title: An InDel-based linkage map of hot pepper (Capsicum annuum).
abstract: Two independent pepper (Capsicum annuum) genomes were published recently, opening a new era of molecular genetics research on pepper. However, pepper molecular marker technologies are still mainly focusing on the simple sequence repeats derived from public database or genomic library. The development and application of the third generation marker system such as single nucleotide polymorphisms, structure variations as well as insertion/deletion polymorphisms (InDels) is still in its infancy. In the present study, we developed InDel markers for pepper genetic mapping with the convenience of two whole-genome re-sequenced inbred lines BA3 (C. annuum) and B702 (C. annuum). A total of 154,519 and 149,755 InDel (1-5 bp) sites were identified for BA3 and B702, respectively, by the alignment of re-sequencing reads to Zunla-1 reference genome. Then, 14,498 InDel sites (only 4 and 5 bp) that are different between BA3 and B702 were predicted. Finally, within a random set of 1,000 primer pairs, 251 InDel markers were validated and mapped onto a linkage map using F2population derived from the intraspecific cross BA3 × B702. The first InDel-based map, named as BB-InDel map, consisted of 12 linkage groups, covered a genetic distance of 1,178.01 cM and the average distance between bin markers was 5.01 cM. Compared to the Zunla-1 reference physical map, high consistency was observed on all 12 chromosomes, and the total length of scaffold anchored and physical distance covered by this map was 299.66 and 2,558.68 Mb, respectively, which accounted for 8.95 and 76.38 % of the Zunla-1 reference genome (3.35 Gb), respectively. Furthermore, 37 scaffolds (total length of 36.21 Mb) from the pseudo-chromosome (P0) of the current genome assembly were newly assigned to the corresponding chromosomes by 40 InDel markers. Thus, this map provided good genome coverage and would be useful for basic and applied research in pepper.
authors.affiliation: College of Horticulture, South China Agricultural University, Wushan Road 483, Guangzhou, 510642 Guangdong China.
authors.forename: Weipeng
authors.initials: W
authors.lastname: Li
authors.affiliation: College of Horticulture, South China Agricultural University, Wushan Road 483, Guangzhou, 510642 Guangdong China.
authors.forename: Jiaowen
authors.initials: J
authors.lastname: Cheng
authors.affiliation: College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Zhongkai Road 501, Guangzhou, 510225 Guangdong China.
authors.forename: Zhiming
authors.initials: Z
authors.lastname: Wu
authors.affiliation: College of Horticulture, South China Agricultural University, Wushan Road 483, Guangzhou, 510642 Guangdong China.|Pepper Institute, Zunyi Academy of Agricultural Sciences, Zunyi, 563102 Guizhou China.|Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130 Sichuan China.
authors.forename: Cheng
authors.initials: C
authors.lastname: Qin
authors.affiliation: College of Horticulture, South China Agricultural University, Wushan Road 483, Guangzhou, 510642 Guangdong China.
authors.forename: Shu
authors.initials: S
authors.lastname: Tan
authors.affiliation: College of Horticulture, South China Agricultural University, Wushan Road 483, Guangzhou, 510642 Guangdong China.
authors.forename: Xin
authors.initials: X
authors.lastname: Tang
authors.affiliation: College of Horticulture, South China Agricultural University, Wushan Road 483, Guangzhou, 510642 Guangdong China.
authors.forename: Junjie
authors.initials: J
authors.lastname: Cui
authors.affiliation: College of Horticulture, South China Agricultural University, Wushan Road 483, Guangzhou, 510642 Guangdong China.
authors.forename: Li
authors.initials: L
authors.lastname: Zhang
authors.affiliation: College of Horticulture, South China Agricultural University, Wushan Road 483, Guangzhou, 510642 Guangdong China.
authors.forename: Kailin
authors.initials: K
authors.lastname: Hu
keywords: Capsicum annuum; Genetic map; InDel; Pepper genome