An ultra-high-density bin map facilitates high-throughput QTL mapping of horticultural traits in pepper (Capsicum annuum)

Koeun Han, Hee Jin Jeong, Hee Bum Yang, Sung Min Kang, Jin Kyung Kwon, Seungill Kim, Doil Choi, Byoung Cheorl Kang

Research output: Contribution to journalArticlepeer-review

85 Scopus citations

Abstract

Most agricultural traits are controlled by quantitative trait loci (QTLs); however, there are few studies on QTL mapping of horticultural traits in pepper (Capsicum spp.) due to the lack of high-density molecular maps and the sequence information. In this study, an ultra-high-density map and 120 recombinant inbred lines (RILs) derived from a cross between C. annuum 'Perennial' and C. annuum 'Dempsey' were used for QTL mapping of horticultural traits. Parental lines and RILs were resequenced at 18x and 1x coverage, respectively. Using a sliding window approach, an ultra-high-density bin map containing 2,578 bins was constructed. The total map length of the map was 1,372 cM, and the average interval between bins was 0.53 cM. A total of 86 significant QTLs controlling 17 horticultural traits were detected. Among these, 32 QTLs controlling 13 traits were major QTLs. Our research shows that the construction of bin maps using low-coverage sequence is a powerful method for QTL mapping, and that the short intervals between bins are helpful for fine-mapping of QTLs. Furthermore, bin maps can be used to improve the quality of reference genomes by elucidating the genetic order of unordered regions and anchoring unassigned scaffolds to linkage groups.

Original languageEnglish
Pages (from-to)81-91
Number of pages11
JournalDNA Research
Volume23
Issue number2
DOIs
StatePublished - 1 Apr 2016

Keywords

  • NGS
  • QTL
  • bin map
  • morphological trait
  • pepper

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