NDLI: An InDel-based linkage map of hot pepper (Capsicum annuum)

Content Provider	Springer Nature Link
Author	Li, Weipeng Cheng, Jiaowen Wu, Zhiming Qin, Cheng Tan, Shu Tang, Xin Cui, Junjie Zhang, Li Hu, Kailin
Copyright Year	2015
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 F$_{2}$ population 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.
Starting Page	1
Ending Page	10
Page Count	10
File Format	PDF
ISSN	13803743
Journal	Molecular Breeding
Volume Number	35
Issue Number	1
e-ISSN	15729788
Language	English
Publisher	Springer Netherlands
Publisher Date	2015-01-21
Publisher Place	Dordrecht
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Capsicum annuum InDel Genetic map Pepper genome Plant Sciences Plant Genetics & Genomics Plant Pathology Plant Physiology Biotechnology
Content Type	Text
Resource Type	Article
Subject	Genetics Plant Science Molecular Biology Biotechnology Agronomy and Crop Science

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

An InDel-based linkage map of hot pepper (Capsicum annuum)

Development of a large number of SSR and InDel markers and construction of a high-density genetic map based on a RIL population of pepper (Capsicum annuum L.)

A SNP-based genetic linkage map of Capsicum baccatum and its comparison to the Capsicum annuum reference physical map

Molecular cloning of the CaLFY, putative pepper ortholog of FLO/LFY

Development of simple sequence repeat markers and construction of a high-density linkage map of Capsicum annuum

An EST-based linkage map reveals chromosomal translocation in Capsicum

Complete genome sequencing and analysis of Capsicum annuum varieties

An SSR-based linkage map of Capsicum annuum

An InDel-based linkage map of hot pepper (Capsicum annuum)

An InDel-based linkage map of hot pepper (Capsicum annuum)

Similar Documents

An InDel-based linkage map of hot pepper (Capsicum annuum)

Development of a large number of SSR and InDel markers and construction of a high-density genetic map based on a RIL population of pepper (Capsicum annuum L.)

A SNP-based genetic linkage map of Capsicum baccatum and its comparison to the Capsicum annuum reference physical map

Molecular cloning of the CaLFY, putative pepper ortholog of FLO/LFY

Development of simple sequence repeat markers and construction of a high-density linkage map of Capsicum annuum

An EST-based linkage map reveals chromosomal translocation in Capsicum

Complete genome sequencing and analysis of Capsicum annuum varieties

An SSR-based linkage map of Capsicum annuum

An InDel-based linkage map of hot pepper (Capsicum annuum)

An InDel-based linkage map of hot pepper (Capsicum annuum)