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Assembly of chromosome-scale and allele-aware autotetraploid genome of the Chinese alfalfa cultivar Zhongmu-4 and identification of SNP loci associated with 27 agronomic traits

Ruicai Long, Fan Zhang, View ORCID ProfileZhiwu Zhang, Mingna Li, Lin Chen, Xue Wang, Wenwen Liu, Tiejun Zhang, Long-Xi Yu, Fei He, Xueqian Jiang, Xijiang Yang, Changfu Yang, Zhen Wang, Junmei Kang, Qingchuan Yang
doi: https://doi.org/10.1101/2021.02.21.428692
Ruicai Long
1Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Fan Zhang
1Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
2Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
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Zhiwu Zhang
2Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
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  • ORCID record for Zhiwu Zhang
Mingna Li
1Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Lin Chen
1Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Xue Wang
1Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Wenwen Liu
1Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Tiejun Zhang
3School of Grassland Science, Beijing Forestry University, Beijing, China
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Long-Xi Yu
4United States Department of Agriculture-Agricultural Research Service, Plant Germplasm Introduction and Testing Research, Prosser, WA, USA
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Fei He
1Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Xueqian Jiang
1Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Xijiang Yang
1Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Changfu Yang
1Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Zhen Wang
1Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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  • For correspondence: wangzhen@caas.cn kangjunmei@caas.cn qchyang66@163.com
Junmei Kang
1Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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  • For correspondence: wangzhen@caas.cn kangjunmei@caas.cn qchyang66@163.com
Qingchuan Yang
1Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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  • For correspondence: wangzhen@caas.cn kangjunmei@caas.cn qchyang66@163.com
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Abstract

Alfalfa (Medicago sativa L.), the most valuable perennial legume crop, referred to as “Queen of the Forages” for its high nutritional value and yield production among forage crops. Comprehensive genomic information of germplasm resources from different ecological regions and modern breeding strategies, such as molecular-marker assisted breeding are of great importance to breed new alfalfa varieties with environmental resilience. Here, we report assembly of the genome sequence of Zhongmu-4 (ZM-4), one of the most planted cultivars in China, and identification of SNPs associated with alfalfa agronomic traits by Genome-wide Association Studies (GWAS). Sequence of 32 allelic chromosomes was assembled successfully by single molecule real time sequencing and Hi-C technique with ALLHiC algorithm. About 2.74 Gbp contigs, accounting for 88.39% of the estimated genome, were assembled with 2.56 Gbp contigs anchored to 32 pseudo-chromosomes. In comparison with M. truncatula A17, distinctive inversion and translocation on chromosome 1, and between chromosome 4 and 8, respectively, were detected. Moreover, we conducted resequencing of 220 alfalfa accessions collected globally and performed GWAS analysis based on our assembled genome. Population structure analysis demonstrated that alfalfa has a complex genetic relationship among germplasm with different geographic origins. GWAS identified 101 SNPs associated with 27 out of 93 agronomic traits. The updated chromosome-scale and allele-aware genome sequence, coupled with the resequencing data of most global alfalfa germplasm, provides valuable information for alfalfa genetic research, and further analysis of major SNP loci will accelerate unravelling the molecular basis of important agronomic traits and facilitate genetic improvement of alfalfa.

Competing Interest Statement

The authors have declared no competing interest.

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Posted February 22, 2021.
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Assembly of chromosome-scale and allele-aware autotetraploid genome of the Chinese alfalfa cultivar Zhongmu-4 and identification of SNP loci associated with 27 agronomic traits
Ruicai Long, Fan Zhang, Zhiwu Zhang, Mingna Li, Lin Chen, Xue Wang, Wenwen Liu, Tiejun Zhang, Long-Xi Yu, Fei He, Xueqian Jiang, Xijiang Yang, Changfu Yang, Zhen Wang, Junmei Kang, Qingchuan Yang
bioRxiv 2021.02.21.428692; doi: https://doi.org/10.1101/2021.02.21.428692
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Assembly of chromosome-scale and allele-aware autotetraploid genome of the Chinese alfalfa cultivar Zhongmu-4 and identification of SNP loci associated with 27 agronomic traits
Ruicai Long, Fan Zhang, Zhiwu Zhang, Mingna Li, Lin Chen, Xue Wang, Wenwen Liu, Tiejun Zhang, Long-Xi Yu, Fei He, Xueqian Jiang, Xijiang Yang, Changfu Yang, Zhen Wang, Junmei Kang, Qingchuan Yang
bioRxiv 2021.02.21.428692; doi: https://doi.org/10.1101/2021.02.21.428692

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