península Ibérica a súa recuperación centrouse na mellora do seu entorno e na repoboación dos ríos, con individuos salvaxes e de piscifactoría, que fracasou. Para una xestión eficiente, os estudos xenéticos teñen unha gran importancia, tanto para manter niveis correctos de variabilidade, como evitar o incremento da consanguinidade. Co desenvolvemento de novas tecnoloxías de xenotipado masivo, coma os SNPs, pódese obter nova información aplicable a programas de conservación. Neste proxecto, utilizarase a información dun array de 220,000 SNP de Affymetrix, datos de microsatélites de distintos anos dende 1990, así como datos de abundancia, información morfolóxica, idade, sexo, datos de capturas,… co obxectivo de deseñar un programa de conservación óptimo para esta especie en Galicia. Evaluarase o estado das poboacións actuais, comparando os datos poblacionais de outros ríos españois e estudando a sua posible introgresión, ademáis da pescuda de xenes determinantes de caracteres de interese e a modelización de tempadas de pesca.Xunta de Galicia | Ref. ED431C-2016-037Instituto Nacional de Investigación y Tecnología Agraria y Alimentari

Detecting local adaptation between North and South European Atlantic salmon populations

Pollution and other anthropogenic effects have driven a decrease in Atlantic salmon (Salmo salar) in the Iberian Peninsula. The restocking effort carried out in the 1980s, with salmon from northern latitudes with the aim of mitigating the decline of native populations, failed, probably due to the deficiency in adaptation of foreign salmon from northern Europe to the warm waters of the Iberian Peninsula. This result would imply that the Iberian populations of Atlantic salmon have experienced local adaptation in their past evolutionary history, as has been described for other populations of this species and other salmonids. Local adaptation can occur by divergent selections between environments, favoring the fixation of alleles that increase the fitness of a population in the environment it inhabits relative to other alleles favored in another population. In this work, we compared the genomes of different populations from the Iberian Peninsula (Atlantic and Cantabric basins) and Scotland in order to provide tentative evidence of candidate SNPs responsible for the adaptive differences between populations, which may explain the failures of restocking carried out during the 1980s. For this purpose, the samples were genotyped with a 220,000 high-density SNP array (Affymetrix) specific to Atlantic salmon. Our results revealed potential evidence of local adaptation for North Spanish and Scottish populations. As expected, most differences concerned the comparison of the Iberian Peninsula with Scotland, although there were also differences between Atlantic and Cantabric populations. A high proportion of the genes identified are related to development and cellular metabolism, DNA transcription and anatomical structure. A particular SNP was identified within the NADP-dependent malic enzyme-2 (mMEP-2*), previously reported by independent studies as a candidate for local adaptation in salmon from the Iberian Peninsula. Interestingly, the corresponding SNP within the mMEP-2* region was consistent with a genomic pattern of divergent selection.Xunta de Galicia | Ref. ED431C 2020/05Ministerio de Economía y Competitividad | Ref. RZ2A12-00011-CO2-01/0