Marker Assisted Plant Breeding: How and Why it works by Gene Hookstra

Issue Date: March 2010

The world of molecular biology; marker systems, instrumentation and bioinformatics keeps advancing at an amazing pace. In the not to distant future whole genome analyses will be able to be completed in a matter of hours not months or years. Even with all these advances some things do remain the same, the direct application of DNA data. Today’s plant breeders still need to incorporate desirable traits into their breeding lines and get their cultivars to market as fast as possible. Marker Assisted Plant Breeding is still that tool. The following article was first published in May of 2008 and even with all the changes it is still valid, applicable and appropriate today and worth another look.

Plant improvement has existed from the time the first hunter-gathers started selecting one plant over another but it wasn’t until Gregor Mendel’s early experiments with peas that we started to understand genetics or the inheritance of traits. A century later Watson and Crick unraveled the actual structure of DNA—the backbone of all heritable traits and since then concepts and applications for plant breeding have been evolving at an unprecedented rate.

While tremendous improvements have been made in plant breeding, it is still a process that requires time and attention to detail, specifically attention to the phenotype or visual traits of your crop. This often requires years of observation but today’s plant breeders know that genetic variation or the combining of superior genetics is the key to most plant improvement and the best way to get to your breeding objectives, your needed phenotype is to understand the genetics.

The most common method of creating genetic variation is though sexual reproduction. Sexual reproduction sets in motion a process known as meiosis. Generally speaking, meiosis occurs with the crossing of one plant’s genes with another creating a mixing of traits or genetic variation. Without going into the wonders of meiosis there are two expressions of major interest; ‘genetic recombination’ and ‘independent assortment’. By definition we have little control over what takes place during genetic recombination but today we do have a way to track what is happening. A technology that developed from Watson and Crick’s research--DNA markers can help you see what’s really going on in the chromosomes and help you attain your breeding goals sooner.

Although there are many avenues to take when considering how best to achieve your plant breeding goals, I am going to focus on only two: backcross selection and forward selection. Backcross breeding methodology is generally applied when you have a superior inbred or variety but it is lacking in some trait(s) such as a specific disease resistance. To incorporate this trait one will cross the superior inbred (parent A) with the source of disease resistance (parent B), generate the “F1” which is composed of 50% of parent A’s genetic traits and 50% parent B’s genetic traits. The F1 plants are then backcrossed to parent A, which is also known as the recurrent parent. The progeny from this cross may simply be called the “BC1” generation and with our knowledge of genetics and inheritance we know that 50% of these plants should have the disease resistance trait we are looking for and that the plants them selves should be 75% recurrent parent genotype. One would then grow out individual plants from the BC1 generation, expose them to the disease, select the plants that show resistance, pick a couple of resistance plants and backcross them again to the recurrent parent making the “BC2” generation which should now be 87.5% recurrent parent; the process is repeated to make the “BC3” generation which is 93.75% recurrent parent and so on until you are satisfied you have recovered the desirable phenotype of parent A along with the desired disease resistance.

This is a tried and true method but requires a considerable amount of time and many generations. Using molecular markers one can be assured that you can recover your genotype and associated phenotype along with the desired traits(s) in two backcrosses and one selfing generation and this is how and why it works:

Remember ‘independent assortment’? That is what makes molecular markers so effective. Table 1 shows actual data of percent recurrent parent in a BC1 generation. There were 94 individual plants (No. of obs) evaluated and if one looks at the average percent recurrent parent, it is 75% as predicted but there is a range represented by individual plants from 60% to 94% recurrent parent. Thus with the right molecular (DNA) markers you could choose plants that would be in the “BC3” generation in one backcross. One more backcross and you can select plants in the BC6 generation! After two backcrosses, all that is left is to self the selected plant to ensure homozygosity in the incorporated trait and you are done. Of course if you happen to have marker linked to the trait being incorporated the whole process is quicker, yet.

Table 1:

This same process works for forward selection as well. In this situation one is crossing two plants, both with positive attributes and trying to combine then to develop a superior progeny. As above, create the F1 but instead of backcrossing one would self the plant creating what may be called F2 plants. The segregation pattern in this generation should be 25% homozygous parent A, 25% homozygous parent B with 50% of the genome being heterozygous. If one screens a representative sample of approximately 100 plants that will be the averages but there is a range of distribution percentages just like in backcross procedure. Using markers one can easily select segments of the genome to ensure it comes from one parent or another plus you can increase the rate to homozygosity in developing a stable inbred or variety. In other words, you have a tailor made inbred with reduced development time.

DNA markers are tools that have been proven to reduce development time and help get your products to market that much sooner. They are tools that need to be used in today’s competitive breeding programs. ESTA has a ‘state of the art’ molecular marker laboratory and personnel with years of experience and knowledge on how to effectively apply marker technology to best achieve your goals. Please give us a call if you have any questions or would like more detail.