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United States Department of Agriculture

Agricultural Research Service

Research Highlights
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New in November, 2014 - Recent Publications, Significant Research Collaborations, Grants Awarded, Technology Transfer, Outreach, Non-technical ArticlesCritical and Emerging Issues


Recent Publications -


ARS Anticipated Product: Plants With Resistance To Diseases


Amei, A., Lee, S., Mysore, K., and Jia, Y.  2014. Statistical inference of selection and divergence of the rice blast resistance gene Pi-ta.  Gene, Genomic and Genetics (G3), doi: 10.1534/g3.114.014969 (Published on line on October 21).


Rice blast disease is one of the most destructive diseases of rice. Over 100 major and minor resistance genes have been identified but only 22 have been cloned. The resistance gene Pi-ta has been effectively used to control rice blast disease in the Southern US and worldwide.  A few recent studies have described the possible evolution of Pi-ta in cultivated and weedy rice, the latter a noxious weed. However, evolutionary statistics used for the studies are too limited to understand selection and divergence of Pi-ta during crop domestication. In this study, we applied a new statistical method to examine the evolution of the Pi-ta gene in cultivated and weedy rice. Our data suggest that the Pi-ta gene may have recently been established in cultivated rice and US weedy rice. In addition, the Pi-ta gene is under positive selection in japonica, tropical japonica, US cultivars, and US weedy rice. We also found that the DNA sequences of two regions of the Pi-ta gene are commonly found among all rice accessions examined. Our results provide a valuable analytical tool for understanding the evolution of disease resistance genes in crop plants.


ARS Anticipated Product: Improved Biotechnology Risk Assessment Methods For The Analysis Of Potential Unintended Consequences In Crop Plants


Thurber, C., Reagon, M., Olsen, K., Jia, Y., and Caicedo, A. 2014.  The evolution of flowering strategies in US weedy rice.  American Journal of Botany 101 (10): 1737 – 1747.  (An invited article for 100 years of celebration of Journal).


The timing of when plants initiate flowering has a large impact on mating success, and on seed production and viability. Multiple environmental variables, such as temperature and day length, can act as cues for flowering time in different species. Many crop varieties have been selected for uniformity in flowering time. In contrast, variable flowering may be important for increased competitiveness of weed species invading the agricultural environment. Given their shared species designation, we assessed the extent to which flowering time differed between cultivated rice and its invasive conspecific weed, weedy rice. We further assessed whether genes affecting flowering time variation could play a role in the evolution of flowering time in US weedy rice. We found that flowering time has diverged between two distinct weedy rice groups, such that straw-hulled (SH) weeds flower earlier and black-hulled awned (BHA) weeds flower later than cultivated rice. Our phenotypic data indicate that there is no single optimal weed flowering strategy. Flowering differences between weed rice groups and their ancestors suggest this trait has evolved rapidly. From a weed management standpoint, there is the potential for overlap in flowering of BHA (not SH) weeds and US rice cultivars.  This could potentially permit gene flow between herbicide resistant rice and weedy rice.

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Significant Research Collaborations


International - none to report.



ARS Anticipated Product: New Tools To Manage High-Throughput Phenotypic And Genotypic Data

Dr. Jeremy Edwards participated in the kick-off meeting for the NSF Track 2 EPSCoR  Arkansas and Missouri Plant Bioimaging Consortium at Arkansas State University. New funding was awarded to the multi-institution group to explore the use of new imaging technologies to quantify biotic and abiotic stress in plants. DBNRRC will serve as a “campus champion” to facilitate accomplishment of the research goals.


Grants Awarded - none to report.


Technology Transfer - 

a.  Formal Events:

To Non-Research Stakeholders - nothing to report

To Research Community - nothing to report

b.  Informal Contacts:

1-   Journalist for Nature regarding research on arsenic in rice                  2 - with rice growers in PA and SC - topics rice diseases, rice milling quality                 

1 - with Tri-Society news media - biofortified rice

2 - local newspaper write-ups on 1 scientist and the research support staff at DBNRRC

1 - Congresswoman Delauro (CT) office, regarding rice quality

1 - FDA, regarding research on mitigating exposure to arsenic in rice

1 - phone call and 1 e-mail; topics- rice and weed management

1 - feature presentation of DBNRRC research on Arkansas’ PBS station “AETN “ Agri Arkansas program

c. New MTAs - nothing to report

d. Germplasm exchanged:

3 elite breeding lines provided to a southern breeder for field study in 2015;1 ARS historical cultivar provided to Dow AgroSciences LLC, Indianapolis, Indiana; and 204 GSOR rice accessions sent to the USA, China, Belgium and England




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Public Outreach/Stakeholder and Collaborator Contacts -

September 3, Dr. Yulin Jia consulted with Dr. Mujeebur Rahman Khan, Professor of Department of Plant Protection, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, India to serve as the foreign examiner for a dissertation of his PhD student. As per Academic Ordinances of the university, the Ph.D. thesis is evaluated by three experts, one from an advanced country (foreign examiner) and two within the country (Indian examiners).

September 8, Dr. Yulin Jia consulted with Dr. James Correll, Professor of Plant Pathology of University of Arkansas to host a discussion and tour with three rice pathologists, Chang-Hsin Kuo, National Chiayi University, Chung Wen-Hsin and Yicheng Chen from National Chung Hsing University, Taiwan.  Dr. Jia presented an update of ARS research on rice blast and sheath blight diseases, and ideas for collaboration subsequently led a tour the ARS facility.

September 10 and September 18, Dr. Yulin Jia consulted with Dr. Muthusamy Manoharan, Director of Regulatory Science Center, Associate Professor of Department of Agriculture, University of Arkansas - Pine Bluff (UA PB) to attend a thesis proposal of Mr. Suresh Pokhrel for his master of science as a member of thesis examining and supervising committee.  Before seminar, Dr. Jia also supervised blast inoculation and evaluation of rice materials at a UA Pine Bluff laboratory.

September 15, Dr. Yulin Jia consulted with John Ridenour, a graduate student of Department of Plant Pathology to meet with Dr. Richard Wilson, an Assistant Professor at the University of Nebraska.   Additional participants for discussions were Johnathon Smith, UA Plant pathology, Dr. Jeremy Edwards (ARS) and Dr. Yeshi Wamishe of University of Arkansas cooperative extension service, Stuttgart, AR.  Subsequently, Dr. Jia led a tour of Plant Pathology lab of DBNRRC.

September 15, Dr. Yulin Jia consulted with Dr. Mike Stout, professor of Louisiana State University for blast infection of adult plants during an investigation of the effect of blast infection on susceptibility of rice to fall armyworm. 

September 16, Dr. Anna McClung provided an overview of the research being conducted at the DBNRRC to a group of 6 representatives from the Federal Grain Inspection Service offices in Washington and Louisiana. A tour of the facility was provided with special stops in the grain chemistry, genomics, and germplasm evaluation laboratories.

September 22, Dr. Yulin Jia attended a qualification examination of a PhD candidate Felix Rotich of Department of Plant Pathology, University of Arkansas-Fayetteville with Dr. Yeshi Wamishe, University of Arkansas Cooperative Extension Service, and Dr. Klaus Scheuermann, a visiting scientist from Brazil.

During September, 800 rice accessions from the Genetics Stocks Oryza (GSOR) collection were distributed to researchers in the USA and Taiwan.

During the last 12 months  2,149 rice accessions were distributed through the NPGS (Aberdeen, ID) to such countries as Bhutan, Canada, Chile, China, France, India, Japan, South Korea, Netherlands, Pakistan, Philippines, Spain, Turkey, United Kingdom, and U.S.  Although the seed is distributed from the Idaho storage center, all rice accessions are rejuvenated and characterized at DBNRRC using summer or winter (in Lajas, Puerto Rico) nursery facilities.



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Write ups in lay media (local paper, Ag. Research magazine, etc.)


Three scientists were featured in the local newspaper, Stuttgart Daily Leader, in an ongoing series to introduce local scientists and highlight the facility’s research mission to the community.  Featured were Drs. Georgia Eizenga, Rolfe Bryant, and David Gealy.


September 15, Dr. Shannon Pinson was quoted in The New York Times article “Fighting Poisons with Bacteria”, which addresses current research with bacteria that can help lower the amount of arsenic in food products by reducing the amount of arsenic that crops uptake from the soil.


Critical or Emerging Issues - none to report



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For more information, please contact Anna McClung, Research Leader,

Last Modified: 11/21/2014
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