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Genome Assembly of Alfalfa Cultivar Zhongmu-4 and Identification of SNPs Associated with Agronomic Traits

Alfalfa (Medicago sativa L.) is the most important legume forage crop worldwide with high nutritional value and yield. For a long time, the breeding of alfalfa was hampered by lacking reliable information on the autotetraploid genome and molecular markers linked to important agronomic traits. We her...

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Autores principales: Long, Ruicai, Zhang, Fan, Zhang, Zhiwu, Li, Mingna, Chen, Lin, Wang, Xue, Liu, Wenwen, Zhang, Tiejun, Yu, Long-Xi, He, Fei, Jiang, Xueqian, Yang, Xijiang, Yang, Changfu, Wang, Zhen, Kang, Junmei, Yang, Qingchuan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9510860/
https://www.ncbi.nlm.nih.gov/pubmed/35033678
http://dx.doi.org/10.1016/j.gpb.2022.01.002
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author Long, Ruicai
Zhang, Fan
Zhang, Zhiwu
Li, Mingna
Chen, Lin
Wang, Xue
Liu, Wenwen
Zhang, Tiejun
Yu, Long-Xi
He, Fei
Jiang, Xueqian
Yang, Xijiang
Yang, Changfu
Wang, Zhen
Kang, Junmei
Yang, Qingchuan
author_facet Long, Ruicai
Zhang, Fan
Zhang, Zhiwu
Li, Mingna
Chen, Lin
Wang, Xue
Liu, Wenwen
Zhang, Tiejun
Yu, Long-Xi
He, Fei
Jiang, Xueqian
Yang, Xijiang
Yang, Changfu
Wang, Zhen
Kang, Junmei
Yang, Qingchuan
author_sort Long, Ruicai
collection PubMed
description Alfalfa (Medicago sativa L.) is the most important legume forage crop worldwide with high nutritional value and yield. For a long time, the breeding of alfalfa was hampered by lacking reliable information on the autotetraploid genome and molecular markers linked to important agronomic traits. We herein reported the de novo assembly of the allele-aware chromosome-level genome of Zhongmu-4, a cultivar widely cultivated in China, and a comprehensive database of genomic variations based on resequencing of 220 germplasms. Approximate 2.74 Gb contigs (N50 of 2.06 Mb), accounting for 88.39% of the estimated genome, were assembled, and 2.56 Gb contigs were anchored to 32 pseudo-chromosomes. A total of 34,922 allelic genes were identified from the allele-aware genome. We observed the expansion of gene families, especially those related to the nitrogen metabolism, and the increase of repetitive elements including transposable elements, which probably resulted in the increase of Zhongmu-4 genome compared with Medicago truncatula. Population structure analysis revealed that the accessions from Asia and South America had relatively lower genetic diversity than those from Europe, suggesting that geography may influence alfalfa genetic divergence during local adaption. Genome-wide association studies identified 101 single nucleotide polymorphisms (SNPs) associated with 27 agronomic traits. Two candidate genes were predicted to be correlated with fall dormancy and salt response. We believe that the allele-aware chromosome-level genome sequence of Zhongmu-4 combined with the resequencing data of the diverse alfalfa germplasms will facilitate genetic research and genomics-assisted breeding in variety improvement of alfalfa.
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spelling pubmed-95108602022-09-27 Genome Assembly of Alfalfa Cultivar Zhongmu-4 and Identification of SNPs Associated with Agronomic Traits Long, Ruicai Zhang, Fan Zhang, Zhiwu Li, Mingna Chen, Lin Wang, Xue Liu, Wenwen Zhang, Tiejun Yu, Long-Xi He, Fei Jiang, Xueqian Yang, Xijiang Yang, Changfu Wang, Zhen Kang, Junmei Yang, Qingchuan Genomics Proteomics Bioinformatics Original Research Alfalfa (Medicago sativa L.) is the most important legume forage crop worldwide with high nutritional value and yield. For a long time, the breeding of alfalfa was hampered by lacking reliable information on the autotetraploid genome and molecular markers linked to important agronomic traits. We herein reported the de novo assembly of the allele-aware chromosome-level genome of Zhongmu-4, a cultivar widely cultivated in China, and a comprehensive database of genomic variations based on resequencing of 220 germplasms. Approximate 2.74 Gb contigs (N50 of 2.06 Mb), accounting for 88.39% of the estimated genome, were assembled, and 2.56 Gb contigs were anchored to 32 pseudo-chromosomes. A total of 34,922 allelic genes were identified from the allele-aware genome. We observed the expansion of gene families, especially those related to the nitrogen metabolism, and the increase of repetitive elements including transposable elements, which probably resulted in the increase of Zhongmu-4 genome compared with Medicago truncatula. Population structure analysis revealed that the accessions from Asia and South America had relatively lower genetic diversity than those from Europe, suggesting that geography may influence alfalfa genetic divergence during local adaption. Genome-wide association studies identified 101 single nucleotide polymorphisms (SNPs) associated with 27 agronomic traits. Two candidate genes were predicted to be correlated with fall dormancy and salt response. We believe that the allele-aware chromosome-level genome sequence of Zhongmu-4 combined with the resequencing data of the diverse alfalfa germplasms will facilitate genetic research and genomics-assisted breeding in variety improvement of alfalfa. Elsevier 2022-02 2022-01-13 /pmc/articles/PMC9510860/ /pubmed/35033678 http://dx.doi.org/10.1016/j.gpb.2022.01.002 Text en © 2022 Beijing Institute of Genomics https://creativecommons.org/licenses/by/4.0/This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Original Research
Long, Ruicai
Zhang, Fan
Zhang, Zhiwu
Li, Mingna
Chen, Lin
Wang, Xue
Liu, Wenwen
Zhang, Tiejun
Yu, Long-Xi
He, Fei
Jiang, Xueqian
Yang, Xijiang
Yang, Changfu
Wang, Zhen
Kang, Junmei
Yang, Qingchuan
Genome Assembly of Alfalfa Cultivar Zhongmu-4 and Identification of SNPs Associated with Agronomic Traits
title Genome Assembly of Alfalfa Cultivar Zhongmu-4 and Identification of SNPs Associated with Agronomic Traits
title_full Genome Assembly of Alfalfa Cultivar Zhongmu-4 and Identification of SNPs Associated with Agronomic Traits
title_fullStr Genome Assembly of Alfalfa Cultivar Zhongmu-4 and Identification of SNPs Associated with Agronomic Traits
title_full_unstemmed Genome Assembly of Alfalfa Cultivar Zhongmu-4 and Identification of SNPs Associated with Agronomic Traits
title_short Genome Assembly of Alfalfa Cultivar Zhongmu-4 and Identification of SNPs Associated with Agronomic Traits
title_sort genome assembly of alfalfa cultivar zhongmu-4 and identification of snps associated with agronomic traits
topic Original Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9510860/
https://www.ncbi.nlm.nih.gov/pubmed/35033678
http://dx.doi.org/10.1016/j.gpb.2022.01.002
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