Abstract

   We used a next-generation high-throughput sequencing platform to
   resequence the Xinguowei and Shouxing melon cultivars, the parents of
   Fengwei melon. We found 84% of the reads (under a coverage rate of
   “13×”) placed on the reference genome DHL92. There were 2,550,000
   single-nucleotide polymorphisms and 140,000 structural variations in
   the two genomes. We also identified 1,290 polymorphic genes between
   Xinguowei and Shouxing. We combined specific length amplified fragment
   sequencing (SLAF-seq) and bulked-segregant analysis (super-BSA) to
   analyze the two parents and the F[2] extreme phenotypes. This combined
   method yielded 12,438,270 reads, 46,087 SLAF tags, and 4,480
   polymorphic markers (average depth of 161.81×). There were six sweet
   trait-related regions containing 13 differential SLAF markers, and 23
   sour trait-related regions containing 48 differential SLAF markers. We
   further fine-mapped the sweet trait to the genomic regions on
   chromosomes 6, 10, 11, and 12. Correspondingly, we mapped the sour
   trait-related genomic regions to chromosomes 2, 3, 4, 5, 9, and 12.
   Finally, we positioned nine of the 61 differential markers in the sweet
   and sour trait candidate regions on the parental genome. These markers
   corresponded to one sweet and eight sour trait-related genes. Our study
   provides a basis for marker-assisted breeding of desirable sweet and
   sour traits in Fengwei melons.

Introduction

   The melon (Cucumis melo L.) is an important horticultural crop, and has
   diverse phenotypes and genotypes that result in variations in fruit
   quality including sugar and acid content, aroma, and fruit shape
   [[36]1]. The principal component of fruit quality in sweet melons is
   the content of sugar, primarily sucrose [[37]2–[38]4]. Details of the
   metabolic pathways involved in sucrose accumulation in melon fruit have
   been previously described [[39]5]. The organic acid content in most
   melon fruit is very low (pH >6.0) [[40]6]. However, some varieties
   accumulate high levels of acid (pH <5) [[41]7–[42]11], and some
   breeders of melons have combined high acidity and high sugar traits to
   develop dessert cultivars [[43]12–[44]14]. The hereditary
   characteristics of citric acid content and titratable acid have been
   studied in melon fruit [[45]7]. A single major QTL for pH has been
   found to co-localize with major QTLs for citric and malic acids
   [[46]8]. Furthermore, the linkage map position for pH genes has been
   reported and an SSR marker was identified as being tightly associated
   with pH [[47]10]. A previous study showed in bred melons that the high
   sugar and low pH traits were inherited independently of each other, and
   that the acidity trait was particularly associated with citric acid
   levels [[48]12]. However, the relationship between genomic variations
   and the sour trait phenotype has not been reported in melon fruit.

   Fengwei melon is a hybrid obtained from the Shouxing and Xinguowei
   varieties, and has a unique sweet and sour taste that results from the
   combined traits of its parents. Shouxing [Cucumis melo L. ssp. melo
   cover. ameri (Pang) Greb] is a crossbred from multiple parents, while
   Xinguowei [Cucumis melo L. ssp. melo convar. ameri (Pang) Greb, a sour
   tasting Hami melon line bred using high-dose Co^60 γ-ray irradiation]
   has a unique sweet and sour taste [[49]13].

   Over the past few years, various genetic and genomic resources for
   melon have become available. New genetic maps have been reported for
   numerous traits such as fruit size and shape, climacteric ripening,
   netting, color, various metabolites, total soluble solids, and pH
   [[50]8,[51]9,[52]15,[53]16]. Resequencing technology and bioinformatics
   tools have helped to unravel the genetic variations and diversity on a
   genome-wide scale [[54]17]. Garcia-Mas et al. [[55]18] sequenced the
   complete genome of the double haploid line, DHL92, and provided
   valuable information about this important cucurbit. Blanca et al.
   [[56]19] resequenced the transcriptomes of 67 melon genotypes using a
   high-throughput SOLiD^™ system. Bulked-segregant analysis (BSA) is used
   for fine-mapping of phenotypic mutants [[57]20] and is substantially
   enhanced by whole genome sequencing [[58]21]. The use of sequence-based
   markers such as restriction site-associated DNA (RAD) markers, helps to
   achieve high-density discovery and genotyping in large populations
   [[59]22]. However, these technologies usually fail in the presence of
   repetitive genomic sequences that usually are not useful in mapping
   experiments. Sun et al. [[60]23] developed an enhanced reduced
   representation library (RRL) sequencing method, known as specific
   length amplified fragment sequencing (SLAF-seq) technology, that
   combines locus-specific amplification and high-throughput sequencing.
   This technique avoids the selection of repetitive genomic sequences and
   is highly accurate, low-cost, and fast.

   Therefore, the present study aimed to localize important genes related
   to the sweet and sour traits in Fengwei melon (the F1 hybrid of the
   Shouxing and Xinguowei varieties). We used parental resequencing and
   comparative genomics to compare whole genome variations and functional
   genes between the two parental lines, in order to provide references