chinense exhibit a relatively closer interspecific relationship with C. annuum is most widely cultivated for use as food, spice, ornaments, and medicine around the world. Introduction Capsicum is a member of the Solanaceae family and consists of the following five most important cultivated species, C. Competing Interests: The authors have declared that no competing interests exist. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. PLOS ONE | DOI:10.1371/journal.pone.0119389 Ma1 / 15 Map Construction and Mapping QTLs Affecting Flowering Time China (No. The InDel/SSR-based interspecific genetic map, QTLs and candidate genes obtained by the present study will be useful for the downstream isolation of flowering timerelated gene and other genetic applications for pepper. With the accomplishment of pepper whole genome sequencing and annotations (release 2.0), 153 candidate genes were predicted to embed in the Nle2.2 region, of which 12 important flowering related genes were obtained. The major QTL on P2 was confirmed based on another subset of the same F2 population (n = 147) in 2014 with selective genotyping of markers from the BY map. Based on the BY map, one major and five minor QTLs affecting the number of leaves on the primary axis (Nle) were detected on chromosomes P2, P7, P10 and P11 in 2012. Comparative analysis of the genetic and physical map based on the anchored markers showed that the BY map covered nearly the whole pepper genome. The BY map consisted of 13 linkage groups (LGs) and spanned a total genetic distance of 1,249.77 cM with an average marker distance of 5.60 cM. Of these, a total of 224 simple PCR-based markers, including 129 InDels and 95 SSRs, were validated and integrated into a map, which was designated as the BY map. To accelerate the development and application of molecular markers and identify the QTLs affecting the flowering time-related trait in pepper, a total of 1,038 pairs of InDel and 674 SSR primers from different sources were used for genetic mapping using the F2 population (n = 154) derived from a cross between BA3 (C. * Abstract Re-sequencing permits the mining of genome-wide variations on a large scale and provides excellent resources for the research community. 201201) and the Guizhou Province and Zunyi City Science and Technology Cooperation Project of 1 College of Horticulture, South China Agricultural University, Guangzhou, China, 2 Pepper Institute, Zunyi Academy of Agricultural Sciences, Zunyi, Guizhou, China, 3 Maize Research Institute of Sichuan Agricultural University / Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, China, 4 College of Agriculture, Guangxi University, Nanning, China, 5 College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China ☯ These authors contributed equally to this work. Funding: This work was supported by the Guangdong Natural Science Foundation of China (S2011030001410), the National High Technology Research and Development Program (“863” Program) of China (2012AA100103), the National Natural Science Foundation of China (31372076), the Zunyi City Natural Science Foundation of China (No. Data Availability Statement: All relevant data are within the paper and its Supporting Information files. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Nelson, The University of Western Australia, AUSTRALIA Received: NovemAccepted: JanuPublished: MaCopyright: © 2015 Tan et al. (2015) Construction of an Interspecific Genetic Map Based on InDel and SSR for Mapping the QTLs Affecting the Initiation of Flower Primordia in Pepper (Capsicum spp.). RESEARCH ARTICLE Construction of an Interspecific Genetic Map Based on InDel and SSR for Mapping the QTLs Affecting the Initiation of Flower Primordia in Pepper (Capsicum spp.) Shu Tan1☯, Jiao-Wen Cheng1☯, Li Zhang1☯, Cheng Qin1,2,3, Ding-Guo Nong4, Wei-Peng Li1, Xin Tang1, Zhi-Ming Wu5, Kai-Lin Hu1* a11111 OPEN ACCESS Citation: Tan S, Cheng J-W, Zhang L, Qin C, Nong D-G, Li W-P, et al.
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