Genome organization in coffee as revealed by EST PCRRFLP, SNPs and SSR analysis

Abstract

An EST-based PCR-RFLP method was employed to gain insight into genome organization in eight allopolyploid Coffea arabica cultivars and seven diploid coffee species. The PCR-amplified products at 19 EST loci were digested with 46 different restriction enzymes and size fractioned in agarose gels. Most often, the sum of the fragments length was double or more than the PCR product. In arabica, this condition could be explained by assuming the presence of duplicated loci in paralogous chromosomes and this was supported by considerable evidence of multiple loci SSR amplification. Based on the RFLP analysis, 12 EST loci were polymorphic. The level of polymorphism was higher in different species compared to the arabica varieties. Sequencing of the amplified products revealed a SNP frequency of 0.021 among diploid species and of 0.007 among arabica varieties. We propose that the involvement of two genomes in C. arabica maintains a residual level of heterozygosity in the form of paralogous chromosomes, while the self-fertilization in this species tends to drive of homozygosity. The heterozygosity of paralogous chromosomes in arabica creates valuable polymorphism essential for species diversity and survival in various ecological niches, while self-fertility tends to preserve in homozygosity many genes of functional significance.

Molecular characterization of arabica and Conilon coffee plants genotypes by SSR and ISSR markers

“…Molecular markers allow direct access to the genome sequences and, thus, isolate the genetic variation of the environmental interferences (Ferrão et al 2007). The potential use of the Simple Sequence Repeats (SSR) and Inter-Simple Sequence Repeats (ISSR), microsatellite primers, has been demonstrated for Coffea related with genetic diversity of native species and germplasm bank accessions, geographical origin detection, domestication degree, coffee plant dispersion history, species identification and genealogy (Masumbuko and Bryngelsson 2006;LopezGartner et al 2009;Tshilenge et al 2009;Missio et al 2010;Setotaw et al 2010;Mishra et al 2011). The good prospects presented by the application of ISSR and SSR markers to assess the diversity in Coffea have led to this study.…”

Genetic Diversity Among Indian Coffee Cultivars Determined via Molecular Markers

“…Different types of molecular markers, such as restriction fragment length polymorphism (RFLP), random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), inter-simple sequence repeat (ISSR), simple sequence repeats (SSR), and expressed sequence tag derived simple sequence repeats (EST-SSR) have been used in coffee genetic diversity studies (Combes et al 2000;Steger et al 2002;Diniz et al 2005;Maluf et al 2005;Missio et al 2010;Mishra et al 2011). Tornincasa et al (2006 made a comparative analysis between the commercial coffee cultivars of American, Indian, and African origin and expressed that Indian cultivars were genetically diverse from the American and African cultivars.…”

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

“…A tetraploid species like arabica has different "copies" which tend to be less similar while the algorithms and software developed for assembly were mainly developed for haploid or diploid genomes may lead to the risk of information loss when using it for genome assembly in polyploid crops (Margarido and Heckerman, 2015). Since arabica is an allotetraploid crop, it is expected to show heterozygosity conditioned by two different alleles derived from two different progenitors (Mishra et al, 2011). Paralogous regions and heterozygous sites create "bubbles" during genome assembly where two or more regions that are highly similar assemble together, and the adjacent dissimilar regions assemble separately but eventually merge again (Michael and VanBuren, 2015) make it hard for assembly.…”

“…However, due to its allotetraploid origin, C. arabica contains a considerable amount of fixed heterozygosity and shows high levels of heterozygosity at individual loci (Lashermes et al, 1999). Similarly, Mishra et al (2011) suggested that since arabica is an allotetraploid crop, it is expected to show heterozygosity conditioned by two different alleles derived from two different progenitors. Heterozygosity within the two ancestral genomes appears to have been lost, since only one allele from each genome remains in arabica, indicating a possible lack of recombination between the ancestral genomes, while recombination within each genome occurs normally (Cubry et al, 2008).…”