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

Genome-wide association study of traits in sacred lotus uncovers MITE-associated variants underlying stamen petaloid and petal number variations

Understanding the genetic variants responsible for floral trait diversity is important for the molecular breeding of ornamental flowers. Widely used in water gardening for thousands of years, the sacred lotus exhibits a wide range of diversity in floral organs. Nevertheless, the genetic variations underlying various morphological characteristics in lotus remain largely unclear. Here, we performed a genome-wide association study of sacred lotus for 12 well-recorded ornamental traits. Given a moderate linkage disequilibrium level of 32.9 kb, we successfully identified 149 candidate genes responsible for seven flower traits and plant size variations, including many pleiotropic genes affecting multiple floral-organ-related traits, such as NnKUP2. Notably, we found a 2.75-kb presence-and-absence genomic fragment significantly associated with stamen petaloid and petal number variations, which was further confirmed by re-examining another independent population dataset with petal number records. Intriguingly, this fragment carries MITE transposons bound by siRNAs and is related to the expression differentiation of a nearby candidate gene between few-petalled and double-petalled lotuses. Overall, these genetic variations and candidate genes responsible for diverse lotus traits revealed by our GWAS highlight the role of transposon variations, particularly MITEs, in shaping floral trait diversity.

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.