Genome-wide association study identifies favorable SNP alleles and candidate genes for waterlogging tolerance in chrysanthemums

Chrysanthemums are sensitive to waterlogging stress,and the development of screening methods for tolerant germplasms or genes and the breeding of tolerant new varieties are of great importance in chrysanthemum breeding.To understand the genetic basis of waterlogging tolerance(WT)in chrysanthemums,we performed a genome-wide association study(GWAS)using 92,811 single nucleotide polymorphisms(SNPs)in a panel of 88 chrysanthemum accessions,including 64 spray cut and 24 disbud chrysanthemums.The results showed that the average MFVW(membership function value of waterlogging)of the disbud type(0.65)was significantly higher than that of the spray type(0.55)at P<0.05,and the MFVW of the Asian accessions(0.65)was significantly higher than that of the European accessions(0.48)at P<0.01.The GWAS performed using the general linear model(GLM)and mixed linear model(MLM)identified 137 and 14 SNP loci related to WT,respectively,and 11 associations were commonly predicted.By calculating the phenotypic effect values for 11 common SNP loci,six highly favorable SNP alleles that explained 12.85—21.85%of the phenotypic variations were identified.Furthermore,the dosage-pyramiding effects of the favorable alleles and the significant linear correlations between the numbers of highly favorable alleles and phenotypic values were identified(r2=0.45;P<0.01).A major SNP locus(Marker6619-75)was converted into a derived cleaved amplified polymorphic sequence(dCAPS)marker that cosegregated with WT with an average efficiency of 78.9%.Finally,four putative candidate genes in the WT were identified via quantitative real-time PCR(qRT-PCR).The results presented in this study provide insights for further research on WT mechanisms and the application of molecular marker-assisted selection(MAS)in chrysanthemum WT breeding programs.

Genomic and transcriptomic alterations following intergeneric hybridization and polyploidization in the Chrysanthemum nankingense×Tanacetum vulgare hybrid and allopolyploid (Asteraceae)

Allopolyploid formation involves two major events:interspecific hybridization and polyploidization.A number of species in the Asteraceae family are polyploids because of frequent hybridization.The effects of hybridization on genomics and transcriptomics in Chrysanthemum nankingense×Tanacetum vulgare hybrids have been reported.In this study,we obtained allopolyploids by applying a colchicine treatment to a synthesized C.nankingense×T.vulgare hybrid.Sequence-related amplified polymorphism(SRAP),methylation-sensitive amplification polymorphism(MSAP),and high-throughput RNA sequencing(RNA-Seq)technologies were used to investigate the genomic,epigenetic,and transcriptomic alterations in both the hybrid and allopolyploids.The genomic alterations in the hybrid and allopolyploids mainly involved the loss of parental fragments and the gain of novel fragments.The DNA methylation level of the hybrid was reduced by hybridization but was restored somewhat after polyploidization.There were more significant differences in gene expression between the hybrid/allopolyploid and the paternal parent than between the hybrid/allopolyploid and the maternal parent.Most differentially expressed genes(DEGs)showed down-regulation in the hybrid/allopolyploid relative to the parents.Among the non-additive genes,transgressive patterns appeared to be dominant,especially repression patterns.Maternal expression dominance was observed specifically for down-regulated genes.Many methylase and methyltransferase genes showed differential expression between the hybrid and parents and between the allopolyploid and parents.Our data indicate that hybridization may be a major factor affecting genomic and transcriptomic changes in newly formed allopolyploids.The formation of allopolyploids may not simply be the sum of hybridization and polyploidization changes but also may be influenced by the interaction between these processes.

The Chrysanthemum nankingense Genome Provides Insights into the Evolution and Diversification of Chrysanthemum Flowers and Medicinal Traits

The Asteraceae (Compositae),a large plant family of approximately 24 000-35 000 species,accounts for^10% of all angiosperm species and contributes a lot to plant diversity.The most representative members of the Asteraceae are the economically important chrysanthemums (Chrysanthemum L.)that diversified through reticulate evolution.Biodiversity is typically created by multiple evolutionary mechanisms such as wholegenome duplication 0NGD)or polyploidization and locally repetitive genome expansion.However,the lack of genomic data from chrysanthemum species has prevented an in-depth analysis of the evolutionary mechanisms involved in their diversification.Here,we used Oxford Nanopore long-read technologyto sequence the diploid Chrysanthemum nankingense genome,which represents one of the progenitor genomes of domesticated chrysanthemums.Our analysis revealed that the evolution of the C.nankingense genome was driven by bursts of repetitive element expansion and WGD events including a recentWGD that distinguishes chrysanthemum from sunflower,which diverged from chrysanthemum approximately 38.8 million years ago.Variations of ornamental and medicinal traits in chrysanthemums are linked to the expansion of candidate gene families by duplication events including paralogous gene duplication.Collectively,our study of the assembled reference genome offers new knowledge and resources to dissect the history and pattern of evolution and diversification of chrysanthemum plants,and also to accelerate their breeding and improvement.