Dissecting genetic diversity and genomic background of Petunia cultivars with contrasting growth habits.

The cultivated petunia (Petunia ×hybrida) is derived from the progenitor species P. axillaris and P. integrifolia. The hybridization dates back only to the 1830s, though intensive breeding efforts have yielded cultivars exhibiting incredible diversity for many traits, including growth habit, flower color, and flower size. Until now, little is known about the genetic diversity and genomic background of modern cultivars. Here we selected a panel of 13 cultivars with contrasting growth habits and three wild species (the progenitors and P. exserta) to estimate the genomic contribution from the ancestral species and to study whether the variation of the genetic origin could be associated with different breeding programs or morphological variability. Transcriptome sequencing identified 1,164,566 SNPs representing 98.4% (32,451) of the transcripts that cover 99.2% (of 52,697,361 bp) of the P. axillaris transcriptome. Cultivars with an upright growth habit had more homozygous alleles and more P. axillaris-derived alleles than trailing cultivars, while mounded cultivars had intermediate heterozygosity. Unlike previous studies, we found the proportions of alleles derived from each progenitor species varied across cultivars but overall were not biased toward one progenitor species, suggesting diverse selection during cultivar development. For trailing cultivars, alleles potentially introgressed from other wild species ("out" alleles) were enriched. The "out" alleles were clustered in particular regions of chromosomes, suggesting that these regions may be hotspots of introgression. Transcripts in these regions were enriched with gene ontology terms associated with growth habit. This study provides novel insight into the contributions of progenitor species to the genomic background of modern petunia cultivars and identifies genome regions that may harbor genes conferring the trailing growth habit for further exploration.

Identification of Quantitative Trait Loci for Component Traits of Flowering Capacity Across Temperature in Petunia.

For ornamental annual bedding plants, flowering performance is critical. Flowering performance includes the length of the flowering period, the longevity of individual flowers, and the number of flowers produced during the flowering period, or flowering capacity. Flowering capacity is a function of several component traits, including the number of branches producing flowers, the number of inflorescences per flowering branch, and the number of flower buds per inflorescence. We employed an F7Petunia axillaris × P. exserta recombinant inbred line population to identify QTL for flowering capacity component traits. The population was phenotyped at 14, 17, and 20° over two years. Fifteen robust QTL (rQTL; QTL detected in two or more temperatures/years) were identified across six of the seven Petunia chromosomes (Chr) for total flower bud number (FlBud), branch number (Branch), flowering branch number (FlBranch), and primary shoot flower bud number (FlBudPS). The largest effect QTL explained up to 28.8, 34.9, 36, and 23.1% of the phenotypic variation for FlBub, FlBudPS, Branch, and FlBranch, respectively. rQTL for FlBud and FlBranch co-localized on Chr 1, and rQTL for FlBud, FlBudPS, and FlBranch co-localized on Chr 4. These regions in particular should be useful for identifying genes controlling flowering capacity of this important ornamental plant.

Genome-wide identification of quantitative trait loci for important plant and flower traits in petunia using a high-density linkage map and an interspecific recombinant inbred population derived from Petunia integrifolia and P. axillaris.

Petunia is a very important flower in the global floriculture industry and has played a critical role as a model in plant genetic studies. Owing to limited genetic variability in commercial germplasm, development of novel petunia phenotypes and new varieties has become increasingly difficult. To enrich petunia germplasm and facilitate genetic improvement, it is important to explore genetic variation in progenitor species that may contain highly valuable genes/alleles. In this study, an interspecific recombinant inbred population (168 recombinant inbreds) derived from Petunia integrifolia × P. axillaris were phenotyped for days to anthesis (DTA), flower count (Flower_C), flower diameter (Flower_D), flower length (Flower_L), plant height (Plant_H), plant spread (Plant_S), and plant size (Plant_Z) in 2014 and 2015. Transgressive segregation was observed for all traits in both years. The broad-sense heritability on a 2-year basis varied from 0.38 (Flower_C) to 0.82 (Flower_L). Ten QTL were consistently identified in both years and by two mapping strategies [multiple QTL mapping (MQM) in MapQTL and inclusive composite interval mapping (ICIM) in IciMapping]. Major QTL explained up to 30.2, 35.5, and 47.1% of the total phenotypic variation for Plant_S, Flower_L, and Flower_D, respectively. These findings should be of significant values for introgression of desirable genes from wild petunias into commercial varieties and future genetic improvement of this important flower.

Genome-Wide Search for Quantitative Trait Loci Controlling Important Plant and Flower Traits in Petunia Using an Interspecific Recombinant Inbred Population of Petunia axillaris and Petunia exserta.

A major bottleneck in plant breeding has been the much limited genetic base and much reduced genetic diversity in domesticated, cultivated germplasm. Identification and utilization of favorable gene loci or alleles from wild or progenitor species can serve as an effective approach to increasing genetic diversity and breaking this bottleneck in plant breeding. This study was conducted to identify quantitative trait loci (QTL) in wild or progenitor petunia species that can be used to improve important horticultural traits in garden petunia. An F7 recombinant inbred population derived between Petunia axillaris and P. exserta was phenotyped for plant height, plant spread, plant size, flower counts, flower diameter, flower length, and days to anthesis in Florida in two consecutive years. Transgressive segregation was observed for all seven traits in both years. The broad-sense heritability estimates for the traits ranged from 0.20 (days to anthesis) to 0.62 (flower length). A genome-wide genetic linkage map consisting of 368 single nucleotide polymorphism bins and extending over 277 cM was searched to identify QTL for these traits. Nineteen QTL were identified and localized to five linkage groups. Eleven of the loci were identified consistently in both years; several loci explained up to 34.0% and 24.1% of the phenotypic variance for flower length and flower diameter, respectively. Multiple loci controlling different traits are co-localized in four intervals in four linkage groups. These intervals contain desirable alleles that can be introgressed into commercial petunia germplasm to expand the genetic base and improve plant performance and flower characteristics in petunia.

Genetic Determinants of Crop Timing and Quality Traits in Two Interspecific Petunia Recombinant Inbred Line Populations.

The rate at which plants develop new nodes (development rate) is a major determinant of crop production time, yet the genetic control of this process, including genetic interactions with crop quality parameters, is poorly understood. We employed a modified genotyping-by-sequencing approach and generated genetic linkage maps with 6,291 and 3,297 single nucleotide polymorphisms (SNPs) for the interspecific Petunia recombinant inbred line (RIL) population - P. axillaris × P. exserta (AE) and P. integrifolia × P. axillaris (IA), respectively. Comparative mapping between the populations revealed perfect collinearity of marker order but different recombination frequency at the corresponding linkage groups (LGs). Quantitative trait loci (QTL) mapping conducted for development traits and other important quality traits indicated QTL clustered on chromosome 1, 2, 4 and 6 for the AE population and chromosome 1, 2, 5 and 6 for the IA population. Additionally, 209 differentially expressed unique transcripts were identified in shoot apex tissue between fast- and slow-developing RILs, 13 of which mapped to within 1 cM of a development rate QTL. These results will facilitate the identification of novel genes controlling crop timing and quality traits in Petunia and highlight the power of using multiple interspecific populations to elucidate genetic determinants of natural variation.

Transcriptome-enabled marker discovery and mapping of plastochron-related genes in Petunia spp.

BACKGROUND: Petunia (Petunia × hybrida), derived from a hybrid between P. axillaris and P. integrifolia, is one of the most economically important bedding plant crops and Petunia spp. serve as model systems for investigating the mechanisms underlying diverse mating systems and pollination syndromes. In addition, we have previously described genetic variation and quantitative trait loci (QTL) related to petunia development rate and morphology, which represent important breeding targets for the floriculture industry to improve crop production and performance. Despite the importance of petunia as a crop, the floriculture industry has been slow to adopt marker assisted selection to facilitate breeding strategies and there remains a limited availability of sequences and molecular markers from the genus compared to other economically important members of the Solanaceae family such as tomato, potato and pepper. RESULTS: Here we report the de novo assembly, annotation and characterization of transcriptomes from P. axillaris, P. exserta and P. integrifolia. Each transcriptome assembly was derived from five tissue libraries (callus, 3-week old seedlings, shoot apices, flowers of mixed developmental stages, and trichomes). A total of 74,573, 54,913, and 104,739 assembled transcripts were recovered from P. axillaris, P. exserta and P. integrifolia, respectively and following removal of multiple isoforms, 32,994 P. axillaris, 30,225 P. exserta, and 33,540 P. integrifolia high quality representative transcripts were extracted for annotation and expression analysis. The transcriptome data was mined for single nucleotide polymorphisms (SNP) and simple sequence repeat (SSR) markers, yielding 89,007 high quality SNPs and 2949 SSRs, respectively. 15,701 SNPs were computationally converted into user-friendly cleaved amplified polymorphic sequence (CAPS) markers and a subset of SNP and CAPS markers were experimentally verified. CAPS markers developed from plastochron-related homologous transcripts from P. axillaris were mapped in an interspecific Petunia population and evaluated for co-localization with QTL for development rate. CONCLUSIONS: The high quality of the three Petunia spp. transcriptomes coupled with the utility of the SNP data will serve as a resource for further exploration of genetic diversity within the genus and will facilitate efforts to develop genetic and physical maps to aid the identification of QTL associated with traits of interest.

Quantitative inheritance of crop timing traits in interspecific hybrid Petunia populations and interactions with crop quality parameters.

The leaf unfolding rate (i.e., development rate) and the number of nodes forming prior to floral initiation are 2 factors determining production times for floriculture crops. Wild relative species of the cultivated petunia (Petunia x hybrida Vilm.) that exhibited faster development rates than modern cultivars and may therefore be useful genetic sources to develop cultivars with decreased production time were identified. Three interspecific F(2) families, Petunia exserta Stehmann x P. axillaris (Lam.) Britton et al., P. x hybrida 'Mitchell' x P. axillaris, and P. axillaris x P. integrifolia (Hook.) Schinz & Thell. all exhibited transgressive segregation for development rate and node number below the first flower. Development rate and time to flower segregated independently in all families. Leaf number below the first flower was positively correlated with leaf unfolding rate in all families except P. axillaris x P. integrifolia. Time to flower was positively correlated with flower bud number in the P. x hybrida 'Mitchell' x P. axillaris and P. axillaris x P. integrifolia families only. Based on these results, wild Petunia germplasm should be useful for developing petunia cultivars with reduced crop production times, but some negative effects on crop quality parameters may need to be overcome.

Vernalization, photoperiod and GA3 interact to affect flowering of Japanese radish (Raphanus sativus Chinese Radish Jumbo Scarlet).

Raphanus sativus L. Chinese Radish Jumbo Scarlet has characteristics that make it an excellent plant model for vernalization studies. This study further characterizes flower induction of R. sativus Chinese Radish Jumbo Scarlet. Seed were imbibed in distilled water containing 0, 10-5 M or 10-3 M GA3 for 24 h and were then exposed to 6 +/- 0.5 degrees C (vernalized) for 0, 2, 4, 6, or 8 days. Seedlings were then grown under a short- (8 h) or long-day photoperiod (8 h with or without a 4-h night interruption; 2200-0200 h). Of unvernalized plants grown under long- and short-day conditions, 45 and 3% flowered, respectively. Saturation of the vernalization response occurred after a 4- or 8-day vernalization treatment when plants were placed under long- or short-days, respectively. Basal leaf number and days to anthesis decreased when seeds were cooled for 2 or 4 days and were imbibed with 10-3 M GA3 compared to distilled water only. These data indicate that R. sativus Chinese Jumbo Scarlet has principally an obligate vernalization requirement when grown under short-days. GA3 application only facilitated flowering when the length of the vernalization treatment was marginal. Taken together, these data support the use of this plant as a model plant for identifying vernalization responses under short-day conditions.