Identification of microsatellite markers in coffee associated with resistance to Meloidogyne exigua

Pereira, Thamiris Bandoni; Setotaw, Tesfahun Alemu; Santos, dos; Mendes, Antônio Nazareno Guimarães; Salgado, Sônia M. L.; Carvalho, G R; Rezende, Ramiro Machado

doi:10.4238/gmr.15038054

Cited by 8 publications

(7 citation statements)

References 23 publications

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“…[40,42,43]. Molecular markers associated with Ck-1 are located on chromosome 1, which have been used in breeding programs to speed up the introgression efficiency ( Figure 1) [44][45][46][47]. Three quantitative trait loci (QTL), qCBD 1-1 on chromosome 1, qCBD 2-1, and qCBD 2-2 on chromosome 2 were identified as responsible for CBD resistance in the C. arabica cultivar Rume Sudan [48].…”

Section: Breeding For Disease Resistancementioning

confidence: 99%

“…QTL for resistance are displayed as bars and the names given by the authors are maintained [44]. Molecular markers are depicted as associated disease and original names given by the authors [41,43,[45][46][47][48][49]. MCBD, MCLR, and MRKN denote molecular markers (M) associated with resistance to coffee berry disease, coffee leaf rust, and root-knot nematodes.…”

Section: Breeding For Disease Resistancementioning

confidence: 99%

“…For many of the other QTLs, it is not clear from the studies whether the resistances inherited dominantly or recessively. With markers that are closely linked to (recessive) resistance genes/QTLs [45][46][47], their physical locations can be defined on chromosomes in order to check whether there is overlap with known S gene candidates. A coffee orthologue of the known Arabidopsis S gene KMD3 (F-box/Kelch-repeat protein) was found to co-localize with a known molecular marker, SSRCafe-39, which was associated with high level of reproduction factor or high susceptibility to root-knot nematodes in a segregating population derived from a cross between resistant C. canephora var.…”

Section: Your Guidelines-how To Find Putative Candidate S Genes In Comentioning

confidence: 99%

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Improving Pathogen Resistance by Exploiting Plant Susceptibility Genes in Coffee (Coffea spp.)

et al. 2020

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Coffee (Coffea spp.) is an economically important crop widely cultivated in (sub) tropical countries worldwide. Commercial coffee production relies mainly on two related species, namely C. arabica and C. canephora. Due to their perennial growth habit, cultivation practices, and narrow genetic diversity, coffees are constantly exposed to many diseases and pests. Coffee leaf rust (Hemileia vastatrix Berk. et Br.), coffee berry disease (Colletotrichum kahawae Bridge and Waller), and coffee wilt disease (Gibberella xylarioides Heim and Saccas/Fusarium xylarioides) are the top fungal diseases affecting C. arabica and C. canephora production areas worldwide. In many regions, chemical-based control measures are widely used and are the only way to control the diseases. Developing resistant cultivars is one of the prerequisites for increasing sustainable market demand and agriculture. However, desired and required resistance traits are not always available in the gene pool. Furthermore, from other crops it is clear that dominant resistance genes introduced into varieties are not durable because of pathogen variability and the emergence of new races of the different pathogens. Utilization of altered susceptibility genes (S genes) offers a novel and alternative strategy for the breeding of durable and broad-spectrum resistance. The S gene encodes a host factor that facilitates a compatible interaction with the pathogen, and impairment of S genes leads to loss-of-susceptibility. In this review, guidelines for effective identification, characterization, and utilization of dysfunctional S genes are proposed to aid breeding activities in order to introduce durable resistance in Coffea spp. Several candidate S genes likely contributing to the susceptibility of Colletotrichum spp., Fusarium spp., and Meloidogyne spp. are discussed. With the rapid development of genetic engineering techniques, including CRISPR-associated systems, we now have the potential to accelerate the application of S genes to achieve durable resistance in coffee.

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Section: Breeding For Disease Resistancementioning

confidence: 99%

Section: Breeding For Disease Resistancementioning

confidence: 99%

Section: Your Guidelines-how To Find Putative Candidate S Genes In Comentioning

confidence: 99%

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Improving Pathogen Resistance by Exploiting Plant Susceptibility Genes in Coffee (Coffea spp.)

et al. 2020

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“…This introgression is facilitated by the use of Hibrido de Timor (HdT), a natural hybrid between the species C. arabica and C. canephora (Lashermes et al 1999). HdT's germplasm carries genes that confer durable resistance to Hemileia vastatrix (Diola et al 2011;Romero et al 2014;Alkimim et al 2017), Colletotrichum kahawae (Gichimu et al 2013;Gichimu et al 2014;Alkimim et al 2017), and Meloidogyne exigua (Bertrand et al 2001;Pereira et al 2016). All cultivars released by this breeding program are derived from HdT and have demonstrated superior cup quality when compared with traditional arabica coffee cultivars (Pereira et al 2010b;Sobreira et al 2015).…”

Section: Communicated By P Ingvarssonmentioning

confidence: 99%

Population structure and genetic diversity of coffee progenies derived from Catuaí and Híbrido de Timor revealed by genome-wide SNP marker

Sousa

Caixeta

Alkimim

et al. 2017

Tree Genetics & Genomes

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The use of single nucleotide polymorphism (SNP) molecular markers has provided advances in selection methodologies used in breeding programs of different crops, reducing cost and time of cultivar release. Despite the great economic and social importance of Coffea arabica, studies with SNP markers are scarce and a small number of SNP are available for this species, when compared with other crops of agronomic importance. Thus, the objective of this study was to identify and validate SNP molecular markers for the species Coffea arabica and to introduce these markers to genetic breeding by means of an accurate analysis of the diversity and genetic structure of breeding populations of this species. After quality filtering, 11,187 SNP markers were selected from the coffee population obtained from crosses between the genotypes Catuaí and Híbrido de Timor. A great number of markers were distributed in the 11 chromosomes, within transcribed regions, and were used to estimate the genetic dissimilarity among the individuals of the breeding population. Dendrogram analysis and a Bayesian approach demonstrated the formation of two groups and the discrimination of all genotypes evaluated. The expressive number of SNP molecular markers distributed throughout C. arabica genome was efficient to discriminate all the accessions evaluated in the experiment, clustering them according to their genealogies. This work identified mixtures within the progenies. The genotyping data also provided detailed information about the parental genotypes and led to the identification of new candidate parents to be introduced to the breeding program. The study discussed population structure and its consequence in obtaining improved varieties of C. arabica.

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“…Penanda simple sequence repeats (SSRs), yang juga disebut microsatellites, short tandem repeats (STRs) atau sequence-tagged microsatellite sites (STMS), merupakan penanda molekuler berbasis polymerase chain reaction (PCR) (Jiang, 2010). Metode SSRs telah digunakan secara luas dalam karakterisasi genetik kopi (Gimase et al, 2011) hingga seleksi sifat ketahanan terhadap nematoda (Pereira et al, 2016) dan penyakit buah kopi (coffee berry disease = CBD) (Kiguongo, Omondi, Gichuru, & Kasili, 2014). Penelitian bertujuan menganalisis variasi genetik dalam populasi kultivar kopi Arabika berbuah kuning berdasarkan penanda SSRs.…”

Section: Pendahuluanunclassified

Variasi Genetik dalam Populasi Kultivar Kopi Arabika Berbuah Kuning di Lahan Petani Berdasarkan Penanda SSRs

Dani¹,

Izzah²,

Randriani³

2016

J. Tanaman Industri dan Penyegar

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Identification of the genetic diversity within populations of yellow-berried Arabica coffee cultivar based on morphological characters faced an obstacle in finding identical environmental conditions at farmers field. Therefore, an approach which is not influenced by differences in environmental conditions is required, for instance based on DNA polymorphism. The research aimed to analyze genetic variation within populations of yellow-berried Arabica coffee cultivar based on SSRs markers. The research was conducted in the Integrated Laboratory, Indonesian Industrial and Beverage Crops Research Institute, Sukabumi, from April until June 2015. The leaf samples for DNA extraction were obtained from yellow-berried Arabica coffee cultivar (AGK-1) and two red-berried cultivars as controls, namely ABP-1 (dwarf type) and Typica (tall type). AGK-1 and ABP-1 cultivars consisted of 17 and 5 individual numbers, respectively, whereas Typica cultivar comprised three individuals. PCR amplification was carried out using 12 SSR primers. Four primers (M24, SSRCa052, M32, and M42) produced polymorphic band. The binary data obtained in this research was subsequently processed using NTSYS-PC program version 2.1. The genotypes were grouped based on a genetic similarity matrix using the unweighted pair group method arithmetic mean (UPGMA). The result showed the existence of genetic variation among individual of AGK-1 cultivars, which forming three clusters at the genetic similarity value of 67%. One cluster exhibited close genetic relationships between some individuals within the population of AGK-1 cultivar and Typica cultivar. Meanwhile, the other two clusters showed high genetic similarity between AGK-1 cultivar and ABP-1 cultivar. The result demonstrated the possibility of gene flow between genotypes or residual heterozygosity within the population of AGK-1 cultivar at farmers field, which required a further study.

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Identification of microsatellite markers in coffee associated with resistance to Meloidogyne exigua

Cited by 8 publications

References 23 publications

Improving Pathogen Resistance by Exploiting Plant Susceptibility Genes in Coffee (Coffea spp.)

Improving Pathogen Resistance by Exploiting Plant Susceptibility Genes in Coffee (Coffea spp.)

Population structure and genetic diversity of coffee progenies derived from Catuaí and Híbrido de Timor revealed by genome-wide SNP marker

Variasi Genetik dalam Populasi Kultivar Kopi Arabika Berbuah Kuning di Lahan Petani Berdasarkan Penanda SSRs

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