Genomic Relationships among Different Timor Hybrid (Coffea L.) Accessions as Revealed by SNP Identification and RNA-Seq Analysis

Herrera, Juan Carlos; Villegas, Andrés Mauricio; Garcı́a, Fernando; Dereeper, Alexis; Combes, Marie‐Christine; Posada, Húver; Lebailly, Philippe

doi:10.1007/978-3-319-01568-2_24

Cited by 4 publications

(2 citation statements)

References 7 publications

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“…The genetic diversity of C. arabica available within the collections outside of Ethiopia is currently exploited for breeding programs to cope with the challenges of climate change around the world. While a global coffee genetic resource conservation consortium is certainly needed to ensure that existing coffee genetic resources are preserved in Ethiopia, the low level of genetic diversity in C. arabica compared to the much higher diversity in the present-day populations of its progenitors suggests that introgression events into the allotetraploid species from the diploid species such as those exploited to achieve coffee rust resistance in derivatives of the Timor hybrid 46,47 are of paramount importance to broaden substantially the genetic diversity in the cultivated germplasm and increase environmental, economic and social sustainability of coffee cultivation.…”

Section: Discussionmentioning

confidence: 99%

A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for the extremely low genetic variation in wild and cultivated germplasm

Scalabrin

Toniutti²,

Gaspero

et al. 2020

Sci Rep

118

111

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the genome of the allotetraploid species Coffea arabica L. was sequenced to assemble independently the two component subgenomes (putatively deriving from C. canephora and C. eugenioides) and to perform a genome-wide analysis of the genetic diversity in cultivated coffee germplasm and in wild populations growing in the center of origin of the species. We assembled a total length of 1.536 Gbp, 444 Mb and 527 Mb of which were assigned to the canephora and eugenioides subgenomes, respectively, and predicted 46,562 gene models, 21,254 and 22,888 of which were assigned to the canephora and to the eugeniodes subgenome, respectively. Through a genome-wide SNP genotyping of 736 C. arabica accessions, we analyzed the genetic diversity in the species and its relationship with geographic distribution and historical records. We observed a weak population structure due to lowfrequency derived alleles and highly negative values of Taijma's D, suggesting a recent and severe bottleneck, most likely resulting from a single event of polyploidization, not only for the cultivated germplasm but also for the entire species. This conclusion is strongly supported by forward simulations of mutation accumulation. However, PCA revealed a cline of genetic diversity reflecting a west-toeast geographical distribution from the center of origin in East Africa to the Arabian Peninsula. The extremely low levels of variation observed in the species, as a consequence of the polyploidization event, make the exploitation of diversity within the species for breeding purposes less interesting than in most crop species and stress the need for introgression of new variability from the diploid progenitors.

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Section: Discussionmentioning

confidence: 99%

A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for the extremely low genetic variation in wild and cultivated germplasm

Scalabrin

Toniutti²,

Gaspero

et al. 2020

Sci Rep

118

111

View full text Add to dashboard Cite

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“…The importance of HDT populations as resistance sources relies on the long durability of some of these resistance factors, which, in some cases, have been in use for more than 30 years. For instance, the genotype HDT CIFC832/2 carries additional genome introgressions compared with other genotypes (Herrera et al ., ) and presents a pre‐haustorial (non‐host‐like) resistance (Diniz et al ., ). Indeed, the post‐haustorial resistance response is typically found in most coffee– H. vastatrix interactions (Silva et al .…”

Section: Disease Controlmentioning

confidence: 99%

The coffee leaf rust pathogen Hemileia vastatrix: one and a half centuries around the tropics

Talhinhas

Batista

Diniz

et al. 2017

Molecular Plant Pathology

198

191

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Although exhibiting limited genetic polymorphism, the very large genome of H. vastatrix (c. 797 Mbp) conceals great pathological diversity, with more than 50 physiological races. Gene expression studies have revealed a very precocious activation of signalling pathways and production of putative effectors, suggesting that the plant-fungus dialogue starts as early as at the germ tube stage, and have provided clues for the identification of avr genes.

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Current Challenges and Genomic Advances Towards the Development Resilient Coffee Genotypes to Abiotic Stresses

Santos

Ferreira

Marques

et al. 2022

Genomic Designing for Abiotic Stress Resistant Technical Crops

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Genomic Relationships among Different Timor Hybrid (Coffea L.) Accessions as Revealed by SNP Identification and RNA-Seq Analysis

Cited by 4 publications

References 7 publications

A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for the extremely low genetic variation in wild and cultivated germplasm

A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for the extremely low genetic variation in wild and cultivated germplasm

The coffee leaf rust pathogen Hemileia vastatrix: one and a half centuries around the tropics

Current Challenges and Genomic Advances Towards the Development Resilient Coffee Genotypes to Abiotic Stresses

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