DNA Marker Technologies and Development of New Rice Varieties for Louisiana

Adam Famoso, Zaunbrecher, Rick, Angira, Brijesh  |  5/22/2019 9:05:14 PM

Adam Famoso, Brijesh Angira, Jennifer Dartez and Rick Zaunbrecher

The development of new rice varieties has been conducted at the H. Rouse Caffey Rice Research Station near Crowley, Louisiana, since 1909. These efforts have led to the development of more than 50 new varieties, which accounted for more than 70% of rice acreage in Louisiana in 2018. New and improved varieties are a central component to increasing yield, sustainability and profit of the Louisiana and U.S. rice industries, which has always been the focus of the variety development program. In the past few years, new and evolving technologies have allowed expansion in new rice variety development.

The applied nature of variety development requires careful evaluation of the costs, benefits and logistical considerations when adopting new technologies. The potential utility of DNA markers in plant breeding has been recognized for decades, but widespread incorporation into variety development programs has been limited in public plant breeding programs. The major hurdles limiting the incorporation of molecular markers have been cost and efficiency.

In recent years, new DNA marker technologies and automated laboratory equipment have made significant headway toward reducing cost and increasing throughput to a point where the time and resource investment is a net positive. In 2016, the Louisiana Rice Research Board supported the development of a state-of-the-art DNA marker lab at the Rice Research Station. This lab uses the KASP SNP genotypic chemistry and the LGC SNPline genotyping platform, which are ideal for routine breeding applications that include many samples (tens of thousands) run across relatively few DNA markers (1-20). The lab has a capacity of 40,000 data points a day and can be operated by a single person, with a cost per data point of 2 cents. This lab has enabled the large-scale implementation of DNA markers into nearly all stages of the breeding process.

A DNA marker is a characterized region of the genome that is different among individuals of interest. It can be associated with a trait of interest, such as disease resistance, and used to determine which individuals will be resistant. Alternatively, a DNA marker may not be associated with a trait but can be useful in creating a genetic profile (fingerprint) that can differentiate varieties. It is critical that DNA marker sets are optimized and validated across the target germplasm (rice lines) for the specific objective that the markers are intended to address.

The rice variety development program now routinely uses DNA markers at every stage of the breeding program, especially for direct selection of target traits prior to field evaluation. Since 2016, KASP DNA SNP markers have been developed and extensively validated for more than 20 key genes controlling key breeding traits, including disease resistance (blast and Cercospora), grain quality (amylose, gel temperature, aroma, and grain length and width), and agronomic characteristics (plant height, leaf pubescence, herbicide resistance and maturity). Through continued method optimization, the program now routinely evaluates 1,600-3,200 individual plants per week and more than 40,000 individual plants per year. This allows selected populations to have only the most desirable plants advanced for field evaluations, significantly increasing the probability of identifying a superior line.

The program has also identified and developed customized KASP DNA SNP marker panels that have been used to characterize all U.S. rice lines and develop DNA fingerprint profiles that can differentiate any two U.S. rice varieties. These marker panels are extensively used in the breeding and foundation seed programs during the purification of new varieties and the maintenance in foundation seed stocks. Foundation seed is a pure form of seed that is the ultimate source of the seed grown in farmers’ fields. Prior to increasing the foundation seed of a new variety, every individual plant that will give rise to foundation seed is characterized using these DNA marker sets, and any plant that appears different is omitted from the seed source. Similarly, once a variety is released, new seed are continually produced as breeder and foundation seed and are routinely monitored for impurities and purified with DNA markers.

Some breeding applications are now conducted that would not be practical without the marker technologies, such as the incorporation of exotic disease resistance genes. Starting in 2016, we began incorporating four new blast disease resistance genes from exotic Asian materials into our elite Louisiana lines. Three of the four new genes confer complete resistance to all the known races of blast present in the Southern United States. The challenge of accomplishing this without the DNA markers is that the two Asian lines were undesirable for most of the other key breeding traits. For example, one of the lines was very low yielding, tall and did not flower in Louisiana until after six months, twice as long as our adapted germplasm. In addition, both lines had pubescent leaves and undesired grain quality, with high chalk and cooking characteristics not typical of standard Southern U.S. market classes. By developing DNA markers that tag the desired genes, we were able to select the desired plants and immediately cross them back to our desired lines, without the need to measure the plants for their disease resistance and agronomic or grain quality characteristics.

By early 2019, we had developed more than 100 lines that are fixed for the desired blast genes from the Asian lines, while containing the desired grain quality and agronomic traits from the Louisiana germplasm. A subset of these lines was evaluated under controlled conditions by our collaborators at the U.S. Department of Agriculture-Agriculture Research Service in Stuttgart, Arkansas, and all have demonstrated the expected resistance to the blast disease. The newly developed lines will be evaluated in 2019 for blast resistance under field conditions at the Rice Research Station and in the breeding nursery for agronomic and grain quality characteristics. A subset of lines with the best blast resistance, grain quality and agronomic characteristics will be used in 2020 to make new breeding crosses.

The impact of these efforts will be a new set of broad-spectrum blast resistance genes for use in variety development, which will help ensure continued development of blast-resistant varieties and help reduce the risk of the blast pathogen from evolving resistance to the available blast resistance genes. By using DNA marker technology, this was accomplished in three years as opposed to 10-15 years with reduced effort in evaluating the thousands of plants for disease, quality and agronomic characteristics.

The utilization of DNA markers is a valuable tool in the breeding and variety development process. It is not a silver bullet and is not a replacement for the foundational breeding activities, which include extensive field testing across years and locations. However, for many breeding activities, the use of DNA markers helps us accomplish the objectives faster, cheaper and with more accuracy.

Acknowledgements: Dr. Yulin Jia with the U.S. Department of Agriculture-Agriculture Research Service in Stuttgart, Arkansas.

Adam Famoso, H. Rouse Caffey Endowed Professor; Brijesh Angira, assistant professor; Jennifer Dartez, research farm specialist; and Rick Zaunbrecher, research associate, all at the H. Rouse Caffey Rice Research Station, Crowley, Louisiana.

This article appears in the spring 2019 issue of Louisiana Agriculture.

Brijesh Angira in his lab

Brijesh Angira, assistant professor-research at the H. Rouse Caffey Rice Research Station, prepares plant tissue to be tested to determine if lines of rice have the desired DNA traits. Photo by Bruce Schultz

Adam in the greenhouse

Adam Famoso, LSU AgCenter rice breeder, checks on the progress of a rice plant that has been used to make a cross in a greenhouse at the H. Rouse Caffey Rice Research Station. Seed from the cross will be grown, and the DNA from the plant’s tissue will be tested to determine if the new line of rice has the desired traits. Photo by Bruce Schultz

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