Identification of Alternaria alternata as a Causal Agent for Leaf Blight in Syringa Species

While many isolates of Alternaria alternata are common saprophytes on trees and shrubs, this study clearly demonstrated that A. alternata is a primary pathogen in lilac (Syringa sp.), causing a leaf-blight that affects different Syringa species. Isolates of Alternaria sp. were collected from leaf blight samples of lilacs in the field. The internal transcribed spacer (ITS) region and morphological characterization were used to identify lilac blight pathogen. Based on 100% ITS nucleotide sequence identities to the Alternaria genus in the GenBank and morphological features, these isolates were identified as A. alternata. Disease symptoms were reproduced in lilac plants inoculated with A. alternata mycelial plugs and sprayed with a fungus-free culture filtrate, indicating that pathogenesis in lilac involves secondary metabolites or toxins. Diagnostic primers were developed to detect Alternaria sp. and A. alternata in lilac leaf blight based on ITS region and four known genes associated with pathogenesis in A. alternata: mixed-linked glucanase precursor, endopolygalacturonase, hsp70, and histone genes. The results from our study indicated A. alternata is a primary pathogen in lilac leaf blight, and these diagnostic primers can be used as a tool for the fast detection of A. alternata associated with lilac leaf blight

Investigation on Various Aboveground Traits to Identify Drought Tolerance in Cowpea Seedlings

Impacts of drought stress on crop production can significantly impair farmer’s revenue, hence adversely impacting the gross national product growth. For cowpea [Vigna unguiculata (L.) Walp.], which is a legume of economic importance, effects of drought at early vegetative growth could lead to substantial yield losses. However, little has been done with respect to breeding for cowpea cultivars withstanding drought at early vegetative growth. In addition, previous investigations have focused on how plantmorphology and root architecture can confer drought tolerance in cowpea, which is not sufficient in efforts to unravel unknown drought tolerance–related genetic mechanisms, potentially of great importance in breeding, and not pertaining to either plantmorphology or root architecture. Therefore, the objective of this study was to evaluate aboveground drought-related traits of cowpea genotypes at seedling stage. A total of 30 cowpea genotypes were greenhouse grown within boxes and the experimental design was completely randomized with three replicates. Drought stress was imposed for 28 days. Data on a total of 17 aboveground-related traits were collected. Results showed the following: 1) a large variation in these traits was found among the genotypes; 2) more trifoliate wilt/chlorosis tolerance but more unifoliate wilt/chlorosis susceptible were observed; 3) delayed senescence was related to the ability of maintaining a balanced chlorophyll content in both unifoliate and trifoliate leaves; and 4) the genotypes PI293469, PI349674, and PI293568 were found to be slow wilting and drought tolerant. These results could contribute to advancing breeding programs for drought tolerance in cowpea

Population Structure of Peronospora effusa in the Southwestern United States

Peronospora effusa is an obligate pathogen that causes downy mildew on spinach and is considered the most economically important disease of spinach. The objective of the current research was to assess genetic diversity of known historical races and isolates collected in 2014 from production fields in Yuma, Arizona and Salinas Valley, California. Candidate neutral single nucleotide polymorphisms (SNPs) were identified by comparing sequence data from reference isolates of known races of the pathogen collected in 2009 and 2010. Genotypes were assessed using targeted sequencing on genomic DNA extracted directly from infected plant tissue. Genotyping 26 historical and 167 contemporary samples at 46 SNP loci revealed 82 unique multi-locus genotypes. The unique genotypes clustered into five groups and the majority of isolates collected in 2014 were genetically closely related, regardless of source location. The historical samples, representing several races, showed greater genetic differentiation. Overall, the SNP data indicate much of the genotypic variation found within fields was produced during asexual development, whereas overall genetic diversity may be influenced by sexual recombination on broader geographical and temporal scales

Investigation on Various Aboveground Traits to Identify Drought Tolerance in Cowpea Seedlings

Impacts of drought stress on crop production can significantly impair farmer’s revenue, hence adversely impacting the gross national product growth. For cowpea [Vigna unguiculata (L.) Walp.], which is a legume of economic importance, effects of drought at early vegetative growth could lead to substantial yield losses. However, little has been done with respect to breeding for cowpea cultivars withstanding drought at early vegetative growth. In addition, previous investigations have focused on how plantmorphology and root architecture can confer drought tolerance in cowpea, which is not sufficient in efforts to unravel unknown drought tolerance–related genetic mechanisms, potentially of great importance in breeding, and not pertaining to either plantmorphology or root architecture. Therefore, the objective of this study was to evaluate aboveground drought-related traits of cowpea genotypes at seedling stage. A total of 30 cowpea genotypes were greenhouse grown within boxes and the experimental design was completely randomized with three replicates. Drought stress was imposed for 28 days. Data on a total of 17 aboveground-related traits were collected. Results showed the following: 1) a large variation in these traits was found among the genotypes; 2) more trifoliate wilt/chlorosis tolerance but more unifoliate wilt/chlorosis susceptible were observed; 3) delayed senescence was related to the ability of maintaining a balanced chlorophyll content in both unifoliate and trifoliate leaves; and 4) the genotypes PI293469, PI349674, and PI293568 were found to be slow wilting and drought tolerant. These results could contribute to advancing breeding programs for drought tolerance in cowpea

Genetic diversity and association analysis of leafminer (Liriomyza langei) resistance in spinach (Spinacia oleracea)

Leafminer (Liriomyza langei) is a major insect pest of many important agricultural crops, including spinach (Spinacia oleracea). Use of genetic resistance is an efficient, economic and environment-friendly method to control this pest. The objective of this research was to conduct association analysis and identify single nucleotide polymorphism (SNP) markers associated with leafminer resistance in spinach germplasm. A total of 300 USDA spinach germplasm accessions were used for the association analysis of leafminer resistance. Genotyping by sequencing (GBS) was used for genotyping and 783 SNPs from GBS were used for association analysis. The distribution of leafminer resistance showed a near normal distribution with a wide range from 1.1 to 11.7 stings per square centimeter leaf area, suggesting that the leafminer resistance in spinach is a complex trait controlled by multiple genes with minor effect in this spinach panel. Association analysis indicated that five SNP markers, AYZV02040968_7171, AYZV02076752_412, AYZV02098618_4615, AYZV02147304_383, and AYZV02271373_398 were associated with the leafminer resistance with a LOD 2.5 or higher. The SNP markers may be useful for breeders to select plants and lines for leafminer resistance in spinach breeding programs through marker-assisted selection.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

<b>Identification of a QTL Region for Tomato Brown Rugose Fruit Virus Resistance in </b><b><i>Solanum pimpinellifolium</i></b>

This is a SNP dataset consisted of 136357 SNPs across 274 tomato F2 plants.</p

Evaluation of Tomato Germplasm against Tomato Brown Rugose Fruit Virus and Identification of Resistance in <i>Solanum pimpinellifolium</i>

The tomato is one of the most important vegetable crops grown worldwide. Tomato brown rugose fruit virus (ToBRFV), a seed-borne tobamovirus, poses a serious threat to tomato production due to its ability to break the resistant genes (Tm-1, Tm-2, Tm-22) in tomatoes. The objective of this work was to identify new resistant source(s) of tomato germplasm against ToBRFV. To achieve this aim, a total of 476 accessions from 12 Solanum species were tested with the ToBRFV US isolate for their resistance and susceptibility. As a result, a total of 44 asymptomatic accessions were identified as resistant/tolerant, including thirty-one accessions of S. pimpinellifolium, one accession of S. corneliomulleri, four accessions of S. habrochaites, three accessions of S. peruvianum, and five accessions of S. subsection lycopersicon hybrid. Further analyses using serological tests identified four highly resistant S. pimpinellifolium lines, PI 390713, PI 390714, PI 390716, and PI 390717. The inheritance of resistance in the selected lines was verified in the next generation and confirmed using RT-qPCR. To our knowledge, this is a first report of high resistance to ToBRFV in S. pimpinellifolium. These new genetic resources will expand the genetic pool available for breeders to develop new resistant cultivars of tomato against ToBRFV

Genome-wide association mapping of resistance to Phytophthora sojae in a soybean [Glycine max (L.) Merr.] germplasm panel from maturity groups IV and V.

Phytophthora sojae, an oomycete pathogen of soybean, causes stem and root rot, resulting in annual economic loss up to $2 billion worldwide. Varieties with P. sojae resistance are environmental friendly to effectively reduce disease damages. In order to improve the resistance of P. sojae and broaden the genetic diversity in Southern soybean cultivars and germplasm in the U.S., we established a P. sojae resistance gene pool that has high genetic diversity, and explored genomic regions underlying the host resistance to P. sojae races 1, 3, 7, 17 and 25. A soybean germplasm panel from maturity groups (MGs) IV and V including 189 accessions originated from 10 countries were used in this study. The panel had a high genetic diversity compared to the 6,749 accessions from MGs IV and V in USDA Soybean Germplasm Collection. Based on disease evaluation dataset of these accessions inoculated with P. sojae races 1, 3, 7, 17 and 25, which are publically available, five accessions in this panel were resistant to all races. Genome-wide association analysis identified a total of 32 significant SNPs, which were clustered in resistance-associated genomic regions, among those, ss715619920 was only 3kb away from the gene Glyma.14g087500, a subtilisin protease. Gene expression analysis showed that the gene was down-regulated more than 4 fold (log2 fold > 2.2) in response to P. sojae infection. The identified molecular markers and genomic regions that are associated with the disease resistance in this gene pool will greatly assist the U.S. Southern soybean breeders in developing elite varieties with broad genetic background and P. sojae resistance

Population Structure and Genetic Diversity Analysis in Sugarcane (Saccharum spp. hybrids) and Six Related Saccharum Species

Sugarcane (Saccharum spp. hybrids) is one of the most important commercial crops for sugar, ethanol, and other byproducts production; therefore, it is of great significance to carry out genetic research. Assessing the genetic population structure and diversity plays a vital role in managing genetic resources and gene mapping. In this study, we assessed the genetic diversity and population structure among 196 Saccharum accessions, including 34 S. officinarum, 69 S. spontaneum, 17 S. robustum, 25 S. barberi, 13 S. sinense, 2 S. edule, and 36 Saccharum spp. hybrids. A total of 624 polymorphic SSR alleles were amplified by PCR with 22 pairs of fluorescence-labeled highly polymorphic SSR primers and identified on a capillary electrophoresis (CE) detection system including 109 new alleles. Three approaches (model-based clustering, principal component analysis, and phylogenetic analysis) were conducted for population structure and genetic diversity analyses. The results showed that the 196 accessions could be grouped into either three (Q) or eight (q) sub-populations. Phylogenetic analysis indicated that most accessions from each species merged. The species S. barberi and S. sinense formed one group. The species S. robustum, S. barberi, S. spontaneum, S. edule, and sugarcane hybrids merged into the second group. The S. officinarum accessions formed the third group located between the other two groups. Two-way chi-square tests derived a total of 24 species-specific or species-associated SSR alleles, including four alleles each for S. officinarum, S. spontaneum, S. barberi, and S. sinense, five alleles for S. robustum. and three alleles for Saccharum spp. hybrids. These species-specific or species-associated SSR alleles will have a wide application value in sugarcane breeding and species identification. The overall results provide useful information for future genetic study of the Saccharum genus and efficient utilization of sugarcane germplasm resources in sugarcane breeding

AMERICAN JOURNAL BIOTECHNOLOGY AND MOLECULAR SCIENCES Identification of molecular markers for Sw-5 gene of tomato spotted wilt virus resistance

ABSTRACT Tomato spotted wilt virus (TSWV) is one of the most destructive viral diseases that threaten worldwide tomato (Solanuum lycopersicum L. syn Lycopersicon esculentum Mill.) production. Use of host resistance appears to be the best way to control the disease. Marker assisted selection (MAS) has become very important and useful in the selection of TSWV resistance genes. The objective of this research was to identify Sw-5 gene-specific PCR-based molecular markers and gene-derived single nucleotide polymorphism (SNP) markers for MAS in tomato breeding. A gene-specific PCR-based marker and two gene-derived SNP markers specific for TSWV resistance Sw5-b allele were identified and validated in different tomato germplasm. It is expected that the present findings will be helpful in advancing the MAS for TSWV resistance in tomato