Identification of favorable SNP alleles and candidate genes responsible for inflorescence-related traits via GWAS in chrysanthemum

被引:34
作者
Chong, Xinran [1 ]
Su, Jiangshuo [1 ]
Wang, Fan [1 ]
Wang, Haibin [1 ]
Song, Aiping [1 ]
Guan, Zhiyong [1 ]
Fang, Weimin [1 ]
Jiang, Jiafu [1 ]
Chen, Sumei [1 ]
Chen, Fadi [1 ]
Zhang, Fei [1 ]
机构
[1] Nanjing Agr Univ, Coll Hort, Weigang 1, Nanjing 210095, Jiangsu, Peoples R China
基金
中国国家自然科学基金;
关键词
Chrysanthemum; Genome-wide association study; Favorable allele; Derived cleaved amplified polymorphic sequence (dCAPS); Candidate gene; Marker-assisted selection; GENOME-WIDE ASSOCIATION; MARKER-ASSISTED SELECTION; MOLECULAR MARKERS; ARABIDOPSIS-THALIANA; TRANSCRIPTION FACTOR; FLOWERING TIME; LINKAGE MAP; GROWTH; RESISTANCE; PROTEINS;
D O I
10.1007/s11103-019-00826-w
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Key message81 SNPs were identified for three inflorescence-related traits, in which 15 were highly favorable. Two dCAPS markers were developed for future MAS breeding, and six candidate genes were predicted.AbstractChrysanthemum is a leading ornamental species worldwide and demonstrates a wealth of morphological variation. Knowledge about the genetic basis of its phenotypic variation for key horticultural traits can contribute to its effective management and genetic improvement. In this study, we conducted a genome-wide association study (GWAS) based on two years of phenotype data and a set of 92,617 single nucleotide polymorphisms (SNPs) using a panel of 107 diverse cut chrysanthemums to dissect the genetic control of three inflorescence-related traits. A total of 81 SNPs were significantly associated with the three inflorescence-related traits (capitulum diameter, number of ray florets and flowering time) in at least one environment, with an individual allele explaining 22.72-38.67% of the phenotypic variation. Fifteen highly favorable alleles were identified for the three target traits by computing the phenotypic effect values for the stable associations detected in 2 year-long trials at each locus. Dosage pyramiding effects of the highly favorable SNP alleles and significant linear correlations between highly favorable allele numbers and corresponding phenotypic performance were observed. Two highly favorable SNP alleles correlating to flowering time and capitulum diameter were converted to derived cleaved amplified polymorphic sequence (dCAPS) markers to facilitate future breeding. Finally, six putative candidate genes were identified that contribute to flowering time and capitulum diameter. These results serve as a foundation for analyzing the genetic mechanisms underlying important horticultural traits and provide valuable insights into molecular marker-assisted selection (MAS) in chrysanthemum breeding programs.
引用
收藏
页码:407 / 420
页数:14
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