Rapid DNA purification kit reduces the seed genotyping workflow by almost a week
For many labs, the ability to deliver pure, high-quality DNA in just five minutes would be enough reason to trial sbeadex Lightning. However, for one South African seed company, the rapid purification kit did far more, cutting their sample testing workflow for their most important product by almost a week and preventing a six-month backlog.
“Initially, I thought it was too good to be true.” says Thandekile Moganedi, Biotech Lab Manager at Starke Ayres.
Starke Ayres offers seeds for a wide variety of crops, which requires extensive genotyping to ensure the quality of their products. Samples for each crop can come from the seeds, the flesh or the roots. “The variety makes our work interesting, but it’s always a challenge to get the best quality DNA from the crops without having too many different protocols,” says Moganedi.
Extracting DNA from the roots of the plant is easier than from the seeds, but that requires waiting for up to a week for the seeds to germinate. To save time, Starke Ayres found protocols to extract DNA directly from the seed for almost all of their crops, with one exception. “For onion, we couldn’t find a way to get good quality DNA from the seeds that is comparable what we get from the roots material.” says Moganedi.
This was particularly unfortunate, as onion makes up almost half of the samples being tested in the lab. The delay caused by germinating the seeds led to a six-month backlog in generating genetic testing results.
Figure 1. Onion is the most important crop for Starke Ayres, accounting for half of its genotyping samples. Source: Starke Ayres.
Successful DNA purification with sbeadex Lightning
The team at Starke Ayres trialled sbeadex™ Lightning as a way to speed up and streamline their DNA purification processes.
sbeadex Lightning is a new kit that uses superparamagnetic microparticles and a novel one-step binding mechanism to reduce washing steps needed in the purification workflow. This can deliver high yields of pure, high-quality DNA in just five minutes, far faster than classic DNA purification kits.
Although sbeadex Lightning has been developed to work for a variety of plant samples, Moganedi was astonished to discover that it could extract high-purity DNA even from onion seeds. “It was great to see that we could extract DNA from the seed for the other crops. But for the onions, I really didn't believe it at all.” she says.
To assess the quality of the sbeadex Lightning purification, Moganedi reviewed the cluster plot after doing KASP genotyping (Figure 2).
“The cluster plot is the deal breaker as it reveals all the impurities that are present.” she says. “When we saw that the sbeadex Lightning clustering was comparable with our existing setup, we were convinced by it.”
Figure 2. KASP genotyping cluster plot after purifying onion seed DNA with sbeadex Lightning. Source: Starke Ayres
Increased lab throughput
Following the successful trial, Starke Ayres switched to using sbeadex Lightning for onion seed and the backlog in extraction vanished within three months. This has massively reduced the turnaround time for samples, with the only limit being data analysis.
“We can report within 10 days from when a seed packet comes in. If there’s an urgent sample, we can now do it within two days, because we extract the DNA on the same day, genotype the following day and then report on it.” says Moganedi.
Onion has a complex growing season, which adds to the pressure on Starke Ayres to plan its production to deliver high-quality seeds to farmers on schedule. “Ensuring that you plant the seed at a specific time is crucial.” Moganedi adds. “So being able to extract DNA much more quickly and report on it has really been a game changer for us. The impact has moved beyond our lab operations to the entire company, including the customer sales department.”
Starke Ayres now plans to transition to sbeadex Lightning for all their crop DNA purification workflows over the next year to take advantage of its efficiency gains.
The faster sbeadex Lightning protocol allows the lab team to increase the samples extracted each day by a third. “I’ve also seen that it gives us more time to prepare for the following day.” says Moganedi. “That is more difficult to quantify, but at the end of the week, you realise we’ve done way more than if we were doing with the normal sbeadex.”
To find out more about the work of Starke Ayres please visit starkeayres.com
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