Apple: Start your domestication journey on the Silk Road

one of the most popular and valuable fruits in the world, the two ancestors of modern apples are Seweth apples and forest apples.
On November 3rd Nature Genetics published online the results of a study by Fei Zhangjun, a professor at Cornell University's Boyce Thompson Institute, who confirmed at the genome-wide level that about 90 percent of the genetic material of modern apples came from these two ancestors, and that apples began to be gradually domesticated by humans along the Silk Road to Europe.Fei Zhangjun, author of the
paper, told China Science that they assembled a complete reference genome of modern apples and their two main wild ancestor species, reordered more than 90 apple species in depth and constructed pan-genomes, and their conclusions provide detailed genetic insights into apple domestication and important fruit traits that can help breeders improve apple flavor, taste and resistance.
Silk Road began in ancient China and flourished from the 2nd century BC to the 14th century AD, connecting Asia, Africa and Europe.
scientists speculate that more than 7,000 kilometers from China to Western Europe, travelers pick apples in one place, eat them on the road, and then leave their cores a few kilometers away. Seeds grow into trees in new places and interbreed with local wild apples to produce new offspring.
process has created more than 7,000 apple varieties that exist in the world today.The USDA Apple Species Resources At Cornell University's Agricultural Laboratory is open to scientists around the world and contains more than 6,000 apple species, some from countries along the Silk Road, said Chung Kanyuan, co-author of the
paper and a scientist with the U.S. Department of Agriculture's Agricultural Research Service (ARS).
one of the wild ancestor species of apples preserved in the resource garden, the Sewes Apple, came from the Silk Road.
records show that the ancestors of modern apples were Seweith apples from Central Asia and forest apples from Europe. Forest apples provide a crisp taste for modern apples. Plant scientists have also confirmed by molecular markers that most of the genomes of modern apples come from these two wild ancestor species.
hybridization with wild species makes modern apples a hybrid with two sets of chromosomes, and their genomes are complex and difficult to study.
's global interdisciplinary research team, led by Fei Zhangjun and Zhong Dryyuan, solved this problem by using state-of-the-art sequencing techniques and bioinsynistic algorithms to assemble two complete chromosomes for the domesticated Apple and its two main wild ancestor species, the Sewes Apple and the Forest Apple, respectively.
the genetic material contributed by the two main wild ancestral species together accounts for about 90 percent of the domesticated apple genome. This confirms at the genome-wide level that the main ancestral species of modern apples are indeed the same as documented, Fei said.
by comparing three complete reference genomes, scientists can learn which ancestral species a segment of the modern apple genome comes from, thus determining which ancestor species contributed to the genes that contributed to the apple's domesticated nature.
, for example, Sewes apples were the dominant ancestors, affecting apple size and yield, while forest apples were the second largest contributor, providing genes that control acidity and taste.
the new study is the result of an early collaboration published in nature-newsletter in 2017 that traces the history of apple domestication and evolution on the Silk Road.
article in nature-newsletter resequenced more than 100 varieties based on Apple's reference genome at the time. Through population genetic analysis, the single nucleotide polymorphism of apples was located. "You can see where parts of the apple genome are fixed during the domestication process, and where they are related to some of the apple's current features, such as sweet acid, hardness, size, and so on." Fei Zhangjun said.
these findings inspired them to apply new sequencing and assembly techniques to other apple materials in the species resource to build new and better apple reference genomes.
results provide a detailed genome roadmap for apple breeders. "We hope to further help us understand apple genetic diversity and to produce excellent new varieties of apples by developing new apple reference genomes, especially those of wild ancestors," Zhong said. Sun xuepeng
lead author of the paper, the team found that the genes that give apples a brittle texture are located near the genes that make them susceptible to blue mold.
"Now that we know exactly where these two genomic regions are, breeders can find a way to preserve the brittle texture of the gene and remove the blue mold susceptible gene to produce better disease-resistant varieties, " Sun said. The
history of apple domestication has led to undeveloped genetic sources that can be used for crop improvements such as size, flavor, sweetness, texture and resistance.
" plant breeders can use these details to improve the most important characteristics for consumers, such as the flavor of apples. More importantly, the information will also help breeders develop apples that are more resistant to adversity and disease. Fei Zhangjun said.
team also conducted a deep resequencing of more than 90 apple species and constructed a pan-genome of cultivated apples and two wild ancestors. Unlike the reference genome, which captures genetic information from individual organisms, pan-genomes can help scientists capture all genetic information in a species. Pan-genome research is particularly important for very diverse species like apples.
, co-authors of the paper, said they identified about 50,000 genes in the pan-genome of domesticated apples, about 2,000 of which did not exist in previously published apple reference genomes.
these 'missing genes' are very important because many of them determine some of the features that apple breeders are most interested in, " said Mr. Jia. In
they also used RNA extracted from different stages of the Gala fruit to identify genes associated with texture, aroma and other fruit characteristics.
found that many genes showed differential expression in two chromosome copies of modern apples. For example, genes that control the acidity or hardness of a fruit rely primarily on highly expressed copies from forest apples, while genes that control fruit size rely on copies of highly expressed copies from Seweith apples.
"this gives us and breeders a deeper understanding of the genetic diversity of specific features. The findings will help them better manage apple species resources and provide breeding scientists with key genetic and genomic information, Zhong said.
team is planning to sequence other wild apple varieties, which Fei said may have valuable properties that can improve the resilience and adaptability of domesticated apples.