Genetically Based Location from Triploid Populations and Gene Ontology of a 3.3-Mb Genome Region Linked to Alternaria Brown Spot Resistance in Citrus Reveal Clusters of Resistance Genes

Abstract

Genetic analysis of phenotypical traits and marker-trait association in polyploid species is generally considered as a challenge. In the present work, different approaches were combined taking advantage of the particular genetic structures of 2n gametes resulting from second division restitution (SDR) to map a genome region linked to Alternaria brown spot (ABS) resistance in triploid citrus progeny. ABS in citrus is a serious disease caused by the tangerine pathotype of the fungus Alternaria alternata. This pathogen produces ACT-toxin, which induces necrotic lesions on fruit and young leaves, defoliation and fruit drop in susceptible genotypes. It is a strong concern for triploid breeding programs aiming to produce seedless mandarin cultivars. The monolocus dominant inheritance of susceptibility, proposed on the basis of diploid population studies, was corroborated in triploid progeny. Bulk segregant analysis coupled with genome scan using a large set of genetically mapped SNP markers and targeted genetic mapping by half tetrad analysis, using SSR and SNP markers, allowed locating a 3.3 Mb genomic region linked to ABS resistance near the centromere of chromosome III. Clusters of resistance genes were identified by gene ontology analysis of this genomic region. Some of these genes are good candidates to control the dominant susceptibility to the ACT-toxin. SSR and SNP markers were developed for efficient early marker-assisted selection of ABS resistant hybrids.

Resistance to Alternaria Brown Spot of New Citrus Hybrids

“…Studies conducted using populations of triploid hybrids (CUENCA et al, 2013) and diploid hybrids (CUENCA et al, 2016) confirmed these results, and the authors suggested that Murcott tangor and Orlando tangelo are both susceptible and heterozygous and that willow leaf mandarins (C. deliciosa Tenore) and clementines (C. clementina) are resistant and homozygous recessive.…”

“…ABS was first identified in Australia in Emperor mandarin (C. reticulata Blanco) around 1903, and the disease soon spread to other places in the world; it is now present in several countries, such as Turkey, Spain, Italy, South Africa, the USA, China, Brazil and Argentina (STUART et al, 2009;CUENCA et al, 2013CUENCA et al, , 2016HUANG et al, 2015). In Brazil, the disease was recorded in Rio de Janeiro in 2001 (GOES et al, 2001) in Dancy mandarin, and it later spread to other states, such as Minas Gerais, Rio Grande do Sul and São Paulo (SPOSITO et al, 2003;STUART et al, 2009).…”

“…Susceptibility is likely simple and controlled by dominant inheritance (DALKILIC et al, 2005;GULSEN et al, 2010;CUENCA et al 2013CUENCA et al , 2016. Thus, the "A" allele would be dominant for susceptibility, and "a" would be recessive for disease resistance.…”

Genetic Structure of Diploid Gametes for the Production of Triploid Citrus Hybrids

“…SNP markers have been used for genetic diversity studies (Chen and Gmitter, 2013;Cuenca et al, 2013a;Garcia-Lor et al, 2013a andb, Curck et al, 2016), marker assisted selection (MAS) for resistance against Alternaria alternata (Cuenca et al, 2013b, discrimination of zygotic and nucellar plants in seedlings and mapping .…”

“…For instance, Cuenca et al (2013b; showed that, the Alternaria brown-spot fungal disease was controlled as a recessive trait by a single locus located at 10.5 cM from the centromere of chromosome III. Therefore in crosses between a heterozygous parent producing diploid gametes and a resistant genotype, PMD is the most favorable mechanisms (50% of resistant hybrids) followed by SDR mechanisms (40%).…”