The I locus of the common bean, Phaseolus vulgaris, controls the development of four different phenotypes in response to inoculation with Bean common mosaic virus, Bean common mosaic necrosis virus, several other related potyviruses, and one comovirus. We have generated a high-resolution linkage map around this locus and have aligned it with a physical map constructed with BAC clones. These clones were obtained from a library of the cultivar ''Sprite,'' which carries the dominant allele at the I locus. We have identified a large cluster of TIR-NBS-LRR sequences associated within this locus, which extends over a distance .425 kb. Bean cultivars from the Andean or Mesoamerican gene pool that contain the dominant allele share the same haplotypes as revealed by gel blot hybridizations with a TIR probe. In contrast, beans with a recessive allele display simpler and variable haplotypes. A survey of wild accessions from Argentina to Mexico showed that this multigene family has expanded significantly during evolution and domestication. RNA gel blot analysis indicated that the TIR family of genes plays a role in the response to inoculations with BCMV or BCMNV.
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.
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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