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

doi:10.1016/j.gpb.2022.01.002

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

Genomics Proteomics Bioinformatics. 2022 Feb;20(1):14-28. doi: 10.1016/j.gpb.2022.01.002. Epub 2022 Jan 13.

Authors

Ruicai Long¹, Fan Zhang², Zhiwu Zhang³, Mingna Li¹, Lin Chen¹, Xue Wang¹, Wenwen Liu¹, Tiejun Zhang⁴, Long-Xi Yu⁵, Fei He¹, Xueqian Jiang¹, Xijiang Yang¹, Changfu Yang¹, Zhen Wang⁶, Junmei Kang⁷, Qingchuan Yang⁸

Affiliations

¹ Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
² Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163, USA.
³ Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163, USA.
⁴ School of Grassland Science, Beijing Forestry University, Beijing 100083, China.
⁵ United States Department of Agriculture-Agricultural Research Service, Plant and Germplasm Introduction and Testing Research, Prosser, WA 99350, USA.
⁶ Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China. Electronic address: wangzhen@caas.cn.
⁷ Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China. Electronic address: kangjunmei@caas.cn.
⁸ Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China. Electronic address: yangqingchuan@caas.cn.

Abstract

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.

Keywords: Alfalfa; Autotetraploid; Genome assembly; Genome-wide association study; Resequencing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

DNA Transposable Elements
Genome-Wide Association Study
Medicago sativa* / genetics
Nitrogen
Polymorphism, Single Nucleotide*

Substances

DNA Transposable Elements
Nitrogen