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Development and Utilization of InDel Markers to Identify Peanut (Arachis hypogaea) Disease Resistance

Peanut diseases, such as leaf spot and spotted wilt caused by Tomato Spotted Wilt Virus, can significantly reduce yield and quality. Application of marker assisted plant breeding requires the development and validation of different types of DNA molecular markers. Nearly 10,000 SSR-based molecular ma...

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Autores principales: Liu, Lifeng, Dang, Phat M., Chen, Charles Y.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4643128/
https://www.ncbi.nlm.nih.gov/pubmed/26617627
http://dx.doi.org/10.3389/fpls.2015.00988
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author Liu, Lifeng
Dang, Phat M.
Chen, Charles Y.
author_facet Liu, Lifeng
Dang, Phat M.
Chen, Charles Y.
author_sort Liu, Lifeng
collection PubMed
description Peanut diseases, such as leaf spot and spotted wilt caused by Tomato Spotted Wilt Virus, can significantly reduce yield and quality. Application of marker assisted plant breeding requires the development and validation of different types of DNA molecular markers. Nearly 10,000 SSR-based molecular markers have been identified by various research groups around the world, but less than 14.5% showed polymorphism in peanut and only 6.4% have been mapped. Low levels of polymorphism limit the application of marker assisted selection (MAS) in peanut breeding programs. Insertion/deletion (InDel) markers have been reported to be more polymorphic than SSRs in some crops. The goals of this study were to identify novel InDel markers and to evaluate the potential use in peanut breeding. Forty-eight InDel markers were developed from conserved sequences of functional genes and tested in a diverse panel of 118 accessions covering six botanical types of cultivated peanut, of which 104 were from the U.S. mini-core. Results showed that 16 InDel markers were polymorphic with polymorphic information content (PIC) among InDels ranged from 0.017 to 0.660. With respect to botanical types, PICs varied from 0.176 for fastigiata var., 0.181 for hypogaea var., 0.306 for vulgaris var., 0.534 for aequatoriana var., 0.556 for peruviana var., to 0.660 for hirsuta var., implying that aequatoriana var., peruviana var., and hirsuta var. have higher genetic diversity than the other types and provide a basis for gene functional studies. Single marker analysis was conducted to associate specific marker to disease resistant traits. Five InDels from functional genes were identified to be significantly correlated to tomato spotted wilt virus (TSWV) infection and leaf spot, and these novel markers will be utilized to identify disease resistant genotype in breeding populations.
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spelling pubmed-46431282015-11-27 Development and Utilization of InDel Markers to Identify Peanut (Arachis hypogaea) Disease Resistance Liu, Lifeng Dang, Phat M. Chen, Charles Y. Front Plant Sci Plant Science Peanut diseases, such as leaf spot and spotted wilt caused by Tomato Spotted Wilt Virus, can significantly reduce yield and quality. Application of marker assisted plant breeding requires the development and validation of different types of DNA molecular markers. Nearly 10,000 SSR-based molecular markers have been identified by various research groups around the world, but less than 14.5% showed polymorphism in peanut and only 6.4% have been mapped. Low levels of polymorphism limit the application of marker assisted selection (MAS) in peanut breeding programs. Insertion/deletion (InDel) markers have been reported to be more polymorphic than SSRs in some crops. The goals of this study were to identify novel InDel markers and to evaluate the potential use in peanut breeding. Forty-eight InDel markers were developed from conserved sequences of functional genes and tested in a diverse panel of 118 accessions covering six botanical types of cultivated peanut, of which 104 were from the U.S. mini-core. Results showed that 16 InDel markers were polymorphic with polymorphic information content (PIC) among InDels ranged from 0.017 to 0.660. With respect to botanical types, PICs varied from 0.176 for fastigiata var., 0.181 for hypogaea var., 0.306 for vulgaris var., 0.534 for aequatoriana var., 0.556 for peruviana var., to 0.660 for hirsuta var., implying that aequatoriana var., peruviana var., and hirsuta var. have higher genetic diversity than the other types and provide a basis for gene functional studies. Single marker analysis was conducted to associate specific marker to disease resistant traits. Five InDels from functional genes were identified to be significantly correlated to tomato spotted wilt virus (TSWV) infection and leaf spot, and these novel markers will be utilized to identify disease resistant genotype in breeding populations. Frontiers Media S.A. 2015-11-13 /pmc/articles/PMC4643128/ /pubmed/26617627 http://dx.doi.org/10.3389/fpls.2015.00988 Text en Copyright © 2015 Liu, Dang and Chen. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Liu, Lifeng
Dang, Phat M.
Chen, Charles Y.
Development and Utilization of InDel Markers to Identify Peanut (Arachis hypogaea) Disease Resistance
title Development and Utilization of InDel Markers to Identify Peanut (Arachis hypogaea) Disease Resistance
title_full Development and Utilization of InDel Markers to Identify Peanut (Arachis hypogaea) Disease Resistance
title_fullStr Development and Utilization of InDel Markers to Identify Peanut (Arachis hypogaea) Disease Resistance
title_full_unstemmed Development and Utilization of InDel Markers to Identify Peanut (Arachis hypogaea) Disease Resistance
title_short Development and Utilization of InDel Markers to Identify Peanut (Arachis hypogaea) Disease Resistance
title_sort development and utilization of indel markers to identify peanut (arachis hypogaea) disease resistance
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4643128/
https://www.ncbi.nlm.nih.gov/pubmed/26617627
http://dx.doi.org/10.3389/fpls.2015.00988
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