Research Project: Broadening and Strengthening the Genetic Base of Rice for Adaptation to a Changing Climate, Crop Production Systems, and Markets

Location: Dale Bumpers National Rice Research Center

Publications (Clicking on the reprint icon will take you to the publication reprint.)

Multi-experiment and multi-locus genome-wide association mapping for grain arsenic in rice population - (Peer Reviewed Journal)

Comparative study of different water management practices on element content in rice grain, yield, and yield components - (Peer Reviewed Journal)

Registration of six Oryza rufipogon Species Complex (ORSC) chromosome segment substitution sine (CSSL) libraries in elite Indica and Japonica rice backgrounds - (Peer Reviewed Journal)

Identification of Blast QTL in a Presidio/Oryza rufipogon rice advanced backcross population - (Abstract Only)

Screening the Presidio/Oryza rufipogon rice advanced backcross population for reaction to leaf blast disease using two techniques - (Abstract Only)

Modern tools for unveiling the genetic basis of prickliness in plants and their applications in plant breeding - (Abstract Only)

AlphaFold application in the rice blast system - (Abstract Only)

Aus sub-population of Oryza sativa L. for bridging food security and water sustainability in rice - (Abstract Only)
Rohila, J.S., Huggins, T.D., Jackson, A.K., Sookaserm, T.B., Mitchell, J.R., Ponniah, S.K., Edwards, J. 2025. Aus sub-population of Oryza sativa L. for bridging food security and water sustainability in rice. Abstract. Plant and Animal Genome Conference. San Diego, California.

Surveys of Magnaporthe oryzae genotypes in breeding stations and commercial rice fields in Arkansas, Louisiana and Puerto Rico from 2017 to 2019 - (Peer Reviewed Journal)
Huang, Y., Jia, Y., Wamishe, Y., Jia, M.H. 2025. Surveys of Magnaporthe oryzae genotypes in breeding stations and commercial rice fields in Arkansas, Louisiana and Puerto Rico from 2017 to 2019. Plant Disease. https://doi.org/10.1094/PDIS-03-24-0652-RE.

Mining the diversity in rice and it’s ancestral species for rice improvement - (Abstract Only)
Eizenga, G.C. 2024. Mining the diversity in rice and it’s ancestral species for rice improvement. Abstract. ASA,CSSA,SSSA International Annual Meeting, San Antonio, Texas. November 10-13, 2024. https://scisoc.confex.com/scisoc/2024am/meetingapp.cgi/Paper/156032

Genome-Wide Association Study for drought response traits in a diverse tropical japonica rice panel - (Abstract Only)
Schafer, S.E., Ting, T., Eizenga, G.C., Henry, A., Wang, D.R. 2024. Genome-Wide Association Study for drought response traits in a diverse tropical japonica rice panel. Crop Science Society of America. Abstract. ASA, CSSA, SSSA International Annual Meeting, San Antonio, Texas. November 10-13, 2024. https://scisoc.confex.com/scisoc/2024am/meetingapp.cgi/Paper/158147

Registration of three long grain rice germplasm lines with improved blast resistance with the Ptr gene, low chalk, excellent milling quality, and good yield - (Peer Reviewed Journal)
Jia, Y., Gibbons, J., Jackson, A.K., Dunlap, H.N., Zhao, H., Wang, X., Jia, M.H., Fomoso, A., Groth, D. 2025. Registration of three long grain rice germplasm lines with improved blast resistance with the Ptr gene, low chalk, excellent milling quality, and good yield. Journal of Plant Registrations. 19:1. https://doi.org/10.1002/plr2.20407.

Characterization and genomic insights for the emerging rice pathogen, Pantoea ananatis - (Abstract Only)
Giebler, M., Luna, E., Jia, Y., Leach, J.E. 2024. Characterization and genomic insights for the emerging rice pathogen, Pantoea ananatis. Abstract. International Phytobiomes Conference, St. Louis, Missouri, November 19-21, 2024.

Manifold and spatiotemporal learning on multispectral unoccupied aerial system imagery for phenotype prediction - (Peer Reviewed Journal)
Farag, F., Huggins, T.D., Edwards, J., McClung, A., Hashem, A., Causey, J., Bellis, E.S. 2024. Manifold and spatiotemporal learning on multispectral unoccupied aerial system imagery for phenotype prediction. The Plant Phenome Journal. https://doi.org/10.1002/ppj2.70006.

Effect of alternate wetting and drying and organic matter addition on greenhouse gas and arsenic dynamics in rice paddy soil - (Abstract Only)
Vega, M., Dignam, W., Slade, A., Weidman, G., Rohila, J.S., Reid, M.C. 2024. Effect of alternate wetting and drying and organic matter addition on greenhouse gas and arsenic dynamics in rice paddy soil. American Geophysical Union. Abstract.

Impacts of multiple dry downs on rice yield, processing grain quality traits and greenhouse gases - (Proceedings)

Genetic variation and population structure of the rice accessions maintained in the AfricaRice genebank using DArTseq - (Peer Reviewed Journal)
Gouda, A., Sangare, J., Wambugu, P., Huggins, T.D., Ndjiondjop, M. 2024. Genetic variation and population structure of the rice accessions maintained in the AfricaRice genebank using DArTseq. Crop Science. https://doi.org/10.1002/csc2.21395.

Polyphenol-mediated covalent bonds on glutelin structural changes in rice with different bran colors - (Peer Reviewed Journal)

Challenges and opportunities of rice disease managements in the USA - (Proceedings)
Jia, Y., Osakina, A., Huang, Y., Pedrozo, R., Wang, L., Huggins, T.D., Jia, M.H., Ponniah, S., Nicolli, C., Dalla Lana, F., Wang, G., Yang, Y., Luna, E., Leach, J. 2024. Challenges and opportunities of rice disease managements in the USA. Meeting Abstract. 2024 International Symposium of Rice Functional Genomics, September 9-11, 2024. Little Rock/Stuttgart, Arkansas.

Identification of genetic loci for grain traits and disease resistance reveals a potential trade off in rice - (Peer Reviewed Journal)
Jia, Y., Jia, M.H., Dunlap, H.N. 2024. Identification of genetic loci for grain traits and disease resistance reveals a potential trade off in rice. PhytoFrontiers. https://doi.org/10.1094/PHYTOFR-03-24-0025-R.

The effects of abiotic stressors on rice resistance responses to the blast fungus Magnaporthe oryzae - (Proceedings)
Huang, Y., Jia, Y. 2024. The effects of abiotic stressors on rice resistance responses to the blast fungus Magnaporthe oryzae. Abstract. 2024 International Symposium on Rice Functional Genomics, September 9-11, 2024. Little Rock/Stuttgart, Arkansas.

Understanding blast resistance through overexpression of the Pita-2 gene in rice - (Proceedings)
Ponniah, S., Mutethia, R., Jia, Y. 2024. Understanding blast resistance through overexpression of the Pita-2 gene in rice. Abstract. 2024 International Symposium on Rice Functional Genomics, September 9-11, 2024. Little Rock/Stuttgart, Arkansas.

Genomic analysis of sheath blight resistance in rice: identifying resistant accessions and key genetic markers - (Proceedings)
Pedrozo, R., Osakina, A., Nicolli, C., Jia, Y. 2024. Genomic analysis of sheath blight resistance in rice: identifying resistant accessions and key genetic markers. Abstract. 2024 International Symposium on Rice Functional Genomics, September 9-11, 2024. Little Rock/Stuttgart, Arkansas.

Functional analysis of a new allele of the broad-spectrum rice blast resistance gene Ptr in weedy species of rice - (Proceedings)
Osakina, A., Olsen, K., Jia, Y. 2024. Functional analysis of a new allele of the broad-spectrum rice blast resistance gene Ptr in weedy species of rice. Abstract. 2024 International Symposium on Rice Functional Genomics, September 9-11, 2024. Little Rock/Stuttgart, Arkansas.

Rice 'Tiara' - High in Antioxidants - (Book / Chapter)
Huggins, T.D., Mcclung, A. 2024. Rice 'Tiara' - High in Antioxidants. Book Chapter. Plant Genetic Resources.

Rice 'Jojutla' - Parboiling Quality - (Book / Chapter)
Huggins, T.D., McClung, A. 2024. Rice 'Jojutla' - Parboiling Quality. Book Chapter. Plant Genetic Resources.

Receptor-ligand interactions in the rice blast system revealed by AlphaFold protein structure prediction - (Proceedings)
Wang, L., Jia, Y., Olsen, K., Huang, Y., Jia, M.H., Sathish, P., Pedrozo, R., Nicolli, C., Edwards, J. 2024. Receptor-ligand interactions in the rice blast system revealed by AlphaFold protein structure prediction. Abstract. 2024 International Symposium on Rice Functional Genomics, September 9-11, 2024. Little Rock/Stuttgart, Arkansas.

Characterization of the uniform regional rice nursery (URRN) for blast and quality using molecular markers for US rice breeding programs. - (Proceedings)
Jia, M.H., Christensen, E.F., Angira, B., Fjellstrom, R.G., Edwards, J., Jia, Y. 2024. Characterization of the uniform regional rice nursery (URRN) for blast and quality using molecular markers for US rice breeding programs. Abstract. 2024 International Symposium on Rice Functional Genomics, September 9-11-2024. Little Rock/Stuttgart, Arkansas.

Development, gene discovery and allele mining of a global tropical japonica core collection - (Proceedings)
Huggins, T.D., Edwards, J., Mcclung, A., Jia, Y., Jia, M.H., Jackson, A.K., Sells, L.J., Lawrence, B.S. 2024. Development, gene discovery and allele mining of a global tropical japonica core collection. Abstract. 2024 International Symposium on Rice Functional Genomics, September 9-11, 2024. Little Rock/Stuttgart, Arkansas.

Mapping yield related traits in a suite of six oryza rufipogon species complex chromosome segment substitution line libraries in Indica and Japonica rice backgrounds - (Proceedings)
Eizenga, G.C. 2024. Mapping yield related traits in a suite of six oryza rufipogon species complex chromosome segment substitution line libraries in Indica and Japonica rice backgrounds. Abstract. 21st International Symposium on Rice Functional Genomics, September 9-11, 2024, Little Rock, Arkansas.

Improving rice milling quality by identifying and deploying loci affecting kernel fissure resistance - (Proceedings)
Pinson, S.R., Jia, Y., Edwards, J. 2024. Improving rice milling quality by identifying and deploying loci affecting kernel fissure resistance. Proceedings. 21st International Symposium on Rice Functional Genomics, Little Rock, Arkansas. September 9-11, 2024.

Aus sub-population of Oryza sativa L.: a unique source for improving rice sustainability and climate resiliency related traits in elite US rice varieties - (Abstract Only)
Rohila, J.S., Mitchell, J., Sookaserm, T.B., Jackson, A.K., Huggins, T.D., Ponniah, S.K., Edwards, J. 2024. Aus sub-population of Oryza sativa L.: a unique source for improving rice sustainability and climate resiliency related traits in elite US rice varieties. Abstract. 21st Internation Symposium on Rice Functional Genomics, Little Rock, Arkansas. September 9-11, 2024.

Rice germplasm characterization and enhancement for the sustainability and resilience of the US rice industry using functional genomics toolsand stress tolerance - (Proceedings)
Jia, Y., Edwards, J., Pinson, S.R., Eizenga, G.C., Huggins, T.D., Rohila, J.S., Jia, M.H., Jackson, A.K. 2024. Rice germplasm characterization and enhancement for the sustainability and resilience of the US rice industry using functional genomics toolsand stress tolerance. Proceedings. 21st International Symposium on Rice Functional Genomics, Little Rock, Arkansas. September 9-11, 2024.

USDA ARS develops a new production system for food sustainability and security - (Other)
Jia, Y., Green, B.W., Fuller, S.A. 2024. USDA ARS develops a new production system for food sustainability and security. Abstract. 2024 University of Arkansas Field Day, August 1, 2024. Stuttgart, Arkansas.

USDA ARS DB NRRC research on rice sustainability and tolerance to biotic & abiotic stresses - (Other)
Edwards, J., Jia, Y., Pinson, S.R., Rohila, J.S., Huggins, T.D., Jia, M.H., Jackson, A.K., Eizenga, G.C. 2024. USDA ARS DB NRRC research on rice sustainability and tolerance to biotic & abiotic stresses. Abstract. 2024 University of Arkansas Field Day, August 1, 2024. Stuttgart, Arkansas.

Protected Rice - Blast resistance genes, genetic markers developed from a cloned major blast resistance gene resulted in more than a dozen U.S. blast resistant rice varieties and germplasm lines - (Book / Chapter)
Jia, Y., Jia, M.H., Edwards, J. 2024. Protected Rice - Blast resistance genes, genetic markers developed from a cloned major blast resistance gene resulted in more than a dozen U.S. blast resistant rice varieties and germplasm lines. Plant Genetic Resources.

USDA ARS develops pre-breeding rice germplasm for enhanced yield, grain quality and stress tolerance - (Other)
Jia, M.H., Jackson, A.K., Edwards, J., Pinson, S.R., Huggins, T.D., Eizenga, G.C., Rohila, J.S., Jia, Y. 2024. USDA ARS develops pre-breeding rice germplasm for enhanced yield, grain quality and stress tolerance. Abstract. University of Arkansas Rice Field Day, August 1, 2024, Stuttgart, Arkansas.

USDA ARS has hidden treasure! genetic discoveries in the USDA collection of world rice varieties - (Other)
Eizenga, G.C., Jia, Y., Edwards, J., Pinson, S.R., Huggins, T.D., Rohila, J.S., Jia, M.H., Jackson, A.K. 2024. USDA ARS has hidden treasure! genetic discoveries in the USDA collection of world rice varieties. Abstract. University of Arkansas 2024 Rice Field Day, August 1, 2024, Stuttgart, Arkansas.

Unraveling the genetic diversity of Magnaporthe oryzae through a graph pangenome approach - (Abstract Only)
Wang, L., Jia, Y., Edwards, J. 2024. Unraveling the genetic diversity of Magnaporthe oryzae through a graph pangenome approach. Abstract. 2024 Plant Health Conference, July 27-30, 2024. Memphia, Tennessee.

Surveys of Magnaporthe oryzae genotypes in breeding stations and commercial rice fields in Arkansas, Louisiana and Puerto Rico from 2017 to 2019 - (Abstract Only)
Yixiao, H., Jia, Y., Wamishe, Y., Jia, M.H. 2024. Surveys of Magnaporthe oryzae genotypes in breeding stations and commercial rice fields in Arkansas, Louisiana and Puerto Rico from 2017 to 2019. Abstract. Plant Health 2024, July 27-30, 2024. Memphia, Tennessee.

Receptor- ligand interactions in plant inmate immunity revealed by artificial intelligence AlphaFold - (Peer Reviewed Journal)
Wang, L., Jia, Y., Osakina, A., Olsen, K., Huang, Y., Jia, M.H., Ponniah, S., Pedrozo, R., Nicolli, C., Edwards, J. 2024. Receptor- ligand interactions in plant inmate immunity revealed by artificial intelligence AlphaFold. Bio-Archives. https://doi.org/10.1101/2024.06.12.598632.

Using major resistance genes to manage rice blast disease in the USA - (Abstract Only)
Jia, Y. 2024. Using major resistance genes to manage rice blast disease in the USA. Meeting Abstract. 9th International Rice and Wheat Blast Conference, June 10-14, 2024. Panama City, Panama.

Convergent evolution of plant prickles is driven by repeated gene co-option over deep time - (Peer Reviewed Journal)
Satterlee, J.W., Alonso, D.D., Gramazio, P.P., Jenike, K.K., He, J.J., Arrones, A.A., Villanueva, G.G., Plazas, M.M., Ramakrishnan, S.S., Benoit, M.B., Gentile, I.I., Hendelman, A.A., Shohat, H.H., Fitzgerald, B.B., Robitaille, G.G., Green, Y.Y., Swartwood, K.K., Passalacqua, M.M., Gagnon, E.E., Hilgenhof, R.R., Huggins, T.D., Eizenga, G.C., Gur, A., Rutten, R., Stein, N., Yao, S.S., Bellot, C.C., Bendahmane, M.M., Frar, A., Knapp, S.S., Sarkinen, T.T., Gills, J., Van Eck, J.J., Schatz, M.M., Eshed, Y., Prohens, J.Y., Vilanova, S.S., Lippman, Z.Z., Poncet, A. 2024. Convergent evolution of plant prickles is driven by repeated gene co-option over deep time. Science. https://doi.org/10.1101/2024.02.21.581474.

Identification of blast resistance QTLs in black hull awn weedy rice (RR14) and Aus-196 rice variety - (Abstract Only)
Osakina, A., Olsen, K., Jia, Y. 2024. Identification of blast resistance QTLs in black hull awn weedy rice (RR14) and Aus-196 rice variety. Abstract. Plant Health 2024, July 27-30, 2024. Memphis, Tennessee.

Genomic insights for enhanced sheath blight resistance in rice (Oryza sativa L.) - (Abstract Only)
Pedrozo, R., Osakina, A., Nicolli, C., Jia, Y. 2024. Genomic insights for enhanced sheath blight resistance in rice (Oryza sativa L.). Abstract. Plant Health 2024, July 27-30, 2024. Memphis, Tennessee.

Understanding the impact of seed-borne pantoea ananatis on rice crop - (Abstract Only)
Pedrozo, R., Huang, Y., Nicolli, C., Jia, Y. 2024. Understanding the impact of seed-borne pantoea ananatis on rice crop. Abstract. Plant Health 2024, July 27-30, 2024. Memphis, Tennessee.

Genomic insights and primer design for the rice pathogen, Pantoea ananatis - (Abstract Only)
Luna, E., Giebler, M., Nicolli, C., Jia, Y., Leach, J.E. 2024. Genomic insights and primer design for the rice pathogen, Pantoea ananatis. Abstract. Plant Health 2024, July 27-30, 2024. Memphia, Tennessee.

Pre-breeding studies focused on rice grown in temperate regions at the USDA-ARS Dale Bumpers National Rice Research Center - (Proceedings)

Elucidating the effect of polyphenol-protein interactions on rheological properties of purple waxy rice - (Peer Reviewed Journal)
Jannasch, A., Wang, Y., Thallapuranam, S., Alraawi, Z., McClung, A.M. 2024. Elucidating the effect of polyphenol-protein interactions on rheological properties of purple waxy rice. Journal of Cereal Science. https://doi.org/10.1016/j.jcs.2024.103877.

Introduction rice as a model for genetics, genomics, and breeding - (Abstract Only)
Jia, Y. 2024. Introduction rice as a model for genetics, genomics, and breeding. Meeting Abstract. Plant and Animal Genome, January 12-17, 2024. San Diego, California.

Establishing a global Tropical Japonica rice core collection for allele mining and gene discovery: construction, sequencing, and phenotyping - (Abstract Only)
Huggins, T.D., Edwards, J., McClung, A., Jia, Y., Jia, M.H., Jackson, A.K., Sells, L.J., Lawrence, B.S. 2024. Establishing a global Tropical Japonica rice core collection for allele mining and gene discovery: construction, sequencing, and phenotyping. Plant and Animal Genome Conference January 12-17, 2024, San Diego, California. Meeting Abstract.