1. An ultra-high-density bin map facilitates high-throughput QTL mapping of horticultural traits in pepper (Capsicum annuum)
- Author
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Doil Choi, Hee-Bum Yang, Seungill Kim, Jin-Kyung Kwon, Koeun Han, Byoung-Cheorl Kang, Hee-Jin Jeong, and Sung-Min Kang
- Subjects
0106 biological sciences ,0301 basic medicine ,Ultra high density ,QTL ,Quantitative Trait Loci ,Biology ,Quantitative trait locus ,01 natural sciences ,Chromosomes, Plant ,Bin ,03 medical and health sciences ,pepper ,Inbred strain ,Family-based QTL mapping ,Pepper ,Genetics ,Molecular Biology ,Crosses, Genetic ,business.industry ,bin map ,Chromosome Mapping ,food and beverages ,Sequence Analysis, DNA ,General Medicine ,Full Papers ,CAPSICUM SPP ,Biotechnology ,Capsicum annuum ,Horticulture ,030104 developmental biology ,NGS ,morphological trait ,Capsicum ,business ,010606 plant biology & botany - 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.
- Published
- 2016
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