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Genomic signatures and candidate genes of lint yield and fibre quality improvement in Upland cotton in Xinjiang

Xinjiang has been the largest and highest yield cotton production region not only in China, but also in the world. Improvements in Upland cotton cultivars in Xinjiang have occurred via pedigree selection and/or crossing of elite alleles from the former Soviet Union and other cotton producing regions...

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Autores principales: Han, Zegang, Hu, Yan, Tian, Qin, Cao, Yiwen, Si, Aijun, Si, Zhanfeng, Zang, Yihao, Xu, Chenyu, Shen, Weijuan, Dai, Fan, Liu, Xia, Fang, Lei, Chen, Hong, Zhang, Tianzhen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7540456/
https://www.ncbi.nlm.nih.gov/pubmed/32030869
http://dx.doi.org/10.1111/pbi.13356
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author Han, Zegang
Hu, Yan
Tian, Qin
Cao, Yiwen
Si, Aijun
Si, Zhanfeng
Zang, Yihao
Xu, Chenyu
Shen, Weijuan
Dai, Fan
Liu, Xia
Fang, Lei
Chen, Hong
Zhang, Tianzhen
author_facet Han, Zegang
Hu, Yan
Tian, Qin
Cao, Yiwen
Si, Aijun
Si, Zhanfeng
Zang, Yihao
Xu, Chenyu
Shen, Weijuan
Dai, Fan
Liu, Xia
Fang, Lei
Chen, Hong
Zhang, Tianzhen
author_sort Han, Zegang
collection PubMed
description Xinjiang has been the largest and highest yield cotton production region not only in China, but also in the world. Improvements in Upland cotton cultivars in Xinjiang have occurred via pedigree selection and/or crossing of elite alleles from the former Soviet Union and other cotton producing regions of China. But it is unclear how genomic constitutions from foundation parents have been selected and inherited. Here, we deep‐sequenced seven historic foundation parents, comprising four cultivars introduced from the former Soviet Union (108Ф, C1470, 611Б and KK1543) and three from United States and Africa (DPL15, STV2B and UGDM), and re‐sequenced sixty‐nine Xinjiang modern cultivars. Phylogenetic analysis of more than 2 million high‐quality single nucleotide polymorphisms allowed their classification two groups, suggesting that Xinjiang Upland cotton cultivars were not only spawned from 108Ф, C1470, 611Б and KK1543, but also had a close kinship with DPL15, STV2B and UGDM. Notably, identity‐by‐descent (IBD) tracking demonstrated that the former Soviet Union cultivars have made a huge contribution to modern cultivar improvement in Xinjiang. A total of 156 selective sweeps were identified. Among them, apoptosis‐antagonizing transcription factor gene (GhAATF1) and mitochondrial transcription termination factor family protein gene (GhmTERF1) were highly involved in the determination of lint percentage. Additionally, the auxin response factor gene (GhARF3) located in inherited IBD segments from 108Ф and 611Б was highly correlated with fibre quality. These results provide an insight into the genomics of artificial selection for improving cotton production and facilitate next‐generation precision breeding of cotton and other crops.
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spelling pubmed-75404562020-10-09 Genomic signatures and candidate genes of lint yield and fibre quality improvement in Upland cotton in Xinjiang Han, Zegang Hu, Yan Tian, Qin Cao, Yiwen Si, Aijun Si, Zhanfeng Zang, Yihao Xu, Chenyu Shen, Weijuan Dai, Fan Liu, Xia Fang, Lei Chen, Hong Zhang, Tianzhen Plant Biotechnol J Research Articles Xinjiang has been the largest and highest yield cotton production region not only in China, but also in the world. Improvements in Upland cotton cultivars in Xinjiang have occurred via pedigree selection and/or crossing of elite alleles from the former Soviet Union and other cotton producing regions of China. But it is unclear how genomic constitutions from foundation parents have been selected and inherited. Here, we deep‐sequenced seven historic foundation parents, comprising four cultivars introduced from the former Soviet Union (108Ф, C1470, 611Б and KK1543) and three from United States and Africa (DPL15, STV2B and UGDM), and re‐sequenced sixty‐nine Xinjiang modern cultivars. Phylogenetic analysis of more than 2 million high‐quality single nucleotide polymorphisms allowed their classification two groups, suggesting that Xinjiang Upland cotton cultivars were not only spawned from 108Ф, C1470, 611Б and KK1543, but also had a close kinship with DPL15, STV2B and UGDM. Notably, identity‐by‐descent (IBD) tracking demonstrated that the former Soviet Union cultivars have made a huge contribution to modern cultivar improvement in Xinjiang. A total of 156 selective sweeps were identified. Among them, apoptosis‐antagonizing transcription factor gene (GhAATF1) and mitochondrial transcription termination factor family protein gene (GhmTERF1) were highly involved in the determination of lint percentage. Additionally, the auxin response factor gene (GhARF3) located in inherited IBD segments from 108Ф and 611Б was highly correlated with fibre quality. These results provide an insight into the genomics of artificial selection for improving cotton production and facilitate next‐generation precision breeding of cotton and other crops. John Wiley and Sons Inc. 2020-02-29 2020-10 /pmc/articles/PMC7540456/ /pubmed/32030869 http://dx.doi.org/10.1111/pbi.13356 Text en © 2020 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd. This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.
spellingShingle Research Articles
Han, Zegang
Hu, Yan
Tian, Qin
Cao, Yiwen
Si, Aijun
Si, Zhanfeng
Zang, Yihao
Xu, Chenyu
Shen, Weijuan
Dai, Fan
Liu, Xia
Fang, Lei
Chen, Hong
Zhang, Tianzhen
Genomic signatures and candidate genes of lint yield and fibre quality improvement in Upland cotton in Xinjiang
title Genomic signatures and candidate genes of lint yield and fibre quality improvement in Upland cotton in Xinjiang
title_full Genomic signatures and candidate genes of lint yield and fibre quality improvement in Upland cotton in Xinjiang
title_fullStr Genomic signatures and candidate genes of lint yield and fibre quality improvement in Upland cotton in Xinjiang
title_full_unstemmed Genomic signatures and candidate genes of lint yield and fibre quality improvement in Upland cotton in Xinjiang
title_short Genomic signatures and candidate genes of lint yield and fibre quality improvement in Upland cotton in Xinjiang
title_sort genomic signatures and candidate genes of lint yield and fibre quality improvement in upland cotton in xinjiang
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7540456/
https://www.ncbi.nlm.nih.gov/pubmed/32030869
http://dx.doi.org/10.1111/pbi.13356
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