Quantitative trait locus mapping in Rosaceae

As the development of genetic maps and genomic resources has progressed, so has the ability to examine the expression of complex traits and associate these traits with specific genomic regions. Traits of interest for Rosaceae breeders include disease resistance, fruit quality (e.g. firmness, size, flavor, content of volatiles, polyphenolics), developmental characteristics (e.g. branching, flowering time, fruiting time) and responses to stress-producing environmental conditions (e.g. drought, cold, heat, salt). I will present specific examples to illustrate how QTL mapping is being utilized in the Rosaceae.

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1.6.1 Apple

Of the economically important Rosaceae crop species, QTL studies have been conducted most often in apple. A number of segregating populations have been employed to detect a variety of different trait/locus associations. Resistance to the causative bacterial pathogen (Erwinia amylovora) for fire blight has received much attention from researchers. Major loci associated with resistance to this disease, which also affects pear, have been mapped to the top of LG3 in three different apple populations derived from ‘Robusta 5’ of 133, 132, and 83 F1 progeny (Gardiner et al. 2012), to the bottom of LG7 in ‘Fiesta’ (Khan et al. 2007), and to the bottom of LG12 in two interspecific apple populations (Durel et al. 2009). Several of these markers are currently being used for marker-assisted selection by apple breeders.

The production and accumulation of polyphenolics in apple fruit has been mapped to several loci, with loci on LG16 involved in the production of epicatechins, catechins, and procyanidins in a population of 170 ‘Royal Gala’ × ‘Braeburn’ F1 progeny (Chagné et al. 2012) and a population of 251 ‘Prima’ × ‘Fiesta’ F1 progeny and 171 ‘Milwa’ × ‘1217’ F1 progeny (Khan et al. 2012). These two studies independently identified leucoanthocyanidin reductase (LAR1) as a candidate gene for the control of these traits. Additional QTL for other polyphenolics were identified on other LG, with a point of difference relating to the production of quercetins. Khan et al. (2012) identified loci on LG1, 8 and 13, whereas Chagné et al. (2012) identified a QTL on LG17.

Flower development is an important trait especially in crops where fruit mature simultaneously. Biennial bearing in apple, where number of flowers and subsequent fruit yield varies from year to year, was investigated over a five year span in a population of 122 ‘Starkrimson’ × ‘Granny Smith’ F1 progeny replicated twice (Guitton et al. 2012). Three large-effect QTL for biennial bearing were identified on LG4, 8 and 10. The candidate gene MdEFL3 (Early Flowering 3) mapped within the QTL interval

on LG8 and genome alignment with the ‘Golden Delicious’ draft whole genome

sequence (Velasco et al. 2010) identified five additional candidate genes involved in plant hormone synthesis or control. Two candidate genes involved in plant hormone synthesis or control were mapped within the QTL interval on LG10. No candidate genes were identified associated with the QTL on LG4.

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1.6.2 Strawberry

The most comprehensive QTL analysis in octoploid commercial strawberry to date combines the analyses of agronomic and fruit quality traits (Zorrilla-Fontanesi et al. 2011a). This study was conducted using a population of 95 F1 progeny of ‘232’ × ‘1392’, which segregated for a number of important traits, such as yield, fruit firmness, and quantities of acids, sugars, anthocyanins (ACY), and L-ascorbic acid. The researchers identified several candidate genes underlying or within the confidence intervals of some QTL. For example, a putative R2R3 MYB transcription factor was identified underlying a QTL for total anthoycanin production on LGII. This class of MYB transcription factor encodes a component of the MYB/bHLH/WD protein complex involved in the regulation of the expression of ACY biosynthetic pathway genes and the subsequent accumulation of ACY in plant tissues (Allan et al. 2008; Baudry et al. 2004). Another locus/candidate gene association was detected for fruit firmness and its co-location with a gene encoding a fruit-specific auxin-independent expansin.

1.6.3 Prunus

A population of 73 F1 progeny of interspecific Prunus persica ‘Summergrand’ × P. davidiana was used to map QTL for resistance of this peach cross to the green peach aphid [Myrus persicae (Sulzer)], as well as aphid feeding behavior (Sauge et al. 2012). QTL for resistance and feeding behavior occurred in close proximity in seven of nine instances, with the strongest effect QTL for both traits occurring within approximately 2 cM on LG3. The co-occurrence of these traits suggest a strong genetic basis for the relationship (Sauge et al. 2012).

Self-incompatibility (SI) in Prunus has been considered a qualitative trait controlled by the S-locus (Crane and Lawrence 1929) and which as been mapped to LG6 (Ballester et al. 1998). Those genotypes that are self-compatible possess an inactive form (Sfi).

However, a recent study in 77 F1 progeny of almond ‘Vivot’ × ‘Blanquerna’ has identified two additional loci, one on LG6 approximately 10 cM from the S-locus, and one on LG8, which may modulate the S-locus (Fernández i Martí et al. 2011).

A recent QTL study was conducted to determine how chilling and heat units influence bloom date in peach (Fan et al. 2010). The goal of this study was to try to understand the genetic control of dormancy break in temperate fruit tree species and attempt to

56 identify loci that can be used for marker assisted selection. The researchers used a population of 378 F2 peach progeny and conducted the study over two years. They identified 20 QTL on all Prunus LG except LG3. The strongest-effect QTL encompassing all three traits was mapped on LG1 in an interval that includes the Evergrowing locus. In most cases the three traits collocated. The authors suggest that the genes regulating the different traits are tightly linked, or alternatively, the presence of a single temperature sensing and response system.

Each of the examples presented above illustrate some of the different complex traits that can be examined using QTL analysis. Population sizes range from 73 F1 individuals to 378 F2 individuals, and in each example small effect QTL are not accurately mapped. However, the studies identify the major genomic regions that are important for the expression of specific traits. The recent increase in genomic information available for apple (Velasco et al. 2010), peach (Sosinski et al. 2010), and strawberry (Shulaev et al. 2011) provides the opportunity to use gene mining for the identification of the putative controlling genes.

I will now present the status of comparative genome mapping in the family, including some of the factors that limit progress in genetic mapping across the Rosaceae.