@article{liu_liu_liu_yu_ma_2023, title={Chickpea C2H2-Type Zinc Finger Protein ZF2 is a Positive Regulator in Drought Response in Arabidopsis}, volume={92}, ISSN={["1851-5657"]}, DOI={10.32604/phyton.2022.023738}, abstractNote={Drought is a major abiotic stress limiting agricultural crops production worldwide.In our study, we isolated a novel C2H2-type zinc finger protein gene ZF2 from chickpea.ZF2 consisted of 232 amino acids with two QALGGH motifs in Cys2/His2 zinc finger domain.Transient expression analysis of ZF2:GFP fusion protein showed that ZF2 was a nuclear localized protein.In the yeast assay system, the full-length of ZF2 did not show transcriptional activation.Expression of ZF2 gene was enhanced by treatments of several abiotic stresses and phytohormones.The promoter region of ZF2 contained multiple stress-and hormone-related cis-elements.Overexpression of ZF2 in Arabidopsis significantly improved the root length and fresh weight at seedling stage and enhanced the survival rates and proline content under drought treatment.These results indicated that ZF2 functioned as a positive regulator in drought response.}, number={2}, journal={PHYTON-INTERNATIONAL JOURNAL OF EXPERIMENTAL BOTANY}, author={Liu, Sushuang and Liu, Yanmin and Liu, Chundong and Yu, Xingwang and Ma, Hao}, year={2023}, pages={577–590} }
 @article{zhou_wang_hu_shen_zhu_liu_wei_yu_liu_ma_2022, title={GmCDPKSK5 Interacting with GmFAD2-1B Participates in Regulation of Seed Development in Soybean Under High Temperature and Humidity Stress}, ISSN={["1572-9818"]}, DOI={10.1007/s11105-021-01329-z}, journal={PLANT MOLECULAR BIOLOGY REPORTER}, author={Zhou, Yali and Wang, Shuang and Hu, Huimin and Shen, Yingzi and Zhu, Yajing and Liu, Xiaolin and Wei, Jiaping and Yu, Xingwang and Liu, Sushuang and Ma, Hao}, year={2022}, month={Jan} }
 @article{yu_lara_carbajal_milla-lewis_2022, title={QTL mapping of morphological characteristics that correlated to drought tolerance in St. Augustinegrass}, volume={17}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0268004}, abstractNote={St. Augustinegrass is a warm-season grass species widely utilized as turf in the southeastern U.S. It shows significant variation in plant growth and morphological characteristics, some of which are potentially associated with drought tolerance. However, the genetic basis of these variations is not well understood. Detecting quantitative trait loci (QTL) associated with morphological traits will provide a foundation for the application of genetic and molecular breeding in St. Augustinegrass. In this study, we report QTL associated with morphological traits, including leaf blade width (LW), leaf blade length (LL), canopy density (CD), and shoot growth orientation (SGO) in a St. Augustinegrass ‘Raleigh’ x ‘Seville’ mapping population containing 115 F1 hybrids. Phenotypic data were collected from one greenhouse and two field trials. Single and joint trial analyses were performed, finding significant phenotypic variance among the hybrids for all traits. Interval mapping (IM) and multiple QTL method (MQM) analysis detected seven QTL for CD, four for LL, five for LW, and two for SGO, which were distributed on linkage groups RLG1, RLG9, SLG3, SLG7, SLG8 and SLG9. In addition, three genomic regions where QTL colocalized were identified on Raleigh LG1 and Seville LG3. One genomic region on Seville LG3 overlapped with two previously reported drought-related QTL for leaf relative water content (RWC) and percent green cover (GC). Several candidate genes related to plant development and drought stress response were identified within QTL intervals. The QTL identified in this study represent a first step in identifying genes controlling morphological traits that might accelerate progress in selection of St. Augustinegrass lines with lower water usage.}, number={5}, journal={PLOS ONE}, author={Yu, Xingwang and Lara, Nicolas A. H. and Carbajal, Esdras M. and Milla-Lewis, Susana R.}, year={2022} }
 @article{wei_zheng_yu_liu_dong_cao_fang_li_jin_mi_et al._2021, title={Comparative Transcriptomics and Proteomics Analyses of Leaves Reveals a Freezing Stress-Responsive Molecular Network in Winter Rapeseed (Brassica rapa L.)}, volume={12}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2021.664311}, abstractNote={Winter rapeseed is susceptible to low temperature during winter in Northwest China, which could lead to a severe reduction of crop production. The freezing temperature could stress the whole plant, especially the leaf, and ultimately harm the survival rate of winter rapeseed. However, the molecular mechanism underlying freezing tolerance is still unclear in winter rapeseed. In this study, a comprehensive investigation of winter rapeseed freezing tolerance was conducted at the levels of transcript, protein, and physiology and biochemistry, using a pair of freezing-sensitive and freezing-resistant cultivars NQF24 and 17NTS57. There were 4,319 unique differentially expressed genes (DEGs) and 137 unique differentially abundant proteins (DAPs) between two cultivars identified in leaf under freezing stress. Function enrichment analysis showed that most of the enriched DEGs and DAPs were involved in plant hormone signal transduction, alpha-linolenic/linoleic acid metabolism, peroxisome, glutathione metabolism, fatty acid degradation, and secondary metabolite biosynthesis pathways. Based on our findings, it was speculated that freezing tolerance formation is caused by increased signal transduction, enhanced biosynthesis of protein, secondary metabolites, and plant hormones, elevated energy supply, greater reactive oxygen species scavenging, and lower lipid peroxidation as well as stronger cell stability in leaf under freezing stress. These results provide a comprehensive profile of leaf response under freezing stress, which have potential to be used as selection indicators of breeding programs to improve freezing tolerance in rapeseed.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Wei, Jiaping and Zheng, Guoqiang and Yu, Xingwang and Liu, Sushuang and Dong, Xiaoyun and Cao, Xiaodong and Fang, Xinling and Li, Hui and Jin, Jiaojiao and Mi, Wenbo and et al.}, year={2021}, month={Apr} }
 @article{brown_yu_holloway_tuong_schwartz_patton_arellano_livingston_milla-lewis_2021, title={Identification of QTL associated with cold acclimation and freezing tolerance in Zoysia japonica}, volume={61}, ISSN={["1435-0653"]}, url={https://doi.org/10.1002/csc2.20368}, DOI={10.1002/csc2.20368}, abstractNote={Abstract}, number={5}, journal={CROP SCIENCE}, publisher={Wiley}, author={Brown, Jessica M. and Yu, Xingwang and Holloway, H. McCamy P. and Tuong, Tan D. and Schwartz, Brian M. and Patton, Aaron J. and Arellano, Consuelo and Livingston, David P. and Milla-Lewis, Susana R.}, year={2021}, month={Sep}, pages={3044–3055} }
 @article{shu_zhou_mu_hu_chen_he_huang_ma_yu_2020, title={A transcriptomic analysis reveals soybean seed pre-harvest deterioration resistance pathways under high temperature and humidity stress}, volume={63}, ISSN={["1480-3321"]}, DOI={10.1139/gen-2019-0094}, abstractNote={ Pre-harvest soybean seeds in the field are susceptible to high temperature and humidity (HTH) stress, leading to pre-harvest seed deterioration, which will result in a reduction in grain quality, yield, and seed vigor. To understand the gene expression involved in seed deterioration response under HTH stress, in this study, we conducted an RNA-Seq analysis using two previously screened soybean cultivars with contrasting seed deterioration resistance. HTH stress induced 1081 and 357 differentially expressed genes (DEGs) in the sensitive cultivar Ningzhen No. 1 and resistant cultivar Xiangdou No. 3, respectively. The majority of DEGs in the resistant cultivar were up-regulated, while down-regulated DEGs were predominant in the sensitive cultivar. KEGG pathway analysis revealed that metabolic pathways, biosynthesis of secondary metabolites, and protein processing in endoplasmic reticulum were the predominant pathways in both cultivars during seed deterioration under HTH stress. The genes involved in photosynthesis, carbohydrate metabolism, lipid metabolism, and heat shock proteins pathways might contribute to the different response to seed deterioration under HTH treatment in the two soybean cultivars. Our study extends the knowledge of gene expression in soybean seed under HTH stress and further provides insight into the molecular mechanism of seed deterioration as well as new strategies for breeding soybean with improved seed deterioration resistance. }, number={2}, journal={GENOME}, author={Shu, Yingjie and Zhou, Yuli and Mu, Kebin and Hu, Huimin and Chen, Ming and He, Qingyuan and Huang, Shoucheng and Ma, Hao and Yu, Xingwang}, year={2020}, month={Feb}, pages={115–124} }
 @article{brown_yu_holloway_dacosta_bernstein_lu_tuong_patton_dunne_arellano_et al._2020, title={Differences in proteome response to cold acclimation in Zoysia japonica cultivars with different levels of freeze tolerance}, volume={60}, ISSN={["1435-0653"]}, DOI={10.1002/csc2.20225}, abstractNote={Abstract}, number={5}, journal={CROP SCIENCE}, author={Brown, Jessica M. and Yu, Xingwang and Holloway, H. McCamy P. and DaCosta, Michelle and Bernstein, Rachael P. and Lu, Jefferson and Tuong, Tan D. and Patton, Aaron J. and Dunne, Jeffrey C. and Arellano, Consuelo and et al.}, year={2020}, pages={2744–2756} }
 @article{yu_mulkey_zuleta_arellano_ma_milla-lewis_2020, title={Quantitative Trait Loci Associated with Gray Leaf Spot Resistance in St. Augustinegrass}, volume={104}, ISSN={["1943-7692"]}, DOI={10.1094/PDIS-04-20-0905-RE}, abstractNote={ Gray leaf spot (GLS), caused by Magnaporthe grisea, is a major fungal disease of St. Augustinegrass (Stenotaphrum secundatum), causing widespread blighting of the foliage under warm, humid conditions. To identify quantitative trait loci (QTL) controlling GLS resistance, an F1 mapping population consisting of 153 hybrids was developed from crosses between cultivar Raleigh (susceptible parent) and plant introduction PI 410353 (resistant parent). Single-nucleotide polymorphism (SNP) markers generated from genotyping-by-sequencing constituted nine linkage groups for each parental linkage map. The Raleigh map consisted of 2,257 SNP markers and spanned 916.63 centimorgans (cM), while the PI 410353 map comprised 511 SNP markers and covered 804.27 cM. GLS resistance was evaluated under controlled environmental conditions with measurements of final disease incidence and lesion length. Additionally, two derived traits, area under the disease progress curve and area under the lesion expansion curve, were calculated for QTL analysis. Twenty QTL were identified as being associated with these GLS resistance traits, which explained 7.6 to 37.2% of the total phenotypic variation. Three potential GLS QTL “hotspots” were identified on two linkage groups: P2 (106.26 to 110.36 cM and 113.15 to 116.67 cM) and P5 (17.74 to 19.28 cM). The two major effect QTL glsp2.3 and glsp5.2 together reduced 20.2% of disease incidence in this study. Sequence analysis showed that two candidate genes encoding β-1,3-glucanases were found in the intervals of two QTL, which might function in GLS resistance response. These QTL and linked markers can be potentially used to assist the transfer of GLS resistance genes to elite St. Augustinegrass breeding lines. }, number={11}, journal={PLANT DISEASE}, author={Yu, Xingwang and Mulkey, Steve E. and Zuleta, Maria C. and Arellano, Consuelo and Ma, Bangya and Milla-Lewis, Susana R.}, year={2020}, month={Nov}, pages={2799–2806} }
 @article{wei_liu_li_zhao_liu_yu_shen_zhou_zhu_shu_et al._2020, title={Quantitative proteomic, physiological and biochemical analysis of cotyledon, embryo, leaf and pod reveals the effects of high temperature and humidity stress on seed vigor formation in soybean}, volume={20}, ISBN={1471-2229}, DOI={10.1186/s12870-020-02335-1}, abstractNote={Abstract}, number={1}, journal={BMC PLANT BIOLOGY}, author={Wei, Jiaping and Liu, Xiaolin and Li, Linzhi and Zhao, Haihong and Liu, Sushuang and Yu, Xingwang and Shen, Yingzi and Zhou, Yali and Zhu, Yajing and Shu, Yingjie and et al.}, year={2020} }
 @article{yu_brown_graham_carbajal_zuleta_milla-lewis_2019, title={Detection of quantitative trait loci associated with drought tolerance in St. Augustinegrass}, volume={14}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0224620}, abstractNote={St. Augustinegrass (Stenotaphrum secundatum) is a warm-season grass species commonly utilized as turf in the southeastern US. Improvement in the drought tolerance of St. Augustinegrass has significant value within the turfgrass industry. Detecting quantitative trait loci (QTL) associated with drought tolerance will allow for advanced breeding strategies to identify St. Augustinegrass germplasm with improved performance for this trait. A multi-year and multi-environment study was performed to identify QTL in a ‘Raleigh’ x ‘Seville’ mapping population segregating for phenotypic traits associated with drought tolerance. Phenotypic data was collected from a field trial and a two-year greenhouse study, which included relative water content (RWC), chlorophyll content (CHC), leaf firing (LF), leaf wilting (LW), green cover (GC) and normalized difference vegetative index (NDVI). Significant phenotypic variance was observed and a total of 70 QTL were detected for all traits. A genomic region on linkage group R6 simultaneously harbored QTL for RWC, LF and LW in different experiments. In addition, overlapping QTL for GC, LF, LW and NDVI were found on linkage groups R1, R5, R7 and S2. Sequence alignment analysis revealed several drought response genes within these regions. The QTL identified in this study have potential to be used in the future to identify genes associated with drought tolerance and for use in marker-assisted breeding.}, number={10}, journal={PLOS ONE}, author={Yu, Xingwang and Brown, Jessica M. and Graham, Sydney E. and Carbajal, Esdras M. and Zuleta, Maria C. and Milla-Lewis, Susana R.}, year={2019}, month={Oct} }
 @article{wei_shen_zhao_liu_jia_yu_ma_2019, title={GmANN, a glutathione S-transferase-interacting annexin, is involved in high temperature and humidity tolerance and seed vigor formation in transgenic Arabidopsis}, volume={138}, ISSN={["1573-5044"]}, DOI={10.1007/s11240-019-01655-x}, number={3}, journal={PLANT CELL TISSUE AND ORGAN CULTURE}, author={Wei, Jiaping and Shen, Yingzi and Zhao, Haihong and Liu, Xiaolin and Jia, Yanfeng and Yu, Xingwang and Ma, Hao}, year={2019}, month={Sep}, pages={583–595} }
 @article{mccamy_holloway_yu_dunne_schwartz_patton_arellano_milla-lewis_2018, title={A SNP-based high-density linkage map of zoysiagrass (Zoysia japonica Steud.) and its use for the identification of QTL associated with winter hardiness}, volume={38}, ISSN={["1572-9788"]}, DOI={10.1007/s11032-017-0763-0}, number={1}, journal={MOLECULAR BREEDING}, publisher={Springer Nature}, author={McCamy, H. and Holloway, P. and Yu, Xingwang and Dunne, Jeffrey C. and Schwartz, Brian M. and Patton, Aaron J. and Arellano, Consuelo and Milla-Lewis, Susana R.}, year={2018}, month={Jan} }
 @misc{yu_kimball_milla-lewis_2018, title={High-density genetic maps of St. Augustinegrass and applications to comparative genomic analysis and QTL mapping of turf quality traits}, volume={18}, ISSN={1471-2229}, url={https://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-018-1554-4}, DOI={10.1186/s12870-018-1554-4}, abstractNote={St. Augustinegrass [Stenotaphrum secundatum (Walt.) Kuntze] is a warm-season, perennial turfgrass species well adapted for home lawns and commercial landscapes with economic and ecological value. However, a lack of genomic resources in St. Augustinegrass has hindered the full utilization of genetic variance for maximizing genetic gain and limited our understanding of the species' evolution.In this study, we constructed the first high-density linkage map for St. Augustinegrass using a genotyping by sequencing (GBS) approach. The integrated linkage map consists of 2871 single nucleotide polymorphism (SNP) and 81 simple sequence repeat (SSR) markers, spanning 1241.7 cM, with an average distance of 0.4 cM between markers, and thus represents the densest genetic map for St. Augustinegrass to date. Comparative genomic analysis revealed inter-chromosome arrangements and independent nested chromosome fusion events that occurred after St. Augustinegrass, foxtail millet, sorghum, and rice diverged from a common ancestor. Forty-eight candidate quantitative trait loci (QTL) were detected for turf quality-related traits, including overall turf quality, leaf texture, genetic color, and turf density. Three hot spot regions were identified on linkage groups LG3 and LG8, where multi-QTL for different traits overlapped. Several leaf development related genes were contained within these identified QTL regions.This study developed the first high-density genetic map and identified putative QTL related to turf quality, which provide valuable genetic resources for marker-assisted selection (MAS) in St. Augustinegrass.}, number={1}, journal={BMC Plant Biology}, publisher={Springer Nature}, author={Yu, X. and Kimball, J.A. and Milla-Lewis, S.R.}, year={2018}, month={Nov}, pages={346} }
 @article{tao_chen_shu_zhu_wang_huang_yu_wang_qian_gu_et al._2018, title={Identification and functional characterization of a novel BEL1-LIKE homeobox transcription factor GmBLH4 in soybean}, volume={134}, ISSN={["1573-5044"]}, DOI={10.1007/s11240-018-1419-4}, number={2}, journal={PLANT CELL TISSUE AND ORGAN CULTURE}, author={Tao, Yuan and Chen, Ming and Shu, Yingjie and Zhu, Yajing and Wang, Shuang and Huang, Liyan and Yu, Xingwang and Wang, Zhankui and Qian, Peipei and Gu, Weihong and et al.}, year={2018}, month={Aug}, pages={331–344} }
 @article{yu_yang_james_2017, title={Comparative proteomic analysis of drought response in roots of two soybean genotypes}, volume={68}, ISSN={["1836-5795"]}, DOI={10.1071/cp17209}, abstractNote={Water deficit is a serious environmental stress during the soybean growth and production season in Australia. Soybean has evolved complex response mechanisms to cope with drought stress through multiple physiological processes. In this study, the roots of a previously identified drought-tolerant soybean genotype, G21210, and a sensitive genotype, Valder, were subjected to comparative proteomic analysis based on 2-dimensional electrophoresis, under mild or severe drought conditions. The analysis showed that the abundance of 179 protein spots significantly changed under stress. In total, 155 unique proteins were identified from these spots, among which 70 protein spots changed only in G2120 and 89 spots only in Valder, with 20 proteins changed in both soybean genotypes. Bioinformatics analysis revealed that these drought-induced changes in proteins were largely enriched in the biological function categories of defence response, protein synthesis, energy metabolism, amino acid metabolism and carbohydrate metabolism. For the drought-tolerant genotype, the differential abundance was decreased for 24 proteins and increased for 46 proteins. For the drought-sensitive genotype, the abundance was reduced for 46 proteins, increased for 40 proteins and changed differently for three proteins in mild and severe drought. The different patterns of change of these proteins in G2120 and Valder might be attributed to the difference in their drought-tolerance capacity. This study, combined with our previously reported proteomics study in soybean leaves, further clarifies the change in proteins under drought stress in different organs and provides a better understanding of the molecular mechanisms under drought stress in soybean production.}, number={7}, journal={CROP & PASTURE SCIENCE}, author={Yu, Xingwang and Yang, Aijun and James, Andrew T.}, year={2017}, pages={609–619} }
 @article{yu_yang_james_2017, title={Selecting soybeans for sulfonylurea herbicide tolerance: a comparative proteomic study of seed germinations}, volume={68}, ISSN={["1836-5795"]}, DOI={10.1071/cp16272}, abstractNote={Sulfonylurea herbicides have attracted renewed interest as an alternative for weed management and control of weed resistance in soybean production. In this proteomic study, we compared changes in the protein profiles in 10-day-old seedlings from a simple roll-paper germination method treated with 0.1 µm metsulfuron methyl (MSM), a compound from the sulfonylurea family. Seeds from susceptible or tolerant soybeans, four lines each, were treated with 0, 0.01, 0.1, 1 or 10 µm MSM and the number of normal seeds germinating was counted after 10 days. MSM at ≥0.1 µm significantly reduced normal germination in the sulfonylurea-susceptible group. Comparative proteomic analysis of the proteins extracted from the germinations treated with 0 or 0.1 µm MSM revealed a much greater number of proteins affected in the sulfonylurea-susceptible genotype than the tolerant type. From a total 227 protein spots with significant differential (>2-fold) accumulation, 142 unique proteins were identified. Functional analysis revealed that about one-third of these proteins were associated with metabolism, followed by energy (24.3%), defence–stress response (22.9%), and protein synthesis and storage (16.7%). Sulfonylurea herbicides, specifically MSM, greatly affected these metabolic pathways in the susceptible genotype through changed accumulation of many enzymes and proteins.}, number={1}, journal={CROP & PASTURE SCIENCE}, author={Yu, Xingwang and Yang, Aijun and James, Andrew T.}, year={2017}, pages={27–32} }
 @article{wang_tao_zhou_niu_shu_yu_liu_chen_gu_ma_2017, title={Translationally controlled tumor protein GmTCTP interacts with GmCDPKSK5 in response to high temperature and humidity stress during soybean seed development}, volume={82}, ISSN={["1573-5087"]}, DOI={10.1007/s10725-017-0250-y}, number={1}, journal={PLANT GROWTH REGULATION}, author={Wang, Shuang and Tao, Yuan and Zhou, Yali and Niu, Juan and Shu, Yingjie and Yu, Xingwang and Liu, Sushuang and Chen, Ming and Gu, Weihong and Ma, Hao}, year={2017}, month={May}, pages={187–200} }