Development of a multi-species SNP array for serrasalmid fish Colossoma macropomum and Piaractus mesopotamicus

AbstractScarce genomic resources have limited the development of breeding programs for serrasalmid fish Colossoma macropomum (tambaqui) and Piaractus mesopotamicus (pacu), the key native freshwater fish species produced in South America. The main objectives of this study were to design a dense SNP array for this fish group and to validate its performance on farmed populations from several locations in South America. Using multiple approaches based on different populations of tambaqui and pacu, a final list of 29,575 and 29,612 putative SNPs was selected, respectively, to print an Axiom AFFYMETRIX (THERMOFISHER) SerraSNP array. After validation, 74.17% (n = 21,963) and 71.25% (n = 21,072) of SNPs were classified as polymorphic variants in pacu and tambaqui, respectively. Most of the SNPs segregated within each population ranging from 14,199 to 19,856 in pacu; and from 15,075 to 20,380 in tambaqui. Our results indicate high levels of genetic diversity and clustered samples according to their hatchery origin. The developed SerraSNP array represents a valuable genomic tool approaching in-depth genetic studies for these species.

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Cross-amplification of heterologous microsatellite markers in Piracanjuba

Ciência Rural ◽

10.1590/0103-8478cr20170374 ◽

2017 ◽

Vol 47 (12) ◽

Cited By ~ 3

Author(s):

Pedro Luiz de Castro ◽

Ricardo Pereira Ribeiro ◽

Silvio Carlos Alves dos Santos ◽

Elenice Souza dos Reis Goes ◽

Felipe Pinheiro de Souza ◽

...

Keyword(s):

Genetic Variability ◽

Microsatellite Markers ◽

Oreochromis Niloticus ◽

Genetic Parameters ◽

Economic Value ◽

Current Analysis ◽

Genetic Studies ◽

Colossoma Macropomum ◽

Piaractus Mesopotamicus ◽

Cross Amplification

ABSTRACT: Brycon orbignyanus, popularly known in Brazil as piracanjuba, is a fish with great economic value but whose natural population drastically decreased in number during the last years. In this context, genetic variability studies of natural stocks and in restocking programs are fundamental for the adoption of conservation measures. Current analysis verifies the cross-amplification of heterologous primers in B. orbignyanus. Fifty-two primers of the species Brycon opalinus, Brycon hilarii, Brycon insignis, Prochilodus sp., Piaractus mesopotamicus, Colossoma macropomum and Oreochromis niloticus were tested. Primers with the best reproducibility were applied to a sample of 20 individuals and the genetic parameters were calculated. Nine primers provided good results for cross-amplification with B. orbignyanus, involving (BoM5 and BoM13) of Brycon opalinus, (Bh5, Bh6, Bh8, Bh13 and Bh16) of Brycon hilarii, (Bc48-10) of Brycon insignis and (Par80) of Prochilodus argenteus. Primers of Piaractus mesopotamicus, Colossoma macropomum and Oreochromis niloticus failed to provide amplification or provided non-specificity. Results demonstrated the possibility of using primers of different species and genera of B. orbignyanus, facilitating genetic studies on the species.

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Genetic Polymorphism of the Glutathione S-Transferase M1 and T1 Genes in Three Distinct Arab Populations

Disease Markers ◽

10.1155/2011/796520 ◽

2011 ◽

Vol 31 (5) ◽

pp. 311-316 ◽

Cited By ~ 7

Author(s):

Abdel Halim Salem ◽

Alaeddin Yaqoob ◽

Muhalab Ali ◽

Shailandra Handu ◽

Raouf Fadel ◽

...

Keyword(s):

Drug Effects ◽

Healthy Individuals ◽

Glutathione S Transferase ◽

Genetic Studies ◽

Increased Risk ◽

Allelic Distribution ◽

Disease Risks ◽

Different Populations ◽

Polymorphic Variants ◽

Risk Of Cancer

Deletion polymorphisms for the glutathione S-transferase (GST) gene are associated with increased risk of cancer, and are implicated in detoxifying mutagenic electrophilic compounds. GST Polymorphic variants were reported for different populations. The aim of this study was to investigate the frequencies ofGSTM1andGSTT1null genotypes among Bahraini, Lebanese and Tunisian Arabs. GST genotyping was done by multiplex PCR-based methods. Study subjects comprised 167 Bahrainis, 141 Lebanese and 186 Tunisians unrelated healthy individuals.GSTM1deletion homozygosity of 49.7%, 52.5% and 63.4% were recorded for Bahraini, Lebanese and Tunisians, respectively. Among Bahrainis, the prevalence ofGSTT1null homozygotes was 28.7%, while in higher rates were seen in Lebanese (37.6%) and Tunisians (37.1%). Our results indicate that there are no major differences in allelic distribution ofGSTM1and GSTT1 genes between the three Arab populations investigated except between Bahrainis and Tunisians regarding the allelic distribution ofGSTM1gene (P= 0.013). Combined analysis of both genes revealed that 14.4% of Bahrainis, 16.3% of Lebanese and 21.0% of Tunisians harbor the deleted genotype of both genes. This is the first study that addressesGSTgene polymorphism in Bahraini and Lebanese Arabs, and will help genetic studies on the association ofGSTM1andGSTT1polymorphisms with disease risks and drug effects in Arab populations.

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First report of Linguadactyloides brinkmanni (Monogenoidea: Linguadactyloidinae) on hybrids of Colossoma macropomum x Piaractus mesopotamicus (Characidae) from South America

Brazilian Journal of Aquatic Science and Technology ◽

10.14210/bjast.v16n2.p61-64 ◽

2012 ◽

Vol 16 (2) ◽

pp. 61 ◽

Cited By ~ 1

Author(s):

Márcia Kelly Reis Dias ◽

Marcos Tavares-Dias ◽

Natalia Marchiori

Keyword(s):

South America ◽

Colossoma Macropomum ◽

Piaractus Mesopotamicus ◽

First Report

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Transferability of heterologous microsatellite primers in Brycon gouldingi

Ciência Rural ◽

10.1590/0103-8478cr20180412 ◽

2018 ◽

Vol 48 (11) ◽

Author(s):

Felipe Pinheiro de Souza ◽

Ed Christian Suzuki de Lima ◽

Natalia Gonçalves Leite ◽

Angela Maria Urrea-Rojas ◽

Andrei Lincoln Yamachita ◽

...

Keyword(s):

Genetic Parameters ◽

Null Alleles ◽

Microsatellite Primers ◽

Neotropical Fish ◽

Genetic Studies ◽

Prochilodus Lineatus ◽

Colossoma Macropomum ◽

Piaractus Mesopotamicus ◽

Future Studies ◽

Environmental Importance

ABSTRACT: Brycon gouldingi is a species of neotropical fish of socioeconomic and environmental importance in the Tocantins-Araguaia Basin. Genetic studies on this species are still limited, making it difficult to evaluate the population structure and genetic diversity in natural and captive stocks. Here, we aimed to evaluate the transferability of heterologous microsatellite primers in B. gouldingi. A total of 30 primers for eight species were evaluated: Brycon hilarii, Brycon opalinus, Brycon cephalus, Brycon orbignyanus, Prochilodus lineatus, Prochilodus argenteus, Piaractus mesopotamicus, and Colossoma macropomum. The primers that showed the best amplification patterns were applied to 20 specimens of B. gouldingi, and their genetic parameters were assessed. Among the 30 primers, seven showed satisfactory transferability, six of which belonged to the genus Brycon: Bh13 (B. hilarii), BoM5, BoM13 (B. opalinus), Borg9, Borg13, and Borg59 (B. orbignyanus), and one belonged to P. argenteus (Par80). The primers for the other species tested showed non-specificity or monomorphism; and were therefore, excluded from the analyses. The number of alleles ranged between two (Borg13 and Borg59) and three (Bh13, BoM5, BoM13, Borg9 and Par80), with sizes varying between 103 bp (BoM5) and 430 bp (Borg9). Four primers showed evidence of null alleles (BoM13, Borg9, Borg13, and Par80), which could probably be attributed to the respective Hardy-Weinberg deviation. Thus, seven primers were validated for cross-amplification in B. gouldingi, which may be used in future studies involving this species.

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INHERITANCE OF RESISTANCE TO NET BLOTCH IN BARLEY. I. FACTORS AFFECTING THE PENETRANCE AND EXPRESSIVITY OF GENE(S) CONDITIONING HOST RESISTANCE

Canadian Journal of Genetics and Cytology ◽

10.1139/g69-068 ◽

1969 ◽

Vol 11 (3) ◽

pp. 587-591 ◽

Cited By ~ 10

Author(s):

T. N. Khan

Keyword(s):

Environmental Conditions ◽

Net Blotch ◽

Host Reaction ◽

Susceptible Parent ◽

Breeding Programs ◽

Genetic Studies ◽

Factors Affecting ◽

Drechslera Teres ◽

Resistant Varieties ◽

High Level

Variability in the host-reaction of barley to infection by Drechslera teres was examined in the parents and progeny of selected crosses under different environmental conditions of testing.The Ethiopian variety C.I. 5791 exhibits a consistently high level of resistance under a range of environmental conditions, which is in contrast to the Manchurian variety C.I. 2330. The sensitivity of the genes for resistance possessed by these varieties to environmental modifications is considered to depend upon their respective genetic backgrounds. Furthermore, variability of host reaction in the progeny of these resistant varieties was shown to be influenced by the genetic background of the susceptible parent used.The implications of these findings in the conduct and interpretation of genetic studies and in backcross breeding programs is discussed.

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Resistência ao estresse e crescimento de larvas de peixes neotropicais alimentadas com diferentes dietas

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2007000100009 ◽

2007 ◽

Vol 42 (1) ◽

pp. 65-72 ◽

Cited By ~ 4

Author(s):

Ronald Kennedy Luz

Keyword(s):

Colossoma Macropomum ◽

Piaractus Mesopotamicus ◽

Astronotus Ocellatus

O objetivo deste trabalho foi avaliar o efeito da alimentação na resistência ao estresse e no crescimento de larvas das espécies de peixes neotropicais: Astronotus ocellatus (Oscar), Piaractus mesopotamicus (pacu) e Pseudoplatystoma coruscans (pintado). As larvas receberam diferentes tipos de alimentos (Artemia sp., larvas de Colossoma macropomum e dieta artificial Fry Feed Kyowa). Foram realizados testes de exposição ao ar e a taxa de sobrevivência, determinada 24 horas depois. A fim de avaliar o crescimento, medidas de peso foram realizadas em larvas dos diferentes tratamentos. Larvas de A. ocellatus alimentadas com náuplios de Artemia sp. apresentaram tendência de maior peso e resistência ao estresse, quando comparadas com o uso de dieta artificial. Larvas de P. mesopotamicus apresentaram melhores valores de peso e taxas de resistência ao estresse, quando alimentadas com Artemia sp. ou alimentação mista (Artemia sp. + dieta artificial). Em P. coruscans, o uso de larvas forrageiras resultou em indivíduos mais resistentes aos testes de exposição ao ar do que os que receberam apenas Artemia sp. Valores de peso, nos dois manejos alimentares, foram semelhantes entre si. O alimento vivo desempenha importante atuação no crescimento em peso e na melhora da resistência ao estresse das espécies estudadas.

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A second rabbit kappa isotype.

Journal of Experimental Medicine ◽

10.1084/jem.156.2.585 ◽

1982 ◽

Vol 156 (2) ◽

pp. 585-595 ◽

Cited By ~ 30

Author(s):

A Benammar ◽

P A Cazenave

Keyword(s):

Light Chain ◽

Immunoglobulin G ◽

Antigenic Determinants ◽

Gene Encoding ◽

Genetic Studies ◽

B Locus ◽

Different Populations ◽

Domestic Rabbits ◽

Chain Type

Immunoglobulin G (IgG) from the rabbit strain Basilea was previously shown to contain two distinct populations of molecules one with light chain belonging to the known lambda isotype and the others to a new kappa-like L chain type. Alloantisera prepared against the Basilea IgG are directed against the kappa-like light chain (anti-bas antisera). All Basilea rabbits express kappa-like chains recognized by anti-bas sera, but IgG from other domestic rabbits did not react with these antisera. Genetic studies of wild rabbits belonging to different populations show that the bas+ phenotype could be found in heterozygous rabbits as well as those homozygous at the b locus. The gene encoding the bas+ light chain is closely linked to the b locus. Moreover, antigenic determinants recognized by anti-bas antibodies and antigenic determinants recognized by antibodies directed against allotypic determinants of the b series are located on distinct IgG molecules. These results show that there are two rabbit kappa isotypes: the kappa 1 isotype, bearing allotypic determinants of the b series, and the kappa 2 isotype, for which bas+ chain is one of the allotypic forms. The kappa 1 and kappa 2 isotypes are controlled by closely linked genes.

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A new source of root-knot nematode resistance from Arachis stenosperma incorporated into allotetraploid peanut (Arachis hypogaea)

Scientific Reports ◽

10.1038/s41598-019-54183-1 ◽

2019 ◽

Vol 9 (1) ◽

Author(s):

Carolina Ballén-Taborda ◽

Ye Chu ◽

Peggy Ozias-Akins ◽

Patricia Timper ◽

C. Corley Holbrook ◽

...

Keyword(s):

Genetic Basis ◽

Snp Array ◽

Nematode Resistance ◽

Major Effect ◽

Root Knot Nematode ◽

Breeding Programs ◽

Genes Encoding ◽

In The Wild ◽

Arachis Batizocoi ◽

Lrr Protein

AbstractRoot-knot nematode is a very destructive pathogen, to which most peanut cultivars are highly susceptible. Strong resistance is present in the wild diploid peanut relatives. Previously, QTLs controlling nematode resistance were identified on chromosomes A02, A04 and A09 of Arachis stenosperma. Here, to study the inheritance of these resistance alleles within the genetic background of tetraploid peanut, an F2 population was developed from a cross between peanut and an induced allotetraploid that incorporated A. stenosperma, [Arachis batizocoi x A. stenosperma]4×. This population was genotyped using a SNP array and phenotyped for nematode resistance. QTL analysis allowed us to verify the major-effect QTL on chromosome A02 and a secondary QTL on A09, each contributing to a percentage reduction in nematode multiplication up to 98.2%. These were validated in selected F2:3 lines. The genome location of the large-effect QTL on A02 is rich in genes encoding TIR-NBS-LRR protein domains that are involved in plant defenses. We conclude that the strong resistance to RKN, derived from the diploid A. stenosperma, is transferrable and expressed in tetraploid peanut. Currently it is being used in breeding programs for introgressing a new source of nematode resistance and to widen the genetic basis of agronomically adapted peanut lines.

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