PHOTO BY KEITH WELLER.
Utilizing single nucleotide polymorphism assessment, Massoudi identifies and advances desirable traits in crops. Single nucleotide polymorphisms, or SNPs, are DNA sequence variations that occur when a single nucleotide in the genome sequence is altered. These differences can provide genetic identification for rapid development of improved cultivars.
In the world of plant breeding, the process of SNP assessment is relatively young. The basic understanding of SNPs came out of the Human Genome Project. The first analytical tools for mapping SNPs and databases to facilitate these activities emerged over a decade ago. The first practical and reliable lab equipment for SNP analysis came a few years later. While there are many other ways to map differences in DNA, SNP technology remains one of the most effective genotyping methods for building a better understanding of plant species.
There are many different SNP genotyping methods, all of them based on some kind of chemical reaction. Massoudi says no method is absolute, and few are practical for high throughput. Ag-Biotech uses the Allele-Specific Polymerase Chain Reaction (AS-PCR) method because it’s economical, versatile and reliable for high-throughput breeding operations. By selectively amplifying individual alleles, this type of PCR detects the presence of SNPs.
“The primary benefit is that it is much faster in determining DNA sequence variations to identify simple or complex genetic traits,” he explains. “It enables breeders to eliminate plants with undesirable traits more rapidly. Instead of the usual five or six backcrosses – hybrids with one of its parents – SNP technology can fast-track a single gene transgression in two backcrosses, producing a recurrent parent line that is 99 percent genetically identical to the original parent line.”
In November 2011, Ag-Biotech released a panel of SNP-based markers to aid tomato breeders worldwide. The markers identified traits for various viruses and fungi, including root knot nematode, fusarium wilt and late blight, the bane of New England’s tomato growers in the summer of 2009. Massoudi claims Ag-Biotech has the most comprehensive proprietary database in the western U.S. of molecular markers for many common vegetables, fruits and other plant varieties. He and his team continuously identify and compile molecular markers in common crops like celery, and in obscure crops like quince, artichoke, cactus and fennel. In the near future, they intend to release panels for various squash and several cultivars of wine grapes. The scientists are currently mapping apples as well.
Changes to breeding and development
Massoudi believes SNP is changing seed breeding and development for the better. “It is exciting when small breeders have the same access to affordable technology as large corporations. Once upon a time a seed researcher couldn’t compete against large operations that had their own in-house laboratory facilities; they would have to partner with these big developers or just not invest in rapid analysis. Now we are finding the more innovative, small plant breeders have begun to understand the advantages of SNP technology. In the meantime, many of those large operations have started using an independent lab like ours because it is more cost-effective,” he says.
One issue faced by technicians using SNP is that the technology is sometimes confused with more controversial DNA technologies. Yet, Massoudi emphasizes, all he and his team do is accelerate a process that humans have done for thousands of years: improving crop yields and, increasing resistance to certain pests or other growing conditions. “In California we have helped with the development of many varieties that are commonly found in the organic and nonorganic sections of produce departments and stores,” he says. Remember, don’t call Massoudi a breeder; Ag-Biotech only performs analysis for breeders so they can get results more rapidly.
The author is a freelance writer based in Massa-chusetts and a monthly contributor to Growing.