Spinach ( Spinacia oleracea ) is an economically important leafy vegetable grown in the United States and world-wide. The downy mildew pathogen, Peronospora effusa ( Pfs ), is a major biotic constraint impacting spinach production and quality. The use of resistant cultivars is an economical and environmentally-friendly management option especially in organic production systems. As new races of the pathogen continue to appear, there is a need to continue to select for resistance to the emerging races. The objectives of this study were to evaluate a set of spinach hybrids and F2 breeding populations for resistance to Pfs race 5 to develop a better understanding of the genetics of downy mildew resistance. Also, we screened 39 commercial spinach cultivars for resistance to a recently identified race, Pfs race 19. The genetics of resistance to Pfs 5 was determined by greenhouse inoculations of F1 progeny (individual crosses between near isogenic lines, NIL3 or NIL1 and susceptible genotype, Viroflay) and F2 population progeny (cross between Califlay and susceptible Viroflay). Two hybrids were examined for resistance to Pfs 5. The results indicated that resistance conferred at the RPF 1 or the RPF 3 loci in a heterozygous (Rr) condition to Pfs 5 was completely dominant. Also, Chi-square analysis of the segregation pattern in the F2 population showed that resistance to Pfs race 5 was conferred by a single dominant gene. A total of 22 out of 39 spinach commercial cultivars were resistant to the newly reported Pfs race 19 and could be used in breeding programs to develop new cultivars with resistance to Pfs 19.

Powdery mildew was observed on common dandelion (Taraxacum officinale), collected in Fayetteville, AR, USA, and was identified using morphology and DNA sequences of ITS and 28S ribosomal RNA (rRNA) gene regions. Four primer pairs were used in this study: (1) the powdery mildew specific primer pair PMITS1/2 produced a 696 bp DNA fragment including full sequence of 563 bp DNA fragment amplified by ITS1/4 (KU563734); (2) CTW13/TW14 created a 279 bp DNA fragment including partial sequence of 28S rRNA gene (KU563735); (3) the 28S rRNA region primer pair NL1f/TW14 amplified a 899 bp DNA fragment (KX610821); and (4) the primer pair ITS1/4 amplified a 563 bp DNA fragment including partial sequence of 18S ribosomal RNA gene and complete sequence of ITS1, the 5.8S rRNA gene, ITS2, and partial sequence of the 28S rRNA gene. The similarity analysis by Blast and phylogenetic analysis indicated that the powdery mildew pathogen in dandelion collected from Arkansas was Podosphaera erigerontis-canadensis.

Understanding the genetic diversity of rice germplasm is important for the sustainable use of genetic materials in rice breeding and production. Africa is rich in rice genetic resources that can be utilized to boost rice productivity on the continent. A major constraint to rice production in Africa is rice blast, caused by the hemibiotrophic fungal pathogen Magnaporthe oryzae. In this report, we present the results of a genotyping-by-sequencing (GBS)-based diversity analysis of 190 African rice cultivars and an association mapping of blast resistance (R) genes and quantitative trait loci (QTLs). The 190 African cultivars were clustered into three groups based on the 184K single nucleotide polymorphisms generated by GBS. We inoculated the rice cultivars with six African M. oryzae isolates. Association mapping identified 25 genomic regions associated with blast resistance (RABRs) in the rice genome. Moreover, PCR analysis indicated that RABR_23 is associated with the Pi-ta gene on chromosome 12. Our study demonstrates that the combination of GBS-based genetic diversity population analysis and association mapping is effective in identifying rice blast R genes/QTLs that contribute to resistance against African populations of M. oryzae. The identified markers linked to the RABRs and 14 highly resistant cultivars in this study will be useful for rice breeding in Africa.

Rice blast disease is emerging as a major constraint to rice production in Africa. Although a traditional gene-tagging strategy using biparental crosses can effectively identify resistance (R) genes or quantitative trait loci (QTL) against Magnaporthe oryzae, the mapping procedure required is time consuming and requires many populations to investigate the genetics of resistance. In this report, we conducted a genome-wide association study (GWAS) to rapidly map rice genes conferring resistance against eight M. oryzae isolates from four African countries. We inoculated 162 rice cultivars, which were part of the rice diversity panel 1 (RDP1) and were previously genotyped with the 44,000 single-nucleotide polymorphism (SNP) chip, with the eight isolates. The GWAS identified 31 genomic regions associated with blast resistance (RABR) in the rice genome. In addition, we used polymerase chain reaction analysis to confirm the association between the Pish gene and a major RABR on chromosome 1 that was associated with resistance to four M. oryzae isolates. Our study has demonstrated the power of GWAS for the rapid identification of rice blast R or QTL genes that are effective against African populations of M. oryzae. The identified SNP markers associated with RABR can be used in breeding for resistance against rice blast in Africa.

Verticillium wilt, caused by Verticillium dahliae Kleb., is an important disease of spinach (Spinacia oleracea L.) and use of genetic resistance is the most economical method of controlling this disease.The objective of this research was to conduct molecular association analysis for Verticillium wilt resistance in spinach.A total of 95 USDA spinach accessions were evaluated for resistance to Verticillium wilt in this study.Phenotyping was conducted using a 0-4 scale of disease severity scores of Verticillium wilt and genotyping was performed using 2,878 SNPs which were postulated from genotyping by sequencing (GBS).STRUCTURE 2.3.4 and MEGA 6 were used for population structure and genetic diversity analysis.The single marker regression (SMR) from QGene, general linear mode (GLM) and mixed linear mode (MLM) from TEASSEL, and compressed mixed linear model (cMLM) and enriched compressed mixed linear model (EcMLM) from GAPIT were used for association analysis of Verticillium wilt resistance.Significant genetic variation of Verticillium wilt disease resistance was observed among the 95 spinach accessions with a wide range from 0.3 to 3.0 on a 0-4 scale.Two well-differentiated genetic populations and admixtures were postulated in the spinach panel.Five SNP markers, AYZV02052595_108, AYZV02112284_14543, AYZV02123399_146, AYZV02164612_331, and AYZV02170942_274 were identified to be associated with Verticillium wilt resistance with R-squared values from 9.3 to 18.2%.These markers may provide a tool utilized in molecular spinach breeding to select Verticillium wilt resistance through markerassisted selection.

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).

Spinach (Spinacia oleracea L.) is an important leafy vegetable crop grown worldwide. Leaf traits, surface texture (smooth, savoy or semi-savoy), petiole colour (different shades of green vs. purple) and edge shape (serrate vs. entire), are important commercial traits of spinach. Association mapping for the three traits was conducted on 323 USDA spinach germplasm accessions, originally collected from 33 countries and representing the entire USDA spinach germplasm collection. The majority of accessions were from Europe (36.3%), Asia (25.3%) and North America (15.8%). The majority of the spinach accessions (82.0%) were smooth (unwrinkled types), whereas the savoy and semi-savoy types (wrinkled types) accounted for 18.0%. The collection contained 74.9% green petiole types, while the purple petioles consisted of 25.1%. The collection consisted of 27.2% serrated leaf types and 72.8% entire leaf edge types. Genotyping-by-sequencing (GBS) was used for single nucleotide polymorphism (SNP) discovery, and SNPs were used as genotypic data to conduct genetic diversity and association mapping of the three leaf traits. Five genetic subpopulations and principal components (PCs) were postulated by structure 2 and JMP Genomics 7 for this association panel. Five, seven and 14 SNPs were identified to be associated with surface texture, edge shape and petiole colour, respectively. This study provides us an approach to identify SNP markers through association analysis in spinach and thus leads to select these three leaf traits through marker-assisted selection in spinach breeding programme.