Association Analysis and Identification of SNP Markers for Stemphylium Leaf Spot (Stemphylium botryosum f. sp. spinacia) Resistance in Spinach (Spinacia oleracea)

Stemphylium leaf spot, caused by Stemphylium botryosum f. sp. spinacia, is an important fungal disease of spinach (Spinacia oleracea L.). The aim of this study was to conduct association analysis to identify single nucleotide polymorphism (SNP) markers associated with Stemphylium leaf spot resistance in spinach. A total of 273 spinach genotypes, including 265 accessions from the USDA spinach germplasm collection and eight commercial cultivars, were used in this study. Phenotyping for Stemphylium leaf spot resistance was evaluated in greenhouse;genotyping was conducted using genotyping by sequencing (GBS) with 787 SNPs;and single marker regression, general linear model, and mixed linear model were used for association analysis of Stemphylium leaf spot. Spinach genotypes showed a skewed distribution for Stemphylium leaf spot resistance, with a range from 0.2% to 23.5% disease severity, suggesting that Stemphylium leaf spot resistance in spinach is a complex, quantitative trait. Association analysis indicated that eight SNP markers, AYZV02052595_115, AYZV02052595_122, AYZV02057770_10404, AYZV02129827_205, AYZV0-2152692_182, AYZV02180153_337, AYZV02225889_197, and AYZV02258563_213 were strongly associated with Stemphylium leaf spot resistance, with a Log of the Odds (LOD) of 2.5 or above. The SNP markers may provide a tool to select for Stemphylium leaf spot resistance in spinach breeding programs through marker-assisted selection (MAS).

Evaluation of Total Seed Protein Content in Eleven Arkansas Cowpea (Vigna unguiculata (L.) Walp.) Lines

Cowpea is cultivated on more than 11 million hectares with a worldwide production of 5.4 million tons of dried seeds. Cowpea is an affordable source of protein, which is used as an alternative to soybean for people who are allergic to soybean protein. The aim of this research was to assess the variability of the total seed protein content in cowpea. Eleven Arkansas breeding lines were used in this study. Field experiment design was a randomized complete block design (RCBD) with 2 blocks, and conducted in three different locations within Arkansas State (Fayetteville, Alma, and Hope) in 2015. A standard chemical protocol was performed involving an analysis of the total nitrogen by combustion using an Elementar Rapid N III instrument to estimate the protein content. The average protein content was 25.4%, and ranged from 23.7% to 27.4% with a standard deviation of 1.9%. The significant effects of genotype, environment (location), and genotype by environment were observed for the total seed protein content in cowpea. The broad sense heritability (H2) for cowpea seed protein was estimated to be 57.8% based on the eleven cowpea genotypes studied. The cowpea lines, “Early Scarlet” and 09-204 had the highest seed protein content with 27.4% and 26.9% dried seed weight, respectively. This study provides valuable information on cowpea protein content for breeders to select and utilize those breeding lines with high seed protein content to develop new high protein cowpea cultivars.

Genome-Wide Identification, Classification and Evolutionary Expansion of KNOX Gene Family in Rice (<i>Oryza sativa</i>) and <i>Populus</i>(<i>Populustrichocarpa</i>)

The KNOX gene family codes for transcriptional regulators with a variety of functions in plant developmental and physiological processes. In this study, a genome-wide comparative analysis of KNOX genes in Poplar (Populustrichocarpa) and rice (Oryza sativa L. ssp. japonica) was carried out. With comprehensive computational analyses, which take into account the gene structures, phylogeny and conserved motifs, 15 and 13 KNOX genes in Poplar and rice were identified, respectively. These KNOX genes were further divided into 3 groups. The Poplar gene POPTR_0012s04040 and the rice genes LOC_Os03g47042 and LOC_Os03g47022 were classified to a new group of KNOX genes without ahomeobox domain together with KNATM, which were proposed to play potential role in plant development and pluripotency. The identification of KNATM homolog in monocotyledons (rice) provided a strong support for proposing an ancient shuffling of HOMEOBOX gene with MEINOX gene took place in the KNOX phylogeny. Using subcellular location information, GO (gene ontology) and expression profile analysis, KNOX genes in rice and poplar were proposed to function similarly to the members in Arabidopsis. Our observations may lay the foundation for future functional analysis of KNOX genes in rice and poplar to unravel their biological roles in cellular pluripotency.

Molecular Markers for Tm-2 Alleles of Tomato Mosaic Virus Resistance in Tomato

Tomato mosaic virus (ToMV) is one of the most infectious virus diseases in tomato (Solanum lycopersicum L). The practical and effective method of controlling this disease is through genetic control by using major resistance genes. So far, three genes Tm-1, Tm-2 and Tm-22 conferring resistance to ToMV have been reported and utilized in tomato culti-var development. Marker assisted selection (MAS) has become very important and useful tool in selection of ToMV re-sistant tomato lines or hybrids. The objective of this research was to identify allele-specific PCR-based, cleaved ampli-fied polymorphic sequence (CAPS), and allele-derived single nucleotide polymorphism (SNP) markers for Tm-2 loci. Four allele-specific PCR-based markers were identified: one for Tm-2, one for Tm-22, and two for the susceptible allele tm-2. Three allele-derived CAPS markers were identified, which can identify and distinguish three alleles, tm-2, Tm-2 and Tm-22 in tomato germplasm. Three SNP markers were developed specific for Tm-2 locus. These markers will pro-vide breeders with a tool in selection of Tm-2 and Tm-22 resistance genes in tomato breeding program.

Effects of Low Temperature and Low Light on Physiology of Tomato Seedlings

The physiological changes and the mechanism of stress tolerance in tomato were studied under low temperature and low light conditions. Two growth chamber experiments evaluated three temperatures regimes under standard and relatively low illumination levels with three tomato genotypes. Both experiments used a completely randomized split-plot design (CRD), with temperature regime as the main plot and tomato genotype as the split-plot. The three tomato varieties were “Fenyan No.1”, “SV0313TG”, and “Ousa”. In both experiments, activity of superoxide dismutase (SOD) and peroxidases (POD) in tomato seedlings decreased under low temperature regime and the combination of low temperature and low light. Decreasing temperature had the greatest effect on the increase in enzyme activity. Decrease in POD activity was the greatest under low light and low temperature. The concentration of malondialdehyde (MDA) in plant tissue also decreased under low temperature (20°C/10°C day/night) compared to the standard temperature control (25°C/16°C day/night), but increased at 15°C/5°C day/night temperatures in both experiments and was the greatest under the lowest light and temperature conditions. In both experiments, proline concentrations were the greatest under the standard light intensity (30,000 lux), and proline concentrations increased as temperature decreased. The content of soluble sugar decreased under only low temperature stress but increased under double stresses. The relative value of osmotic potential increased a little under low temperature stress but decreased under double stresses.

Skim resequencing finely maps the downy mildew resistance loci RPF2 and RPF3 in spinach cultivars whale and Lazio

Commercial production of spinach(Spinacia oleracea L.)is centered in California and Arizona in the US,where downy mildew caused by Peronospora effusa is the most destructive disease.Nineteen typical races of P.effusa have been reported to infect spinach,with 16 identified after 1990.The regular appearance of new pathogen races breaks the resistance gene introgressed in spinach.We attempted to map and delineate the RPF2 locus at a finer resolution,identify linked single nucleotide polymorphism(SNP)markers,and report candidate downy mildew resistance(R)genes.Progeny populations segregating for RPF2 locus derived from resistant differential cultivar Lazio were infected using race 5 of P.effusa and were used to study for genetic transmission and mapping analysis in this study.Association analysis performed with low coverage whole genome resequencing-generated SNP markers mapped the RPF2 locus between 0.47 to 1.46 Mb of chromosome 3 with peak SNP(Chr3_1,221,009)showing a LOD value of 61.6 in the GLM model in TASSEL,which was within 1.08 Kb from Spo12821,a gene that encodes CC-NBS-LRR plant disease resistance protein.In addition,a combined analysis of progeny panels of Lazio and Whale segregating for RPF2 and RPF3 loci delineated the resistance section in chromosome 3 between 1.18–1.23 and 1.75–1.76 Mb.This study provides valuable information on the RPF2 resistance region in the spinach cultivar Lazio compared to RPF3 loci in the cultivar Whale.The RPF2 and RPF3 specific SNP markers,plus the resistant genes reported here,could add value to breeding efforts to develop downy mildew resistant cultivars in the future.

A Rapid Method for Measuring Seed Protein Content in Cowpea (<i>Vigna unguiculata</i>(L.) Walp)

Cowpea (Vigna unguiculata (L.) Walp), a legume crop that is grown in the worldwide, provides beneficial proteins for human consumption and animal feeding. In comparison, Rapid N analyzer as traditional method, has been widely used to measure protein content through the percentage of total nitrogen in the seed’s grounded powder. Near-Infrared Reflectance (NIR) has commonly been used to measure protein content in soybean seeds using whole grain without the need of seed grinding, which makes it possible to obtain fast results at a lower cost-per-analysis than the traditional combustion method. The specific objective of this study is to test a rapid method for measuring cowpea seed protein content by the NIR analyzer comparing to the traditional rapid N analyzer. A total of 240 cowpea genotypes were used in this study, including six seed coat colors, black, blackeye, browneye, cream, pinkeye, and red with 40 cowpea genotypes. The results showed that a linear relationship exists between the NIR analyzer and the Rapid N analyzer in the six different color groups. The correlation efficiency (r) between the seed protein contents from NIR and Rapid N was higher for pinkeye seed (r = 0.867), blackeye (0.771), cream (0.729), browneye (0.700), and red (0.623), respectively, but lower for black seeds, indicating that the NIR analyzer can be used to measure protein content for cowpea seeds with the five types of seed coat except black. Overview, the cowpea seed protein content measured from the NIR analyzer showed a little higher seed protein content. A series of regression models with different seed coat color have been built to adjust to protein content of colorful cowpea seeds from the NIR analyzer. But, it is not recommended to use for black color seeds due to a very low correlation efficiency (r) value with 0.184.

Screening of Seed Soluble Sugar Content in Cowpea (<i>Vigna unguiculata</i>(L.) Walp)

Cowpea (Vigna unguiculata (L.) Walp) is a legume crop grown worldwide to provide protein, starch, soluble sugar, amino acids, fatty acids, minerals, and vitamins for human consumption and animal feed. Soluble sugar is an important physiological trait in cowpea seeds. It not only plays an important role in storability and abiotic stress tolerance in seeds, but also provides energy to the human body and improves cooking quality by giving a desirable taste and mouth feel. Therefore, this research aimed to evaluate variation of cowpea seed soluble sugar content, and assess the soluble sugar content of cowpea varieties with different seed coat colors for cowpea consumers. A total of 113 cowpea genotypes were used, including 89 USDA GRIN germplasm accessions and 24 advanced breeding lines developed from University of Arkansas, AR, USA. Seed soluble sugar content was measured using a Spectrophotometer by phenol-sulphuric acid method. The results showed that the seed soluble sugar contents among 113 cowpea genotypes exhibited a wide range varying from 32.6 mg/g to 86.1 mg/g with an average of 54.5 mg/g. The five highest soluble sugar contents in seeds were found in the Arkansas cultivar Empire (86.1 mg/g), USDA germplasm accession PI583202 (84.5 mg/g), Arkansas advanced breeding line 09-655 (82.1 mg/g), USDA accession PI601085 (81.6 mg/g), and Arkansas advanced breeding line 09-529 (80.9 mg/g), and they can be used in cowpea breeding programs to develop new cowpea cultivars with higher seed soluble sugar content. It was also observed that the soluble sugar contents in Arkansas commercial cultivars and advanced breeding lines were higher than those in USDA germplasm and the seeds with colorful coat may have soluble sugar levels desirable by consumers.

Research advances and prospects of spinach breeding,genetics,and genomics

Spinach(Spinacia oleracea)is a diploid(2n=2x=12),wind-pollinated and highly heterozygous crop.The plants are mostly dioecious,although some monoecious plants exist.Spinach is an economically important cool-season leafy vegetable crop.Demand for spinach is increasing worldwide,particularly due to its high nutritional content.Spinach is a versatile crop eaten raw or cooked and used as salads or mixed with other cuisines.This review article provides an overview of origin and domestication,genetic diversity and population structure,genetic and genomic resources,major diseases threatening spinach production,breeding progress,and synthesizing how these resources can help in spinach improvement.The rapid development of genomic and sequence resources of spinach has increased biological and genetics research and laid the foundation for adopting molecular breeding.Downy mildew is the most serious disease affecting spinach and breeding programs focus on developing cultivars resistant to continually emerging new races of downy mildew pathogens.The use of genomic and molecular resources and approaches offers promises in population improvement and hybrid development to address biotic and abiotic stresses production challenges and provide improved breeding materials and strategies against the rapidly changing pathogen races and climatic conditions.

Loci discovery, network-guided approach, and genomic prediction for drought tolerance index in a multi-parent advanced generation intercross (MAGIC) cowpea population

Cowpea is a nutrient-dense legume that significantly contributes to the population’s diet in sub-Saharan Africa and other regions of the world.Improving cowpea cultivars to be more resilient to abiotic stress such as drought would be of great importance.The use of a multi-parent advanced generation intercross(MAGIC)population has been shown to be efficient in increasing the frequency of rare alleles that could be associated with important agricultural traits.In addition,drought tolerance index has been reported to be a reliable parameter for assessing crop tolerance to water-deficit conditions.Therefore,the objectives of this study were to evaluate the drought tolerance index for plant growth habit,plant maturity,flowering time,100-seed weight,and grain yield in a MAGIC cowpea population,to conduct genome-wide association study(GWAS)and identify single nucleotide polymorphism(SNP)markers associated with the drought tolerance indices,to investigate the potential relationship existing between the significant loci associated with the drought tolerance indices,and to conduct genomic selection(GS).These analyses were performed using the existing phenotypic and genotypic data published for the MAGIC population which consisted of 305 F8 recombinant inbred lines(RILs)developed at University of California,Riverside.The results indicated that:(1)large variation in drought tolerance indices existed among the cowpea genotypes,(2)a total of 14,18,5,5,and 35 SNPs were associated with plant growth habit change due to drought stress,and drought tolerance indices for maturity,flowering time,100-seed weight,and grain yield,respectively,(3)the network-guided approach revealed clear interactions between the loci associated with the drought tolerance traits,and(4)the GS accuracy varied from low to moderate.These results could be applied to improve drought tolerance in cowpea through marker-assisted selection(MAS)and genomic selection(GS).To the best of our knowledge,this is the first report on marker loci associated with drought tolerance indices in cowpea.

Impact of nutrient solutions under inorganic substrate soilless cultivation on plant growth,fruit yield and quality of tomato

Soilless cultivation has been widely used in tomato(Solanum lycopersicum)production.The objectives of this research are to evaluate the impacts of five nutrient solutions under soilless cultivation on plant growth,fruit yield and fruit quality in tomatoes.Four experiments were conducted with six treatments(five nutrient solutions plus one control)in six-cherry tomato cultivars and two big fruited tomato cultivars and 12 traits were observed and evaluated.The results showed that each of the five solutions increased plant growth and fruit yield,and improved the fruit quality.Compared to the control,the nutrient solution treatments increased 91.3%for number of fruits on base fruit cluster,12.1%for height,and 26.3%for stem diameter in the 2017-experiment;17.1%for vitamin C,13.8%for soluble solids,and 20.8%for total soluble sugar content in 2018-experiment one;28.1%for number of fruit cluster,25.8%for fruit yield,9.4%for number of fruit per cluster,and 13.3%for single fruit weight in 2018-experiment two;and 27.7%for vitamin C,14.0%for soluble solids,18.1%for total soluble sugar content,and 14.6%for fruit yield in the 2019-experiment.The solution decreased the chemical nitrate content 16.2%in the 2018-experiment and 43.7%in the 2019-experiment,and decreased the fruit cracking rate by 87%.Treatment 2 with higher nutrient component content showed the best results of the five treatments.The significant high positive correlation among the beneficial traits,fruit yield,soluble solids,total soluble sugar content,and vitamin C,and high negative correlation between each of the four traits and nitrate content were observed,indicating that soilless cultivation can increase tomato yield with higher nutritional components and decreased nitrate content.This research provides useful information for utilizing nutrient solutions supplied to tomato soilless cultivation.

Compact solar-powered plasma water generator: enhanced germination of aged seed with the corona dielectric barrierdischarger

Seed aging adversely affects agricultural productivity by reducing germination rates and seedling vigor,leading to significant costs for seed banks and companies due to the need for frequent seed renewals.This study demonstrated the use of plasma-activated water(PAW),generated by a solar-powered corona dielectric barrier discharger,to enhance germination rates of spinach seeds that had been stored at 4℃ for 23 years.Treating seeds with PAW at 17 kV for 15 min improved germination(by 135%)and seedling growth compared to untreated seeds.Through detailed analysis,beneficial PAW properties for seed development were identified,and a molecular mechanism for this rejuvenation is proposed.The solar-powered microreactor used in this study is considered to represent a significant advancement in seed treatment technology,offering a sustainable solution to meet growing food demands while addressing environmental and resource sustainability challenges.