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Pear (Pyrus spp.) belongs to the tribe Maleae in family Rosaceae together with apple. Almost all major cultivated pears are functionally diploid (2n = 2x = 34) with 17 as the basic chromosome number (n = 17). Genus Pyrus comprises almost 22 species which are widespread in pear growing areas of the world. However the three major species P. communis. L (European pear.), P. pyrifolia Nakai (Japanese pear) and P.

bretschneideri Rehd (Chinese pear.) are the most popular and are grown

commercially.

1.4.5.1 Pyrus genotyping

The advent of new high throughput technologies has enabled the availability of more and more sequenced plant genome and large numbers of SNPs discovery. QTL mapping has become easier and more popular for fruit plants than in previous years. Considerable amount of QTL mapping work in fruit crops have been performed in the last two decades, especially in the last few years (Chen et al., 1999; Etienne et al., 2002; Dondini et al., 2004; Arbelbide and Bernardo, 2006; Dunemann et al., 2009; Costa et al., 2010; Khan et al., 2012; Costa et al., 2013).

Recently, whole genome sequencing of Chinese pear (Pyrus bretschneideri) with a coverage 194× was reported by (Wu et al., 2013). The genome was sequenced using a combination of NGS and BAC-by-BAC sequencing technology and covered almost

97.1 % of the estimated genome size. The whole genome sequence of the European pear 'Bartlett' obtained using NGS technology has also been published recently (Chagné et al., 2014). Mapping of ‘Old Home’ and ‘Louise Bonne de Jersey’ low coverage sequence data to ‘Bartlett’ scaffolds enabled discovery of a total of of 3,893,643 putative SNPs. Average SNP frequency after filtration was one SNP per 674 bp. The ‘Bartlett’ genome assembly can be used to compare synteny of the pear genome with other related species, including other members from Rosaceae family. Comparison of ‘Bartlett’ protein cluster with 13 other species including P. bretschneideri Rehd and apple revealed that a set of 1,433 protein clusters present in both pear species (European and Chinese pear) and apple that were absent from other species and this set of proteins may include genes responsible for the pome fruit character (Chagné et al., 2014).

1.4.5.2 Construction of linkage maps in Pyrus

Construction of a high density map is a prerequisite in plant genetic improvement programmes. Pear genetics and genomics are not as advanced as in other major crops, including apple. Iketani et al. (2001) was the pioneer, developing the first pear linkage map, using Japanese pear (P. pyrifolia Nakai) varieties ‘Kinchaku’ and ‘Kosui’ and RAPD markers to develop maps. They developed two separate maps for each parent by using 82 individuals (Iketani et al., 2001). These maps were estimated to cover almost half of the pear genome when compared to apple maps. The second set of linkage maps was developed by Yamamoto et al. (2002, 2004) using 63 seedlings from interspecific crosses between ‘Bartlett’ (P. communis) and ‘Hosui’ (P. pyrifolia) pear. They used the AFLP and SSR markers from apple, pear and peach, isozymes and phenotypic markers to construct two maps. Their maps were first reported reference maps for pear eg ‘Bartlett’ had 256 loci spanning 1020cM. Average distance between the loci reported is 4 cM (Yamamoto et al., 2002; Yamamoto et al., 2004).

Linkage maps from two European pear cultivars ‘Passe Crassane’ and ‘Harrow Sweet’ were developed by Dondini et al. (2004). These maps were constructed by using 99 F1 individuals with SSR, MFLPs (microsatellite-anchored fragment length polymorphism), AFLPs, RGAs (resistance gene analog) and AFLP-RGA (amplified 39

fragment length polymorphism- resistance gene analog) markers from apple and pear origin. These maps were used to map QTL controlling resistance to fire blight, one of the important diseases of European pears. The map for ‘Passe Crassane’ comprised 155 loci in 18 groups over the distance of 912cM and for ‘Harrow Sweet’ comprised 156 loci spanning over distance of 930cM and 19 groups. Pierantoni et al. (2004) used two European populations to construct maps using 100 apple SSRs. Syntenic relationships between apple and pear was also confirmed by at least carrying two or more common SSR markers. Pierantoni et al. (2007) used one of the same population to construct a high density map from 157 AFLP and 41 SSR markers and to identify QTLs for scab resistance.

Genetic maps for Chinese pear ‘Yali’ and ‘Jingbaili’ were constructed by using AFLP and SSR markers from 145 F1 individuals by Sun et al. (2010) in order to identifyQTLs for leaf traits. Their maps consisted of 402 markers (AFLP and SSR) which covered 1395.9 cM area and average distance between pair of loci was 3.8 cM (Sun et al., 2009). Zhang et al. (2011) used a population of 97 F1 seedlings from a cross between the interspecific hybrid pear ‘Bayuehong’(European × Chinese species) and the Chinese pear ‘Dangshansuli’, for construction of parental linkage maps for the purpose of QTL analysis of fruit traits. Both these maps consisted of 17 linkage groups with 214 and 122 markers spanning over 1,352.7 cM and 1,044.3 cM for Bayuehong’and ‘Dangshansuli’ respectively.

Recently Wu. et al (2014) published a dense integrated pear map consisting of 3143 SNPs and 98 SSR markers developed by restriction-association DNA sequencing (RAD). This map consisted of 17 LG spanning 2243.4 cM.

1.4.5.3 Pyrus QTL analysis

Extensive research involving QTL mapping has been reported in apple (Korban and Tartarini, 2009), however only a few studies have been reported for Pyrus species. Generally these researches were conducted to study the disease resistance, one about leaf characteristics and last focuses on fruit characters.

QTL mapping was carried out for fire blight resistance in European pears by Dondini et al. (2004). They identified four putative QTLs for control of fire blight (Erwinia amylovora) in a resistant parent ‘Harrow Sweet’, and no QTLs were detected in the

susceptible parent ‘Passe Crassane’. Another important disease for European pear is

scab (Venturia inaequalis). Pierantoni et al. (2007) used the linkage maps from

‘Abbé Fétel’ × ‘Max Red Bartlett’ to identify QTLs linked to scab resistance. They detected two putative major QTLs for scab resistance on LG3 and 7 these QTLs explained a total of 88% of phenotypic variance.

QTL mapping in Chinese pear was reported by Sun et al. (2009) for vegetative traits including leaf length, width, leaf length/leaf width ratio and petiole length. So far two studies have been reported for fruit trait QTLs in pear. A population developed from interspecific hybrid pear ‘Bayuehong’ (P. communis × P. bretschneideri ) and the Chinese pear ‘Dangshansuli’ has been used in two different studies for genetic map construction and QTL mapping for fruit traits (Zhang et al., 2011; Wu et al., 2014). Zhang et al. (2011) developed two parental linkage maps using AFLP and SRAP markers and detected nine QTLs for five fruit traits (fruit weight, transverse diameter of fruit, vertical diameter of fruit, soluble solids content and fruit shape index). Recently a total of 32 potential QTLs for 11 fruit traits including pedicel length, fruit weight, transverse diameter, vertical diameter, flesh colour, number of seeds, juice content, calyx status, skin colour, skin smoothness and TSS were identified using the same population (Wu et al., 2014).