Genome Heterozygosity And Origin Study Of Sweet Orange Based On Second Generation Sequencing Technology

With the fast development of next generation sequencing (NGS) technology, genomics and other-omics researches enter into a high-throughput and quantitative study era. Genome-wide resequencing based on NGS methods contributes to studying genetic diversity, population structure, species’ origin and evolution, and genome-wide association study. As the world’s first largest fruit, Citrus is one of the most important species for studying genetics, breeding, and genomics of fruit plants. Previous study showed that sweet orange (Citrus sinensis) originated from the hybrid of mandarin (Citrus reticulata) and pummelo (Citrus grandis). It reproduces asexually by nucellar embryony, and often propagates via grafting, which lead to the highly heterozygous genome of sweet orange. And heterozygosity is related to heterosis of plants. All previous study about heterozygosity and origin of sweet orange can’t provide a genome-wide view and evidence for assigning the genetic origin and determining the origin pattern.By utilizing whole genome resequencing data, we comprehensively studied the heterozygosity of sweet orange, analyzed the gene expression of heterozygous loci, and studied its origin pattern. The mainly contents of our researches are described as below:1) Based on bioinformatic analysis of genome-wide resequencing data from the parent of reference genome of sweet orange, we found868,490SNPs,151,080InDels, and3,517SVs including2,615deletions,836insertions, and66inversions. We also assembled42MB of novel sequence not found in the reference sequence of a haploid sweet orange by de novo assembly of unmapped reads, and annotated134protein-coding genes within these novel sequences.2) According to the annotation of heterozygous loci, we defined large-effect for effects of SNPs and InDels on genes. Combining the expression analysis result of RNA-seq data sets from different tissues, we found that nearly half of genes containing large-effect SNPs or InDels presented tissue-differential expression level, and1,062genes were allelic differentially expressed.3) By analyzing the genome resequencing data sets from mandarin and pummelo, we assigned39.7Mb and118.2Mb genome regions to pummelo and mandarin, respectively. The ratio of genetic origin between pummelo and mandarin was1:3. We inferred that sweet orange originated from an hybridization with female-parent pummelo and male-parent mandarin, followed by a backcross with a male mandarin and follow-up breeding.