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High-quality genome assembly and pan-genome studies facilitate genetic discovery in mung bean and its improvement

Mung bean is an economically important legume crop species that is used as a food, consumed as a vegetable, and used as an ingredient and even as a medicine. To explore the genomic diversity of mung bean, we assembled a high-quality reference genome (Vrad_JL7) that was ∼479.35 Mb in size, with a con...

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Autores principales: Liu, Changyou, Wang, Yan, Peng, Jianxiang, Fan, Baojie, Xu, Dongxu, Wu, Jing, Cao, Zhimin, Gao, Yunqing, Wang, Xueqing, Li, Shutong, Su, Qiuzhu, Zhang, Zhixiao, Wang, Shen, Wu, Xingbo, Shang, Qibing, Shi, Huiying, Shen, Yingchao, Wang, Bingbing, Tian, Jing
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9700124/
https://www.ncbi.nlm.nih.gov/pubmed/35752938
http://dx.doi.org/10.1016/j.xplc.2022.100352
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author Liu, Changyou
Wang, Yan
Peng, Jianxiang
Fan, Baojie
Xu, Dongxu
Wu, Jing
Cao, Zhimin
Gao, Yunqing
Wang, Xueqing
Li, Shutong
Su, Qiuzhu
Zhang, Zhixiao
Wang, Shen
Wu, Xingbo
Shang, Qibing
Shi, Huiying
Shen, Yingchao
Wang, Bingbing
Tian, Jing
author_facet Liu, Changyou
Wang, Yan
Peng, Jianxiang
Fan, Baojie
Xu, Dongxu
Wu, Jing
Cao, Zhimin
Gao, Yunqing
Wang, Xueqing
Li, Shutong
Su, Qiuzhu
Zhang, Zhixiao
Wang, Shen
Wu, Xingbo
Shang, Qibing
Shi, Huiying
Shen, Yingchao
Wang, Bingbing
Tian, Jing
author_sort Liu, Changyou
collection PubMed
description Mung bean is an economically important legume crop species that is used as a food, consumed as a vegetable, and used as an ingredient and even as a medicine. To explore the genomic diversity of mung bean, we assembled a high-quality reference genome (Vrad_JL7) that was ∼479.35 Mb in size, with a contig N50 length of 10.34 Mb. A total of 40,125 protein-coding genes were annotated, representing ∼96.9% of the genetic region. We also sequenced 217 accessions, mainly landraces and cultivars from China, and identified 2,229,343 high-quality single-nucleotide polymorphisms (SNPs). Population structure revealed that the Chinese accessions diverged into two groups and were distinct from non-Chinese lines. Genetic diversity analysis based on genomic data from 750 accessions in 23 countries supported the hypothesis that mung bean was first domesticated in south Asia and introduced to east Asia probably through the Silk Road. We constructed the first pan-genome of mung bean germplasm and assembled 287.73 Mb of non-reference sequences. Among the genes, 83.1% were core genes and 16.9% were variable. Presence/absence variation (PAV) events of nine genes involved in the regulation of the photoperiodic flowering pathway were identified as being under selection during the adaptation process to promote early flowering in the spring. Genome-wide association studies (GWASs) revealed 2,912 SNPs and 259 gene PAV events associated with 33 agronomic traits, including a SNP in the coding region of the SWEET10 homolog (jg24043) involved in crude starch content and a PAV event in a large fragment containing 11 genes for color-related traits. This high-quality reference genome and pan-genome will provide insights into mung bean breeding.
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spelling pubmed-97001242022-11-27 High-quality genome assembly and pan-genome studies facilitate genetic discovery in mung bean and its improvement Liu, Changyou Wang, Yan Peng, Jianxiang Fan, Baojie Xu, Dongxu Wu, Jing Cao, Zhimin Gao, Yunqing Wang, Xueqing Li, Shutong Su, Qiuzhu Zhang, Zhixiao Wang, Shen Wu, Xingbo Shang, Qibing Shi, Huiying Shen, Yingchao Wang, Bingbing Tian, Jing Plant Commun Research Article Mung bean is an economically important legume crop species that is used as a food, consumed as a vegetable, and used as an ingredient and even as a medicine. To explore the genomic diversity of mung bean, we assembled a high-quality reference genome (Vrad_JL7) that was ∼479.35 Mb in size, with a contig N50 length of 10.34 Mb. A total of 40,125 protein-coding genes were annotated, representing ∼96.9% of the genetic region. We also sequenced 217 accessions, mainly landraces and cultivars from China, and identified 2,229,343 high-quality single-nucleotide polymorphisms (SNPs). Population structure revealed that the Chinese accessions diverged into two groups and were distinct from non-Chinese lines. Genetic diversity analysis based on genomic data from 750 accessions in 23 countries supported the hypothesis that mung bean was first domesticated in south Asia and introduced to east Asia probably through the Silk Road. We constructed the first pan-genome of mung bean germplasm and assembled 287.73 Mb of non-reference sequences. Among the genes, 83.1% were core genes and 16.9% were variable. Presence/absence variation (PAV) events of nine genes involved in the regulation of the photoperiodic flowering pathway were identified as being under selection during the adaptation process to promote early flowering in the spring. Genome-wide association studies (GWASs) revealed 2,912 SNPs and 259 gene PAV events associated with 33 agronomic traits, including a SNP in the coding region of the SWEET10 homolog (jg24043) involved in crude starch content and a PAV event in a large fragment containing 11 genes for color-related traits. This high-quality reference genome and pan-genome will provide insights into mung bean breeding. Elsevier 2022-06-26 /pmc/articles/PMC9700124/ /pubmed/35752938 http://dx.doi.org/10.1016/j.xplc.2022.100352 Text en © 2022 The Author(s) https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Research Article
Liu, Changyou
Wang, Yan
Peng, Jianxiang
Fan, Baojie
Xu, Dongxu
Wu, Jing
Cao, Zhimin
Gao, Yunqing
Wang, Xueqing
Li, Shutong
Su, Qiuzhu
Zhang, Zhixiao
Wang, Shen
Wu, Xingbo
Shang, Qibing
Shi, Huiying
Shen, Yingchao
Wang, Bingbing
Tian, Jing
High-quality genome assembly and pan-genome studies facilitate genetic discovery in mung bean and its improvement
title High-quality genome assembly and pan-genome studies facilitate genetic discovery in mung bean and its improvement
title_full High-quality genome assembly and pan-genome studies facilitate genetic discovery in mung bean and its improvement
title_fullStr High-quality genome assembly and pan-genome studies facilitate genetic discovery in mung bean and its improvement
title_full_unstemmed High-quality genome assembly and pan-genome studies facilitate genetic discovery in mung bean and its improvement
title_short High-quality genome assembly and pan-genome studies facilitate genetic discovery in mung bean and its improvement
title_sort high-quality genome assembly and pan-genome studies facilitate genetic discovery in mung bean and its improvement
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9700124/
https://www.ncbi.nlm.nih.gov/pubmed/35752938
http://dx.doi.org/10.1016/j.xplc.2022.100352
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