Evidence of Intergenomic Relationships in Triploid Hybrids of Coffee (Coffea sp.) as Revealed by Meiotic Behavior and Genomic in Situ Hybridization

Herrera, Juan-Carlos; Romero, Juan Vicente; Camayo, Gloria-Cecilia; Caetano, Creucí María; Cortina, Hernando-Alfonso

doi:10.1007/s12042-012-9105-x

Cited by 3 publications

(4 citation statements)

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“…The two sub‐genomes of C. arabica (Ca and Ea) indicated sufficient sequence differences, and thus obtaining a whole‐genome sequence would be an important resource for the allotetraploid genome of C. arabica . Results also revealed that C. eugenioides was more closely related to C. arabica than to C. liberica , which was in agreement with the ancestral history of the allotetraploid C. arabica …”

Section: Coffee Genomic Resourcessupporting

confidence: 73%

“…Among coffee species, comparison of genomes showed a high gene synteny between C. arabica (EaEaCaCa) and C. canephora (CC) and C. arabica (EaEaCaCa), C. eugenioides (EE) and C. liberica (LL), but numerous chromosomal rearrangements were detected . The two sub‐genomes of C. arabica (Ca and Ea) indicated sufficient sequence differences, and thus obtaining a whole‐genome sequence would be an important resource for the allotetraploid genome of C. arabica .…”

Section: Coffee Genomic Resourcesmentioning

confidence: 99%

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Advances in genomics for the improvement of quality in coffee

et al. 2016

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Coffee is an important crop that provides a livelihood to millions of people living in developing countries. Production of genotypes with improved coffee quality attributes is a primary target of coffee genetic improvement programs. Advances in genomics are providing new tools for analysis of coffee quality at the molecular level. The recent report of a genomic sequence for robusta coffee, Coffea canephora, is a major development. However, a reference genome sequence for the genetically more complex arabica coffee (C. arabica) will also be required to fully define the molecular determinants controlling quality in coffee produced from this high quality coffee species. Genes responsible for control of the levels of the major biochemical components in the coffee bean that are known to be important in determining coffee quality can now be identified by association analysis. However, the narrow genetic base of arabica coffee suggests that genomics analysis of the wild relatives of coffee (Coffea spp.) may be required to find the phenotypic diversity required for effective association genetic analysis. The genomic resources available for the study of coffee quality are described and the potential for the application of next generation sequencing and association genetic analysis to advance coffee quality research are explored.Key words: Coffee quality, genetics, genomics, biochemical compounds, next generation sequencing, association studies.This article is protected by copyright. All rights reserved. Accepted Article GENERAL INTRODUCTIONCoffee is an important crop and the second most traded commodity in the world (after petroleum) providing a living to more than 125 million people .Commercial coffee production is dominated by only two species belonging to the Coffea genus: C. arabica and C. canephora (the latter generally referred to as robusta coffee). All coffee species are diploid (2n=2x=22) and generally self-incompatible, except for C. arabica which is a self-fertile tetraploid (2n=4x=44) derived from a spontaneous hybridization between C. canephora (as paternal progenitor) and C.eugenioides (as maternal progenitor) 8 9.Although C. arabica is considered to have better cupping quality than C. canephora, improving the quality of both commercial species 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 quality, thereby helping improve the efficiency of breeding programs.This review will discuss current knowledge regarding the genetics of those biochemical compounds which are considered quality determinants, for use as a foundation for improving coffee quality by breeding. Available genomic resources for the study of the genetics of biochemical compounds that are likely to be playing a role in coffee flavour will also be discussed. In addition, the potential value of the study of genetics of coffee This article is protected by copyright. All rights reserved.Ac...

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Section: Coffee Genomic Resourcessupporting

confidence: 73%

Section: Coffee Genomic Resourcesmentioning

confidence: 99%

Advances in genomics for the improvement of quality in coffee

et al. 2016

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“…In cassava ( M. esculenta ), breeding with the wild relative M. glaziovii allowed for the transmission of useful traits such as increased water uptake, virus and pest resistance, and apomictic seed development ( Nassar and Ortiz, 2010 ); the latter would be beneficial because it would allow the propagation of hybrids without the need for cuttings that enable viruses and bacteria to contaminate the plants ( Nassar and Ortiz, 2010 ). Introgression of useful traits from wild relatives has also been reported in the breeding of fruit tree papaya ( Carica papaya ) ( Coppens d’Eeckenbrugge et al, 2014 ) and coffee ( Herrera et al, 2012 ) and was proposed in cacao ( Dantas and Guerra, 2010 ). These are tropical cash crops that are not usually considered orphan crops but whose social impact is considerable in developing countries ( Myrick et al, 2014 ; Giuliani et al, 2017 ; Wickramasuriya and Dunwell, 2018 ).…”

Section: Genomics and Breeding Of Orphan Cropsmentioning

confidence: 99%

Meiosis Research in Orphan and Non-orphan Tropical Crops

Bolaños-Villegas

Argüello-Miranda

2019

Front. Plant Sci.

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Plant breeding is directly linked to the development of crops that can effectively adapt to challenging conditions such as soil nutrient depletion, water pollution, drought, and anthropogenic climate change. These conditions are extremely relevant in developing countries already burdened with population growth and unchecked urban expansion, especially in the tropical global southern hemisphere. Engineering new crops thus has potential to enhance food security, prevent hunger, and spur sustainable agricultural growth. A major tool for the improvement of plant varieties in this context could be the manipulation of homologous recombination and genome haploidization during meiosis. The isolation or the design of mutations in key meiotic genes may facilitate DNA recombination and transmission of important genes quickly and efficiently. Genome haploidization through centromeric histone mutants could be an option to create new crosses rapidly. This review covers technical approaches to engineer key meiotic genes in tropical crops as a blueprint for future work and examples of tropical crops in which such strategies could be applied are given.

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“…Among coffee species, comparison of genomes showed a high gene synteny between C. arabica (EaEaCaCa) and C. canephora (CC) and among C. arabica (EaEaCaCa), C. eugenioides (EE) and C. liberica (LL) (Cenci et al, 2012;Herrera et al, 2012;Yu et al, 2011), but numerous chromosomal rearrangements were detected (Yu et al, 2011). The two sub-genomes of C. arabica (Ca and Ea) indicated sufficient sequence differences, and thus obtaining a whole-genome sequence would be an important resource for the allotetraploid genome of C. arabica.…”

Section: Coffee Whole Genome and Syntenymentioning

confidence: 99%

Genomic studies of biochemical compounds determining arabica coffee (Coffea arabica L.) quality

Tran¹

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Coffee is an important crop globally. Improving coffee quality is a primary breeding target that would benefit from understanding of trait inheritance and ancestral genetic information. However, comparatively little information exists on the genetics of quality and the relationships between wild and cultivated coffee genotypes, especially arabica coffee (Coffea arabica L.) which accounts for almost 60% of coffee production globally. The complex polyploidy genome and limited genomic information for C. arabica have impeded the progress of genetic studies. Arabica coffee is among the major organisms that do not have a reference genome. This project aimed to develop and utilise genomic resources in genetic studies of arabica coffee quality. The relationship between coffee species and the position of arabica within the Coffeeae tribe were investigated using complete chloroplast genome sequences to determine the value of these genetic resources in breeding. A draft genome sequence of arabica coffee was developed. Marker-trait associations were studied for caffeine and trigonelline, the two principal compounds known to be related to coffee quality, paving the way for developing new improved varieties with preferred levels of these compounds in the coffee beans.Chloroplast genomes of 16 coffee species were sequenced and their phylogeny constructed. Results support distinct Psilanthus and Coffea clades. It is likely that C. canephora is a hybrid that has a Psilanthus maternal genome but received much of its nuclear genome from Coffea. The maternal genomes of C. arabica and C. canephora are divergent. This result is in agreement with the fact that the chloroplast genome of arabica should be that of the maternal parent i.e. C. eugenioides. There were two species (C. humblotiana and C. tetragona) close to C. arabica and one species (P. ebracteolatus) close to C. canephora containing almost no caffeine. They could serve as important materials in arabica quality breeding and research.For the association study, 232 diverse arabica coffee accessions originating from 27 countries were harvested from the germplasm collection at CATIE (Tropical Agricultural Research and Higher Education Centre), Costa Rica. Substantial variation between genotypes was observed for bean morphology attributes. Non-volatiles including caffeine and trigonelline showed larger variation in range than was previously reported. Results of targeted analysis of 18 volatiles from 35 accessions also showed significant variation. No strong correlation was found between bean morphology and the levels of non-volatile or volatile compounds, implying that it is difficult to select for low or high non-volatile and volatile compounds based on bean physical characteristics. However, it also indicates that breeding for desirable combinations of traits (i.e. large bean size, low caffeine, high trigonelline, and favourable volatiles) is possible.ii The genome of the most popular arabica variety (K7) in Australia was sequenced. Genome assembly was performed using b...

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Evidence of Intergenomic Relationships in Triploid Hybrids of Coffee (Coffea sp.) as Revealed by Meiotic Behavior and Genomic in Situ Hybridization

Cited by 3 publications

References 27 publications

Advances in genomics for the improvement of quality in coffee

Advances in genomics for the improvement of quality in coffee

Meiosis Research in Orphan and Non-orphan Tropical Crops

Genomic studies of biochemical compounds determining arabica coffee (Coffea arabica L.) quality

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