The impact of herbicide-resistant rice technology on phenotypic diversity and population structure of United States weedy rice

Authors: BURGOS, NILDA - University Of Arkansas; SINGH, VIJAY - University Of Arkansas; TSENG, TE MING - University Of Arkansas; Black, Howard; YOUNG, NELSON - University Of Massachusetts; HUANG, ZHONGYUN - University Of Massachusetts; HYMA, KATIE - University Of Massachusetts; Gealy, David; CAICEDO, ANA - University Of Massachusetts

Submitted to: Plant Physiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/3/2014
Publication Date: 8/13/2014
Publication URL: http://handle.nal.usda.gov/10113/60672
Citation: Burgos, N.R., Singh, V., Tseng, T., Black, H.L., Young, N.D., Huang, Z., Hyma, K.E., Gealy, D.R., Caicedo, A.L. 2014. The impact of herbicide-resistant rice technology on phenotypic diversity and population structure of United States weedy rice. Plant Physiology. 166:1208-1220.

Interpretive Summary: Rice varieties with herbicide resistance (HR) to the chemical, imazethapyr, have been used to control a weedy, red-seeded form of crop rice (called red rice) for more than a decade, and are now grown on about 60% of the rice acreage in Arkansas, the largest producer of rice in the USA. Although this system has had good success in general, the HR gene can be inadvertently transferred from HR rice to the red rice at low rates through a natural process called outcrossing. This can create unwieldy populations of red rice plants that have gained resistance to the herbicide, and thus are no longer controllable using these HR varieties, resulting in difficult and expensive management problems for farmers. In order to assess how the use of HR rice varieties have been affecting the herbicide resistance levels, plant composition, and genetic makeup of red rice in Arkansas, we collected weedy red rice biotypes from commercial farm fields with a history of HR rice production. Seed heads from representatives of various red rice biotypes were harvested and tested for resistance to imazethapyr, the herbicide applied to HR rice (commercially known as Clearfield® rice). Most of the plants sampled had at least 20% resistant offspring, suggesting that they had recently acquired the HR gene from HR rice. Generally, these resistant weeds were taller than commercial rice cultivars and began flowering later than did our historical red rice biotypes. Less than 1/3 of contemporary HR red rice had straw-colored hulls (i.e. more than 2/3 had dark-colored awns), which was a dramatic reduction from the 2/3 strawhulls found in historical red rice biotypes in Arkansas. This shift in the frequency of hull color suggested that HR rice outcrossing and gene flow to red rice might have been favored in the dark-hulled biotypes of the weed at the expense of the straw-hulled types. Significantly, a sizeable portion of the DNA known to have originated from chromosomes of the HR rice crop was found in the chromosomes of the HR red rice. Additional DNA analyses showed that HR red rice biotypes contained DNA segments in the region of chromosome 2 which contained the specific HR gene that confers resistance to imazethapyr herbicide. The HR red rice described in this research represents a new and distinct population of red rice. It is characterized by a strong resistance to imazethapyr herbicide and inheritance of genetic material directly from HR rice cultivars through outcrossing. Its acquired HR trait, in combination with other modifications in plant development, provide this HR red rice with additional biological ‘tools’ that render its management even more difficult than that of historic red rice biotypes.

Technical Abstract: The use of imazethapyr herbicide-resistant (HR) Clearfield® rice (Oryza sativa L.) to control weedy rice has increased in the past 12 years to comprise about 60% of rice acreage in Arkansas, where 43% of rice in the USA was planted in 2013. To assess the impact of HR cultivated rice on herbicide resistance and population structure of weedy rice, weedy samples were collected from commercial fields with a history of Clearfield® rice production. Panicles from representatives of various weedy types were harvested and tested for resistance to imazethapyr. The majority of plants sampled had at least 20% resistant offspring. These resistant weeds were 97 to 199 cm tall and initiated flowering from 78 d to 128 d, generally later than recorded for historical weedy rice accessions. Whereas the majority (70%) of historical weedy accessions had straw-colored hulls, only 30% of contemporary HR weedy rice had strawhulls. Results of genotyping by sequencing (GBS) data showed that contemporary HR weedy rice was not genetically structured according to hull color, whereas historical weedy rice separated into strawhull and blackhull populations. Moreover, a significant portion of the cultivated rice crop genome has been introgressed into HR weedy rice, which was rare in historical weedy accessions. Analysis of admixtures show that HR weedy rice tends to possess cultivated rice haplotypes in the region of chromosome 2 containing the ALS gene, which confers resistance to imazethapyr. US HR weedy rice is thus a distinct population relative to historical weedy rice, and shows modifications in morphological and phenological profiles that are relevant to weed management.