Genetic diversity of coffee (Coffea spp.) in Mexico evaluated by using DArTseq and SNP markers

Spinoso-Castillo, José Luis; Prado, Esteban; Aguilar-Rincón, Víctor Héber; Morales-Ramos, Victorino; Santos, Gabino García de los; Pérez‐Rodríguez, Paulino; Corona-Torres, Tarsicio

doi:10.1007/s10722-020-00940-5

Cited by 19 publications

(12 citation statements)

References 34 publications

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“…The genetic variability of C. arabica accessions from other countries, such as Costa Rica [94], Mexico [95], Nicaragua [96], India [97][98][99], Indonesia [100], China [101], Kenya [102] and Ethiopia [34,[103][104][105], has also been analyzed using markers such as ISSRs, SSRs, sequence-related amplified polymorphisms (SRAPs), AFLPs, and SNPs. In Ethiopia, different studies have shown the presence of great genetic variability in coffee plants.…”

Section: Genetic Diversity Based On Molecular Markersmentioning

confidence: 99%

Genetic Diversity ofCoffea arabica

Ferreira¹,

Caixeta²,

Caniato³

et al. 2021

Genetic Variation

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Coffea arabica L. is a native coffee species probably originated in Abyssinia, now Ethiopia. The genetic diversity of C. arabica has economic implications directly related to profits by breeding for developing new varieties to a global market. The economic value of C. arabica genetic resources are estimated at US$ 420 million, considered a 10% discount rate. Understanding the extent of traits variability and genetic diversity is essential to guide crosses between genotypes, targeting the development of new varieties with high economic value. This chapter will present the C. arabica economic importance, primarily to Brazil, the most significant world producer; we will outline the origin and dispersion of arabica coffee and briefly show the leading germplasm banks. We will also point out contribution of genetic diversity studies based on morphological, agronomic traits, and molecular markers supporting the development of new varieties. Finally, we present an outline for the future.

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Section: Genetic Diversity Based On Molecular Markersmentioning

confidence: 99%

Genetic Diversity ofCoffea arabica

Ferreira¹,

Caixeta²,

Caniato³

et al. 2021

Genetic Variation

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“…These accessions were selected from the National Coffee Germplasm Bank located at 19°10′ 27" N and 96° 57′ 50" W and 1345 masl, in Huatusco, Veracruz, Mexico. Accessions were previously characterized by DArTseq™ method and SNP markers in Spinoso-Castillo et al [66].…”

Section: Dartseq™: An Effective Tool For Genome Diversity In C Arabicamentioning

confidence: 99%

“…The development of a new coffee variety takes about 25 years. An efficient selection can be addressed when sequencing approaches are adopted in the variety Genetic Diversity of Coffea arabica L.: A Genomic Approach DOI: http://dx.doi.org/10.5772/intechopen.96640 development process [66,76]. In the 1990s, Marker-Assisted Selection (MAS) was proposed, which enabled selecting individuals with specific alleles.…”

Section: A Future In Genomic Resources Of C Arabicamentioning

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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“…is an allotetraploid species (2n = 2x = 44) that exhibits a diploid-like meiotic behavior (Lashermes and Combes, 2018). C. arabica is the only tetraploid species of the Coffea genus while the rest of the species are diploid (Spiniso-Castillo et al, 2020). The C. arabica is believed to have been formed as a result of spontaneous hybridization between two diploid species, C. canephora and Coffea eugenioides (Lashermes et al, 1999(Lashermes et al, , 2011.…”

Section: Introductionmentioning

confidence: 99%

“…Next-generation sequencing (NGS) technologies, such as genotyping-by-sequencing (GBS) and Diversity Arrays Technology sequencing (DArTseq), provide markers that are widely used in genome-wide analysis (Spiniso-Castillo et al, 2020). The GBS approach is more informative than predesigned single nucleotide polymorphism (SNP) arrays especially on wild germplasm as it is unbiased and provide information on rare alleles while the DArTseq method is based on the complexity reduction approach, using restriction enzymes that target the genome coding regions (Pailles et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

Genetic relationship and the occurrence of multiple gene resistance to coffee berry disease (Colletotrichum kahawae, Waller Bridge) within selected Coffea arabica varieties in Kenya

Gimase¹,

Thagana²,

Omondi³

et al. 2021

Afr. J. Plant Sci.

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The Coffee Berry Disease (CBD) epidemics destroy up to 100% of the crop on a susceptible variety. Resistance to CBD is conferred by the T-gene in Hibrido De Timor (HDT), R-gene in Rume Sudan (RS), and k-gene in K7, which were assembled in resistance varieties Ruiru 11(R11) and Batian. This study aimed to evaluate the genetic relationship between R11 and Batian with their parents' HDT, RS, SL8 and confirm the occurrence of T and R genes using DNA markers. Genome-wide single nucleotide polymorphism (SNP) markers were obtained through Diversity Arrays Technology sequencing (DArTseq). The genetic relationship was analyzed by Principal Component Analysis and hierarchical clustering. The Tgene was confirmed using Microsatellite primer, Sat 235 while the R gene was by marker sequence search within the DArTseq result files. The PC1 accounted for 42% of the total variation. Hierarchical clustering revealed less than 10% dissimilarity index apart from HDT that recorded above 20%. All the R11 and Batian genotypes carry the T gene. Eleven genotypes carry both T and R genes, therefore, with broad-based resistance to CBD. The study confirmed the narrow genetic relations within the Coffea arabica coffee varieties and further confirmed the occurrence of multiple gene resistance in R11 and Batian that will not break easily to new pathogen races.

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Genetic diversity of coffee (Coffea spp.) in Mexico evaluated by using DArTseq and SNP markers

Cited by 19 publications

References 34 publications

Genetic Diversity ofCoffea arabica

Genetic Diversity ofCoffea arabica

Genetic Diversity of Coffea arabica L.: A Genomic Approach

Genetic relationship and the occurrence of multiple gene resistance to coffee berry disease (Colletotrichum kahawae, Waller Bridge) within selected Coffea arabica varieties in Kenya

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