Genome-wide genetic variation and comparison of fruit-associated traits between kumquat (Citrus japonica) and Clementine mandarin (Citrus clementina)
Genome-wide genetic variation and comparison of fruit-associated traits between kumquat (Citrus japonica) and Clementine mandarin (Citrus clementina)
复制标题
金橘（Citrus japonica）和柑橘（Citrus clementina）之间的全基因组遗传变异和果实相关性状的比较
DOI：
10.1007/s11103-018-0712-2
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发表时间：
2018-03-01
影响因子：
5.1
通讯作者：
Zhang, Jin-Zhi
中科院分区：
文献类型：
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作者：
Liu, Tian-Jia;Li, Yong-Ping;Zhang, Jin-Zhi
关键信息在基因组和转录组水平上分析了两个柑橘品种的综合遗传变异。通过RNA测序，在果实发育过程中总共发现了1090个差异表达基因。 摘要：果实大小（果实赤道直径）和重量（鲜重）是决定许多园艺作物产量和消费者可接受性的两个最重要的组成部分。然而，人们对这些性状的遗传控制知之甚少。在这里，我们进行了全基因组重测序，以揭示金橘（Citrus japonica）和柑橘（Citrus clementina）之间果实发育的综合遗传变异。在这两个柑橘品种中总共鉴定出 5,865,235 个单核苷酸多态性 (SNP) 和 414,447 个插入/缺失 (InDels)。基于水果基因组和转录组的综合分析，鉴定出 640,801 个 SNP 和 20,733 个 InDels。探讨了这些遗传变异的特征、基因组分布、功能效应和其他特征。 RNA 测序鉴定出金橘和柑橘果实发育过程中的 1090 个差异表达基因 (DEG)。基因本体论揭示这些基因参与各种分子功能和生物过程。此外，还鉴定了之前报道的939个DEG和74个多重果实发育途径基因的遗传变异。一项全球调查在两个柑橘物种中鉴定出了 24,237 个特定的选择性剪接事件，并表明内含子保留是最普遍的选择性剪接模式。这些基因组变异数据为进一步探索柑橘多样性和基因表型关系以及未来分子育种研究以改良金橘、柑橘和相关物种奠定了基础。
Key messageThe comprehensive genetic variation of two citrus species were analyzed at genome and transcriptome level. A total of 1090 differentially expressed genes were found during fruit development by RNA-sequencing.AbstractFruit size (fruit equatorial diameter) and weight (fresh weight) are the two most important components determining yield and consumer acceptability for many horticultural crops. However, little is known about the genetic control of these traits. Here, we performed whole-genome resequencing to reveal the comprehensive genetic variation of the fruit development between kumquat (Citrus japonica) and Clementine mandarin (Citrus clementina). In total, 5,865,235 single-nucleotide polymorphisms (SNPs) and 414,447 insertions/deletions (InDels) were identified in the two citrus species. Based on integrative analysis of genome and transcriptome of fruit, 640,801 SNPs and 20,733 InDels were identified. The features, genomic distribution, functional effect, and other characteristics of these genetic variations were explored. RNA-sequencing identified 1090 differentially expressed genes (DEGs) during fruit development of kumquat and Clementine mandarin. Gene Ontology revealed that these genes were involved in various molecular functional and biological processes. In addition, the genetic variation of 939 DEGs and 74 multiple fruit development pathway genes from previous reports were also identified. A global survey identified 24,237 specific alternative splicing events in the two citrus species and showed that intron retention is the most prevalent pattern of alternative splicing. These genome variation data provide a foundation for further exploration of citrus diversity and gene–phenotype relationships and for future research on molecular breeding to improve kumquat, Clementine mandarin and related species.