Association between DNA Markers and Loci Controlling Avocado Traits

Abstract

<jats:p>The detection of association between DNA markers and traits of interest in an outbred population is complicated and requires highly polymorphic markers. A genetic linkage map of avocado (<jats:italic>Persea americana</jats:italic> Mill.) recently generated consists of simple sequence repeat (SSR) markers as well as DNA fingerprint (DFP) and randomly amplified polymorphic DNA (RAPD) markers. These markers were used to detect putative quantitative trait loci (QTLs) of eight avocado fruit traits. Two statistical methods were used: one-way analysis of variance and interval mapping. Six traits were found to be associated with at least one of the 90 DNA markers. Based on the two statistical approaches, a putative QTL associated with the presence of fibers in the flesh, was found to be located on linkage group 3. This putative QTL was found to be associated with the SSR marker AVA04 having a high significant value (<jats:italic>P</jats:italic> = 4.4 × 10<jats:sup>-8</jats:sup>). The haplotype analysis of linkage group 3 showed a putative dominant interaction between the alleles of this locus.</jats:p>

From forest to field: Perennial fruit crop domestication

“…Neither the development nor the maintenance of a mapping population are trivial undertakings for a long-lived organism, but QTL studies have been conducted in many fruit tree genera, including Castanea ( Casasoli et al, 2004 ), Citrus ( Garc í a et al, 2000 ), Coffea ( Amidou et al, 2007 ), Cocos ( Baudouin et al, 2006 ), Malus ( Kenis et al, 2008 ), Prunus ( Quilot et al, 2004 ;Zhang et al, 2010 ), Persea ( Sharon et al, 1998 ), Theobroma ( Crouzillat et al, 1996 ;Crouzillat et al, 2000 ), and Vitis ( Cabezas et al, 2006 ). Because the goal of most of these studies has been crop improvement, crosses have mainly been within the domesticated species (e.g., apple cultivars Telamon × Braeburn; Kenis et al, 2008 ), but also include some wide crosses between two domesticated species (e.g., almond × peach; Illa et al, 2010 ) or between a domesticated species and a wild species that is not a progenitor of the crop [e.g., Citrus limon (L.) Osbeck × Poncirus trifoliata (L.) Raf.…”

“…Because the goal of most of these studies has been crop improvement, crosses have mainly been within the domesticated species (e.g., apple cultivars Telamon × Braeburn; Kenis et al, 2008 ), but also include some wide crosses between two domesticated species (e.g., almond × peach; Illa et al, 2010 ) or between a domesticated species and a wild species that is not a progenitor of the crop [e.g., Citrus limon (L.) Osbeck × Poncirus trifoliata (L.) Raf. One clear pattern is the instability of the majority of QTLs across years, which requires measurement of the traits of interest across multiple seasons (e.g., Sharon et al, 1998 ;Garc í a et al, 2000 ;Casasoli et al, 2004 ;Quilot et al, 2004 ;Cabezas et al, 2006 ;Kenis et al, 2008 ;Zhang et al, 2010 ). These crosses do not lend themselves easily to answering questions about domestication genetics, but some conclusions can be drawn from them.…”

“…These crosses do not lend themselves easily to answering questions about domestication genetics, but some conclusions can be drawn from them. One clear pattern is the instability of the majority of QTLs across years, which requires measurement of the traits of interest across multiple seasons (e.g., Sharon et al, 1998 ;Garc í a et al, 2000 ;Casasoli et al, 2004 ;Quilot et al, 2004 ;Cabezas et al, 2006 ;Kenis et al, 2008 ;Zhang et al, 2010 ). One extreme example of this pattern is from a 15-yr mapping project in cacao, where only two of 10 QTLs contributing to yield were detected in more than 3 years ( Crouzillat et al, 2000 ).…”

Creation of an avocado unambiguous genotype SNP database for germplasm curation and as an aid to breeders

“…Previous studies have developed molecular markers for avocado including SNPs from targeted resequencing (Chen et al 2008), and microsatellite markers (Alcaraz and Hormaza 2007;Ashworth et al 2004;Borrone et al 2007;Ge et al 2019;Gross-German and Viruel, 2013;Lavi et al 1994;Mhameed et al 1997;Sharon et al 1997). These markers have been combined with phenotypic data including heritability of nutritional components (Calderon-Vazquez et al 2013) and have been used to identify marker trait associations in avocado (Mhameed et al 1995;Sharon et al 1998). A recent study identified > 250,000 polymorphic SNPs from 22 avocado individuals (Ge et al 2019).…”

Outcrossing Rate and Genetic Variability in Mexican Race Avocado

“…Molecular markers in avocado have been used to assess genetic diversity among and within racial groups (Boza et al, 2018;Cuiris-P erez et al, 2009;Gross-German and Viruel, 2013), in phylogenetic studies (Ashworth and Clegg, 2003;Reyes-Alem an et al, 2013), and in construct linkage maps ; to identify quantitative trait loci (Sharon et al, 1998), and in outcrossing studies (Alcaraz and Hormaza, 2011;Borrone et al, 2008;Chen et al, 2007;Garner et al, 2008;Kobayashi et al, 2000;Schnell et al, 2009;Violi et al, 2009). Outcrossing rate studies based on molecular markers have been done in different plant species such as Brassica carinata A. Braun (Teklewold et al, 2013), Foeniculum vulgare Mill.…”