Genomic tools speed up classic plant breeding

Published: 21-01-2014

The world population is growing by 1.2 to 1.5% a year. The production of many crops is unable to keep up with such growth, however. This means new varieties are needed that use nutrients and water more efficiently and are more heat, salt, disease and pest resistant, resulting in less loss and higher yields. In a separate development, plant breeders are breeding new varieties that meet the color, shape and flavor preference of farmers, supermarkets and consumers. In developing new varieties with these traits plant breeders are benefiting greatly from data generation and sequencing techniques, largescale genotyping techniques and bioinformatics. These tools have significantly accelerated and improved the application of genetic information in plant breeding programs.


Genetic markers
Farmers have been using marker-assisted selection to grow vegetable crops and field crops like corn and rapeseed for a number of years. “Molecular markers have been in use for more than ten years. But recently it has become easier to trace those markers, because now other types of marker are being used: SNPs instead of SSRs, RFLPs or AFLPs,” says Annemieke Jungerius of Genetwister. A decade ago, markers were mainly used for research purposes, for fingerprinting, that is being able to distinguish lines/varieties at DNA-level. But now it is possible to costeffectively identify the genetic basis of traits that are important to breeding programs in practical breeding. Developing anonymous markers (SNPs) for a new crop takes only six months. An important factor is the availability of lines that are a good representation of the core plasma of the breeder’s crop. But Jungerius says “the most important thing is linking these anonymous genetic ‘mile markers’ to traits that are relevant to the breeder. This requires cross-breeding, phenotyping and linkage studies, which takes another 18 months to two years.”

Guusje Bonnema, researcher at Wageningen University Research Center’s department of Plant Breeding, says genetic markers, in combination with accurate phenotyping (determining and measuring traits), can seriously speed up the breeding process. “Just consider the simple example of the color of your apples. If you plant an apple seed, the tree doesn’t bear fruit for another seven years. However, if I can determine at the seedling stage whether this tree is going to bear red or green apples, I can then focus my efforts on green apples alone. This increases efficiency and lowers costs,” Bonnema adds. The genetic markers also come in handy when you want to preserve multiple traits, such as resistance to several diseases, in your descendants, or when you would like to select for a new trait from the genome of a wild species. “What it comes down to is that much less crossbreeding is needed to get descendants with the desired combination of traits,” says Bonnema.

mutagenesis KeyGene, a molecular genetics R&D company with many international clients, researches which genes are responsible for certain traits and develops molecular markers for them. As Mark van Haaren of KeyGene said in his presentation at the April ‘Genomics in Business’ conference in Amsterdam: “This knowledge is crucial for us because we want to discover the natural genetic variation of crops and use it to produce new varieties that meet the current demands of the market.” He emphasized that most of the desired traits are already present in nature and that the use of GMO crops is therefore not an absolute necessity. “We’ve seen how big of a role GMO is playing in field crops, but it has also narrowed the genetic distribution of new varieties of these crops, while variation is necessary if you want to keep selecting for new traits,” Van Haaren says.

One technique for increasing natural variation is molecular mutagenesis. KeyGene has optimized this process and made it applicable for a large number of crops. Van Haaren: “Mutagenesis itself has been used for decades in the breeding of crops, but molecular mutagenesis is relatively new. Using our KeyPoint®MT technology (based on molecular mutagenesis), we can select plants with the very genetic mutations we’re interested in, and do it with great efficiency on a large scale. The advantages are huge: it means a new trait can be expressed in a crop in just a year or two.”


Opportunities for smaller scale crops
With the advent of molecular mutagenesis and the introduction of more and more molecular markers breeders can predict ever more accurately and quickly what the result of crossbreeding will be. Van Haaren believes these new techniques will help expand our knowledge of key traits such as abiotic and biotic stress and will heighten the economic return of a variety. Bonnema of Wageningen UR Plant Breeding says the new techniques have increased the profit potential of many food crops.

Bonnema: “Just think of phytophthora-resistant potatoes, virus-resistant tomatoes, xanthomonas-resistant cabbage or pest-resistant crops and biobased crops with added value (such as antioxidant tocopherols in rapeseed or certain fatty acids in crambe).” Genetwister’s Jungerius also believes there is plenty of room for improvement in crops. She says the genetic tools are getting cheaper and are therefore becoming more readily available for use on smaller scale crops. This is also why Marcus Weidler at Bayer sees great opportunities for wheat. Weidler, who also spoke at the ‘Genomics in Business’ conference, says wheat is about to undergo a technological revolution because the relatively poorly funded wheat research can now benefit from the groundwork done on corn. Van Haaren of KeyGene agrees with Weidler. He says the introduction of hybrids in corn has led to a spectacular increase in yields. “This has not been the case for wheat, and Weidler’s right: if we seriously invest in crops like wheat, we can expect to see improved yields that far outstrip normal growth through traditional breeding,” says Van Haaren. Keygene recently entered into a research partnership with Bayer CropScience aimed specifically at improving wheat.

Jungerius, at Genetwister, says there are great expectations in the field of sequencing. “Right now, generating sequencing data is fairly simple and we’re able to obtain much larger amounts than we were ten years ago. But it’s still a bit like finding a needle in the haystack. Identifying the relevant genetic basis for profitable traits remains a big challenge,” Jungerius says. She stresses that new techniques such as the use of molecular markers will always remain supplementary to plant breeding. “It’s not as if plant breeding will soon only take place on computers. You still have to go out into the field or the greenhouse to see and select the plants, which are the end products of genetics and their environment.”

Phenotyping gains importance
We are steadily gaining more insight into the genetic makeup of plants. It has become relatively cheap to generate unlimited numbers of genetic markers. Therefore, it is all the more important to accurately determine which traits the industry is interested in. Hence the growth of phenotyping (measuring traits and physical characteristics). Only if a phenotype is reliably established in a population is it possible to use marker technology to identify the genetic location and the genes behind this phenotype. KeyGene and the German company LemnaTec have jointly invested in a state-of-the-art phenotyping facility in Wageningen called PhenoFab. There, hundreds of plants a day can be phenotyped automatically. The precision with which this is done enables researchers to discover the relationships that breeders have difficulty detecting in the field.