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Prakash, N. S.; Combes, Marie‐Christine; Naveen, Somanna; Lebailly, Philippe

doi:10.1023/a:1015736220358

Cited by 56 publications

(7 citation statements)

References 14 publications

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“…Both AFLP and SSR markers appeared to be efficient for the generation of DNA markers. In previous studies using molecular markers, a large part if not all of the detected polymorphism in C. arabica introgressed plants was related to the introgression of foreign genetic material (Prakash et al 2002(Prakash et al , 2004. However, in contrast with earlier studies on other Timor Hybrid-derived genotypes , in the present study, a low number of AFLP markers and only three SSR loci appeared to be polymorphic between Caturra and the DI.200 line.…”

Section: Discussioncontrasting

confidence: 96%

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Genetic analysis of partial resistance to coffee leaf rust (Hemileia vastatrix Berk & Br.) introgressed into the cultivated Coffea arabica L. from the diploid C. canephora species

et al. 2008

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The objective of this study was to identify polymorphic molecular markers associated with partial resistance to coffee leaf rust, Hemileia vastarix. A segregating F 2 population derived from a cross between the susceptible Coffea arabica cv. Caturra and a C. canephora-introgressed Arabica line exhibiting high partial resistance was analyzed. Rust resistance measured as rust incidence (RI) and defoliation (DEF) was evaluated in field conditions in three consecutive years (2003)(2004)(2005). During the 2003 season, which was characterized by favorable conditions for a rust epidemic, the F 2 plants exhibited different levels of resistance ranging from very susceptible (50.1% for DEF and 49.5% for RI) to highly partial resistance (9.1% for DEF and 3.7% for RI). Molecular analysis enabled identification of seven polymorphic markers (5 AFLP and 2 SSR) exhibiting significant association with partial resistance. Coexistence of resistance homozygous alleles (RR) at codominant SSR loci was correlated with high resistance. This study is the first attempt to develop PCR-based sequence specific markers linked to partial rust resistance in coffee.

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Section: Discussioncontrasting

confidence: 96%

“…In total, 33 primer combinations were tested in this study. The experimental protocol for AFLP assays, including PCR amplifications and radioactive labeling was as described by Prakash et al (2002). PCR products (5 ll) were separated on 6% denaturing polyacrylamide gels with 8 M urea and 19 TBE buffer.…”

Section: Genetic Marker Analysismentioning

confidence: 99%

Genetic analysis of partial resistance to coffee leaf rust (Hemileia vastatrix Berk & Br.) introgressed into the cultivated Coffea arabica L. from the diploid C. canephora species

et al. 2008

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“…The S.288 line is derived from a selfed offspring of S.26, a natural hybrid between C. arabica and C. liberica (Vishveshwara 1974). This line has been reported to carry the S H 3 resistance factor against the coffee leaf rust, introgressed from C. liberica (Rodrigues et al 1975;Prakash et al 2002Prakash et al , 2004. Therefore, it has been used as one of the main sources for rust resistance in India (Vishveshwara 1974).…”

Section: Plant Materialsmentioning

confidence: 99%

Use of fluorescence in situ hybridization as a tool for introgression analysis and chromosome identification in coffee (Coffea arabica L.)

Herrera

D’Hont

Lebailly

2007

Genome

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Fluorescence in situ hybridization (FISH) was used to study the presence of alien chromatin in interspecific hybrids and one introgressed line (S.288) derived from crosses between the cultivated species Coffea arabica and the diploid relatives C. canephora and C. liberica. In situ hybridization using genomic DNA from C. canephora and C. arabica as probes showed elevated cross hybridization along the hybrid genome, confirming the weak differentiation between parental genomes. According to our genomic in situ hybridization (GISH) data, the observed genomic resemblance between the modern C. canephora genome (C) and the C. canephora-derived subgenome of C. arabica (C a ) appears rather considerable. Poor discrimination between C and C a chromosomes supports the idea of low structural modifications of both genomes since the C. arabica speciation, at least in the frequency and distribution of repetitive sequences. GISH was also used to identify alien chromatin segments on chromosome spreads of a C. liberica-introgressed line of C. arabica. Further, use of GISH together with BAC-FISH analysis gave us additional valuable information about the physical localization of the C. liberica fragments carrying the SH3 factor involved in resistance to the coffee leaf rust. Overall, our results illustrate that FISH analysis is a complementary tool for molecular cytogenetic studies in coffee, providing rapid localization of either specific chromosomes or alien chromatin in introgressed genotypes derived from diploid species displaying substantial genomic differentiation from C. arabica.Key words: coffee, BAC-FISH, interspecific hybridization, GISH, introgression, genome evolution.Résumé : L'hybridation in situ fluorescente (« FISH ») a été utilisée pour étudier la présence de chromatine introgressée chez des hybrides interspécifiques mais aussi chez une lignée cultivée, issues du croissement entre l'espèce cultivée Coffea arabica et ses proches diploïdes C. canephora et C. liberica, respectivement. L'hybridation in situ en utilisant l'ADN gé-nomique des espèces C. canephora et C. arabica comme sondes, a montré une hybridation croisée importante chez les gé-nomes hybrides, ce qui confirme une étroite différentiation génomique entre les parents. Cette ressemblance entre le génome actuel de C. canephora et le sous-génome de C. arabica dérivant de l'espèce C. canephora (C a ), semble très éle-vée. De plus, la faible discrimination entre les chromosomes du type C et ceux du type C a , suggère des modifications structurales mineures dès l'origine même de l'espèce C. arabica, au moins dans ce qui concerne la fréquence et distribution des séquences répétées. L'hybridation génomique in situ (« GISH ») a permis aussi l'identification de différents fragments d'introgression chez une lignée de C. arabica introgressée par C. liberica, ce qui a conduit à l'identification de quatre fragments d'introgression. De plus, l'analyse combiné GISH plus BAC-FISH a donné des informations importantes sur la localisation physique du fragment issu d...

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“…The only allotetraploid is C. arabica L. with 2n = 4x = 44 [12], which was originated from the natural cross between Coffea eugenioides S. Moore and C. canephora Pierre ex A. Froehner [13], C. arabica is the only self-fertile among the other cultivated species. This specie is genetically less diverse when compared to the diploid species [14,15], a situation that has been associated with its susceptibility to the common coffee diseases [16].…”

Section: Genetic Diversity Of Coffea Arabica Lmentioning

confidence: 99%

Genetic Diversity of Coffea arabica L.: A Genomic Approach

Spinoso-Castillo¹,

Corona-Torres²,

Prado³

et al. 2021

Landraces - Traditional Variety and Natural Breed

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Coffea arabica L. produces a high-quality beverage, with pleasant aroma and flavor, but diseases, pests and abiotic stresses often affect its yield. Therefore, improving important agronomic traits of this commercial specie remains a target for most coffee improvement programs. With advances in genomic and sequencing technology, it is feasible to understand the coffee genome and the molecular inheritance underlying coffee traits, thereby helping improve the efficiency of breeding programs. Thanks to the rapid development of genomic resources and the publication of the C. canephora reference genome, third-generation markers based on single-nucleotide polymorphisms (SNPs) have gradually been identified and assayed in Coffea, particularly in C. arabica. However, high-throughput genotyping assays are still needed in order to rapidly characterize the coffee genetic diversity and to evaluate the introgression of different cultivars in a cost-effective way. The DArTseq™ platform, developed by Diversity Arrays Technology, is one of these approaches that has experienced an increasing interest worldwide since it is able to generate thousands of high quality SNPs in a timely and cost-effective manner. These validated SNP markers will be useful to molecular genetics and for innovative approaches in coffee breeding.

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Cited by 56 publications

References 14 publications

Genetic analysis of partial resistance to coffee leaf rust (Hemileia vastatrix Berk & Br.) introgressed into the cultivated Coffea arabica L. from the diploid C. canephora species

Genetic analysis of partial resistance to coffee leaf rust (Hemileia vastatrix Berk & Br.) introgressed into the cultivated Coffea arabica L. from the diploid C. canephora species

Use of fluorescence in situ hybridization as a tool for introgression analysis and chromosome identification in coffee (Coffea arabica L.)

Genetic Diversity of Coffea arabica L.: A Genomic Approach

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