InDel markers: An extended marker resource for molecular breeding in chickpea
Date
2019-03-18ISI journal
Impact factor: 2.776 (Year: 2019)
Author(s)
Citation
Ankit Jain, Manish Roorkiwal, Sandip Kale, Garg Vanika, Ramakrishna Yadala, Rajeev Varshney. (18/3/2019). InDel markers: An extended marker resource for molecular breeding in chickpea. PLoS ONE, 3(14), pp. 1-13.
Abstract
Chickpea is one of the most important food legumes that holds the key to meet rising global food and nutritional demand. In order to deploy molecular breeding approaches in crop improvement programs, user friendly and cost effective marker resources remain prerequisite. The advent of next generation sequencing (NGS) technology has resulted in the generation of several thousands of markers as part of several large scale genome sequencing and re-sequencing initiatives. Very recently, PCR based Insertion-deletions (InDels) are becoming a popular gel based genotyping solution because of their co-dominant, inexpensive, and highly polymorphic nature. With an objective to expand marker resources for genomics assisted breeding (GAB) in chickpea, whole genome re-sequencing data generated on five parental lines of one interspecific (ICC 4958 × PI 489777) and two intra-specific (ICC 283 × ICC 8261 and ICC 4958 × ICC 1882) mapping populations, were used for identification of InDels. A total of 231,658 InDels were identified using Dindel software with default parameters. Further, a total of 8,307 InDels with ≥20 bp size were selected for development of gel based markers, of which primers could be designed for 7,523 (90.56%) markers. On average, markers appeared at a frequency of 1,038 InDels/LG with a maximum number of markers on CaLG04 (1,952 InDels) and minimum on CaLG08 (360 InDels). In order to validate these InDels, a total of 423 primer pairs were randomly selected and tested on the selected parental lines. A high amplification rate of 80% was observed ranging from 46.06 to 58.01% polymorphism rate across parents on 3% agarose gel. This study clearly reflects the usefulness of available sequence data for the development of genome-wide InDels in chickpea that can further contribute and accelerate a wide range of genetic and molecular breeding activities in chickpea.
Author(s) ORCID(s)
Roorkiwal, Manishhttps://orcid.org/0000-0001-6595-281X
Subject(s)
AGROVOC Keywords
Click to enable
Related items
Showing items related by title, author, creator and subject.
-
Title: Salt tolerance analysis of chickpea, faba bean and durum wheat varieties I. Chickpea and faba bean
Author(s)Katerji, Nader; van Hoorn, J.W.; Hamdy, Atef; Mastrorilli, Marcello; Oweis, Theib (Elsevier Masson, 2005-04-02)Date: 2005-01-12Type: Journal ArticleStatus: Limited accessTwo varieties of chickpea (Cicer arietinum L.) and faba bean (Vicia faba), differing in drought tolerance according to the classification of the International Center for Agronomic Research in Dry Areas (ICARDA), were ... -
Title: Developing an artificial inoculation technique for screening chickpea genotypes against a Syrian isolate of Chickpea chlorotic stunt virus
Author(s)Nader, Asaad; Kumari, Safaa; Kasem, Amin; Al-Chaabi, Salah; Arab, Ateh (Arab Society for Plant Protection, 2020-06-30)Date: 2020-06-30Type: Journal ArticleStatus: Open accessChickpea chlorotic stunt virus (CpCSV) is the most important virus affecting chickpea crop in several countries of West Asia and North Africa (WANA), including Syria. The main objective of this study was to develop a ... -
Title: Effect of Heterodera Ciceri On Yield of Chickpea and Lentil and Development of This Nematode On Chickpea in Syria
Author(s)Greco, N.; Di Vito, M.; Saxena, Mohan C.; Reddy, M.V.Date: 1988-01-01Type: Journal ArticleStatus: Timeless limited accessExperiments were undertaken in 1984-1986 to assess losses caused by Heterodera ciceri to chickpea and lentil and to investigate the development of the nematode in Syria. Pots containing 5.5 dm 3 of soil were sown to spring ...