Barcode system unlocks hidden chromosome instability in alfalfa
image: Validation of large chromosomal segment deletions by chromosome painting. (a, b) FISH assays of the chr2 barcode probes and chr2 painting probes on metaphase chromosomes prepared from LeiTing. The white rectangle shows the special homologous copy of chromosome 2 with large chromosomal segment deletions. (c) A schematic diagram explaining the occurrence of large chromosomal segment deletions at both ends of a homologous copy of chromosome 2. Chromosome 2 homologous copies were digitally excised from the same image of (a). (d) chromosome 2 homologous copies were digitally excised from the same image of (b). The white dotted line represents the position of centromeres on the chromosome. Scale bars, 10 μm.
Credit: Horticulture Research
Alfalfa, a globally important forage crop, has long lacked efficient tools for chromosome identification due to its complex polyploid genome. Researchers have now created a powerful oligo-fluorescence in situ hybridization (oligo-FISH) barcode system capable of distinguishing all eight chromosomes simultaneously. Applying this method, they discovered previously hidden chromosomal variations—aneuploidy and large segment deletions—occurring at low frequency, with chromosome 2 emerging as especially prone to instability. DNA sequence analysis further revealed significant presence/absence variation (PAV) among homologous copies of chromosome 2, providing a genetic basis for this susceptibility. This breakthrough tool not only advances molecular cytogenetics in alfalfa but also enhances understanding of polyploid inheritance and genome evolution.
Karyotype analysis is fundamental to understanding genetic makeup, diversity, and adaptation in plants. Yet, distinguishing individual chromosomes remains challenging in species with small, uniform chromosomes and complex polyploid genomes such as alfalfa. Traditional cytogenetic probes, including repetitive sequences and bacterial artificial chromosomes, are labor-intensive, prone to background noise, and limited in specificity. Although newer oligo-based probes have improved chromosome studies in several crops, their application in alfalfa had not been fully explored. This limitation has hindered both fundamental genomic research and applied breeding strategies. Due to these problems, there is a need to develop efficient tools for chromosome identification and karyotyping in alfalfa to enable deeper research.
A research team from Shihezi University, Northwest A&F University, and the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, has developed a novel chromosome identification system for alfalfa. The study, published (DOI: 10.1093/hr/uhae266) on September 20, 2024, and corrected on January 1, 2025, in Horticulture Research, introduces an oligo-fluorescence in situ hybridization (oligo-FISH) barcode method that distinguishes all alfalfa chromosomes with precision. Applying this system, the researchers identified chromosomal instabilities, particularly on chromosome 2, revealing new insights into natural aberration tendencies during inheritance in autotetraploid alfalfa.
The team designed 21 oligo probes covering specific chromosomal regions, creating a “barcode” capable of simultaneously distinguishing all eight alfalfa chromosomes within a single cell. This system worked consistently across 10 cultivated alfalfa varieties, proving its robustness against DNA polymorphisms. Comparative karyotype analysis showed all varieties had metacentric chromosomes, but subtle structural differences were detected. Unexpectedly, cytological analyses revealed two major types of natural variations: aneuploidy (extra chromosome copies) and large chromosomal segment deletions. These aberrations appeared in about 4% of seeds from three alfalfa varieties, indicating overall genomic stability but highlighting localized instability. Strikingly, chromosome 2 accounted for the majority of these abnormalities. DNA sequence comparisons uncovered extensive presence/absence variation (PAV) among homologous copies of chromosome 2, particularly a ∼120 kb divergent region, which may underlie its susceptibility. In contrast, chromosomes 3 and 6 showed occasional but less consistent variation. These results suggest that specific sequence divergence contributes to chromosome-specific instability. The oligo-FISH barcode not only provides a much-needed cytogenetic tool for alfalfa but also serves as a reference for studying chromosome behavior, assisting genome assembly, and guiding breeding strategies.
“Our barcode chromosome identification system overcomes a longstanding bottleneck in alfalfa cytogenetics,” said lead author Dr. Zhuang Meng. “By enabling simultaneous visualization of all chromosomes, we can now detect subtle variations that were previously hidden. The finding that chromosome 2 is disproportionately prone to aberrations opens a new window into understanding how polyploid genomes maintain stability while allowing occasional variation. This system will not only support basic chromosome research but also provide valuable references for hybrid breeding and genome improvement in alfalfa and related species.”
The oligo-FISH barcode system offers wide-ranging applications for both fundamental and applied research. By providing a reliable means of distinguishing chromosomes, it will enhance genome mapping, karyotype analysis, and comparative cytogenetics in alfalfa and other polyploid crops. For breeders, the ability to monitor chromosomal variations opens opportunities to harness hybrid vigor more effectively and reduce risks associated with genomic instability. Moreover, its potential use in genome assembly and quality control will improve reference genomes, aiding molecular breeding programs. Ultimately, this innovation strengthens the toolkit for advancing alfalfa genetics and offers a framework adaptable to other complex plant species.
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References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhae266
Funding information
This work was supported equally by Tianchi Talent Project of Xinjiang (Grant number CZ001604), High-level Talents Scientific Startup Project of Shihezi University (Grant number RCZK202362), Natural Science Foundation of China (Grant number 32400496), Science and Technology Innovation Talent Project of Bingtuan (grant number 23CB008-01), and Science and Technology Research Project of Bingtuan (grant number 2023AB070).
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.