eprintid: 9955
rev_number: 11
eprint_status: archive
userid: 1305
dir: disk0/00/00/99/55
datestamp: 2017-04-13 04:30:05
lastmod: 2017-04-13 04:31:46
status_changed: 2017-04-13 04:30:05
type: article
metadata_visibility: show
creators_name: Singh, V K
creators_name: Khan, A W
creators_name: Saxena, R K
creators_name: Sinha, P
creators_name: Kale, S M
creators_name: Parupalli, S
creators_name: Kumar, V
creators_name: Chitikineni, A
creators_name: Vechalapu, S
creators_name: Sameer Kumar, C V
creators_name: Sharma, M
creators_name: Ghanta, A
creators_name: Yamini, K N
creators_name: Muniswamy, S
creators_name: Varshney, R K
icrisatcreators_name: Singh, V K
icrisatcreators_name: Khan, A W
icrisatcreators_name: Saxena, R K
icrisatcreators_name: Sinha, P
icrisatcreators_name: Kale, S M
icrisatcreators_name: Parupalli, S
icrisatcreators_name: Kumar, V
icrisatcreators_name: Chitikineni, A
icrisatcreators_name: Vechalapu, S
icrisatcreators_name: Sameer Kumar, C V
icrisatcreators_name: Sharma, M
icrisatcreators_name: Varshney, R K
affiliation: ICRISAT (Patancheru)
affiliation: Agricultural Research Station (ARS) (Tandur) Professor Jayashankar Telangana State Agricultural University (PJTSAU) (Hyderabad)
affiliation: Agricultural Research Station (ARS)(Gulbarga), University of Agricultural Sciences (UAS)(Raichur)
country: India
title: Indel-seq: a fast-forward genetics approach for identification of trait-associated putative candidate genomic regions and its application in pigeonpea (Cajanus cajan)
ispublished: pub
subjects: s1.2
subjects: s2.13
divisions: CRPS3
crps: crp1.5
full_text_status: public
keywords: Bulked segregant analysis, fusarium wilt, Indels, sterility mosaic disease, whole-genome resequencing, pigeonpea, Indel-seq approach
note: Authors are thankful to the United States Agency for International
Development (USAID); Biotechnology Industry Partnership
Programme (BIPP) and Department of Biotechnology of Government
of India; Ministry of Agriculture, Government of Karnataka
state of India for funding various projects related to pigeonpea
genomics. This work has been undertaken as part of the CGIAR
Research Program on Grain Legumes. ICRISAT is a member of
CGIAR Consortium.
abstract: Identification of candidate genomic regions associated with target traits using conventional mapping methods is challenging and time-consuming. In recent years, a number of single nucleotide polymorphism (SNP)-based mapping approaches have been developed and used for identification of candidate/putative genomic regions. However, in the majority of these studies, insertion–deletion (Indel) were largely ignored. For efficient use of Indels in mapping target traits, we propose Indel-seq approach, which is a combination of whole-genome resequencing (WGRS) and bulked segregant analysis (BSA) and relies on the Indel frequencies in extreme bulks. Deployment of Indel-seq approach for identification of candidate genomic regions associated with fusarium wilt (FW) and sterility mosaic disease (SMD) resistance in pigeonpea has identified 16 Indels affecting 26 putative candidate genes. Of these 26 affected putative candidate genes, 24 genes showed effect in the upstream/downstream of the genic region and two genes showed effect in the genes. Validation of these 16 candidate Indels in other FW- and SMD-resistant and FW- and SMD-susceptible genotypes revealed a significant association of five Indels (three for FW and two for SMD resistance). Comparative analysis of Indel-seq with other genetic mapping approaches highlighted the importance of the approach in identification of significant genomic regions associated with target traits. Therefore, the Indel-seq approach can be used for quick and precise identification of candidate genomic regions for any target traits in any crop species.
date: 2017
date_type: published
publication: Plant Biotechnology Journal
publisher: John Wiley & Sons, Inc
pagerange: 1-9
id_number: 10.1111/pbi.12685
refereed: TRUE
issn: 1467-7644
official_url: http://dx.doi.org/10.1111/pbi.12685
related_url_url: https://scholar.google.co.in/scholar?q=Indel-seq%3A+a+fast-forward+genetics+approach+for+identification+of+trait-associated+putative+candidate+genomic+regions+and+its+application+in+pigeonpea+%28Cajanus+cajan%29&btnG=&hl=en&as_sdt=0%2C5
related_url_type: pub
citation:   Singh, V K and Khan, A W and Saxena, R K and Sinha, P and Kale, S M and Parupalli, S and Kumar, V and Chitikineni, A and Vechalapu, S and Sameer Kumar, C V and Sharma, M and Ghanta, A and Yamini, K N and Muniswamy, S and Varshney, R K  (2017) Indel-seq: a fast-forward genetics approach for identification of trait-associated putative candidate genomic regions and its application in pigeonpea (Cajanus cajan).  Plant Biotechnology Journal.  pp. 1-9.  ISSN 1467-7644     
document_url: http://oar.icrisat.org/9955/1/Singh_et_al-2017-Plant_Biotechnology_Journal.pdf