The most important disease of Coffea arabica is coffee leaf rust caused by the fungus Hemileia vastatrix. The purpose of this study was to characterize the inheritance of coffee resistance gene(s) to race II of this pathogen and to identify and map molecular markers linked to this trait. Different populations were used: F 2 (160 plants), BCr (20), and BCs (135), derived from a cross between the resistant genotype Híbrido de Timor UFV 427-15 and the susceptible cultivar Catuaí Amarelo UFV 2143-236 (IAC 30). The segregation analysis showed that the resistance of Híbrido de Timor to race II of the H. vastatrix is conferred by a single dominant gene. The amplification of 176 AFLP (Amplified fragment length polymorphism) primer combinations using bulked segregant analysis (BSA) allowed the identification of three molecular markers linked to the resistance gene. Genetic mapping of these three markers in the F 2 population indicated that they are distributed on both sides, flanking the resistance gene. The markers E.CTC/M.TTT405 and E.CGT/M.TGT 300 were found linked to the resistance gene at 8.69 cM (LOD 18.91) and 25.10 cM (LOD 5.37), respectively, while E.CCT/M.TTC230 was localized on the other side of the gene, at 20.50 cM (LOD 6.15). These markers are the first rust resistance markers identified in Híbrido de Timor and can be useful for marker assisted selection in coffee breeding programs.

Coffee leaf rust (CLR) caused by Hemileia vastatrix Berk. et Br. is one of the major Coffea arabica diseases worldwide. CLR resistance has been attributed to at least nine dominant genes, as single or in combination. We present an inheritance study and mapping loci involved in the Híbrido de Timor (HDT) UFV 443-03 resistance to race I, race II, and pathotype 001 of H. vastatrix. Molecular markers were used to ascertain the phenotypic results and to map the putative resistance loci. For all tree isolates, the inheritance study indicated that the resistance of HDT UFV 443-03 is conditioned by two independent dominant loci or by three independent loci (two dominant and one recessive). Molecular marker analyses ascertained that the resistance of HDT UFV 443-03 to race II is conditioned by at least two independent dominant loci, while the resistance to race I and pathotype 001 is conditioned by at least four independent dominant loci. Gene pyramiding might result in a cultivar with durable resistance; however, it is difficult to distinguish between plants with one or more resistance genes due to epistatic effects. Molecular markers linked to these genes were indicated for marker-assisted selection, as it is an efficient breeding alternative for CLR resistance with no such epistatic effects.

Angular leaf spot is one of the major diseases of the common bean. The extensive genetic variability of this pathogen requires the constant development of new resistant cultivars. Different sources of resistance have been identified and characterized. For the State of Minas Gerais, Brazil, four main resistance sources were found: Mexico 54, AND 277, MAR 2 and Cornell 49-242. Independent characterization of these genotypes demonstrates that resistance in all four sources is dominant and monogenic. However, there are no studies on the relationship and independence of these genes. In the present work, allelism tests were carried out to understand the relationship among the resistance genes present in these four resistance sources. The data revealed a much higher complexity in the resistance inheritance of these genes than previously reported. It was demonstrated that Cornell 49-242 possesses a dominant gene (Phg-3); Mexico 54 possesses three genes, denominated Phg-2, Phg-5 and Phg-6. In MAR 2, two genes were found, one independent designated Phg-4 and the other, an allelic form of Phg-5, denominated of Phg-5 2 . Allelic forms were also found in AND 277, Phg-2 2 , Phg-3 2 and Phg-4 2 . These results have special importance for breeding programs aiming to pyramid resistance genes.

Coffee leaf rust is the most limiting disease for coffee cultivation in Brazil. Despite its importance, relatively little is known about the genetic diversity of Hemileia vastatrix, the rust causal agent. In this work, the DNA from 112 monopustule isolates from different geographic locations and coffee genotypes were analysed by amplified fragment length polymorphisms (AFLP). The objectives were to assess the influence of the host and geographic origin on the diversity and population differentiation in H. vastatrix. The fungal population showed a low level of genotypic diversity. Gene diversity (h) was 0·027 and the hypothesis of random mating in the total population was rejected, but evidence for recombination was found for two subpopulations (São Paulo and Paraná). The analysis of molecular variance revealed that 90% of the genetic distribution of the pathogen occurs among isolates within the subpopulation (states or host of origin). There was no correlation between geographic and genetic distance (r = −0·024, P = 0·74), which together with the high number of migrants and the low degree of differentiation in populations of H. vastatrix, is consistent with the fact that the inoculum is probably easily dispersed by wind over long distances, allowing dispersal of the pathogen among coffee growing areas in Brazil. Therefore, it is difficult to predict the durability of resistant sources to coffee rust. The recommendation for the breeding programmes is thus to incorporate multigenic resistance as a control strategy.

Acrocomia aculeata (Arecaceae), a palm endemic to South and Central America, is a potential oil crop. Knowledge of the mating system of this species is limited to its reproductive biology and to studies using molecular markers. The present study analyzed genetic diversity between its developmental stages and determined its prevailing mating system in order to support genetic conservation and breeding programs. We tested 9 microsatellite markers in 27 mother trees (adult plants) and 157 offspring (juvenile plants) from the southeastern region of Brazil. Heterozygosity levels differed between the 2 studied life stages, as indicated by the fixation index of adult and juvenile trees, suggesting that selection against homozygotes occurs during the plant life cycle. The mating system parameters analyzed indicate that A. aculeata is predominantly outcrossing (allogamous). However, its low levels of selfing suggest that there is individual variation with regard to self-incompatibility, which can be a survival strategy in isolated or fragmented habitats. Deviations in variance effective size were detected because of high mating rates among relatives and correlated matings. These findings indicate that the main source of inbreeding results from biparental inbreeding in the population and that the progenies are predominantly composed of full-sibs. The information provided by this study on the ecology and reproduction dynamics of A. aculeata should be useful to both breeding and genetic conservation programs, allowing the development of more precise mathematical models and the estimation of the appropriate number of mother trees for seed collection.

The coefficient of parentage among 121 cultivars of Coffea arabica L. in Brazil released from 1939 to 2009 was estimated and used to study the genetic diversity and the breeding pattern of the breeding programs. A low genetic diversity was observed within the C. arabica cultivars of Brazil. The genetic base of 121 cultivars released in Brazil between 1939 and 2009 was defined by 13 ancestors. Seven ancestors contribute with 97.55% of the genetic base of C. arabica cultivars. Bourbon Vermelho contributed with 52.76% for the genetic pool of the C. arabica cultivars of Brazil followed by Sumatra (19.05%) and Híbrido de Timor (11.59%). Mundo Novo and Icatu Vermelho contributed with 87.65% for the genetic base of the C. arabica cultivars. It was calculated that 97.55% of the genetic base of the Brazilian C. arabica cultivars is derived from seven ancestors, indicating a narrow genetic base. Among the first progenies, Mundo Novo contributed with 69.39% of the genetic base of C. arabica cultivars in Brazil. The increase in the genetic diversity among C. arabica cultivars observed in recent decades is due to the introduction of parental lines with diverse genetic base. High genetic diversity was observed among cultivars released by Empresa de Pesquisa Agropecuária de Minas Gerais/Universidade Federal de Viçosa, Fundação Procafé, and Instituto Agronômico do Paraná. The 121 Brazilian cultivars were clustered into four groups based on coefficient of parentage. The distributions of genotypes over the cluster groups showed the effect of parental line contribution.

Genomic Selection (GS) has allowed the maximization of genetic gains per unit time in several annual and perennial plant species. However, no GS studies have addressed Coffea arabica, the most economically important species of the genus Coffea. Therefore, this study aimed (i) to evaluate the applicability and accuracy of GS in the prediction of the genomic estimated breeding value (GEBV); (ii) to estimate the genetic parameters; and (iii) to evaluate the time reduction of the selection cycle by GS in Arabica coffee breeding. A total of 195 Arabica coffee individuals, belonging to 13 families in generation of F2, susceptible backcross and resistant backcross, were phenotyped for 18 agronomic traits, and genotyped with 21,211 SNP molecular markers. Phenotypic data, measured in 2014, 2015, and 2016, were analyzed by mixed models. GS analyses were performed by the G-BLUP method, using the RKHS (Reproducing Kernel Hilbert Spaces) procedure, with a Bayesian algorithm. Heritabilities and selective accuracies were estimated, revealing moderate to high magnitude for most of the traits evaluated. Results of GS analyses showed the possibility of reducing the cycle time by 50%, maximizing selection gains per unit time. The effect of marker density on GS analyses was evaluated. Genomic selection proved to be promising for C. arabica breeding. The agronomic traits presented high complexity for they are controlled by several QTL and showed low genomic heritabilities, evidencing the need to incorporate genomic selection methodologies to the breeding programs of this species.

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