Alfalfa (Medicago sativa L.)

Database: Legume Information System

                          PGSB Medicago MT3 genome database

Shen et al. (2020) genome assembly available here.

Karyotype: 2n=2x=16; cultivated 2n=4x=32

Blondon F, Marie D, Brown S et al. (1994). Genome size and base composition in Medicago sativa and M. truncatula species. Genome 37: 264-270. link

Barnes DK, Goplen BP, Baylor JE. (1988). Highlights in the USA and Canada. In: Hanson, AA, Barnes DK, and Baylor RR (eds.) Alfalfa and Alfalfa improvement. Journal of the American Society of Agronomy Monograph 29: 1-24. link

Genome size (1C, Mb): 1682 (2n=4x=32)

Pustahija F, Brown SC, Bogunic F et al. (2013). Small genomes dominate in plants growing on serpentine soils in West Balkans, an exhaustive study of 8 habitats covering 308 taxa. Plant and Soil 373: 427-453. link

Genetic maps:

He F, Long R, Zhang T et al. (2020). Quantitative trait locus mapping of yield and plant height in autotetraploid alfalfa (Medicago sativa L.). The Crop Journal 8(5): 812-818. link

He F, Kang J, Zhang F et al. (2019). Genetic mapping of leaf-related traits in autotetraploid alfalfa (Medicago sativa L.). Molecular Breeding 39: 147. link

Li X, Wei Y, Acharya A et al. (2014). A saturated genetic linkage map of autotetraploid Alfalfa (Medicago sativa L.) developed using genotyping-by-sequencing is highly syntenous with the Medicago truncatula. Genome. G3 4: 1971-1979. link

Kaló P, Endre G, Zimánneyi L et al. (2000). Construction of an improved linkage map of diploid alfalfa (Medicago sativa). Theoretical and Applied Genetics 100: 641-657. link


cpDNA sequencing: 128,574 bp

Wu S, Chen J, Li Y et al. (2021). Extensive genomic rearrangements mediated by repetitive sequences in plastomes of Medicago and its relatives. BMC Plant Biology 21: 1-16. link

Yang C, Wu X, Guo X et al. (2019). The complete chloroplast genome of Medicago sativa cv. Hangmu No.1, a plant of space mutation breeding. Mitochondrial DNA Part B 4: 603-604. link

Tao X, Ma L, Zhang Z et al. (2017). Characterization of the complete chloroplast genome of alfalfa (Medicago sativa) (Leguminosae). Gene Reports 6: 67-73. link

Whole genome sequencing:

Shen C, Du H, Chen Z et al. (2020). The chromosome-level genome sequence of the autotetraploid alfalfa and resequencing of core germplasms provide genomic resources for Alfalfa research. Molecular Plant. link

Transcriptome sequencing:

Liu J, Wang T, Weng Y et al. (2022). Identification and Characterization of Regulatory Pathways Controlling Dormancy Under Lower Temperature in Alfalfa (Medicago sativa L.). Frontiers in Plant Science 1930. link

Li J, Ma M, Sun Y et al. (2022). Comparative physiological and transcriptome profiles uncover salt tolerance mechanisms in Alfalfa. Frontiers in Plant Science 1930. link

Wang X, Kang W, Wu F et al. (2022). Comparative transcriptome analysis reveals new insight of alfalfa (Medicago sativa L.) cultivars in response to abrupt freezing stress. Frontiers in Plant Science 937. link

Bhattarai S, Fu Y-B, Coulman B et al. (2021). Transcriptomic analysis of differentially expressed genes in leaves and roots of two alfalfa (Medicago sativa L.) cultivars with different salt tolerance. BMC Plant Biology 21:1-16. link

Qiaoli M, Xie Y, Xu X et al. (2021). Comparative analysis of alfalfa (Medicago sativa L.) seedling transcriptomes reveals genotype-specific drought tolerance mechanisms. Plant Physiology and Biochemistry. link

Ma D, Liu B, Ge L et al. (2021). Identification and characterization of regulatory pathways involved in early flowering in the new leaves of alfalfa (Medicago sativa L.) by transcriptome analysis. BMC Plant Biology 21:1-14. link

Duan HR, Wang LR, Cui GX et al. (2020). Identification of the regulatory networks and hub genes controlling alfalfa floral pigmentation variation using RNA-sequencing analysis. BMC Plant Biology 20:1-17. link

Yuan J, Sun X, Guo T et al. (2020). Global transcriptome analysis of alfalfa reveals six key biological processes of senescent leaves. PEERJ 8: e8426. link

Chao Y, Yuan J, Guo T et al. (2019). Analysis of transcripts and splice isoforms in Medicago sativa L. by single-molecule long-read sequencing. Plant Molecular Biology 99: 219-235. link

Luo D, Zhou Q, Wu Y et al. (2019). Full-length transcript sequencing and comparative transcriptomic analysis to evaluate the contribution of osmotic and ionic stress components towards salinity tolerance in the roots of cultivated alfalfa (Medicago sativa L.). BMC Plant Biology 19: 32. link

Luo D, Wu Y, Liu J et al. (2019). Comparative transcriptomic and physiological analyses of Medicago sativa L. indicates that multiple regulatory networks are activated during continuous aba treatment. International Journal of Molecular Sciences 20: 47. link

Zeng N, Yang Z, Zhang Z et al. (2019). Comparative transcriptome combined with proteome analyses revealed key factors involved in Alfalfa (Medicago sativa) response to waterlogging stress. International Journal of Molecular Sciences 20: 1359. link

Tu XB, Zhao HL, Zhang ZH (2018). Transcriptome approach to understand the potential mechanisms of resistant and susceptible alfalfa (Medicago sativa L.) cultivars in response to aphid feeding. Journal of Integrative Agriculture 17: 2518-2527. link

O'Rourke JA, Fu F, Bucciarelli B et al. (2015). The Medicago sativa gene index 1.2: a web-accessible gene expression atlas for investigating expression differences between Medicago sativa subspecies. BMC Genomics 16: 502. link

Postnikova OA, Hult M, Shao J et al. (2015). Transcriptome analysis of resistant and susceptible alfalfa cultivars infected with root-knot nematode Meloidogyne incognita. PLoS One 10: e0118269. link

Zhang S, Shi Y, Cheng N et al. (2015). De novo characterization of fall dormant and nondormant alfalfa (Medicago sativa L.) leaf transcriptome and identification of candidate genes related to fall dormancy. PLoS One, 10: e0122170. link

Liu Z, Chen T, Ma L et al. (2013). Global transcriptome sequencing using the illumina platform and the development of EST-SSR markers in autotetraploid Alfalfa. PloS One 8: e83549. link

Han Y, Kang Y, Torres-Jerez I et al. (2011). Genome-wide SNP discovery in tetraploid alfalfa using 454 sequencing and high resolution melting analysis. BMC Genomics 12: 1-11. link

Yang SS, Tu ZJ, Cheung F et al. (2011). Using RNA-seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems. BMC Genomics 12: 1-19. link

Yang SS, Xu WW, Tesfaye M et al. (2009). Single-feature polymorphism discovery in the transcriptome of tetraploid Alfalfa. Plant Genome 2: 224-232. link


He F, Wei C, Zhang Y et al. (2022). A Genome-wide association analysis coupled with transcriptome analysis reveals candidate genes related to salt stress in Alfalfa (Medicago sativa L.). Frontiers in Plant Science 12: 826584-826584. link

Lin S, Medina CA, Boge B et al. (2020). Identification of genetic loci associated with forage quality in response to water deficit in autotetraploid alfalfa (Medicago sativa L.). BMC Plant Biology 20(1): 1-18. link

Wang Z, Wang X, Zhang H et al. (2020). A genome-wide association study approach to the identification of candidate genes underlying agronomic traits in alfalfa (Medicago sativa L.). Plant Biotechnology Journal 18(3): 611-613. link

Shen C, Du H, Chen Z et al. (2020). The chromosome-level genome sequence of the autotetraploid alfalfa and resequencing of core germplasms provide genomic resources for Alfalfa research. Molecular Plant. link

Kang Y, Torres-Jerez I, An Z et al. (2018). Genome-wide association analysis of salinity responsive traits in Medicago truncatula. Plant, Cell & Environment 42: 1513-1531. link

Liu XP, Yu LX (2017). Genome-Wide Association Mapping of Loci Associated with Plant Growth and Forage Production under Salt Stress in Alfalfa (Medicago sativa L.). Frontiers in Plant Science 8:853. link

Kang Y, Sakiroglu M, Krom M et al. (2015). Genome-wide association of drought-related and biomass traits with HapMap SNPs in Medicago truncatula. Plant, Cell & Environment 38: 1997-2011. link

Stanton-Geddes J, Paape T, Epstein B et al. (2013). Candidate genes and genetic architecture of symbiotic and agronomic traits revealed by whole-genome, sequence-based association genetics in Medicago truncatula. PLoS One 8:e65688. link