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

Abstract

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.

Early Selection Enabled by the Implementation of Genomic Selection in Coffea arabica Breeding

“…The DNA concentration of the samples was standardized and sent to RAPiD GENOMICS, Florida/USA, for probes construction, sequencing, and identification of SNP molecular markers (Sousa et al, 2017).…”

“…From 40,000 probes, 10,000 polymorphic probes were selected, and 21,211 SNP molecular markers were identified. Details on probes construction and SNPs identification can be obtained from Sousa et al (2017). The SNP set was subject to quality analysis implemented in the Rbio software (Bhering, 2017).…”

“…Therefore, the use of the mixed models methodology, Residual or Restricted Maximum Likelihood/Best Linear Unbiased Prediction (REML/BLUP) (Patterson and Thompson, 1971; Henderson, 1975) has allowed, from phenotypic information, the accurate, and unbiased prediction of genetic values of individuals (Resende and Thompson, 2004; Viana et al, 2011; Barbosa et al, 2012; Ferreira et al, 2012; Pereira et al, 2013; Corrêa et al, 2015; Spinelli et al, 2015). For coffee, genetic gains have also been reported using molecular markers in studies on genetic diversity (Sousa et al, 2017), genetic maps (Pestana et al, 2015; Moncada et al, 2016), and assisted selection (Alkimim et al, 2017; Favoretto et al, 2017). However, due to the complexity and number of genes that control most of the agronomic traits of this species, GS studies are promising for they allow estimating the effects of all loci that explain the genetic variation (Heffner et al, 2009) and the genomic estimated breeding value (GEBV) (Meuwissen et al, 2001).…”

Genetic Diversity ofCoffea arabica

“…Thus, genotype discrimination based on differences in phenotypic characteristics may be difficult because individuals who are genetically distinct may be phenotypically similar, which reduces the selective efficiency. To overcome this difficulty, molecular markers have been used as an important tool in the accurate discrimination of genotypes [71,72].…”

“…Different molecular markers, such as simple sequence repeats (SSRs), sequencecharacterized amplified regions (SCARs), and single-nucleotide polymorphisms (SNPs), have been identified and made available for coffee [71,72,[74][75][76][77][78][79][80][81][82]. These species-specific markers combined with random markers, such as inter-simple sequence repeats (ISSRs), random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphisms (AFLPs); support the genetic breeding of this crop.…”