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Genomic Insight into Differentiation and Selection Sweeps in the Improvement of Upland Cotton

Upland cotton is the most economically important fibre crop. The human-mediated selection has resulted in modern upland cultivars with higher yield and better fibre quality. However, changes in genome structure resulted from human-mediated selection are poorly understood. Comparative population geno...

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Autores principales: Nazir, Mian Faisal, Jia, Yinhua, Ahmed, Haris, He, Shoupu, Iqbal, Muhammad Shahid, Sarfraz, Zareen, Ali, Mushtaque, Feng, Chenfan, Raza, Irum, Sun, Gaofei, Pan, Zhaoe, Du, Xiongming
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7356552/
https://www.ncbi.nlm.nih.gov/pubmed/32503111
http://dx.doi.org/10.3390/plants9060711
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author Nazir, Mian Faisal
Jia, Yinhua
Ahmed, Haris
He, Shoupu
Iqbal, Muhammad Shahid
Sarfraz, Zareen
Ali, Mushtaque
Feng, Chenfan
Raza, Irum
Sun, Gaofei
Pan, Zhaoe
Du, Xiongming
author_facet Nazir, Mian Faisal
Jia, Yinhua
Ahmed, Haris
He, Shoupu
Iqbal, Muhammad Shahid
Sarfraz, Zareen
Ali, Mushtaque
Feng, Chenfan
Raza, Irum
Sun, Gaofei
Pan, Zhaoe
Du, Xiongming
author_sort Nazir, Mian Faisal
collection PubMed
description Upland cotton is the most economically important fibre crop. The human-mediated selection has resulted in modern upland cultivars with higher yield and better fibre quality. However, changes in genome structure resulted from human-mediated selection are poorly understood. Comparative population genomics offers us tools to dissect the genetic history of domestication and helps to understand the genome-wide effects of human-mediated selection. Hereby, we report a comprehensive assessment of Gossypium hirsutum landraces, obsolete cultivars and modern cultivars based on high throughput genome-wide sequencing of the core set of genotypes. As a result of the genome-wide scan, we identified 93 differential regions and 311 selection sweeps associated with domestication and improvement. Furthermore, we performed genome-wide association studies to identify traits associated with the differential regions and selection sweeps. Our study provides a genetic basis to understand the domestication process in Chinese cotton cultivars. It also provides a comprehensive insight into changes in genome structure due to selection and improvement during the last century. We also identified multiple genome-wide associations (GWAS associations) for fibre yield, quality and other morphological characteristics.
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spelling pubmed-73565522020-07-30 Genomic Insight into Differentiation and Selection Sweeps in the Improvement of Upland Cotton Nazir, Mian Faisal Jia, Yinhua Ahmed, Haris He, Shoupu Iqbal, Muhammad Shahid Sarfraz, Zareen Ali, Mushtaque Feng, Chenfan Raza, Irum Sun, Gaofei Pan, Zhaoe Du, Xiongming Plants (Basel) Article Upland cotton is the most economically important fibre crop. The human-mediated selection has resulted in modern upland cultivars with higher yield and better fibre quality. However, changes in genome structure resulted from human-mediated selection are poorly understood. Comparative population genomics offers us tools to dissect the genetic history of domestication and helps to understand the genome-wide effects of human-mediated selection. Hereby, we report a comprehensive assessment of Gossypium hirsutum landraces, obsolete cultivars and modern cultivars based on high throughput genome-wide sequencing of the core set of genotypes. As a result of the genome-wide scan, we identified 93 differential regions and 311 selection sweeps associated with domestication and improvement. Furthermore, we performed genome-wide association studies to identify traits associated with the differential regions and selection sweeps. Our study provides a genetic basis to understand the domestication process in Chinese cotton cultivars. It also provides a comprehensive insight into changes in genome structure due to selection and improvement during the last century. We also identified multiple genome-wide associations (GWAS associations) for fibre yield, quality and other morphological characteristics. MDPI 2020-06-03 /pmc/articles/PMC7356552/ /pubmed/32503111 http://dx.doi.org/10.3390/plants9060711 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Nazir, Mian Faisal
Jia, Yinhua
Ahmed, Haris
He, Shoupu
Iqbal, Muhammad Shahid
Sarfraz, Zareen
Ali, Mushtaque
Feng, Chenfan
Raza, Irum
Sun, Gaofei
Pan, Zhaoe
Du, Xiongming
Genomic Insight into Differentiation and Selection Sweeps in the Improvement of Upland Cotton
title Genomic Insight into Differentiation and Selection Sweeps in the Improvement of Upland Cotton
title_full Genomic Insight into Differentiation and Selection Sweeps in the Improvement of Upland Cotton
title_fullStr Genomic Insight into Differentiation and Selection Sweeps in the Improvement of Upland Cotton
title_full_unstemmed Genomic Insight into Differentiation and Selection Sweeps in the Improvement of Upland Cotton
title_short Genomic Insight into Differentiation and Selection Sweeps in the Improvement of Upland Cotton
title_sort genomic insight into differentiation and selection sweeps in the improvement of upland cotton
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7356552/
https://www.ncbi.nlm.nih.gov/pubmed/32503111
http://dx.doi.org/10.3390/plants9060711
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