Association mapping for agronomic traits in two-row barley
Dr. Aaron Beattie
Assistant Professor, Plant Sciences
University of Saskatchewan
Timeline: April 2013 – March 2018
Alberta Barley funding: $10,218
Total funding from other partners: $208,227
Benefits for barley farmers
The project should help breeders become more efficient at selecting traits that are important to Alberta barley farmers (e.g., lodging resistance, yield, etc.), which will result in better varieties.
The project will identify molecular markers associated with important agronomic traits that will help breeders improve these traits via molecular marker-assisted selection or genomic selection strategies.
As reported previously, the association mapping (AM) population was genotyped with the 9K SNP Infinium iSelect chip. A total of 6,265 polymorphic SNP markers were identified and can be used for association mapping. The population was evaluated for structure and kinship was determined. This information will also be used in the association mapping analysis.
In order to collect field data to be analyzed in conjunction with the genotyping data, the AM population was grown as a two replicate RCBD in 2015 at Lacombe, AB, Saskatoon, SK and Brandon, MB. However, the Lacombe, AB site suffered hail damage so did not provide useful data.
Objectives for the upcoming year – June 2016
The original work plan proposed to evaluate a number of agronomic traits (e.g. yield, lodging) at 3 locations (Brandon, Saskatoon, Lacombe) in both 2014 and 2015. However, due to flooding issues at Brandon in 2014, water logging issues in Saskatoon in 2014 and hail damage in Lacombe in 2015 we did not collected any useful data from these sites.
We had originally planned to create a 2nd association mapping population with a set of more recent 2RCoop barley lines and test these at the same three sites in 2016 and 2017. Given that we have had issues collecting good data on the first association mapping population, we suggested (and received permission from AAFC and the industry partners in November/December 2015) that we continue to grow this association mapping population in 2016 and 2017 to increase the data collected and ensure we have a good set of data on which to do the mapping. If we see a similar attrition rate over the next two years it will mean that over the 4 years of the project we will have collected the intended 2 years of data.
Although the absence of a second association mapping population means that some interesting marker-trait association will not be discovered, the data collected from the first association mapping population will still be very useful to breeders.
The goals of this project were to identify molecular markers associated with important agronomic traits that will help breeders improve these traits via molecular marker-assisted selection or genomic selection strategies. This should help breeders become more efficient at selecting traits that are important to Alberta barley growers (e.g. yield) which will result in better varieties.
A 92 member association mapping panel consisting of two-row malting germplasm, derived from eight breeding programs, adapted to western Canada was assessed over a four year period (2014-2017) at Lacombe, AB, Saskatoon, SK and Brandon, MB. A total of 10 site years of data were collected for grain yield, heading date, plant height and lodging. This data was used in conjunction with genotyping data obtained from the barley Infinium iSelect 9K genotyping beadchip to conduct association analysis using a linear mixed model that incorporated kinship to control population structure.
A total of three loci were significantly associated with the agronomic traits studied (1 for yield, 1 for heading date, 1 for plant height and 0 for lodging). All loci explained a relatively large proportion of the phenotypic variation for these traits and two of the loci (those associated with yield and plant height) had not been previously associated with these traits.
The loci identified in this study were present in germplasm adapted to western Canada, thus making them useful to breeders focused on this production area. Incorporation of these markers into genomic selection strategies for these traits should help breeders improve yield (which improves grower returns), reduce plant height (to reduce the chance of lodging and assist with management of straw) and maintain or reduce days to maturity (to ensure timely harvest).
Updated July 6, 2018