Identifying the genome-wide genetic variation between precocious trifoliate orange and its wild type and developing new markers for genetics research.
To increase our understanding of the genes involved in flowering in citrus, we performed genome resequencing of an early flowering trifoliate orange mutant (Poncirus trifoliata L. Raf.) and its wild type. At the genome level, 3,932,628 single nucleotide polymorphisms (SNPs), 1,293,383 insertion/deletion polymorphisms (InDels), and 52,135 structural variations were identified between the mutant and its wild type based on the citrus reference genome. Based on integrative analysis of resequencing and transcriptome analysis, 233,998 SNPs and 75,836 InDels were also identified between the mutant and its wild type at the transcriptional level. Also, 272 citrus homologous flowering-time transcripts containing genetic variation were also identified. Gene Ontology and Kyoto Encyclopaedia of Genes and Genomes annotation revealed that the transcripts containing the mutant- and the wild-type-specific InDel were involved in diverse biological processes and molecular function. Among these transcripts, there were 131 transcripts that were expressed differently in the two genotypes. When 268 selected InDels were tested on 32 genotypes of the three genera of Rutaceae for the genetic diversity assessment, these InDel-based markers showed high transferability. This work provides important information that will allow a better understanding of the citrus genome and that will be helpful for dissecting the genetic basis of important traits in citrus.
Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China.
Jin-Zhi
JZ
Zhang
Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China.
Sheng-Rui
SR
Liu
Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China chungen@mail.hzau.edu.cn.
Chun-Gen
CG
Hu
D032084:Citrus sinensis / Q000235:genetics* / Q000254:growth & development; D035264:Flowers / Q000235:genetics / Q000254:growth & development; D005819:Genetic Markers; D018745:Genome, Plant; D054643:INDEL Mutation; D018895:Microsatellite Repeats; D020641:Polymorphism, Single Nucleotide; D059467:Transcriptome
D005819:Genetic Markers
SNP; citrus; flowering; genetic variation; genome resequencing