Adhikari L, Mohseni-Moghadam M, Missaoui A (2018) Allelopathic effects of cereal rye on weed suppression and forage yield in Alfalfa. American Journal of Plant Sciences 9:685
Annicchiarico P, Nazzicari N, Li X, Wei Y, Pecetti L, Brummer EC (2015) Accuracy of genomic selection for alfalfa biomass yield in different reference populations. BMC genomics 16:1-13
Avci M, Hatipoglu R, Çinar S, Kiliçalp N (2018) Assessment of yield and quality characteristics of alfalfa (Medicago sativa L.) cultivars with different fall dormancy rating. Legume Research 41:369-373
Barnes D (1977) Alfalfa germplasm in the United States: Genetic vulnerability, use, improvement, and maintenance. Department of Agriculture, Agricultural Research Service
Barnes D, RE S, LJ E (1979) Fall dormancy in alfalfa: A valuable predictive tool
Bertrand A, Bipfubusa M, Claessens A, Rocher S, Castonguay Y (2017) Effect of photoperiod prior to cold acclimation on freezing tolerance and carbohydrate metabolism in alfalfa (Medicago sativa L.). Plant Science 264:122-128
Biazzi E, Nazzicari N, Pecetti L, Brummer EC, Palmonari A, Tava A, Annicchiarico P (2017) Genome-wide association mapping and genomic selection for alfalfa (Medicago sativa) forage quality traits. PLoS One 12:e0169234
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114-2120
Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633-2635
Chao Y, Zhang T, Yang Q, Kang J, Sun Y, Gruber MY, Qin Z (2014) Expression of the alfalfa CCCH-type zinc finger protein gene MsZFN delays flowering time in transgenic Arabidopsis thaliana. Plant Science 215:92-99
Chen H, Zeng Y, Yang Y, Huang L, Tang B, Zhang H, Hao F, Liu W, Li Y, Liu Y (2020) Allele-aware chromosome-level genome assembly and efficient transgene-free genome editing for the autotetraploid cultivated alfalfa. Nature communications 11:1-11
Chen J-R, Lü J-J, Liu R, Xiong X-Y, Wang T-x, Chen S-Y, Guo L-B, Wang H-F (2010) DREB1C from Medicago truncatula enhances freezing tolerance in transgenic M. truncatula and China Rose (Rosa chinensis Jacq.). Plant Growth Regulation 60:199-211
Cunningham S, Gana J, Volenec J, Teuber L (2001) Winter hardiness, root physiology, and gene expression in successive fall dormancy selections from ‘Mesilla’and ‘CUF 101’alfalfa. Crop science 41:1091-1098
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST (2011) The variant call format and VCFtools. Bioinformatics 27:2156-2158
Du H, Shi Y, Li D, Fan W, Wang G, Wang C (2017) Screening and identification of key genes regulating fall dormancy in alfalfa leaves. PloS one 12:e0188964
Du H, Shi Y, Li D, Fan W, Wang Y, Wang G, Wang C (2018) Proteomics reveals key proteins participating in growth difference between fall dormant and non-dormant alfalfa in terminal buds. Journal of proteomics 173:126-138
Heller R, Yekutieli D (2014) Replicability analysis for genome-wide association studies. The Annals of Applied Statistics 8:481-498
Herrmann D, Barre P, Santoni S, Julier B (2010) Association of a CONSTANS-LIKE gene to flowering and height in autotetraploid alfalfa. Theoretical and applied genetics 121:865-876
Huang M, Liu X, Zhou Y, Summers RM, Zhang Z (2019) BLINK: a package for the next level of genome-wide association studies with both individuals and markers in the millions. GigaScience 8:giy154
Huang X, Kurata N, Wang Z-X, Wang A, Zhao Q, Zhao Y, Liu K, Lu H, Li W, Guo Y (2012) A map of rice genome variation reveals the origin of cultivated rice. Nature 490:497-501
Jia C, Wu X, Chen M, Wang Y, Liu X, Gong P, Xu Q, Wang X, Gao H, Wang Z (2017) Identification of genetic loci associated with crude protein and mineral concentrations in alfalfa (Medicago sativa) using association mapping. BMC plant biology 17:1-7
Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK (2012) VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome research 22:568-576
Li H (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv:13033997
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078-2079
Li X, Alarcón‐Zúñiga B, Kang J, Nadeem Tahir MH, Jiang Q, Wei Y, Reyno R, Robins JG, Brummer EC (2015) Mapping fall dormancy and winter injury in tetraploid alfalfa. Crop Science 55:1995-2011
Li X, Brummer EC (2012) Applied genetics and genomics in alfalfa breeding. Agronomy 2:40-61
Li X, Han Y, Wei Y, Acharya A, Farmer AD, Ho J, Monteros MJ, Brummer EC (2014) Development of an alfalfa SNP array and its use to evaluate patterns of population structure and linkage disequilibrium. PLoS One 9:e84329
Ligges U, Mächler M (2002) Scatterplot3d-an r package for visualizing multivariate data. Technical Report
Lin S, Medina CA, Boge B, Hu J, Fransen S, Norberg S, Yu L-X (2020) Identification of genetic loci associated with forage quality in response to water deficit in autotetraploid alfalfa (Medicago sativa L.). BMC Plant Biology 20:1-18
Lin X (2019) Reproducibility and replicability in large scale genetic studies. National Academies Press
Liu X-P, Yu L-X (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
Liu Z-Y, Baoyin T, Li X-L, Wang Z-L (2019) How fall dormancy benefits alfalfa winter-survival? Physiologic and transcriptomic analyses of dormancy process. BMC plant biology 19:1-13
Long R, Zhang F, Zhang Z, Li M, Chen L, Wang X, Liu W, Zhang T, Yu L-X, He F (2021) 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. bioRxiv
Michaud R, Lehman W, Rumbaugh M (1988) World distribution and historical development. Alfalfa and alfalfa improvement 29:25-91
Munjal G, Hao J, Teuber LR, Brummer EC (2018) Selection mapping identifies loci underpinning autumn dormancy in alfalfa (Medicago sativa). G3: Genes, Genomes, Genetics 8:461-468
Novillo F, Alonso JM, Ecker JR, Salinas J (2004) CBF2/DREB1C is a negative regulator of CBF1/DREB1B and CBF3/DREB1A expression and plays a central role in stress tolerance in Arabidopsis. Proceedings of the National Academy of Sciences 101:3985-3990
Peterson BG, Carl P, Boudt K, Bennett R, Ulrich J, Zivot E, Cornilly D, Hung E, Lestel M, Balkissoon K (2018) Package ‘performanceanalytics’. R Team Cooperation
Prosperi J-M, Jenczewski E, Muller M-H, Fourtier S, Sampoux J-P, Ronfort J (2014) Alfalfa domestication history, genetic diversity and genetic resources. Legume Perspectives 4:13-14
Qiang H, Chen Z, Zhang Z, Wang X, Gao H, Wang Z (2015) Molecular diversity and population structure of a worldwide collection of cultivated tetraploid alfalfa (Medicago sativa subsp. sativa L.) germplasm as revealed by microsatellite markers. PLoS One 10:e0124592
Rietveld CA, Conley D, Eriksson N, Esko T, Medland SE, Vinkhuyzen AA, Yang J, Boardman JD, Chabris CF, Dawes CT (2014) Replicability and robustness of genome-wide-association studies for behavioral traits. Psychological science 25:1975-1986
Sakiroglu M, Brummer EC (2017) Identification of loci controlling forage yield and nutritive value in diploid alfalfa using GBS-GWAS. Theoretical and applied genetics 130:261-268
Şakiroğlu M, Doyle JJ, Brummer EC (2010) Inferring population structure and genetic diversity of broad range of wild diploid alfalfa (Medicago sativa L.) accessions using SSR markers. Theoretical and applied genetics 121:403-415
Scossa F, Alseekh S, Fernie AR (2021) Integrating multi-omics data for crop improvement. Journal of Plant Physiology 257:153352
Sheaffer C, Barnes D, Warnes D, Lueschen W, Ford H, Swanson D (1992) Seeding‐year cutting affects winter survival and its association with fall growth score in alfalfa. Crop Science 32:225-231
Shen C, Du H, Chen Z, Lu H, Zhu F, Chen H, Meng X, Liu Q, Liu P, Zheng L (2020) The Chromosome-level genome sequence of the autotetraploid alfalfa and resequencing of core germplasms provide genomic resources for alfalfa research. Molecular Plant 13:1250-1261
Shu Y, Li W, Zhao J, Zhang S, Xu H, Liu Y, Guo C (2017) Transcriptome sequencing analysis of alfalfa reveals CBF genes potentially playing important roles in response to freezing stress. Genetics and molecular biology 40:824-833
Smith D (1961) Association of fall growth habit and winter survival in alfalfa. Canadian Journal of Plant Science 41:244-251
STOUT DG (1985) Fall growth and stand persistence of alfalfa in interior British Columbia. Canadian journal of plant science 65:935-941
STOUT DG, HALL JW (1989) Fall growth and winter survival of alfalfa in interior British Columbia. Canadian Journal of Plant Science 69:491-499
Teuber L, Taggard K, Gibbs L, McCaslin M, Peterson M, Barnes D (1998) Fall dormancy. Standard tests to characterize alfalfa cultivars:A-1
Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, Del Angel G, Levy‐Moonshine A, Jordan T, Shakir K, Roazen D, Thibault J (2013) From FastQ data to high‐confidence variant calls: the genome analysis toolkit best practices pipeline. Current protocols in bioinformatics 43:11.10. 11-11.10. 33
Wang J, Zhang Z (2020) GAPIT Version 3: Boosting Power and Accuracy for Genomic Association and Prediction. bioRxiv
Wang Z, Qiang H, Zhao H, Xu R, Zhang Z, Gao H, Wang X, Liu G, Zhang Y (2016) Association mapping for fiber-related traits and digestibility in alfalfa (Medicago sativa). Frontiers in plant science 7:331
Wang Z, Wang X, Zhang H, Ma L, Zhao H, Jones CS, Chen J, Liu G (2020) A genome‐wide association study approach to the identification of candidate genes underlying agronomic traits in alfalfa (Medicago sativa L.). Plant biotechnology journal 18:611
Wickham H (2011) ggplot2. Wiley Interdisciplinary Reviews: Computational Statistics 3:180-185
Yu L-X, Liu X, Boge W, Liu X-P (2016) Genome-wide association study identifies loci for salt tolerance during germination in autotetraploid alfalfa (Medicago sativa L.) using genotyping-by-sequencing. Frontiers in plant science 7:956
Yu LX, Zheng P, Zhang T, Rodringuez J, Main D (2017) Genotyping‐by‐sequencing‐based genome‐wide association studies on Verticillium wilt resistance in autotetraploid alfalfa (Medicago sativa L.). Molecular plant pathology 18:187-194
Zhang C, Dong S-S, Xu J-Y, He W-M, Yang T-L (2019) PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. Bioinformatics 35:1786-1788
Zhang T, Yu L-X, Zheng P, Li Y, Rivera M, Main D, Greene SL (2015) Identification of loci associated with drought resistance traits in heterozygous autotetraploid alfalfa (Medicago sativa L.) using genome-wide association studies with genotyping by sequencing. PLoS One 10:e0138931
Zhou J, Liu L, Chen CJ, Zhang M, Lu X, Zhang Z, Huang X, Shi Y (2019) Genome-wide association study of milk and reproductive traits in dual-purpose Xinjiang Brown cattle. BMC genomics 20:1-11
Zhou Z, Jiang Y, Wang Z, Gou Z, Lyu J, Li W, Yu Y, Shu L, Zhao Y, Ma Y (2015) Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nature biotechnology 33:408-414