Registro Completo |
Biblioteca(s): |
Embrapa Semiárido. |
Data corrente: |
05/09/2022 |
Data da última atualização: |
06/01/2023 |
Tipo da produção científica: |
Artigo em Periódico Indexado |
Autoria: |
MEDEIROS, F. L. V.; SANTOS, C. A. F.; COSTA, A. E. S. |
Afiliação: |
F. L. B. MEDEIROS, UFRPE; CARLOS ANTONIO FERNANDES SANTOS, CPATSA; A. E. S. COSTA, UFRPE. |
Título: |
Comparing SNP-based genetic linkage and physical maps in guava (Psidium guajava). |
Ano de publicação: |
2022 |
Fonte/Imprenta: |
Genetics and Molecular Research, v. 21, n. 2, gmr19033, 2022. |
DOI: |
DOI http://dx.doi.org/10.4238/gmr19033 |
Idioma: |
Inglês |
Conteúdo: |
Genome mapping is a simplified representation of molecular markers or nucleotide sequences in chromosomes; developing accurate and dense maps is crucial for marker-assisted selection. We developed and compared genetic linkage maps obtained using JoinMap 4.0 and GACD with a physical map obtained using BLAST analysis based on Eucalyptus SNPs transferred to guava, Psidium guajava (Myrtaceae) - to serve as a reference for trait mapping in this crop. Genotyping was conducted on 112 individuals from an experimental cross between a well-known commercial cultivar and an exotic genotype (Pedro Sato × Purple guava), using the Euchip60K SNP chip, version 2.0 (72,202 SNPs); 79% of the SNPs were monomorphic. After data filtering, 1120 markers were used for map construction. The JoinMap 4.0 linkage map had 203 markers, spanning 1405.2 cM, with an average marker distance of 7.7 cM. The GACD linkage map had 186 markers and spanned 1392.7 cM, with an average marker distance of 8.8 cM. JoinMap and GACD disagreed on the estimated distances and SNP ordering. GACD showed a greater limitation than JoinMap 4.0 as it ordered markers according to their parental origin. The physical map developed using BLAST consisted of 694 hits (e-values from 8xE-10 to 1.15xE-26), spanning 434.88 Mb, with an average marker interval of 0.62 Mb. Both linkage maps showed linkage groups with segments from several chromosomes compared to the physical map, indicating limitations. These results highlight the effectiveness of physical mapping through BLAST to overcome linkage mapping limitations, such as in marker grouping and ordering. The physical maps proposed here can serve as a reference for mapping and QTL estimates in guava. MenosGenome mapping is a simplified representation of molecular markers or nucleotide sequences in chromosomes; developing accurate and dense maps is crucial for marker-assisted selection. We developed and compared genetic linkage maps obtained using JoinMap 4.0 and GACD with a physical map obtained using BLAST analysis based on Eucalyptus SNPs transferred to guava, Psidium guajava (Myrtaceae) - to serve as a reference for trait mapping in this crop. Genotyping was conducted on 112 individuals from an experimental cross between a well-known commercial cultivar and an exotic genotype (Pedro Sato × Purple guava), using the Euchip60K SNP chip, version 2.0 (72,202 SNPs); 79% of the SNPs were monomorphic. After data filtering, 1120 markers were used for map construction. The JoinMap 4.0 linkage map had 203 markers, spanning 1405.2 cM, with an average marker distance of 7.7 cM. The GACD linkage map had 186 markers and spanned 1392.7 cM, with an average marker distance of 8.8 cM. JoinMap and GACD disagreed on the estimated distances and SNP ordering. GACD showed a greater limitation than JoinMap 4.0 as it ordered markers according to their parental origin. The physical map developed using BLAST consisted of 694 hits (e-values from 8xE-10 to 1.15xE-26), spanning 434.88 Mb, with an average marker interval of 0.62 Mb. Both linkage maps showed linkage groups with segments from several chromosomes compared to the physical map, indicating limitations. These results highlight the effectiveness... Mostrar Tudo |
Palavras-Chave: |
BLAST; Mapeamento de características qualitativas e quantitativas em goiaba; Transferibilidade de SNPs. |
Thesagro: |
Genoma; Goiaba; Marcador Molecular; Melhoramento Genético Vegetal; Psidium Guajava. |
Thesaurus Nal: |
Guavas. |
Categoria do assunto: |
G Melhoramento Genético |
Marc: |
LEADER 02565naa a2200265 a 4500 001 2146109 005 2023-01-06 008 2022 bl uuuu u00u1 u #d 024 7 $aDOI http://dx.doi.org/10.4238/gmr19033$2DOI 100 1 $aMEDEIROS, F. L. V. 245 $aComparing SNP-based genetic linkage and physical maps in guava (Psidium guajava).$h[electronic resource] 260 $c2022 520 $aGenome mapping is a simplified representation of molecular markers or nucleotide sequences in chromosomes; developing accurate and dense maps is crucial for marker-assisted selection. We developed and compared genetic linkage maps obtained using JoinMap 4.0 and GACD with a physical map obtained using BLAST analysis based on Eucalyptus SNPs transferred to guava, Psidium guajava (Myrtaceae) - to serve as a reference for trait mapping in this crop. Genotyping was conducted on 112 individuals from an experimental cross between a well-known commercial cultivar and an exotic genotype (Pedro Sato × Purple guava), using the Euchip60K SNP chip, version 2.0 (72,202 SNPs); 79% of the SNPs were monomorphic. After data filtering, 1120 markers were used for map construction. The JoinMap 4.0 linkage map had 203 markers, spanning 1405.2 cM, with an average marker distance of 7.7 cM. The GACD linkage map had 186 markers and spanned 1392.7 cM, with an average marker distance of 8.8 cM. JoinMap and GACD disagreed on the estimated distances and SNP ordering. GACD showed a greater limitation than JoinMap 4.0 as it ordered markers according to their parental origin. The physical map developed using BLAST consisted of 694 hits (e-values from 8xE-10 to 1.15xE-26), spanning 434.88 Mb, with an average marker interval of 0.62 Mb. Both linkage maps showed linkage groups with segments from several chromosomes compared to the physical map, indicating limitations. These results highlight the effectiveness of physical mapping through BLAST to overcome linkage mapping limitations, such as in marker grouping and ordering. The physical maps proposed here can serve as a reference for mapping and QTL estimates in guava. 650 $aGuavas 650 $aGenoma 650 $aGoiaba 650 $aMarcador Molecular 650 $aMelhoramento Genético Vegetal 650 $aPsidium Guajava 653 $aBLAST 653 $aMapeamento de características qualitativas e quantitativas em goiaba 653 $aTransferibilidade de SNPs 700 1 $aSANTOS, C. A. F. 700 1 $aCOSTA, A. E. S. 773 $tGenetics and Molecular Research$gv. 21, n. 2, gmr19033, 2022.
Download
Esconder MarcMostrar Marc Completo |
Registro original: |
Embrapa Semiárido (CPATSA) |
|