Josh A. Honig

Genetic Variation of Spartina alterniflora in the New York Metropolitan Area and Its Relevance for Marsh Restoration

We examined the genetic population structure of Spartina alterniflora in Jamaica Bay, Queens, NY and the surrounding area in order to assist the ongoing restoration of Jamaica Bay. AMOVA (Analysis of Molecular Variance) indicated that population differences accounted for 15% of molecular variance (ΦPT = 0.15, p = 0.001). Observed heterozygosity (Ho) ranged from 0.61 to 0.73 among populations. A Mantel test indicated a weak and non-significant correlation between pairwise ΦPT and geographic distance matrices (r = 0.34, p = 0.12). A PCA revealed no obvious grouping pattern for sampled populations. Based on these data, we determined that the studied populations contained similar genetic variability to other populations in the New York vicinity and to those of the entire region. It seems likely that collection of germplasm from within the region will prove sufficient in maintaining overall genetic variation in restoration plantings. Given the small amount of genetic structure among populations within Jamaica Bay, however, it would be prudent to collect widely within the target marsh. We also recommend the practice of propagating plugs of S. alterniflora from wild seed, as opposed to using vegetative cuttings, when creating planting stock, in order to maximize genetic diversity in restored marshes.

Classification of bentgrass (Agrostis) cultivars and accessions based on microsatellite (SSR) markers

Genetic relationships among Agrostis species used for turf have been difficult to discern. Recent studies have either confirmed or contradicted previously proposed genetic relationships based on chromosome pairing behavior of inter-specific hybrids. The objective of the current study was to assess genetic relationships among Agrostis cultivars and accessions by using newly available A. stolonifera microsatellite (SSR) markers. Nuclear SSR (nuSSR) and chloroplast SSR (cpSSR) markers were used to genotype 16 individuals from each of 74 Agrostis cultivars and accessions. Genetic relationships based on nuSSR markers most closely resembled species relationships proposed by Jones in the 1950s. Contrary to the work of Jones, genetic relationships based on cpSSR markers indicated that A. canina was more closely related to A. stolonifera than to A. capillaris. We hypothesize that chloroplast introgression via interspecific hybridization between A. canina and A. stolonifera resulted in these species sharing common chloroplast genome lineages, while maintaining disparate nuclear genome lineages. Genetic relationships within Agrostis species based on nuSSR markers closely matched known pedigree relationships. Bayesian clustering analysis of nuSSR markers indicated that most modern seeded A. stolonifera cultivars exhibited high levels of admixture. Our study confirms that nuSSR markers distinguish Agrostis species and cultivars, and are valuable for studying genetic diversity and genetic relationships within the genus Agrostis.

A first linkage map and downy mildew resistance QTL discovery for sweet basil (Ocimum basilicum) facilitated by double digestion restriction site associated DNA sequencing (ddRADseq)

Limited understanding of sweet basil (Ocimum basilicum L.) genetics and genome structure has reduced efficiency of breeding strategies. This is evidenced by the rapid, worldwide dissemination of basil downy mildew (Peronospora belbahrii) in the absence of resistant cultivars. In an effort to improve available genetic resources, expressed sequence tag simple sequence repeat (EST-SSR) and single nucleotide polymorphism (SNP) markers were developed and used to genotype the MRI x SB22 F2 mapping population, which segregates for response to downy mildew. SNP markers were generated from genomic sequences derived from double digestion restriction site associated DNA sequencing (ddRADseq). Disomic segregation was observed in both SNP and EST-SSR markers providing evidence of an O. basilicum allotetraploid genome structure and allowing for subsequent analysis of the mapping population as a diploid intercross. A dense linkage map was constructed using 42 EST-SSR and 1,847 SNP markers spanning 3,030.9 cM. Multiple quantitative trait loci (QTL) model (MQM) analysis identified three QTL that explained 37–55% of phenotypic variance associated with downy mildew response across three environments. A single major QTL, dm11.1 explained 21–28% of phenotypic variance and demonstrated dominant gene action. Two minor QTL dm9.1 and dm14.1 explained 5–16% and 4–18% of phenotypic variance, respectively. Evidence is provided for an additive effect between the two minor QTL and the major QTL dm11.1 increasing downy mildew susceptibility. Results indicate that ddRADseq-facilitated SNP and SSR marker genotyping is an effective approach for mapping the sweet basil genome.