Fine Mapping for Identification of Citrus Alternaria Brown Spot Candidate Resistance Genes and Development of New SNP Markers for Marker-Assisted Selection

Abstract

Alternaria brown spot (ABS) is a serious disease affecting susceptible citrus genotypes, which is a strong concern regarding citrus breeding programs. Resistance is conferred by a recessive locus (ABSr) previously located by our group within a 3.3 Mb genome region near the centromere in chromosome III. This work addresses fine-linkage mapping of this region for identifying candidate resistance genes and develops new molecular markers for ABS-resistance effective marker-assisted selection (MAS). Markers closely linked to ABSr locus were used for fine mapping using a 268-segregating diploid progeny derived from a heterozygous susceptible × resistant cross. Fine mapping limited the genomic region containing the ABSr resistance gene to 366 kb, flanked by markers at 0.4 and 0.7 cM. This region contains nine genes related to pathogen resistance. Among them, eight are resistance (R) gene homologs, with two of them harboring a serine/threonine protein kinase domain. These two genes along with a gene encoding a S-adenosyl-L-methionine-dependent-methyltransferase protein, should be considered as strong candidates for ABS-resistance. Moreover, the closest SNP was genotyped in 40 citrus varieties, revealing very high association with the resistant/susceptible phenotype. This new marker is currently used in our citrus breeding program for ABS-resistant parent and cultivar selection, at diploid, triploid and tetraploid level.

Resistance to Alternaria Brown Spot of New Citrus Hybrids

“…Throughout the population, 165 (70%) asymptomatic individuals were observed, and 70 (30%) other individuals showed different levels of symptoms (Figure 2). Studies on inheritance of ABS resistance in citrus were based on crosses between mandarins varieties (CUENCA et al, 2013) and between mandarin and sweet orange (CUENCA et al, 2016). These studies stated that the inheritance of ABS resistance in citrus is controlled by a single recessive allele (DALKILIC et al, 2005;GULSEN et al, 2010;CUENCA et al, 2013).…”

“…These studies stated that the inheritance of ABS resistance in citrus is controlled by a single recessive allele (DALKILIC et al, 2005;GULSEN et al, 2010;CUENCA et al, 2013). Thus, the "A" allele would be dominant for susceptibility, and "a" would be recessive for disease resistance (CUENCA et al, 2013(CUENCA et al, , 2016. Therefore, segregation is expected in progeny arising from crosses between resistant and heterozygous ABS-susceptible parents or even between two heterozygous ABS susceptible ones.…”

“…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.…”