Construction of high-density genetic maps and detection of QTLs associated with Huanglongbing infection in citrus

Abstract

No true resistance to Huanglongbing (HLB), a citrus disease associated with infection of Candidatus Liberibacter asiaticus (CLas), is found within commercial citrus cultivars, though trifoliate orange (Poncirus trifoliata) has been described as resistant or tolerant. Through genotyping an intergeneric F1 population by Genotyping-by-Sequencing, high-density SNP-based genetic maps were constructed separately for trifoliate orange and sweet orange (Citrus sinensis). Both genetic maps exhibited high synteny and high coverage of citrus genome. After exposure to intense HLB pressure for two years, Ct value of qPCR for CLas detection in leaves throughout ten time points during the next three years was above 35 in trifoliate oranges, under 28 in sweet oranges, and ranged from 24 to 38 and exhibited obvious segregation among progenies. Phenotypic data of percentage of healthy trees showed high correlation with the Ct value. By mapping the two traits at all time points, a total of nine clusters of QTLs were detected, of which five, respectively located on LG-t7 and LG-t8 of trifoliate orange map and LG-s3, LG-s5 and LG-s9 of sweet orange map, collectively explained a major part of the phenotypic variation. This study provides a starting point for citrus breeding to support long-term control of this devastating disease.Highlight1). Constructed the first high-density genetic map for trifoliate orange (Poncirus trifoliata)2). The first report on identification of QTLs related to Huanglongbing in citrus.AbbreviationsACPAsian citrus psyllidCLasCandidatus Liberibacter asiaticuscMcentiMorgansCtCycle thresholdHLBHuanglongbingIMInterval mappingKWKruskal-WallisLGLinkage groupLODLogarithm of oddsQTLQuantitative trait locusRADRestriction site associated DNArMQMrestricted multiple QTL mappingSNPSingle nucleotide polymorphism.

A High-Density Linkage Map of the Forage Grass Eragrostis curvula and Localization of the Diplospory Locus

“…In addition, many other genotypes used as pollen donors were incompatible with the maternal plant. Despite these limitations, this is a high density map which is consistent with data collected by other authors using similar models and techniques (Worthington et al, 2016, Huang et al, 2018).…”

“…In addition, recombination rates are known to differ between sexes in both plants and animals (Lorch, 2005). For example, Huang et al (2018) found that the male genetic map of Clementine mandarin was notably larger than its female counterpart. Another possible reason for the difference in the sizes of the linkage maps is that OTA-S was obtained by bulk seed harvest produced in isolation from four tetraploid (2 n = 40) clones derived from PI 299929 and from a cross between PI 299928 and PI 299929 (Voigt, 1976).…”

Preferential Homologous Chromosome Pairing in a Tetraploid Intergeneric Somatic Hybrid (Citrus reticulata + Poncirus trifoliata) Revealed by Molecular Marker Inheritance

“… Bernet et al (2010) reported high collinearity between Fortune “mandarin” and Poncirus trifoliata . More recently, the availability of reference whole genome sequence allowed to compare genetic and physical maps and globally confirmed the good conservation of marker order between P. trifoliata and “Sunki” mandarin ( Curtolo et al, 2018 ) and P. trifoliata and sweet orange ( Huang et al, 2018 ).…”