title: An ultra-high-density bin map facilitates high-throughput QTL mapping of horticultural traits in pepper (Capsicum annuum).
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 18× and 1× 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.
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea.
authors.forename: Koeun
authors.initials: K
authors.lastname: Han
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea.
authors.forename: Hee-Jin
authors.initials: HJ
authors.lastname: Jeong
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea.
authors.forename: Hee-Bum
authors.initials: HB
authors.lastname: Yang
authors.affiliation: Department of Computer Science, College of Information Science and Technology, KAIST, Daejeon 305-701, Republic of Korea.
authors.forename: Sung-Min
authors.initials: SM
authors.lastname: Kang
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea.
authors.forename: Jin-Kyung
authors.initials: JK
authors.lastname: Kwon
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 599 Gwanak-ro Gwank-gu, Seoul 151-921, Republic of Korea.
authors.forename: Seungill
authors.initials: S
authors.lastname: Kim
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 599 Gwanak-ro Gwank-gu, Seoul 151-921, Republic of Korea bk54@snu.ac.kr doil@snu.ac.kr.
authors.forename: Doil
authors.initials: D
authors.lastname: Choi
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea bk54@snu.ac.kr doil@snu.ac.kr.
authors.forename: Byoung-Cheorl
authors.initials: BC
authors.lastname: Kang
mesh_terms: D002212:Capsicum / Q000235:genetics*; D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D003433:Crosses, Genetic; D040641:Quantitative Trait Loci; D017422:Sequence Analysis, DNA
keywords: NGS; QTL; bin map; morphological trait; pepper