Development of technologies and methods

Last changed: 15 May 2017

Does genomic selection have a future in plant breeding?

Selection based on genomic information, often called genomic selection, is a recently developed concept that aims to use genetic markers across the whole genome as a selection tool in breeding programmes. Genomic selection is a so-called “black box” approach because associations rather than knowledge of the biological functions of genes are used. This technique has been developed from previous marker-based techniques and became useful when genotyping became more affordable. Today this method has been integrated into dairy cattle breeding programmes and is being tested in other livestock and plant species.

In the process of crop breeding few favourable plants are being selected among numerous lines. Selection starts at early stage of the development and is based on measurable traits during those stages, often visible information such as height or colour. However, the genetic progress for traits measurable at later stages (for example, increases in yield) is predicted to be low, compared to more accurate assessments of phenotypes and information showing high correlation with the final traits, such as the breeding value. Therefore, many plant-breeding companies aim to integrate genomic information into their programmes. Furthermore, numerous studies using simulated and empirical data have been published, often promising high reliabilities when using breeding values based on genetic markers, so-called “genomic breeding values”.

But how realistic are those assessments? In a paper by Elisabeth Jonas and Dirk Jan de Koning, they conclude that in many approaches genetic markers can be used as an additional tool with a better predictive value compared to some of the current selection steps in a breeding cycle. Genomic selection has been proposed to both provide a more accurate estimate of genetic merit as well as to shorten the generation interval. At present, however, strategies to shorten the breeding cycle are rarely discussed.

Jonas and de Koning emphasise that a functioning collaboration between geneticists, farmers, breeders, and seed producing companies is needed to integrate novel approaches for improved breeding into realistic breeding schemes. Also, because there is a huge difference between cattle breeding and plant breeding, methods successfully applied in the former have to be carefully considered for the latter.

Scientific paper:
Jonas, E., & de Koning, D.J. 2013. Does genomic selection have a future in plant breeding? Trends in Biotechnology 31: 497–504

For more information:
Elisabeth Jonas

Protein navigation in plant breeding

By the development of methods for analyzing plant proteins, it is possible to find out which plants are the best to cultivate. The researchers have found proteins in potato typical for high yield, and resistance against late blight. They suggest a new workflow, including both DNA- and protein analyses, to accelerate the breeding for important crop traits.

Senior lecturer Fredrik Levander, at the Department of Immunotechnology at Lund University, is one of the researchers behind a study showing that it is possible to determine which potato plants are high-yielding, and which are resistant to late blight, by analyzing the potato plants' proteins.

– It can be tricky to predict the cultivation characteristics of, for example, a potato by just looking at genes. Proteins bring us closer to what actually happens when the plant grows. Although, at the same time, it is experimentally easier to measure DNA variations, he explains.

Using mass spectrometry, more specifically the technology selected reaction monitoring, it is possible to find out the amounts of selected peptides and proteins in a plant. First of all, it is important to find out which of these molecules are specific to the plants with good properties. Then, plant breeders can use the peptides and proteins as markers for the properties such as resistance to disease, drought tolerance or adaptation to a particular region.

The markers can thus tell the plant breeder what properties the plants have, without having to wait and identify the properties per se, among the grown up plants. This saves energy, time and money.

There are already methods for making selections based on the genome, using DNA markers. But the researchers see benefits of supplementing DNA markers with protein markers. The proteins say more about which biological processes are "going on" in the plant, compared to DNA markers. Some genes are not expressed, and some genes give rise to several different proteins.

– There are often several copies of genes present in plant genomes, and several variants of genes that are very similar to each other. That makes it difficult to predict plant characteristics from DNA. Especially in plants that are tetraploid, hexaploid, and so forth, says Fredrik Levander.

You get closer to the truth with protein analyzes, compared to DNA analyzes, but it's trickier to analyze the proteins. DNA sequences consist of four different bases, and there are easy methods for amplifying large amounts of DNA. The proteins consist of many more constituents (amino acids), and the researchers are limited by how much protein they manage to get from a leaf or a potato tuber.

- Different proteins behave very differently, therefore it is more complicated to analyze them, compared to analyzing DNA.

In the current study, the researchers selected 104 protein markers. Some of these could be used to predict higher potato yield, and resistance to the oomycete Phytophthora infestans causing late blight in foliage and tubers. In other words, they found protein markers for properties for which there are no commercial DNA markers yet.

The study was funded by Mistra Biotech and the Swedish Foundation for Strategic Research.

For more information:
Fredrik Levander or Erik Andreasson 


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