@article{shi_jin_nifong_shew_lewis_2021, title={Homoeologous chromosome exchange explains the creation of a QTL affecting soil-borne pathogen resistance in tobacco}, ISSN={["1467-7652"]}, DOI={10.1111/pbi.13693}, abstractNote={Crop plant partial resistance to plant pathogens controlled by quantitative trait loci (QTL) is desirable in cultivar development programmes because of its increased durability. Mechanisms underlying such resistance are difficult to study. We performed RNA-seq analyses for tobacco (Nicotiana tabacum) nearly isogenic lines (NILs) with and without favourable allele(s) at Phn7.1, a major QTL influencing partial resistance to the soil-borne pathogens Phytophthora nicotianae and Ralstonia solanacearum. Based upon combined analyses of transcriptome-based sequence variation and gene expression profiles, we concluded that allelic variability at the Phn7.1 locus was likely generated from homoeologous exchange, which led to deletion of low-expressing members of the SAR8.2 gene family and duplication of high-expressing SAR8.2 genes from a different subgenome of allotetraploid tobacco. The high expression of endogenous Phn7.1-associated SAR8.2 genes was correlated with observed resistance to P. nicotianae. Our findings suggest a role for genomic rearrangements in the generation of favourable genetic variability affecting resistance to pathogens in plants.}, journal={PLANT BIOTECHNOLOGY JOURNAL}, author={Shi, Rui and Jin, Jing and Nifong, Jessica M. and Shew, David and Lewis, Ramsey S.}, year={2021}, month={Oct} }
 @article{ma_heim_humphry_nifong_lewis_2020, title={Characterization of Phn15.1, a Newly Identified Phytophthora nicotianae Resistance QTL in Nicotiana tabacum}, volume={104}, ISSN={["1943-7692"]}, DOI={10.1094/PDIS-10-19-2257-RE}, abstractNote={Phytophthora nicotianae is an oomycete that causes black shank, one of the most economically important diseases affecting tobacco production worldwide. Identification and introgression of novel genetic variability affecting partial genetic resistance to this pathogen is important because of the increased durability of partial resistance over time as compared with genes conferring immunity. A previous mapping study identified a quantitative trait locus (QTL), hereafter designated as Phn15.1, with a major effect on P. nicotianae resistance in tobacco. In this research, we describe significantly improved resistance of nearly isogenic lines (NILs) of flue-cured tobacco carrying the introgressed Phn15.1 region derived from highly resistant cigar tobacco cultivar Beinhart 1000. The Phn15.1 region appeared to act in an additive or partially dominant manner to positively affect resistance. To more finely resolve the position of the gene or genes underlying the Phn15.1 effect, the QTL was mapped with an increased number of molecular markers (single-nucleotide polymorphisms) identified to reside within the region. Development and evaluation of subNILs containing varying amounts of Beinhart 1000-derived Phn15.1-associated genetic material permitted the localization of the QTL to a genetic interval of approximately 2.7 centimorgans. Importantly, we were able to disassociate the Beinhart 1000 Phn15.1 resistance alleles from a functional NtCPS2 allele(s) which contributes to the accumulation of a diterpene leaf surface exudate considered undesirable for flue-cured and burley tobacco. Information from this research should be of value for marker-assisted introgression of Beinhart 1000-derived partial black shank resistance into flue-cured and burley tobacco breeding programs.}, number={6}, journal={PLANT DISEASE}, author={Ma, Justin M. and Heim, Crystal B. and Humphry, Matt and Nifong, Jessica M. and Lewis, Ramsey S.}, year={2020}, month={Jun}, pages={1638–1646} }
 @article{ma_hancock_nifong_kernodle_lewis_2020, title={Identification and editing of a hybrid lethality gene expands the range of interspecific hybridization potential in Nicotiana}, volume={133}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-020-03641-w}, number={10}, journal={THEORETICAL AND APPLIED GENETICS}, author={Ma, Justin and Hancock, Wesley G. and Nifong, Jessica M. and Kernodle, Sheri P. and Lewis, Ramsey S.}, year={2020}, month={Oct}, pages={2915–2925} }
 @article{zeng_nifong_liu_huang_fang_lewis_li_2019, title={Evaluating diverse systems of tobacco genetic resistance to Phytophthora nicotianae in Yunnan, China}, volume={68}, ISSN={["1365-3059"]}, DOI={10.1111/ppa.13091}, abstractNote={Black shank, caused by the soilborne pathogen Phytophthora nicotianae , is one of the most devastating diseases affecting tobacco production in China. The most effective strategy for reducing economic loss from this pathogen is development and use of resistant tobacco varieties. Multiple sources and systems of resistance have been developed in the Western Hemisphere; however, populations of P. nicotianae are variable around the world, including the predominance of different races. Different P. nicotianae isolates may react differently on tobacco plants with different systems of resistance, a possibility that could complicate the breeding of cultivars with resistance that is effective in different tobacco production regions worldwide. The objective of this research was to evaluate an array of tobacco germplasm possessing different systems of genetic resistance to black shank disease in tobacco‐growing regions of Yunnan, China. Resistance types included simply inherited resistance mechanisms introgressed from wild Nicotiana relatives and polygenic partial resistance systems of N. tabacum origin. The loci of Wz exhibited high level resistance to black shank in the five diverse disease environments in Yunnan, China. K326 Php /− Wz /− genotype and Beinhart 1000 exhibited the greatest levels of resistance in both 2015 and 2016. Field observed results for 13 tobacco genotypes were highly correlated with those tested in growth chamber evaluation. These findings suggest that both Wz − and Beinhart 1000‐mediated resistance have important commercial value in flue‐cured tobacco breeding programmes in China. Cultivars developed for black shank resistance in China may also have utility in other tobacco‐growing areas.}, number={9}, journal={PLANT PATHOLOGY}, author={Zeng, J. M. and Nifong, J. and Liu, Y. and Huang, C. J. and Fang, D. H. and Lewis, R. S. and Li, Y. P.}, year={2019}, month={Dec}, pages={1616–1623} }
 @article{ma_heim_humphry_nifong_lewis_2019, title={Genetic analysis of Phn7.1, a major QTL conferring partial resistance to Phytophthora nicotianae in Nicotiana tabacum}, volume={39}, DOI={10.1007/s11032-018-0923-x}, number={1}, journal={MOLECULAR BREEDING}, author={Ma, Justin M. and Heim, Crystal and Humphry, Matt and Nifong, J. M. and Lewis, Ramsey S.}, year={2019} }