Researchers from wide range of disciplines advance plant genetics

Wednesday, October 5, 2016

Lana Koepke Johnson

Yerka team
Research Assistant Professor Melinda Yerka and Assistant Professor James Schnable collect data in a sorghum field for a phenotyping project with postdoc Yang Zhang and graduate students Xianjun Lai, Zhikai Liang, Jake Ziggafoos, Chenyong Miao and Daniel Carvalho. | Photo by Lana Koepke Johnson

University of Nebraska–Lincoln faculty from a wide range of disciples are working together to advance the field of plant genetics, specifically with sorghum. This was evidenced this past summer by interactions among faculty, postdocs, graduate and undergraduate students working with Melinda Yerka, agronomy research assistant professor and plant geneticist, to collect data from a field of grain sorghum varieties at the Agricultural Research & Development Center near Mead, Nebraska.

“One of the exciting things about being a plant geneticist at UNL is that you get to act as a ‘hub,’ using your research to connect disciplines as diverse as biochemistry, weed ecology, crop evolution, computational biology, and even computer science,” Yerka said.

Melinda Yerka holding wide variety of sorghum panicles
Melinda Yerka holds a wide variety of sorghum panicles
collected from her research field near Mead, Neb.,
demonstrating the range of phenotypes and genetic
diversity available in this historically important Nebraska crop.

The first of these collaborations involves plant genetics, biochemistry and weed ecology.

The male reproductive parts of flowers shed pollen grains, which may land on a single stigma – the outermost, sometimes sticky part of a pistil – which is the flower’s female reproductive organ. If fertilization occurs, new seeds may develop.

While different plants shed pollen at different times, some species do overlap and shed their pollen at the same time. Trees, grasses and roses all shed pollen at the same time, but only the pollen from roses can fertilize rose plants. The pollen from many species may land on a single stigma, but only the right kind of pollen will be accepted into the pistil and set seed. Pollen-pistil interactions involve extensive molecular cross-talk that determines which pollen is allowed into the ovule to set seed, and which is excluded.

Pollen-pistil interactions are actively studied in a number of other plant species, including poppy, lily, potato, and increasingly maize; however, relatively little is known about sorghum. Yerka and Rebecca Roston, biochemistry assistant professor and plant biochemist, worked with UNL sophomore Taylor O’Brien this summer to develop and test sorghum pollen growth assays. They are interested in the ways sorghum pollen and pistils communicate during self-pollination as opposed to when sorghum pollinates its wild or weedy relatives.

“Identifying the range of pollen-pistil interactions among sorghum species may provide insight as to whether certain genes could be used to prevent gene flow from crops to neighboring fields or related weed species.” Yerka said. “This becomes especially important for grain sorghum when you have herbicide-resistant crops growing in places where related species exist as weeds, because herbicide resistance could transfer to them through pollen and make them much more difficult to control.”

These genetic reproductive barriers will also be important in protecting the quality of new sorghum varieties with specialized starch traits, like waxy sorghum. Normal sorghum starch is typically comprised of 30 percent amylose and 70 percent amylopectin, but several recessive mutations confer waxy endosperm with nearly 100 percent amylopectin. This unique composition results in increased digestibility and shortened fermentation times in ethanol production. It also improves the texture and shelf life of breads and cakes.

Yerka led the release of several waxy hybrid parent lines in 2014–2015 while working for the U.S. Department of Agriculture – Agricultural Research Service. She continues this work at Nebraska with Earl Roemer, president of Nu Life Market.

Roemer used the grain of hybrids made from Yerka's parent lines in pilot studies with the ethanol and food industries, with encouraging results. In order to explore their full market potential, protecting starch quality will require preventing cross-pollination by normal sorghum or related weeds, which would carry the dominant gene to produce amylose in newly developing seeds.

Nu Life Market provides more information about the nutrient content of waxy whole grain sorghum flour.

The second collaboration involves plant genetics, computational biology, and computer science.

How do you combine data on genetic and phenotypic variations from several related grain crops like corn, sorghum and millet in order to identify the specific functions of individual genes in each species?

University agronomy experts are working to figure out new approaches to collecting and analyzing this data. Leading the effort is James Schnable, assistant professor of agronomy and computational biologist and working with him are Yerka, Oscar Rodriguez, research professor and maize breeder, and Dipak Santra, associate professor and millet breeder.

Yerka and Schnable, along with postdoc Yang Zhang and graduate students Xianjun Lai, Zhikai Liang, Jake Ziggafoos, Chenyong Miao and Daniel Carvalho, recently spent a day near Mead measuring several traits of grain sorghum varieties, including height, stem width and the angle formed between the stem and the leaf of sorghum plants.

Xianjun Lai, visiting graduate student from China, and postdoc Yang Zhang
Xianjun Lai, visiting graduate student from China, and postdoc
Yang Zhang measuring traits of grain sorghum varieties.
| Photo by Lana Koepke Johnson

Schable said plants with more erect leaves tend to be better at growing in really crowded fields than plants where the leaves grow almost straight out from the stem. Being able to crowd more plants onto the same acreage has been a big driver of how plant breeders have continued to increase yields year after year.

“On the other hand, in drier regions like western Nebraska, farmers will often plant fewer plants per acre so each plant will have access to a bigger share of the water in the soil. Under those conditions flatter leaves let plants capture more of the sunlight falling on the field.” Schnable said.

It is useful to understand the genes involved in erect or flat leaves to help breed for the best plant architecture suited to different growing conditions. Corn and sorghum share many of the same genes, and it is likely that control of leaf angle variation in both species proceeds along similar genetic pathways. According to Schnable, identifying new genes involved in controlling this trait wouldn’t have been possible using data from just maize or just sorghum, both are needed.

The researchers’ goal is to combine data from the field measurements of leaf angles in sorghum with data from sets of diverse maize hybrids and inbreds grown at Mead and in the new automated phenotyping greenhouse at the Greenhouse Innovation Center on Nebraska Innovation Campus. They hope to identify new genes involved in controlling these traits – and ultimately help farmers plant the best varieties for different growing conditions in Nebraska and the world in general.

More information on Schnable’s phenotyping research at NIC available at https://go.unl.edu/schnable-phenotyping-research

The third collaboration involves plant genetics and crop evolution.

Did you know that the bristles on brooms used to be made from a plant called broomcorn, and that making brooms was a thriving industry in Nebraska years ago?

Broomcorn is actually a type of sorghum, and the long bristles are branches on the sorghum panicle, or head. Modern sorghum hybrids typically grown on the Great Plains have very short panicle branches, resulting in the familiar compact seed head. Panicle branch extension, or the lack thereof, is determined by meristems – small patches of cells at each branch point that keep the plant growing. They are the plant equivalent of stem cells.

Variation in the DNA sequence of certain genes regulating meristems, by activating or de-activating them during plant development, were used by early maize breeders in Mexico to create a highly compact female flower – the cob. University agronomy researchers Brandi Sigmon, research assistant professor, and Jeff Mower, associate professor, are working with Yerka to study the wide variety of panicle architecture present in sorghum to see if early African sorghum breeders targeted similar genes when adapting the crop to the wide range of geographies and climates where sorghum is traditionally grown.

These and other collaborations offer new and exciting research possibilities into the world of plant genetics.

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