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Genome Sequencing of Artificial Allopolyploid of Muskmelon


Whole Genome Sequencing of Artificial Allopolyploid of Muskmelon Reveals the Important Evolution of Allopolyploid Genome

The team of Professor Jinfeng Chen from Nanjing Agricultural University and collaborators completed the chromosome-level genome assembly of artificially synthesized polyploidy for the first time through whole-genome sequencing. 

In the comparative analysis at the whole-genome level, it was detected that there were sub-genes in the early genome evolution of allotetraploid in Melon Genome dominance, found that heterologous doubling leads to phenotypic dominance and initially revealed its regulatory mechanism.

Cucumber Crop  

Cucumber (CucumissativusL.) (2n=2x=14) is an important vegetable crop in the world. It has experienced an evolutionary bottleneck in the process of domestication, so its genetic basis is particularly narrow. 

Professor Chen Jinfeng made an interspecific hybridization between cultivated cucumbers and wild pickled cucumbers (C. hystrixChakr., 2n=24) in 2000. 

Through embryo rescue and chromosome doubling, he created the first artificial allotetraploid species of the genus "Golden Melon". Named Cucumis×hytivusChen and Kirkbr., it is an important material to expand cucumber genetic base and broaden cucumber breeding resources.


In this study, the multi-level strategy of PacBio+BioNano+Hi-C+Illumina was used to complete the chromosome-level genome assembly of Jinggua and accurately distinguish its subgenome. 

Based on the analysis of the parental pickled cucumber genomes in the early stage of the project team, this study compared the parental cultivated cucumber and wild pickled cucumber genomes and found that although most of the genomes of the two parents are retained in the pumpkin genome. 

The subgenome has obvious subgenome advantages, which is characterized by fewer missing sequences and higher expression levels of homologous genes.


Genome Sequencing of Artificial Allopolyploid of Muskmelon

Further comparative genomics analysis carried out with the interspecific hybrid F1, the first generation S0 of Jinggua, and other early generations (S4-S13) showed that three important stages in the process of heteropolyploidization (interspecific hybridization, genome doubling, and two Ploidization) has different effects on allopolyploid genomes, with interspecies hybridization being the most significant. 

In other words, the phenomenon of subgenomic dominance that is widely found in polyploidy has been basically determined in the process of interspecific hybridization, and gradually accumulated in the subsequent evolutionary process. 

In the process of diploidization, the changes in the genome also mainly occurred in the first few generations (S0~S3), after which only a few sites were changed.


Why crop varieties through polyploidy has become an urgent need for agricultural production?

The world’s population continues to grow rapidly, the global climate is changing rapidly, and extreme events continue to occur frequently, making agricultural production face unprecedented challenges. 

The creation of new high-yield, high-efficiency, environment-friendly, and broadly adaptable crop varieties through polyploidy has become an urgent need for agricultural production, environmental protection and sustainable development of human society. 

Reference value for creating new polyploid crops from scratch is very limited

Although there have been a large number of polyploid plant research and application results, since most of the existing natural polyploid plants have existed for thousands of years, the reference value for creating new polyploid crops from scratch is very limited. 

In this study, a new synthetic polyploid species, pumpkin, was identified for heat tolerance and resistance to Meloidogyne incognita. 

The results showed that pumpkin not only showed obvious heterosis (strong growth and high nutritional value), but also had very strong environmental adaptability, able to grow in the hot Nanjing in summer, is a real example of using polyploidization to develop new crop varieties.


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