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Uncovering of natural allelic variants of key yield contributing genes by targeted resequencing in rice (Oryza sativa L.)
In rice (Oryza sativa L.), during the course of domestication, numerous beneficial alleles remain untapped in the progenitor wild species and landraces. This study aims at uncovering these promising alleles of six key genes influencing the yield, such as DEP1, Ghd7, Gn1a, GS3, qSW5 and sd1 by target...
Autores principales: | , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6547710/ https://www.ncbi.nlm.nih.gov/pubmed/31160789 http://dx.doi.org/10.1038/s41598-019-44708-z |
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author | Vemireddy, Lakshminarayana R. Kadambari, Gopalakrishnamurty Reddy, G. Eswar Kola, Vijaya Sudhakara Rao Ramireddy, Eswarayya Puram, Venkata Ramana Rao Badri, Jyothi Eslavath, Suresh N. Bollineni, Swarajyalakshmi N. Naik, Bukya J. Chintala, Sreelakshmi Pottepalem, Rameshbabu Akkareddy, Srividhya Nagireddy, Ranjithkumar Reddy, Lachagari V. B. Bodanapu, Reddaiah Lekkala, Sivarama P. Chakravartty, Navajeet Siddiq, E. A. |
author_facet | Vemireddy, Lakshminarayana R. Kadambari, Gopalakrishnamurty Reddy, G. Eswar Kola, Vijaya Sudhakara Rao Ramireddy, Eswarayya Puram, Venkata Ramana Rao Badri, Jyothi Eslavath, Suresh N. Bollineni, Swarajyalakshmi N. Naik, Bukya J. Chintala, Sreelakshmi Pottepalem, Rameshbabu Akkareddy, Srividhya Nagireddy, Ranjithkumar Reddy, Lachagari V. B. Bodanapu, Reddaiah Lekkala, Sivarama P. Chakravartty, Navajeet Siddiq, E. A. |
author_sort | Vemireddy, Lakshminarayana R. |
collection | PubMed |
description | In rice (Oryza sativa L.), during the course of domestication, numerous beneficial alleles remain untapped in the progenitor wild species and landraces. This study aims at uncovering these promising alleles of six key genes influencing the yield, such as DEP1, Ghd7, Gn1a, GS3, qSW5 and sd1 by targeted resequencing of the 200 rice genotypes. In all, 543 nucleotide variations including single nucleotide polymorphisms and insertion and deletion polymorphisms were identified from the targeted genes. Of them, 225 were novel alleles, which identified in the present study only and 91 were beneficial alleles that showed significant association with the yield traits. Besides, we uncovered 128 population-specific alleles with indica being the highest of 79 alleles. The neutrality tests revealed that pleiotropic gene, Ghd7 and major grain size contributing gene, GS3 showed positive and balanced selection, respectively during the domestication. Further, the haplotype analysis revealed that some of the rice genotypes found to have rare haplotypes, especially the high yielding variety, BPT1768 has showed maximum of three genes such as Gn1a-8, qSW5-12 and GS3-29. The rice varieties with novel and beneficial alleles along with the rare haplotypes identified in the present study could be of immense value for yield improvement in the rice breeding programs. |
format | Online Article Text |
id | pubmed-6547710 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-65477102019-06-10 Uncovering of natural allelic variants of key yield contributing genes by targeted resequencing in rice (Oryza sativa L.) Vemireddy, Lakshminarayana R. Kadambari, Gopalakrishnamurty Reddy, G. Eswar Kola, Vijaya Sudhakara Rao Ramireddy, Eswarayya Puram, Venkata Ramana Rao Badri, Jyothi Eslavath, Suresh N. Bollineni, Swarajyalakshmi N. Naik, Bukya J. Chintala, Sreelakshmi Pottepalem, Rameshbabu Akkareddy, Srividhya Nagireddy, Ranjithkumar Reddy, Lachagari V. B. Bodanapu, Reddaiah Lekkala, Sivarama P. Chakravartty, Navajeet Siddiq, E. A. Sci Rep Article In rice (Oryza sativa L.), during the course of domestication, numerous beneficial alleles remain untapped in the progenitor wild species and landraces. This study aims at uncovering these promising alleles of six key genes influencing the yield, such as DEP1, Ghd7, Gn1a, GS3, qSW5 and sd1 by targeted resequencing of the 200 rice genotypes. In all, 543 nucleotide variations including single nucleotide polymorphisms and insertion and deletion polymorphisms were identified from the targeted genes. Of them, 225 were novel alleles, which identified in the present study only and 91 were beneficial alleles that showed significant association with the yield traits. Besides, we uncovered 128 population-specific alleles with indica being the highest of 79 alleles. The neutrality tests revealed that pleiotropic gene, Ghd7 and major grain size contributing gene, GS3 showed positive and balanced selection, respectively during the domestication. Further, the haplotype analysis revealed that some of the rice genotypes found to have rare haplotypes, especially the high yielding variety, BPT1768 has showed maximum of three genes such as Gn1a-8, qSW5-12 and GS3-29. The rice varieties with novel and beneficial alleles along with the rare haplotypes identified in the present study could be of immense value for yield improvement in the rice breeding programs. Nature Publishing Group UK 2019-06-03 /pmc/articles/PMC6547710/ /pubmed/31160789 http://dx.doi.org/10.1038/s41598-019-44708-z Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Vemireddy, Lakshminarayana R. Kadambari, Gopalakrishnamurty Reddy, G. Eswar Kola, Vijaya Sudhakara Rao Ramireddy, Eswarayya Puram, Venkata Ramana Rao Badri, Jyothi Eslavath, Suresh N. Bollineni, Swarajyalakshmi N. Naik, Bukya J. Chintala, Sreelakshmi Pottepalem, Rameshbabu Akkareddy, Srividhya Nagireddy, Ranjithkumar Reddy, Lachagari V. B. Bodanapu, Reddaiah Lekkala, Sivarama P. Chakravartty, Navajeet Siddiq, E. A. Uncovering of natural allelic variants of key yield contributing genes by targeted resequencing in rice (Oryza sativa L.) |
title | Uncovering of natural allelic variants of key yield contributing genes by targeted resequencing in rice (Oryza sativa L.) |
title_full | Uncovering of natural allelic variants of key yield contributing genes by targeted resequencing in rice (Oryza sativa L.) |
title_fullStr | Uncovering of natural allelic variants of key yield contributing genes by targeted resequencing in rice (Oryza sativa L.) |
title_full_unstemmed | Uncovering of natural allelic variants of key yield contributing genes by targeted resequencing in rice (Oryza sativa L.) |
title_short | Uncovering of natural allelic variants of key yield contributing genes by targeted resequencing in rice (Oryza sativa L.) |
title_sort | uncovering of natural allelic variants of key yield contributing genes by targeted resequencing in rice (oryza sativa l.) |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6547710/ https://www.ncbi.nlm.nih.gov/pubmed/31160789 http://dx.doi.org/10.1038/s41598-019-44708-z |
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