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ARS Home » Pacific West Area » Pullman, Washington » Plant Germplasm Introduction and Testing Research » Research » Publications at this Location » Publication #388910
Research Project: Enhancing Resistance to Biotic and Abiotic Stresses in Alfalfa

Location: Plant Germplasm Introduction and Testing Research

Title: Genome assembly of alfalfa cultivar Zhongmu-4 and identification of SNPs associated with agronomic traits

Author
item LONG, RUICAI - Chinese Academy Of Agricultural Sciences
item ZHANG, FAN - Chinese Academy Of Agricultural Sciences
item ZHANG, ZHIWU - Washington State University
item LI, MINGNA - Chinese Academy Of Agricultural Sciences
item CHEN, LIN - Chinese Academy Of Agricultural Sciences
item WANG, XUE - Chinese Academy Of Agricultural Sciences
item LIU, WENWEN - Chinese Academy Of Agricultural Sciences
item ZHANG, TIEJUN - Chinese Academy Of Agricultural Sciences
item Yu, Long-Xi
item HE, FEI - Chinese Academy Of Agricultural Sciences
item JIANG, XUEQIAN - Chinese Academy Of Agricultural Sciences
item YANG, XIJIAN - Chinese Academy Of Agricultural Sciences
item YANG, CHANGFU - Chinese Academy Of Agricultural Sciences
item WANG, ZHEN - Chinese Academy Of Agricultural Sciences
item KANG, JUNMEI - Chinese Academy Of Agricultural Sciences
item YANG, Q - Chinese Academy Of Agricultural Sciences

Submitted to: Genomics, Proteomics and Bioinformatics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/7/2022
Publication Date: 1/13/2022
Citation: Long, R., Zhang, F., Zhang, Z., Li, M., Chen, L., Wang, X., Liu, W., Zhang, T., Yu, L., He, F., Jiang, X., Yang, X., Yang, C., Wang, Z., Kang, J., Yang, Q. 2022. Genome assembly of alfalfa cultivar Zhongmu-4 and identification of SNPs associated with agronomic traits. Genomics, Proteomics and Bioinformatics. 20(1):14-28. https://doi.org/10.1016/j.gpb.2022.01.002.
DOI: https://doi.org/10.1016/j.gpb.2022.01.002

Interpretive Summary: 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. In the present study, we report the whole genome sequence of Zhongmu-4 (ZM-4), one of the most planted cultivars in China. The sequence information can be used as reference genetic and genomic assessments for all alfalfa varieties.

Technical Abstract: 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.