The Dominant and Poorly Penetrant Phenotypes of Maize Unstable factor for orange1 Are Caused by DNA Methylation Changes at a Linked Transposon.

The maize (Zea mays) mutant Unstable factor for orange1 (Ufo1) has been implicated in the epigenetic modifications of pericarp color1 (p1), which regulates the production of the flavonoid pigments phlobaphenes. Here, we show that the ufo1 gene maps to a genetically recalcitrant region near the centromere of chromosome 10. Transcriptome analysis of Ufo1-1 mutant and wild-type plants identified a candidate gene in the mapping region using a comparative sequence-based approach. The candidate gene, GRMZM2G053177, is overexpressed by >45-fold in multiple tissues of Ufo1-1, explaining the dominance of Ufo1-1 and its phenotypes. In the mutant stock, GRMZM2G053177 has a unique transcript originating within a CACTA transposon inserted in its first intron, and it is missing the first four codons of the wild-type transcript. GRMZM2G053177 expression is regulated by the DNA methylation status of the CACTA transposon, explaining the incomplete penetrance and poor expressivity of Ufo1-1 Transgenic overexpression lines of GRMZM2G053177 (Ufo1-1) phenocopy the p1-induced pigmentation in coleoptiles, tassels, leaf sheaths, husks, pericarps, and cob glumes. Transcriptome analysis of Ufo1 versus wild-type tissues revealed changes in several pathways related to abiotic and biotic stress. Thus, this study addresses the enigma of Ufo1 identity in maize, which had gone unsolved for more than 50 years.

Resistance to Phytophthora infestans Clonal Lineage US-23 in Potato Cultivars and Its Relationship with Early Blight Resistance and Tuber Yield.

Resistance to late blight caused by Phytophthora infestans clonal lineage US-23 in 217 old and modern potato cultivars was evaluated in field trials in 2016 and 2017 in Pennsylvania. Significant differences in resistance were found among these cultivars (P < 0.0001). Significant interaction between cultivars and environments was found (P < 0.0001). The values of relative area under the disease progress curve ranged from 0 to 0.5841 in 2016 and from 0 to 0.5469 in 2017. Broad-sense heritability of late blight resistance was estimated to be 0.91, with a 95% confidence interval of 0.88 to 0.93. Cluster analysis classified the cultivars into five groups: resistant, moderately resistant, intermediate, moderately susceptible, and susceptible. Thirty cultivars showing resistance and 32 cultivars showing moderate resistance were identified. The 217 cultivars were also evaluated for foliar maturity, tuber yield, and resistance to early blight caused by Alternaria solani. A few cultivars with late blight resistance independent of late maturity were found. Late blight resistance and early blight resistance were positively correlated, and 17 cultivars possessed resistance to both diseases. Yield trade-off associated with late blight resistance was not observed among the cultivars in the absence of disease pressure.

Genome wide association mapping of epi-cuticular wax genes in Sorghum bicolor.

Sorghum accumulates epi-cuticular wax (EW) in leaves, sheaths, and culms. EW reduces the transpirational and nontranspirational (nonstomatal) water loss and protects the plant from severe drought stress in addition to imparting resistance against insect pests. Results presented here are from the analysis of EW content of 387 diverse sorghum accessions and its genome-wide association study (GWAS). EW content in sorghum leaves ranged from 0.1 to 29.7 mg cm-2 with a mean value of 5.1 mg cm-2. GWAS using 265,487 single nucleotide polymorphisms identified thirty-seven putative genes associated (P < 9.89E-06) with EW biosynthesis and transport in sorghum. Major EW biosynthetic genes identified included 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, an Ankyrin repeat protein, a bHLH-MYC, and an R2R3-MYB transcription factor. Genes involved in EW regulation or transport included an ABC transporter, a Lipid exporter ABCA1, a Multidrug resistance protein, Inositol 1, 3, 4-trisphosphate 5/6-kinase, and a Cytochrome P450. This GWA study thus demonstrates the potential for genetic manipulation of EW content in sorghum for better adaptation to biotic and abiotic stress.

The plant hormone auxin directs timing of xylem development by inhibition of secondary cell wall deposition through repression of secondary wall NAC-domain transcription factors.

Wood formation in higher plants is a complex and costly developmental process regulated by a complex network of transcription factors, short peptide signals and hormones. Correct spatiotemporal initiation of differentiation and downstream developmental stages is vital for proper wood formation. Members of the NAC (NAM, ATAF1/2 and CUC) family of transcription factors are described as top level regulators of xylem cell fate and secondary cell wall (SCW) deposition, but the signals initiating their transcription have yet to be elucidated. We found that treatment of Populus stems with auxin repressed transcription of NAC transcription factors associated with fiber and SCW formation and induced vessel-specific NACs, whereas gibberellic acid (GA) induced the expression of both classes of NAC domain transcription factors involved in wood formation. These transcriptional changes were reflected in alterations of stem anatomy, i.e. auxin treatment reduced cell wall thickness, whereas GA had a promotive effect on SCW deposition and on the rate of wood formation. Similar changes were observed on treatment of Arabidopsis thaliana stems with GA or the synthetic auxin NAA. We also observed corresponding changes in PIN5 overexpressing lines, where interference with auxin transport leads to premature SCW deposition and formation of additional fiber bundles. Together, this suggests wood formation is regulated by an integrated readout of both auxin and GA, which, in turn, controls expression of fiber and vessel specific NACs.

Characterization of Early Blight Resistance in Potato Cultivars.

Early blight, caused by the fungus Alternaria solani, is one of the most economically important foliar diseases of potatoes worldwide. In this study, 217 tetraploid old and modern potato cultivars were evaluated for foliar resistance to early blight in field experiments in Pennsylvania in 2016 and 2017. Relative area under the disease progress curve (RAUDPC) was calculated based on visual assessment of foliar disease during the growing season each year. RAUDPC ranged from 0.0090 to 0.7372 in 2016 and from 0.0215 to 0.7889 in 2017, respectively. Significant differences in resistance to A. solani among cultivars were found (P < 0.0001). A significant interaction was found between cultivar and environment (P < 0.0001). Cluster analysis classified the cultivars into five groups: resistant, moderately resistant, intermediate, moderately susceptible, and susceptible. Broad-sense heritability for early blight resistance was estimated as 0.89 with a 95% confidence interval of 0.86 to 0.92. All cultivars were also evaluated for foliage maturity in separate field trials in 2016 and 2017, and a strong negative correlation between early blight resistance and maturity was found. Maturity-adjusted RAUDPC was calculated by regressing maturity on RAUDPC; predicted values more than two standard deviations greater or less than observed values were used to identify cultivars with greater genetic susceptibility or resistance to early blight, respectively, independent of maturity. Although most resistant and moderately resistant cultivars showed late maturity and most susceptible cultivars showed early maturity, a few exceptions were found.

Genetic Dissection of Early Blight Resistance in Tetraploid Potato.

Early blight, caused by the fungus Alternaria solani, is one of the most economically important diseases of potatoes worldwide. We previously identified a tetraploid potato clone, B0692-4, which is resistant to early blight. To dissect the genetic basis of early blight resistance in this clone, a full-sib tetraploid potato population including 241 progenies was derived from a cross between B0692-4 and a susceptible cultivar, Harley Blackwell, in this study. The population was evaluated for foliage resistance against early blight in field trials in Pennsylvania in 2018 and 2019 and relative area under the disease progress curve (rAUDPC) was determined. The distribution of rAUDPC ranged from 0.016 to 0.679 in 2018, and from 0.017 to 0.554 in 2019. Broad sense heritability for resistance, as measured as rAUDPC, was estimated as 0.66-0.80. The population was also evaluated for foliar maturity in field trials in Maine in 2018 and 2020. A moderate negative correlation between rAUDPC and foliar maturity was detected in both years. A genetic linkage map covering a length of 1469.34 cM with 9124 SNP markers was used for mapping quantitative trait loci (QTL) for rAUDPC and foliar maturity. In 2018, three QTLs for early blight were detected; two of them on chromosome 5 overlapped with QTLs for maturity, and one of them on chromosome 7 was independent of maturity QTL. In 2019, six QTLs for early blight were detected; two QTLs on chromosome 5 overlapped with QTLs for maturity, and the other four QTLs did not overlap with QTLs for maturity. The identification of these QTLs provides new insight into the genetic basis of early blight resistance and may serve as sources for marker-assisted selection for early blight resistance breeding.

Genetic basis of drought resistance at reproductive stage in rice: separation of drought tolerance from drought avoidance.

Drought tolerance (DT) and drought avoidance (DA) are two major mechanisms in drought resistance of higher plants. In this study, the genetic bases of DT and DA at reproductive stage in rice were analyzed using a recombinant inbred line population from a cross between an indica lowland and a tropical japonica upland cultivar. The plants were grown individually in PVC pipes and two cycles of drought stress were applied to individual plants with unstressed plants as the control. A total of 21 traits measuring fitness, yield, and the root system were investigated. Little correlation of relative yield traits with potential yield, plant size, and root traits was detected, suggesting that DT and DA were well separated in the experiment. A genetic linkage map consisting of 245 SSR markers was constructed for mapping QTL for these traits. A total of 27 QTL were resolved for 7 traits of relative performance of fitness and yield, 36 QTL for 5 root traits under control, and 38 for 7 root traits under drought stress conditions, suggesting the complexity of the genetic bases of both DT and DA. Only a small portion of QTL for fitness- and yield-related traits overlapped with QTL for root traits, indicating that DT and DA had distinct genetic bases.

QTL analysis for flag leaf characteristics and their relationships with yield and yield traits in rice.

Photosynthesis of carbohydrate is the primary source of grain yield in rice (Oryza sativa L.). It is important to genetically analyze the morphological and the physiological characteristics of functional leaves, especially flag leaf, in rice improvement. In this study, a recombinant inbred population derived from a cross between an indica (O. sativa L. ssp. indica) cultivar and a japonica (O. sativa L. ssp. japonica) cultivar was employed to map quantitative traits loci (QTLs) for the morphological (i.e., leaf length, width, and area) and physiological (i.e., leaf color rating and stay-green) characteristics of flag leaf and their relationships with yield and yield traits in 2003 and 2004. A total of 17 QTLs for morphological traits (flag leaf length, width, and area), 6 QTLs for degree of greenness and 14 QTLs for stay-green-related traits (retention-degrees of greenness, relative retention of greenness, and retention of the green area) were resolved, and 10 QTLs were commonly detected in both the years. Correlation analysis revealed that flag leaf area increased grain yield by increasing spikelet number per panicle. However, the physiological traits including degree of greenness and stay-green traits were not or negatively correlated to grain yield and yield traits, which may arise from the negative relation between degree of greenness and flag leaf size and the partial sterility occurred in a fraction of the lines in this population. The region RM255-RM349 on chromosome 4 controlled the three leaf morphological traits simultaneously and explained a large part of variation, which was very useful for genetic improvement of grain yield. The region RM422-RM565 on chromosome 3 was associated with the three stay-green traits simultaneously, and the use of this region in genetic improvement of grain yield needs to be assessed by constructing near-isogenic lines.

Identification of quantitative trait loci for ABA sensitivity at seed germination and seedling stages in rice.

Abscisic acid (ABA) is one of the important plant hormones, which plays a critical role in seed development and adaptation to abiotic stresses. The sensitivity of rice (Oryza sativa L.) to exogenous ABA at seed germination and seedling stages was investigated in the recombinant inbred line (RIL) population derived from a cross between irrigated rice Zhenshan 97 and upland rice IRAT109, using relative germination vigor (RGV), relative germination rate (RGR) and leaf rolling scores of spraying (LRS) or culturing (LRC) with ABA as sensitivity indexes. The phenotypic correlation analysis revealed that only RGV at germination stage was positively correlated to ABA sensitivity at seedling stage. QTL detection using composite interval mapping (CIM) and mixed linear model was conducted to dissect the genetic basis of ABA sensitivity, and the single-locus QTLs detected by both methods are in good agreement with each other. Five single QTLs and six pairs of epistatic QTLs were detected for ABA sensitivity at germination stage. Eight single QTLs and five pairs of epistatic QTLs were detected for ABA sensitivity at seedling stage. Two QTLs were common between LRS and LRC; and one common QTL was detected for RGV, LRS and LRC simultaneously. These results indicated that both single and epistatic loci were involved in the ABA sensitivity in rice, and the genetic basis of ABA sensitivity at seed germination and seedling stage was largely different.

Genome-Wide Association Analysis Reveals Different Genetic Control in Panicle Architecture Between and Rice.

Panicle architecture determines the number of spikelets per panicle (SPP) and is highly associated with grain yield in rice ( L.). Understanding the genetic basis of panicle architecture is important for improving the yield of rice grain. In this study, we dissected panicle architecture traits into eight components, which were phenotyped from a germplasm collection of 529 cultivars. Multiple regression analysis revealed that the number of secondary branch (NSB) was the major factor that contributed to SPP. Genome-wide association analysis was performed independently for the eight particle architecture traits observed in the and rice subpopulations compared with the whole rice population. In total, 30 loci were associated with these traits. Of these, 13 loci were closely linked to known panicle architecture genes, and 17 novel loci were repeatedly identified in different environments. An association signal cluster was identified for NSB and number of spikelets per secondary branch (NSSB) in the region of 31.6 to 31.7 Mb on chromosome 4. In addition to the common associations detected in both and subpopulations, many associated loci were unique to one subpopulation. For example, and were specifically associated with panicle length (PL) in and rice, respectively. Moreover, the -mediated flowering genes and were associated with the formation of panicle architecture in rice. These results suggest that different gene networks regulate panicle architecture in and rice.

Evolution and association analysis of Ghd7 in rice.

Plant height, heading date, and yield are the main targets for rice genetic improvement. Ghd7 is a pleiotropic gene that controls the aforementioned traits simultaneously. In this study, a rice germplasm collection of 104 accessions (Oryza sativa) and 3 wild rice varieties (O.rufipogon) was used to analyze the evolution and association of Ghd7 with plant height, heading date, and yield. Among the 104 accessions, 76 single nucleotide polymorphisms (SNPs) and six insertions and deletions were found within a 3932-bp DNA fragment of Ghd7. A higher pairwise π and θ in the promoter indicated a highly diversified promoter of Ghd7. Sixteen haplotypes and 8 types of Ghd7 protein were detected. SNP changes between haplotypes indicated that Ghd7 evolved from two distinct ancestral gene pools, and independent domestication processes were detected in indica and japonica varietals respectively. In addition to the previously reported premature stop mutation in the first exon of Ghd7, which caused phenotypic changes of multiple traits, we found another functional C/T mutation (SNP S_555) by structure-based association analysis. SNP S_555 is located in the promoter and was related to plant height probably by altering gene expression. Moreover, another seven SNP mutations in complete linkage were found to be associated with the number of spikelets per panicle, regardless of the photoperiod. These associations provide the potential for flexibility of Ghd7 application in rice breeding programs.

Paramutation-like interaction of T-DNA loci in Arabidopsis.

In paramutation, epigenetic information is transferred from one allele to another to create a gene expression state which is stably inherited over generations. Typically, paramutation describes a phenomenon where one allele of a gene down-regulates the expression of another allele. Paramutation has been described in several eukaryotes and is best understood in plants. Here we describe an unexpected paramutation-like trans SALK T-DNA interaction in Arabidopsis. Unlike most of the previously described paramutations, which led to gene silencing, the trans SALK T-DNA interaction caused an increase in the transcript levels of the endogenous gene (COBRA) where the T-DNA was inserted. This increased COBRA expression state was stably inherited for several generations and led to the partial suppression of the cobra phenotype. DNA methylation was implicated in this trans SALK T-DNA interaction since mutation of the DNA methyltransferase 1 in the suppressed cobra caused a reversal of the suppression. In addition, null mutants of the DNA demethylase ROS1 caused a similar COBRA transcript increase in the cobra SALK T-DNA mutant as the trans T-DNA interaction. Our results provide a new example of a paramutation-like trans T-DNA interaction in Arabidopsis, and establish a convenient hypocotyl elongation assay to study this phenomenon. The results also alert to the possibility of unexpected endogenous transcript increase when two T-DNAs are combined in the same genetic background.

Identification of quantitative trait loci for four morphologic traits under water stress in rice (Oryza sativa L.).

Late season drought coinciding with the rice booting to heading stage affects the development of plant height, panicle exsertion, and flag leaf size, and causes significant yield loss. In this study, a recombinant inbred line population derived from a cross between paddy and upland cultivars was used for data collection of the morphologic traits under well water and drought stress conditions. Drought stress was applied at the stage of panicle initiation in the field in 2002 and at the booting stage in PVC pipes in 2003. The data from stress conditions and their ratios (trait measured under stress condition/trait measured under well water condition) or differences (trait measured under stress condition minus trait measured under well water condition) were used for QTL analysis. Totally, 17 and 36 QTLs for these traits were identified in 2002 and 2003, respectively, which explained a range of 2.58%-29.82% of the phenotypic variation. Among them, six QTLs were commonly identified in the two years, suggesting that the drought stress in the two years was different. The genetic basis of these traits will provide useful information for improving rice late season drought resistance, and their application as indirect indices in rice late season drought resistance screening was also discussed.

Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice.

Yield potential, plant height and heading date are three classes of traits that determine the productivity of many crop plants. Here we show that the quantitative trait locus (QTL) Ghd7, isolated from an elite rice hybrid and encoding a CCT domain protein, has major effects on an array of traits in rice, including number of grains per panicle, plant height and heading date. Enhanced expression of Ghd7 under long-day conditions delays heading and increases plant height and panicle size. Natural mutants with reduced function enable rice to be cultivated in temperate and cooler regions. Thus, Ghd7 has played crucial roles for increasing productivity and adaptability of rice globally.

Genetic analysis for drought resistance of rice at reproductive stage in field with different types of soil.

Drought resistance of rice is a complex trait and is mainly determined by mechanisms of drought avoidance and drought tolerance. The present study was conducted to characterize the genetic basis of drought resistance at reproductive stage in field by analyzing the QTLs for drought response index (DRI, normalized by potential yield and flowering time), relative yield, relative spikelet fertility, and four traits of plant water status and their relationships with root traits using a recombinant inbred population derived from a cross between an indica rice and upland rice. A total of 39 QTLs for these traits were detected with individual QTL explained 5.1-32.1% of phenotypic variation. Only two QTLs for plant water status were commonly detected in two environments, suggesting different mechanisms might exist in two types of soil conditions. DRI has no correlation with potential yield and flowering time under control, suggesting that it can be used as a good drought resistance index in field conditions. The co-location of QTLs for canopy temperature and delaying in flowering time suggested a usefulness of these two traits as indexes in drought resistance screening. Correlation and QTL congruence between root traits and putative drought tolerance traits revealed that drought avoidance (via thick and deep root traits) was the main genetic basis of drought resistance in sandy soil condition, while drought tolerance may play more role in the genetic basis of drought resistance in paddy soil condition. Therefore, both drought mechanisms and soil textures must be considered in the improvement of drought resistance at reproductive stage in rice.