Rescued by wild genes
In the ever-ongoing arms race between crops and their pest scientist are kept busy by identifying new resistance mechanisms against new pests. Often these new resistance mechanisms are brought in through wild relatives, but pinning down the responsible genes is not easy. Now a new study by Israeli scientists illustrates that looking at the genomes of those contributing wild relatives might help.
The scientists where particular interested in the mechanisms behind the resistance of sunflowers to the parasite broomrape. Studies so far identified multiple resistant varieties, but ended up with the identification of only a single responsible gen, even though different mechanisms behind the resistance was expected.
Circumventing resistance
As broomrape is constantly finding new ways to circumvent sunflowers resistance, the first thing the researchers did was finding new resistant lines against two broomrape populations. For this they used a population of 287 varieties of cultivated sunflowers consisting out of inbred lines, open-pollinated varieties and landraces, but no wild relatives.
After finding the resistant lines, the researchers identified the genomic regions that are likely responsible for this. They used multiple tactics for this, resulting in the identification of 782 genomic regions. First, they identified those genomic regions on a sunflower reference genome. But the researchers did not stop there, they also mapped the regions to three other sunflower reference genomes. Through doing this they found that of the 782 genomic regions identified as likely to be involved in resistance to broomrape, only 30 of them were found in all four sunflower refence genomes analysed.
Found in wild relatives
In addition, the researchers mapped those resistance linked regions to the genome of six sunflower wild relatives. In total 19 of the resistance linked regions the researchers could find back in three of the wild relatives. Indicating that commercial sunflower lines obtained at least 19 traits from wild relatives. As only the refence genomes of six wild relative were consulted, there is the possibility that more resistance traits originated in sunflower’s wild relatives.
Having all these 782 genomic regions located in the multiple sunflower genomes enabled the researchers to make a start with the identification of the underlying resistance genes. Scanning the genome around these regions resulted in the identification of 474 candidate resistance genes.
Combined these results show why pangenomes, a collection of genomes of many individuals or varieties of a species, are valuable resources for finding novel traits. Especially, as novel traits when brought in from the outside, are likely to be more than a minor mutation. As such they are not captured in the main reference genome used, as shown in this study. A pangenome, in contrast, captures the complete width of a species and as such allows the mapping of the traits to the genome and the subsequent gene identification.
Literature
Dana Sisou, Hammam Ziadna, Mika Eizenberg-Weiss, Hanan Eizenberg, Sariel Hübner, Wild genes to the rescue: High-throughput genomics reveals the wild source of broomrape resistance in sunflower, Journal of Experimental Botany, 2026;, erag141, https://doi.org/10.1093/jxb/erag141
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