Yulin Jia

• PhD
• Research Leader/Center Director at United States Department of Agriculture

Robust disease resistance may require an expenditure of energy that may limit crop yield potential. In the present study, a subset of a USDA rice core collection consisting of 151 accessions was selected using a major blast resistance (R) gene Pi-ta marker, and was genotyped with 156 simple sequence repeat (SSR) markers. Disease reactions to Magnap...

The Pi-ta gene in rice is effective in preventing infections by Magnaporthe oryzae strains that contain the corresponding avirulence gene, AVR-Pita1. Genome sequencing and mapping studies demonstrated that AVR-Pita1 is highly unstable, and diverse haplotypes of AVR-Pita1 have been identified from isolates of M. oryzae from rice production areas in...

Crop domestication provided the calories that fueled the rise of civilization. For many crop species, domestication was accompanied by the evolution of weedy crop relatives, which aggressively outcompete crops and reduce harvests. Understanding the genetic mechanisms that underlie the evolution of weedy crop relatives is critical for agricultural w...

Plant resistance genes typically encode proteins with nucleotide binding site-leucine rich repeat (NLR) domains. Here we show that Ptr is an atypical resistance gene encoding a protein with four Armadillo repeats. Ptr is required for broad-spectrum blast resistance mediated by the NLR R gene Pi-ta and by the associated R gene Pi-ta2. Ptr is express...

Rice (Oryza sativa L.) is a critical crop for global food security; however, under certain conditions, rice grains can accumulate elevated levels of arsenic (As) and cadmium (Cd). Research has shown that alternate wetting and drying (AWD) of rice fields, rather than maintaining a continuous flood (FLD), can lower concentrations of both total As (tA...

Rice blast, caused by Magnaporthe oryzae, is a major threat to global rice production, necessitating the development of resistant cultivars through genetic improvement. Breakthroughs in rice genomics, including the complete genome sequencing of japonica and indica subspecies and the availability of various sequence-based molecular markers, have gre...

Major resistance (R) gene mediated resistance to rice blast fungus Magnaporthe oryzae is often overcome by the fungus due to the occurrences of new races with altered corresponding avirulence (AVR) genes. In this study, blast diseased rice tissue samples were collected from breeding stations and commercial rice fields in Arkansas, Louisiana, and Pu...

Rice blast disease (caused by the fungus Magnaporthe oryzae B.C. Couch) is the most threatening disease of rice (Oryza sativa L.) worldwide. Three rice germplasm lines, designated as CS272 (Reg. no. GP‐151, GSOR 201), CS324 (Reg. no. GP‐152, GSOR 202), and CS353 (Reg. no. GP‐153, GSOR 203) were selected from among nine 900 recombinant inbred lines...

Understanding how plants utilize limited resources for reproductivity and disease resistance can improve the efficiency of plant breeding. In the present study, we mapped genes for grain traits, including grain length and width and thousand grain weight (TGW). A previously constructed linkage map of a recombinant inbred line population (MHM) was us...

One of the common mechanisms to trigger plant innate immunity is recognition of pathogen avirulence gene products directly by products of major resistance ( R ) genes in a gene for gene manner. In the USA, the R genes, Pik-s, PiKh/m , and Pi-ta, Pi-39(t) , and Ptr genes have been effectively deployed to prevent the infections of M. oryzae races, IB...

Weedy rice ( Oryza spp.) is a weedy relative of the cultivated rice that competes with the crop and causes significant production loss. The BHA (blackhull awned) US weedy rice group has evolved from aus cultivated rice and differs from its ancestors in several important weediness traits, including flowering time, plant height and seed shattering. P...

Rice blast, caused by Magnaporthe oryzae, is the most destructive rice disease worldwide. The disease symptoms are usually expressed on the leaf and panicle. The leaf disease intensity in controlled environmental conditions is frequently quantified using a 0 to 5 scale, where 0 represents the absence of symptoms, and 5 represents large eyespot lesi...

Weeds that infest crops are a primary factor limiting agricultural productivity worldwide. Weedy rice, also called red rice, has experienced independent evolutionary events through gene flow from wild rice relatives and de-domestication from cultivated rice. Each evolutionary event supplied/equipped weedy rice with competitive abilities that allowe...

Weeds that infest crops are a primary factor limiting agricultural productivity world-wide. Weedy rice, also called red rice, has experienced independent evolutionary events through gene flow from wild rice relatives and de-domestication from cultivated rice. Each evolutionary event supplied/equipped weedy rice with competitive abilities that allow...

Easy-to-use methods to disinfect microbes on seeds are not available. In the present study, rice 30 seeds were irradiated by 274 nanometer germicidal ultraviolet proton in a biosafe flow cabinet. Seeds (10) without any barrier, in a sterilized mesh bag, or in a sterilized coin envelope were removed each day with sterilized forceps for seven days af...

In August 2021, bacterial leaf blight-like symptoms were observed on 14 out of 570 rice genotypes (Oryza sativa) in research field plots of global rice germplasm grown in Arkansas (eXtra Figure S1. A & B). The disease was characterized by spreading lesions on leaves, panicle sterility and reduced yield in highly susceptible, mature rice germplasm....

Eclipse (Reg. no. GP‐149, PI 701081) is a blast‐resistant and ‘Calrose’ type medium‐grain‐quality rice (Oryza sativa L.) germplasm that was developed by the USDA‐ARS Dale Bumpers National Rice Research Center, Stuttgart, AR. It was selected from a backcross between a blast‐resistant tropical japonica rice cultivar ‘Katy’ and a temperate japonica me...

Rice resistance (R) genes have been effectively deployed to prevent blast disease caused by the pathogen Magnaporthe oryzae, one of the most serious threats for stable rice production worldwide. Weedy rice competing with cultivated rice may carry novel or lost R genes. The QTL qBR12.3b was previously mapped between two single nucleotide polymorphis...

Two mapping populations were developed from crosses of the Asian indica rice (Oryza sativa L.) cultivar ‘Dee Geo Woo Gen’ (DGWG; PI 699210 Parent, PI 699212 Parent) and two weedy rice ecotypes, an early‐flowering straw hull (SH) biotype AR‐2000‐1135‐01 (PI 699209 Parent) collected in Arkansas and a late‐flowering black hull (BHA) biotype MS‐1996‐9...

Rice blast disease caused by the fungus Magnaporthe oryzae (syn. M. grisea) is one of the most lethal diseases for sustainable rice production worldwide. Blast resistance mediated by major resistance genes are often broken-down after a short period of deployment, while minor blast resistance genes, each providing a small effect on disease reactions...

Sheath blight is a serious rice disease worldwide and genes involved in resistance remain unclear. In the present study, a virulent field isolate of Rhizoctonia solani was used to inoculate detached leaves of a sheath blight resistant rice cultivar ‘Jasmine 85’, a suppression subtractive cDNA library was constructed using RNA isolated 16 hours post...

Rice blast disease caused by fungus Magnaporthe oryzae (syn. Pyricularia oryzae) is one of the most damaging diseases of rice, reducing plant production worldwide. In the present study, Bacillus subtilis strain GB519 was identified from the rhizosphere based on predicted signatures of 16S ribosomal DNA and gyrA gene and morphological, biochemical,...

Rice is one of the most important food crops for mankind and suffers significant crop loss annually due to rice diseases. Availability of genome sequences of rice has served as a springboard to utilize its innate immunity to prevent rice diseases. Knowledge on interactions of rice and rice pathogens has rapidly accumulated. Effective resistance gen...

The isoflavones are a group of plant secondary metabolites primarily synthesized in legumes and are known for their role in improving human health and plant disease resistance. The isoflavones, especially genistein, act as precursors for the production of phytoalexins, which may induce broad-spectrum disease resistance in plants. In the present stu...

Magnaporthe oryzae is the causal agent for the devastating disease rice blast. The avirulence (AVR) genes in M. oryzae are required to initiate robust disease resistance mediated by the corresponding resistance (R) genes in rice. Therefore, monitoring pathogen AVR genes is important to predict the stability of R gene-mediated blast resistance. In t...

Rice has been produced for thousands of years in a wide range of ecological and cultural systems around the globe becoming a primary food crop for more than 3.5 billion people. Recent advances in the study of rice genetics, genomics, pathology and interactions with the environment have resulted in a growing appreciation of how science may help in s...

Rice foot rot disease caused by the pathogen Dickeya zeae (formerly known as Erwinia chrysanthemi pv. zeae), is a newly emerging damaging bacterial disease in China and the southeast of Asia, resulting in the loss of yield and grain quality. However, the genetic resistance mechanisms mediated by miRNAs to D. zeae are unclear in rice. In the present...

Sheath blight caused by the soil borne fungus Rhizoctonia solani AG1-IA is one of the major diseases of rice in the world. Genetic resistance in rice against this disease has not been very successful. Brachypodium distachyon is considered as a model species for several cereal crops and it has been studied in the past to identify novel sources of di...

Weedy rice (Oryza spp.) is a problematic weed of cultivated rice (O. sativa) around the world. Recent studies have established multiple independent evolutionary origins of weedy rice, raising questions about the traits and genes that are essential for the evolution of this weed. Among world regions, South Asia stands out due to the heterogeneity of...

Magnaporthe oryzae avirulence (AVR) genes are predicted to be involved in pathogen invasion and their virulence functions are restricted by the presence of the cognate resistance (R) genes. In this study, the distribution and variation of avirulence (AVR‐Pii) gene of M. oryzae in Yunnan province, China were analyzed to understand haplotype diversit...

Rice blast, caused by the fungus Magnaporthe oryzae, is the most damaging disease for rice worldwide. However, the reactions of rice to M. oryzae at different growth stages are largely unknown. In the present study, two temperate japonica rice cultivars, M-202 and Nipponbare, were inoculated synchronously at different vegetative growth stages, V1 t...

Kernel fissures in rice (Oryza sativa L.) caused by pre-or postharvest stresses are the leading cause of breakage among milled rice. Such breakage causes economic losses for producers, millers, and marketers. Five quantitative trait loci (QTLs) for kernel fissure resistance (FR) were identified among a set of 271 recombinant inbred lines derived fr...

Weedy red rice (Oryza sativa; WRR), a close relative of cultivated rice, is a highly competitive weed that commonly infests rice fields and can also naturally interbreed with rice. Useful genes for biotic stress have been maintained in WRR and can be explored for breeding. Here we describe genetic and physiological traits of WRR that can be benefic...

Major blast resistance (R) genes confer resistance in a gene-for-gene manner. However, little information is available on interactions between R genes. In this study, interactions between two rice blast R genes, Pi-ta and Pi-b, and other minor blast resistance quantitative trait loci (QTL) were investigated in a recombinant inbred line (RIL) popula...

Agricultural weeds serve as productive models for studying the genetic basis of rapid adaptation, with weed-adaptive traits potentially evolving multiple times independently in geographically distinct but environmentally similar agroecosystems. Weedy relatives of domesticated crops can be especially interesting systems because of the potential for...

Burkholderia glumae presumably induces a grain rot symptom of rice that isthreatening to rice production in most rice producing states of the USA. The present study was to identify the causal agent of bacteria panicle blight (BPB),virulence based on hypersensitive reactions and distribution of the pathogen within a plant. 178 rice panicles samples...

The blast (Magnaporthe oryzae) resistance (R) gene is the most economical and environmental method to control rice blast disease. Characterization of molecular identity and pathogenicity of M. oryzae benefits the deployment of effective blast R genes. In order to identify blast R genes that would be effective in Hunan Province,182 M. oryzae strains...

Rice blast disease caused by Magnaporthe oryzae (Mo) is one of the most destructive diseases of rice. Field isolates of Mo rapidly adapt to their hosts and climate. Tracking the genetic and pathogenic variability of field isolates is essential to understand how Mo interacts with hosts and environments. In this study, a total of 1022 US field isolat...

Weedy rice (Oryza spp.), a weedy relative of cultivated rice (O. sativa), infests and persists in cultivated rice fields worldwide. Many weedy rice populations have evolved similar adaptive traits, considered part of the "agricultural weed syndrome," making this an ideal model to study the genetic basis of parallel evolution. Understanding parallel...

Weedy rice is a conspecific form of cultivated rice (Oryza sativa L.) that infests rice fields and results in severe crop losses. Weed strains in different world regions appear to have originated multiple times from different domesticated and/or wild rice progenitors. In the case of Malaysian weedy rice, a multiple-origin model has been proposed ba...

Rice blast disease caused by the filamentous ascomycete fungus Magnaporthe oryzae Cav. [Magnaporthe grisea (Herbert) Barr.] is one of the most threatening rice (Oryza sativa L.) diseases in the southern United States. Forty-two rice blast resistant genetic stocks (Reg. No. GS-34 to Reg. No. GS-75, GSOR 102501 to GSOR 102542) were developed and rele...

The Pi9 gene in rice, originating from Oryza minuta, is an effective resistance gene for controlling rice blast disease. However, currently available linked DNA markers do not accurately identify the function of Pi9, thus hindering its efficient incorporation into new cultivars through marker assisted selection (MAS). In addition, no known Pi9 cont...

Tiller number (TN) is a key determinant of final grain yield in the small grains crops, including rice ( Oryza sativa L.), and is desired to enhance competition with weeds. Quantitative trait loci (QTLs) associated with TN were mapped within a set of recombinant inbred lines developed from a cross between the low‐tillering tropical japonica cultiva...

Outbreaks of bacterial panicle blight (BPB) of rice in recent past years have resulted in severe yield losses in the Southern United States including Arkansas. Bacterial species, Burkholderia glumae was identified as the main causative agent among others causing BPB in rice. The symptoms of BPB include sheath rot, panicle blighting, panicle blankin...

The rice nursery located in the Lajas Valley, in the southwestern corner of Puerto Rico has been used by US rice breeders for the past 43 years to produce one to two extra generations per year. In April, 2015, blast disease lesions were observed on rice breeding lines belong to the USDA ARS DB NRRC and to the University of Arkansas Rice Research an...

Molecular markers are useful for the identifi­cation of critical genes controlling agricultural traits of interest in crop germplasm and for the use of these genes in crop improvement using marker-assisted selection (MAS). The improve­ment of blast disease resistance of rice (Oryza sativa L.) varieties is one of the major goals for rice breeders. T...

Quantitative trait loci (QTL) play important roles in controlling rice blast disease. In the present study, 10 field isolates of the races IA1, IB1, IB17, and IC1 of US rice blast fungus Magnaporthe oryzae collected in 1996 and 2009 were used to identify blast resistance QTL with a recombinant inbred line (RIL) population consisting of 227 F7 indiv...

Due to the harmful nature of the rice blast fungus, Magnaporthe oryzae, it is beneficial to characterize field isolates to help aid in the deployment of resistance (R) genes in rice. In the present study, 252 field isolates of M. oryzae, collected from rice fields of Yunnan Province in China, were assessed for mating type, DNA fingerprinting, and d...

Many different crop species were selected for a common suite of "domestication traits," which facilitates their use for studies of parallel evolution. Within domesticated rice (Oryza sativa), there has also been independent evolution of weedy strains from different cultivated varieties. This makes it possible to examine the genetic basis of paralle...

Understanding the genetic architecture of adaptation is of great importance in evolutionary biology. US weedy rice is well-adapted to the local conditions in US rice fields. Rice blast disease is one of the most destructive diseases of cultivated rice worldwide. However, information about resistance to blast in weedy rice is limited. Here, we evalu...

Robust disease resistance may require an expenditure of energy that may limit crop yield potential. In the present study, a subset of a United States Department of Agriculture rice core collection consisting of 151 accessions was selected using a major blast resistance (R) gene, Pi-ta, marker and was geno-typed with 156 simple sequence repeat (SSR)...

Studying natural variation in rice resistance genes of cultivated and wild rice relatives can predict resistance stability to rice blast fungus. In the present study, the protein coding regions of the rice R gene Pi-d2 in 35 rice accessions, including Oryza sativa L. subsp. indica Kato (Aus), indica (IND), temperate japonica (TEJ), tropical japonic...

The indica rice variety Dee Geo Woo Gen (DGWG) was the source of the semidwarf gene (SD1) which played an important role in the Green Revolution. In the present study, resistance (R) genes to the US race (isolate) IB54 of Magnaporthe oryzae, causal agent of rice blast disease, was investigated. Two recombinant inbred line mapping populations, consi...

The indica rice variety Dee Geo Woo Gen (DGWG) was the source of the semidwarf gene (SD1) which played an important role in the Green Revolution. In the present study, resistance (R) genes to the US race (isolate) IB54 of Magnaporthe oryzae, causal agent of rice blast disease, was investigated. Two recombinant inbred line mapping populations, consi...

The indica rice variety Dee Geo Woo Gen (DGWG) was the source of the semidwarf gene (SD1) which played an important role in the Green Revolution. In the present study, resistance (R) genes to the US race (isolate) IB54 of Magnaporthe oryzae, causal agent of rice blast disease, was investigated. Two recombinant inbred line mapping populations, consi...

A mapping population developed from a cross of rice (Oryza sativa L.) tropical japonica cultivar Lemont and indica cultivar Jasmine 85 was developed to facilitate genetic studies for important agronomic traits. The indica- and tropical japonica-based rice recombinant inbred line (RIL) mapping population has been used to identify genomic regions ass...

The fungus Magnaporthe oryzae is the causal agent of a wide range of cereal diseases. For long-term preservation, the fungus is grown and stored desiccated on filter papers at –20 °C. Inoculated filter papers are cut into pieces of 0.5–1.0 cm diameter prior to storage. In the present study, a fast (11 min) and simple method of preparing DNA suitabl...

• Premise of the study: Local adaptation in plants often involves changes in flowering time in response to day length and temperature. Many crops have been selected for uniformity in flowering time. In contrast, variable flowering may be important for increased competitiveness in weed species invading the agricultural environment. Given the shared...

The resistance gene Pi-ta has been effectively used to control rice blast disease, but some populations of cultivated and wild rice have evolved resistance. Insights into the evolutionary processes that led to this resistance during crop domestication may be inferred from the population history of domesticated and wild rice strains. In this study,...

Magnaporthe oryzae, the rice blast pathogen, causes significant annual yield loss of rice worldwide. Currently, the most effective disease control approach is deployment of host resistance through introduction of resistance (R) genes into elite cultivars. The function of each R gene relies on the specific recognition of an avirulence (AVR) gene of...

Identification of resistance (R) genes to races of Magnaporthe oryzae in rice (Oryza sativa) germplasm is essential for the development of rice cultivars with long-lasting blast resistance. In the present study, one major quantitative trait locus, qPi93-3, was fine mapped using a recombinant inbred line (RIL), F-8 RIL171, derived from the cross bet...

The polymerase chain reaction (PCR) is particularly useful for plant pathogen detection. In the present study, multiplex PCR and SYBR Green real-time PCR were developed to facilitate the simultaneous detection of three important rice pathogens, Xanthomonas oryzae pv. oryzae, X. oryzae pv. oryzicola, and Burkholderia glumae. The unique PCR primer se...