Science1 publisher2 min readPublished
Southern crabapple genome ties 242 DNA regions to the climates where wild trees grew
Ben Mansfeld's team built a Southern crabapple reference genome and sequenced over 150 wild samples, finding 242 DNA regions linked to local climate. The links are to where each tree grew, so the regions are hardiness candidates that still have to be tested in living trees.
The Scientist · Science desk
What happened
- The wild samples came from crabapple seeds that sat in storage for decades, overlooked until USDA scientist Christopher Gottschalk found them.
- The Southern crabapple resists fire blight, a deadly bacterial disease, and copes with heat, drought and severe weather that commercial apple varieties struggle with.
- Beyond single-letter DNA changes, the team also searched the genomes for larger structural variants.
- The seeds hold diversity missing from the USDA's living orchard, including trees from Missouri, a state the orchard does not represent.
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Why it matters
- capability Breeders chasing heat and drought hardiness now have candidate regions from a species outside apple's breeding history, reachable by gene editing or by new rootstocks for grafting.
- constraint The scan covered climate, so breeders after the species' fire blight resistance still wait on disease mapping; Mansfeld's lab takes that work next to Malus coronaria and Malus ioensis.
- precedent A seed lot left unsequenced for decades is now filling gaps in the living USDA orchard, a model other gene banks holding stored wild seed could copy.
The study, published in Horticulture Research [1], is a genotype-environment scan. Working with Christopher Gottschalk of the USDA and Zoe Migicovsky of Acadia University [3], Mansfeld's team took each wild genome from across the species' native range [5], attached climate data from the place the sample originated, and searched for variants associated with seasonal precipitation and temperature [6]. The 242 regions are the hits from that search [7].
Each hit is a correlation with place. A variant can be common where summers run hot and dry because it helps trees survive there. It can also be common there because the trees in that part of the range share ancestry, and the variant came along with it. Telling those apart takes a statistical correction for relatedness and, in the end, trees grown side by side under the same stress. The summary of the work does not report effect sizes, the ancestry correction used, or how many of the 242 regions are structural variants.
The structural-variant work is the most ambitious part of the design. The reference genome is haplotype-resolved [4], meaning the two parental copies of each chromosome are assembled separately. "We're coming to understand that it's not just single 'letter' mutations, but large changes in genomes that can contribute to traits," Mansfeld said. "I was surprised by how amazingly diverse these apples are in their structural variation." [9]
The Southern crabapple is one of four crabapple species native to North America [2]. "These species are really not included in the history of the breeding and domestication of apples at all," Mansfeld said. "They're what we call a genetic treasure trove." [21] Until now there was little to study. The USDA Apple Collection in Geneva, N.Y., holds a small collection of Southern crabapple trees, too few for proper genetic studies [13]. Of the stored seeds that made this work possible, Mansfeld said: "It's a valuable collection that's never been sequenced before." [15] He and Gottschalk had earlier assembled the genome of another native, the Pacific crabapple, and studied its fire blight resistance [11].
I think the resource is sound, and the 242 regions are a list of places to look. A rootstock breeder would want grafted trees tested under drought or heat before any of them goes into a program. The genome and sequences are open to any researcher, whatever trait they are after [20], so that testing does not have to wait on one lab. The pace is set by the crop: apples grow year after year from the same plant [19]. "You're not planting for next year," Mansfeld said. "You're planning for the next 25 years." [19]
What to watch
- The full Horticulture Research paper's effect sizes, its correction for shared ancestry, and how many of the 242 regions are structural variants.
- Any trial that grows trees carrying these regions under controlled drought or heat and measures how they perform.
- Fire blight mapping results from Mansfeld's lab in Malus coronaria and Malus ioensis.