4.5 Article

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

Journal

DNA RESEARCH
Volume 23, Issue 2, Pages 81-91

Publisher

OXFORD UNIV PRESS
DOI: 10.1093/dnares/dsv038

Keywords

pepper; NGS; bin map; QTL; morphological trait

Funding

  1. Cooperative Research Program for Agriculture Science and Technology Development (Plant Molecular Breeding Center), Rural Development Administration, Republic of Korea [PJ01120501]
  2. Cooperative Research Program for Agriculture Science and Technology Development (Agricultural Genome Center), Rural Development Administration, Republic of Korea [PJ01120401, PJ01127501]
  3. Seoul National University
  4. National Research Foundation of Korea [22A20130012530] Funding Source: Korea Institute of Science & Technology Information (KISTI), National Science & Technology Information Service (NTIS)

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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.

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