Scientists solving inbreeding barrier to more sustainable, nutritious hay

Using powerful computers and genome sequencers in their Washington State University lab, scientists Deven See and Zhiwu Zhang are part of a national team solving genetic hurdles to better alfalfa (Photo by Seth Truscott, WSU).

By Seth Truscott, College of Agricultural, Human, and Natural Resource Sciences

Helping provide a more valuable and sustainable hay crop for farmers and dairy producers, geneticists at Washington State University this fall launched a high‑tech search for genetic keys unlocking improvements to alfalfa fertility.

Zhiwu Zhang, the Washington Grain Commission Distinguished Professor for Statistical Genomics in WSU’s Department of Crop and Soil Sciences, leads the $250,000 research project, funded by the U.S. Department of Agriculture’s National Institute for Food and Agriculture, aimed at solving a breeding bottleneck to better alfalfa.

Innate barrier to fertility

Alfalfa is one of the most widely cultivated hay crops in the world, with about 55 million tons grown annually in the United States. Relied on by cattle producers for nutritious feed, “It’s one of our best and most important feeds for dairy cows,” said Zhang.

By improving simple traits controlled by major genes, breeders have already developed alfalfa that resists disease and survives cold winters. However, scientists have had little success improving hay quality and seed and forage yields, which are controlled by multiple genes.

That’s because of a challenge innate to alfalfa called inbreeding depression. Unlike some crops, such as wheat, some alfalfa genes contain a self‑defense mechanism that prevents inbreeding, stopping breeders from developing inbred lines — an important step in breeding hybrids with favorable traits, such as more nutritious, high‑yielding hay.

“Alfalfa has self‑incompatibility genes,” explained Deven See, USDA research geneticist and adjunct professor with the WSU Department of Plant Pathology. “If it mates with itself, it quickly becomes sterile”.

“Rarely will a purebred plant survive a fourth generation of inbreeding,” See added. “But we need seven or eight generations to reach a pure line that we can cross to achieve a healthy, desirable hybrid.” “We need a good way to accumulate valuable genes that increase yields and quality,” Zhang said. “Inbreeding is the only way we can do it.”

Gathering valuable genes

Co‑investigators Zhang, See, and USDA research geneticists Longxi Yu, at WSU’s Irrigated Agriculture Research and Extension Center at Prosser, and Michael Peel, at the USDA Forage & Range Research Lab in Logan, Utah, are using next‑generation sequencing to identify the alleles, or areas of genetic code, responsible for inbreeding depression.

In Washington and Utah, scientists will grow and genetically sample thousands of alfalfa plants over the next three years, winnowing them for good and bad traits with the goal of developing 200 distinct inbred lines.

“Using a tiny sample of a plant, we can find markers for inbreeding depression, then kick those plants out early in the breeding process,” Zhang said. “Alfalfa breeders will then be able to use true inbred lines to produce vigorous hybrids with better seed and forage quality.”

Zhang is excited about the potential impact of the research. Because alfalfa fixes nitrogen in the soil, more profitable alfalfa production could boost yields in many other crops through rotation.

“By solving inbreeding depression, we’re opening the door to better breeding, better crops, and improved yields,” Zhang said. “New, hardy alfalfa that can survive harsh climates and disease, while offering more seeds and forage and better nutrition, will feed livestock more economically and sustainably, ultimately helping everyone.”