The Difficult Task of Breeding Chickpeas - Pulse Research
July 03, 2019
Since 1997, Saskatchewan Pulse Growers (SPG) has commercialized 125 pulse crop varieties, in many market classes, through its Variety Commercialization Program.
It is important work aimed at developing new, publicly available pulse crop varieties with improved performance for growers across Saskatchewan.
SPG wants every farmer in Saskatchewan to have viable pulse crop options for their rotation, no matter where they farm, and that can only happen when work into varietal improvement is funded, much like the chickpea work undertaken by Dr. Bunyamin Tar’an.
By developing better breeding tools and better understanding the chickpea genome, he and his team can help achieve their goals of improving yield and reducing the agronomic constraints surrounding pulse production. In the case of chickpeas, finding sources of disease resistance and early maturity will go a long way to do that.
Chickpeas have been grown in Saskatchewan for many years, at varying acreage levels. In 2018, high prices had farmers seeding over double the acres they did in 2017 (from 160,000 acres in 2017 to 368,600 acres in 2018).
While many chickpeas were harvested successfully, others faced challenges related to disease, as chickpeas are highly susceptible. Breeding for disease resistance and early maturity in chickpeas takes time.
“The four most important traits in chickpeas, especially for Canadian farmers, are resistance to Ascochyta blight, large seed size – especially for the Kabuli-type, early maturity, and acceptable yield,” says Dr. Bunyamin Tar’an, a chickpea breeder at the Crop Development Centre (CDC) at the University of Saskatchewan. “Putting all those traits together in a single variety still poses a big challenge to the breeding program. Adding some additional and desirable traits, like tolerance to herbicide, upright plant stature, and a better nutritional profile adds another layer of challenge.”
Tar’an explains that a central problem for breeders is the lack of genetic diversity among chickpeas. All of the varieties commercially grown today are genetically related – even Desi and Kabuli types share a lot of the same DNA – so finding chickpea germplasm that carries desirable traits, like disease tolerance, means researchers have to dig through wild relatives of chickpea to find what they are looking for.
That leads to a second key problem, which is getting those traits from wild relatives into chickpea elite breeding lines and developing tools to make that breeding process accurate and efficient. In other words, finding the genes that govern early maturity, say, in a wild relative is only part of the battle. Crossing genetically diverse lines can be challenging so breeders need tools that will help them quickly assess the lines resulting from these crosses, to identify which ones have the traits they want to carry forward.
Even that description makes the task sound a lot easier than it actually is. While much work has been done to better understand and sequence chickpea DNA and also identify wild germplasm with desirable traits, there is still much more to do in terms of developing the kinds of tools breeders need to finally bring new varieties to Canadian growers. This is the important work Tar’an and his team has been doing with funding from SPG.
Building a Breeders' Toolbox
Tar’an recently completed three studies aimed at developing new breeding tools for chickpeas. One looked at the genome architecture and dynamics of 109 elite Canadian chickpea lines. The second project focused on re-sequencing 251 chickpea accessions (or chickpea
germplasm). The third was aimed at developing a new genomic breeding tool for chickpeas.
All three projects were linked and, in many ways, they all started with the need to sequence the chickpea genomes.
The genome of CDC Frontier was sequenced in 2013. Tar’an explains that this gave breeders a general blueprint of the genetic makeup of chickpeas – kind of a reference genome, as it were. “The next step was to examine thoroughly the variability of the genetic makeup of other existing varieties through a process called re-sequencing, and linking that genetic variability with the actual field performance of those varieties.”
Tar’an says that by re-sequencing these chickpea varieties, researchers were able to better understand the genetic origins of physical traits they observed in the plants. “This provided us with a tremendous resource of information of DNA sequence variability across cultivars, which we used to develop the SNP chip.”
What is a SNP chip? “It is also known as a SNP array and is a collection of thousands of single nucleotide variations in one chip,” says Tar’an. “In the case of chickpea, there are over 60 thousand SNP variabilities in the chip.”
In layman’s terms, SNPs, or single nucleotide polymorphisms, are regions on the genome that are variable and could be associated with specific traits. A SNP chip is a collection of thousands of SNP variations across the chickpea genome that are put together into one place. It is a tool that allows breeders to much more quickly screen large chickpea populations for the variability and the traits they are interested in, keeping the ones they want to advance and letting the others go.
“SNP chip technology has been widely used in many major crops, like wheat, soybeans, corn, and rice,” says Tar’an. It has not been available for chickpeas and other legumes because the genomic information needed to develop such a tool has, until now, been very thin.
This is particularly useful when it comes to the wild chickpea germplasm being introduced into breeding programs. “The output from these three projects can be used as a tool to screen the materials form the wild chickpea projects,” says Tar’an. “The progeny of the wild crosses possess characteristics that are lacking in cultivated varieties, such as better tolerance to frost and heat conditions, as well as better resistance to some root diseases.”
Still Some Road to Walk
A better understanding of the chickpea genome, access to wild germplasm with desirable traits, and new breeding tools all bode well for the arrival of improved chickpea cultivars with traits farmers want.
“Currently, worldwide chickpea production exceeds demand. Buyers are looking for top quality, so it is critical that Canadian chickpeas meet these expectations,” says Laurie Friesen, SPG’s Seed Program Manager.
She says that Tar’an’s focus on disease resistance, early maturity (which should greatly reduce green seed content thereby improving quality), and large seed size are key to achieving better market access for Canadian farmers.
Tar’an says that while breeders are much farther along the road toward these goals, there is still a lot of work to be done, including work to test the utility of the SNP chip his team has just developed. The genetic mechanisms that influence agronomic traits, like yield and
disease resistance, are highly complex in themselves, never mind how changes in the growing environment from year-to-year impact how those traits are expressed.
“These projects were geared toward breeding tool development that will allow for a more effective and quick selection process,” says Tar’an. “At the same time, this work has generated a wealth of information about the genetics of the important traits in chickpeas, including
traits that are important to farmers for successful chickpea production under Canadian conditions, as well as traits that are important to processors and consumers, such as nutritional profile.”
Tar’an warns that a herbicide-resistant, Ascochyta-tolerant, early maturing, highyielding, upright chickpea, may still be a ways off, but with the new tools he and his team have developed, they are much closer than they used to be. “In the meantime, we will continue to develop and deliver improved chickpea cultivars to Western Canadian farmers.”