Alfalfa (Medicago sativa ssp. sativa L.) is known as “the queen of forage crops” and a perennial legume forage that is widely cultivated for hay, pasture and silage production. It is used as a rotation crop to increase soil fertility and also has a broad market space and potential for in-depth exploration in medicine and functional health care. Alfalfa has long been used as a medicinal herb. Its seeds or dried leaves can be used as a nutritional supplement and are sold as a bulk powdered herb, capsules, and tablets in health food stores. The extracts from alfalfa seeds and leaves have hypocholesterolemic, neuroprotective, antioxidant, hypolipidemic, and antimicrobial effects. Despite the high economic value of and increasing industrial demand for alfalfa, improvements through breeding are very limited, partly due to a lack of information on the whole genome. Alfalfa is suggested to be an autotetraploid (2n = 4x = 32) subspecies in the M. sativa complex. The recently published genome assembly of an autotetraploid alfalfa is expected to greatly facilitate the future improvement of molecular breeding strategies. However, assembling a complete autotetraploid genome is still challenging due to essential features of tetrasomic inheritance. In this case, assembling the genome of the diploid progenitor could be an alternative way to obtain full genomic information for alfalfa.

Fig. 1 Photographs of alfalfa uses and products.

Recently, Horticulture Research published a research paper “A chromosome-scale genome assembly of a diploid alfalfa, the progenitor of autotetraploid alfalfa” by Prof. Jian-Quan Liu’s team from Lanzhou University.

Medicago sativa spp. caerulea (voucher PI464715; 2n = 2x = 16) was chosen for genome sequencing and assembly. To accurately assemble this highly heterozygous genome, Illumina, Nanopore and Hi-C technologies were adopted for sequencing, and a series of methods were performed for assembly. Approximately 793.2 Mb of genome sequence was oriented on eight pseudochromosomes and its Contig N50 of 3.9 Mb. The transposable elements (TEs) accounted for about 55.55% of the genome, and identified 47,202 protein-coding genes.

Fig. 2 Overview of the PI464715 genome assembly.

Based on the phylogenetic tree and differentiation time of single copy genes. PI464715 displayed a close relationship with M. truncatula and phylogenetically diverged from its common ancestor approximately 5.12 million years ago. Synteny analysis was conducted between the PI464715 genome assembly, the four monoploid genomes of alfalfa and the M. truncatula ecotype Jemalong A17 genome v5.0 to explore their evolution. High collinearity was revealed between our genome with all four subgenomes of alfalfa and for five chromosomes between our genome and the A17 genome by visualizing syntenic blocks. We further detected a pair of large interchromosomal rearrangements between chromosome 4 and chromosome 8 and a large inversion on chromosome 1, as also evident in the dot plots comparing our genome and the A17 genome. In addition, in the PI464615 genome, 489 R genes were detected and 82 and 85 candidate genes involved in the lignin and cellulose biosynthesis pathways, respectively. The near-complete and accurate diploid alfalfa reference genome obtained herein serves as an important complement to the recently assembled autotetraploid alfalfa genome and will provide valuable genomic resources for investigating the genomic architecture of autotetraploid alfalfa as well as for improving breeding strategies in alfalfa.

Fig. 3 Gene synteny between the M. truncatula ecotype Jemalong A17, PI464715 and alfalfa genomes.

Fig. 4 Expression of lignin and cellulose biosynthesis genes in leaf and stem tissues.

Young researcher Guang-Peng Ren and Yong-Zhi Yang are authors for correspondence. PhD students Li Ao and Liu Ai are first authors. This work was supported equally by the Second Tibetan Plateau Scientific Expedition and Research (STEP) program (2019QZKK0502) and the National Natural Science Foundation of China (31971391) and further supported by the National Natural Science Foundation of China (41901056).

Link: https://www.nature.com/articles/s41438-020-00417-7