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Recent genomic analysis of species within the genus Malus, which encompasses the domesticated apple and its wild counterparts, has shed light on their evolutionary relationships and genomic changes over the last nearly 60 million years. The research team uncovered structural variations within these genomes and devised methodologies to pinpoint genes linked to favorable attributes such as taste quality, disease resistance, and cold tolerance, which could potentially inform future apple breeding initiatives.
A study detailing these findings, involving an international collaboration that includes biologists from Penn State, was published this week (April 16) in the journal Nature Genetics.
“There are approximately 35 species in the genus Malus, yet, despite the prominence of apples as a fruit crop, comprehensive studies on the evolutionary development of their genomes have been scarce,” stated Hong Ma, Huck Chair in Plant Reproductive Development and Evolution and professor of biology at Penn State, who co-authored the paper. “This study provides an in-depth analysis of Malus genomes, allows us to construct a phylogenetic tree for apples, document significant events such as whole-genome duplications and interspecies hybridizations, and identify genomic regions related to specific traits, including resistance to apple scab disease.”
The researchers sequenced and assembled the genomes of 30 Malus species, including the well-known golden delicious variety. Among the species analyzed, 20 are diploid, possessing two chromosome sets, similar to humans, while 10 are polyploid, containing three or four sets of chromosomes, likely due to recent hybridization events with diploid relatives of Malus. By comparing nearly 1,000 genes from each species, the team constructed a family tree of the genus and traced its origins back to approximately 56 million years ago in Asia through biogeographical analysis.
“The evolutionary narrative of this genus is intricate, with frequent hybridizations and a common whole-genome duplication event, complicating comparative studies,” Ma remarked. “The availability of high-quality genomes for a significant number of species, along with insights into their interrelations, has allowed us to explore the evolutionary processes of the genus more thoroughly.”
Further exploration of Malus genomic history employed a pan-genomics strategy. This method involved a detailed comparison of both conserved genes and other sequences, including transposons—often referred to as jumping genes due to their mobility within the genome—across the 30 species as well as specific genes unique to subsets. Pan-genomic analyses leverage the genomic data from closely related species to elucidate evolutionary conservation and divergence, significantly enhanced by the pan-genome graph tool.
“The pan-genome analysis of these 30 species proved instrumental in detecting structural variations, gene duplications, and rearrangements that might otherwise go unnoticed when analyzing a limited number of genomes,” Ma noted. “One such discovered structural variant allowed us to identify the genomic segment linked to resistance against apple scab, a worldwide fungal threat to apples.”
The team also developed a pan-genome analysis tool to uncover evidence of selective sweeps, a process where advantageous traits spread quickly within a population. This approach led to the identification of a genomic region linked to cold and disease resistance in wild Malus species, which may also correlate with less desirable fruit flavors.
“There’s a chance that efforts to yield the tastiest fruits have inadvertently compromised the resilience of cultivated apples,” Ma cautioned. “Gaining insights into structural variations in Malus genomes, the intricate relationships among species, and their hybridization history through pan-genome analysis can significantly inform future breeding programs, ensuring that desirable taste and disease resistance traits are preserved in apples.”
Alongside Ma, the research team includes postdoctoral researcher Taikui Zhang from Penn State. Their contributions benefited from the support of the Eberly College of Science and the Huck Institutes of the Life Sciences at Penn State. A complete list of collaborators and funding sources is available in the published paper.
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