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

Long, R.; Zhang, F.; Zhang, Z.; Li, M.; Chen, L.; Wang, X.; Liu, W.; Zhang, T.; Yu, L.-X.; He, F.; Jiang, X.; Yang, X.; Yang, C.; Wang, Z.; Kang, J.; Yang, Q.

doi:10.1101/2021.02.21.428692

bioRxiv · 10.1101/2021.02.21.428692

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

Long, R.·Zhang, F.·Zhang, Z.·Li, M.·Chen, L.·Wang, X.·Liu, W.·Zhang, T.·Yu, L.-X.·He, F.·Jiang, X.·Yang, X.·Yang, C.·Wang, Z.·Kang, J.·Yang, Q.

View original source ↗Export metadata ↓

Abstract

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. Here, 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.

Explore related subjects

plant biology Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Long, R., Zhang, F., Zhang, Z., Li, M., Chen, L., Wang, X., Liu, W., Zhang, T., Yu, L.-X., He, F., Jiang, X., Yang, X., Yang, C., Wang, Z., Kang, J., Yang, Q.. 2021-02-22. 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. https://doi.org/10.1101/2021.02.21.428692

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Melanoidins Suppress Cucumber and Tomato Diseases Incited by Pathogens that are Oomycetes, Bacteria and a Virus

We recently reported that solutions of the nitrogenous compounds melanoidins (M), that are formed during the final stages of the Maillard Reaction, are inducers of plant resistance (Elad et al. 2026). M promoted immunity and induced disease resistance through an effect on the transcriptome, primarily through the salicylic acid pathway. Here we tested the effect of M on plant diseases that are caused by Oomycetes, bacteria and a tobamovirus. Drench and spray of M suppressed Pythium aphanidermatum damping off in cucumber, cucumber downy mildew (Pseudoperonospera cubensis), tomato late blight (Phytophthora infestans), bacterial speck (Pseudomonas syringae pv. tomato), bacterial canker (Clavibacter michiganensis subsp. michiganensis) and the Tobamovirus Tomato brown rugose fruit virus (ToBRFV) in tomato. In various experiments control was achieved by concentrations of 0.03 and 0.1% and on older and younger leaves and even in long term experiments where the M was applied for ca 11 weeks. It can be concluded that the disease resistance inducer M can suppress soilborne and foliar diseases that are caused by Oomycetes, bacteria and a virus of the genus Tobamovirus, in addition to the fungal pathogen Botrytis cinerea reported earlier.

plant biology↗

bioRxiv2026

Expansion and Comprehensive Evaluation of the Peacock Eye Disease Management (PedMan) System across Olive Cultivars Differing in Susceptibility to Venturia oleaginea

Peacock eye disease, caused by Venturia oleaginea , is an important foliar disease of olive that is primarily managed through fungicide applications. Integrating host resistance into disease-warning systems could improve spray timing and reduce unnecessary fungicide use. PedMan (Peacock eye disease Manager) was previously developed and validated for highly susceptible olive cultivars. The objectives of the present study were to expand PedMan to cultivars differing in susceptibility to V. oleaginea and to evaluate the expanded system under commercial grove conditions. A sensitivity analysis of the rainfall and temperature criteria used for highly susceptible cultivars was conducted to establish criteria for moderately susceptible and moderately resistant cultivars. The rainfall threshold of [≥]15 mm was retained, whereas the temperature range triggering an infection alert was narrowed from 12-18 {degrees}C for highly susceptible cultivars to 13-17 {degrees}C for moderately susceptible and 14-16 {degrees}C for moderately resistant cultivars. The expanded system was subsequently evaluated in 33 field trials and observations under natural infection conditions. PedMan recommendations were classified as correct or incorrect based on statistical comparisons of leaf abscission between fungicide-treated and untreated trees. Overall, 30 of 33 recommendations were correct, resulting in an accuracy of 90.9%. Sensitivity was 87.0%, while specificity and positive predictive value were both 100%. These results demonstrate that incorporating cultivar susceptibility into PedMan broadens its applicability and provides reliable cultivar-specific fungicide recommendations. The system has potential to reduce unnecessary fungicide applications while maintaining effective management of peacock eye disease across olive cultivars differing in susceptibility.

plant biology↗

bioRxiv2026

Large seed size accompanying GmSDP1 suppression is linked to cellular remodeling and phytohormone regulation

Soybean (Glycine max) seeds contain approximately 20% oil and 40% protein and are important for food, feed, and biofuel. Improving soybean productivity and seed quality requires optimizing carbon partitioning during seed development. Previously, seed-specific suppression of the lipase-encoding gene Sugar-Dependent 1 (SDP1) increased seed oil content by approximately 5% while slightly reducing raffinose family oligosaccharides without compromising protein content. Seed-specific SDP1 suppression also increased seed size by 18-25% without affecting seed number, resulting in greater seed biomass per plant. To determine the developmental basis of the increased seed size, we investigated the cellular and molecular mechanisms underlying this phenotype. Microscopy and biochemical analyses showed that larger seeds were associated with increased seed cell size and enhanced lignocellulosic cell wall accumulation. Temporal biochemical and transcriptomic analyses further revealed coordinated changes in hormone homeostasis, including altered levels of abscisic acid, 12-oxo-phytodienoic acid, and jasmonoyl-isoleucine, together with differential expression of F-box and RING/U-box family genes. The results indicate that the enhanced seed size resulting from SDP1 suppression is associated with coordinated changes in cellular development, cell wall accumulation, hormone homeostasis, and regulation of gene expression during seed development. Developmental and metabolic changes associated with the increased seed size phenotype support SDP1 manipulation as a potential strategy for improving soybean seed yield and quality.

plant biology↗