Linkage map for chromosome-level genome anchoring and genome-wide association study for resistance to Aeromonas hydrophila in Colossoma macropomum

Ariede, Raquel B.; Freitas, Milena V.; Lira, Lieschen V.G.; Agudelo, John F.G.; Borges, Carolina H.S.; Mastrochirico-Filho, Vito A.; Cáceres, Pablo; Yáñez, José M.; Hashimoto, Diogo Teruo

doi:10.1016/j.aquaculture.2022.738462

Cited by 8 publications

(5 citation statements)

References 65 publications

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“…Recently, the tambaqui C. macropomum was described as having an XY hypothetical sex determination system [55], despite not presenting heteromorphic sex chromosomes. [56] found that the tambaqui female linkage map was larger than the male (1.55x). Differences in map length can result from a variation in the number of recombination events in the two parents as well as variations in the number and location of the mapped loci.…”

Section: Discussionmentioning

confidence: 99%

De novo assembly and characterization of a highly degenerated ZW sex chromosome in the fish Megaleporinus macrocephalus

Borges,

Utsunomia,

Varani

et al. 2024

Preprint

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Background: Megaleporinus macrocephalus (piaucu) is a Neotropical fish within Characoidei that presents a well-established heteromorphic ZZ/ZW sex-determination system and thus, constitutes a good model for studying W and Z chromosomes in fishes. We used PacBio reads and Hi-C to assemble a chromosome-level reference genome for M. macrocephalus. We generated family segregation information to construct a genetic map, pool-seq of males and females to characterize its sex system, and RNA-seq to highlight candidate genes of M. macrocephalus sex determination. Results: M. macrocephalus reference genome is 1,282,030,339 bp in length and has a contig and scaffold N50 of 5.0 Mb and 45.03 Mb, respectively. Based on patterns of recombination suppression, coverage, Fst, and sex-specific SNPs, three major regions were distinguished in the sex chromosome: W-specific (highly differentiated), Z-specific (in degeneration), and PAR. The sex chromosome gene repertoire was composed of genes from the TGF-beta family (amhr2, bmp7) and Wnt/beta-catenin pathway (wnt4, wnt7a), and some of them were differentially expressed. Conclusions: The chromosome-level genome of piaucu exhibits high quality, establishing a valuable resource for advancing research within the group. Our discoveries offer insights into the evolutionary dynamics of Z and W sex chromosomes in fish, emphasizing ongoing degenerative processes and indicating complex interactions between Z and W sequences in specific genomic regions. Notably, amhr2 and bmp7 are potential candidate genes for sex determination in M. macrocephalus.

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Section: Discussionmentioning

confidence: 99%

De novo assembly and characterization of a highly degenerated ZW sex chromosome in the fish Megaleporinus macrocephalus

Borges,

Utsunomia,

Varani

et al. 2024

Preprint

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“…Cooney et al [ 39 ] evaluated the recombination landscape of 61 fish species and found that 42 species had higher recombination rates in females than males. Although there is no clear adaptative explanation for such differences between sexes, some hypotheses were proposed, such as the meiotic drive (i.e., alleles have an advantage during the process of female meiosis changing recombination rates) and protection against aneuploidy (i.e., failure of chromosomes to separate during cell division) [ 40 – 42 ]. In crustaceans, a previous study showed similar recombination rates between males and females for Daphnia pulex [ 43 ], which conflicts with our results in shrimp.…”

Section: Discussionmentioning

confidence: 99%

A high-density linkage map and sex-determination loci in Pacific white shrimp (Litopenaeus vannamei)

Garcia,

Mastrochirico-Filho,

Gallardo-Hidalgo

et al. 2024

BMC Genomics

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Background Expansion of genomic resources for the Pacific white shrimp (Litopenaeus vannamei), such as the construction of dense genetic linkage maps, is crucial for the application of genomic tools in order to improve economically relevant traits. Sexual dimorphism exists in Pacific white shrimp, and the mapping of the sex-determination region in this species may help in future reproductive applications. We have constructed male, female, and sex-averaged high-density genetic maps using a 50 K single-nucleotide polymorphism (SNP) array, followed by a genome-wide association study (GWAS) to identify genomic regions associated with sex in white shrimp. Results The genetic map yielded 15,256 SNPs assigned to 44 linkage groups (LG). The lengths of the male, female, and sex-averaged maps were 5,741.36, 5,461.20 and 5,525.26 cM, respectively. LG18 was found to be the largest for both sexes, whereas LG44 was the shortest for males and LG31 for females. A sex-determining region was found in LG31 with 21 statistically significant SNPs. The most important SNP was previously identified as a sex-linked marker and was able to identify 99% of the males and 88% of the females. Although other significant markers had a lower ability to determine sex, putative genes were intercepted or close to them. The oplophorus-luciferin 2-monooxygenase, serine/arginine repetitive matrix protein and spermine oxidase genes were identified as candidates with possible participation in important processes of sexual differentiation in shrimp. Conclusions Our results provide novel genomic resources for shrimp, including a high-density linkage map and new insights into the sex-determining region in L. vannamei, which may be usefulfor future genetics and reproduction applications.

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“…Cooney et al (2021) evaluated the recombination landscape of 61 sh species and found that 42 of them have higher recombination rates in females in comparison to males. Although there is no clear adaptative explanation for such differences between sexes, some hypotheses were proposed, such as the meiotic drive (i.e., alleles have an advantage during the process of female meiosis changing recombination rates) and protection against aneuploidy (i.e., failure of chromosomes to separate during cell division) [41][42][43].…”

Section: Discussionmentioning

confidence: 99%

A high-density linkage map and sex-determination loci in Pacific white shrimp (Litopenaeus vannamei)

Garcia,

Mastrochirico-Filho,

Gallardo-Hidalgo

et al. 2023

Preprint

View full text Add to dashboard Cite

Background Expansion of genomic resources for the Pacific white shrimp (Litopenaeus vannamei) such as the construction of dense genetic linkage maps, is crucial for the application of genomic tools to improve economic relevant traits. Sexual dimorphism exists in Pacific white shrimp, and mapping of the sex determination region in this species may help in the future reproductive applications for this species. We constructed male, female and sex-averaged high-density genetic maps using a 50K single-nucleotide polymorphism (SNP) array followed by a genome-wide association study (GWAS) to identify genomic regions associated to sex in white shrimp.Results The genetic map yielded 15,256 SNPs assigned to 44 linkage groups (LG). The length of the male, female and sex-averaged maps were 5,741.36, 5,461.20 and 5,525.26 cM, respectively. The LG18 was the largest for both sexes while the LG44 was the shortest for males and LG31 for females. A sex determination region was found on LG31 with 21 statistically significant SNPs. The most important SNP was previously identified as a sex-linked marker and it was able to identify 99% of males and 88% of females. Although, the other significant markers had lower ability to determine sex, putative genes were found intercepted or close to them. The oplophorus-luciferin 2-monooxygenase, serine/arginine repetitive matrix protein and spermine oxidase genes were identified as candidate with possible participation in important processes of sexual differentiation in shrimp.Conclusions Our results provided novel genomic resources for shrimp, including a high-density linkage map and new insights regarding the sex determining region in L. vannamei, and may be both useful in future genetics and reproduction applications.

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Linkage map for chromosome-level genome anchoring and genome-wide association study for resistance to Aeromonas hydrophila in Colossoma macropomum

Cited by 8 publications

References 65 publications

De novo assembly and characterization of a highly degenerated ZW sex chromosome in the fish Megaleporinus macrocephalus

De novo assembly and characterization of a highly degenerated ZW sex chromosome in the fish Megaleporinus macrocephalus

A high-density linkage map and sex-determination loci in Pacific white shrimp (Litopenaeus vannamei)

A high-density linkage map and sex-determination loci in Pacific white shrimp (Litopenaeus vannamei)

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