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Abstract
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.
Highlights
The chrysanthemum (Chrysanthemum morifoliumRamat.) is the second-most important ornamental species in the world, and it accounts for a large proportion of the total commercial production of these plants[1]
The objectives of this study were to (1) detect single nucleotide polymorphisms (SNPs) loci associated with waterlogging tolerance (WT) chrysanthemums, (2) mine favorable alleles underlying the WT and assess their pyramiding effects, (3) develop derived cleaved amplified polymorphic sequence (dCAPS) markers that cosegregated with WT, and (4) identify potential candidate genes for WT
A substantial number of SNP markers were used in a genome-wide association study (GWAS) to investigate the genetic control of WT in chrysanthemums
Summary
Ramat.) is the second-most important ornamental species in the world, and it accounts for a large proportion of the total commercial production of these plants[1]. Cut chrysanthemums can be divided into the following two types depending on the flower diameter: spray cut type and disbud-cut type. The disbud type bears a large flower of Waterlogging stress is a common constraint in the chrysanthemum industry around the world, in the southern production regions of China[2]. Screening for tolerant germplasms or genes and developing waterlogging-tolerant chrysanthemum cultivars are efficient solutions to this challenge. To genetically improve crops for waterlogging tolerance (WT), the possible mechanisms underlying water stress and the genetic variations associated with WT within a species must be investigated.
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