Genome-Wide Assessment of Avocado Germplasm Determined from Specific Length Amplified Fragment Sequencing and Transcriptomes: Population Structure, Genetic Diversity, Identification, and Application of Race-Specific Markers
文献类型： 外文期刊
作者： Ge, Yu 1 ; Zhang, Teng 2 ; Wu, Bin 1 ; Tan, Lin 1 ; Ma, Funing 1 ; Zou, Minghong 3 ; Chen, Haihong 4 ; Pei, Jinli 5 ; Liu, Y 1 ;
作者机构： 1.Chinese Acad Trop Agr Sci, Haikou Expt Stn, Haikou 570102, Hainan, Peoples R China
2.Tianjin Derit Seed Ind Co Ltd, Tianjin 300384, Peoples R China
3.Chinese Acad Trop Agr Sci, South Subtrop Crops Res Inst, Zhanjiang 524091, Peoples R China
4.Guangxi Vocat & Tech Coll, Coll Agr, Nanning 530226, Peoples R China
5.Hainan Univ, Coll Hort & Landscape Architecture, Haikou 570228, Hainan, Peoples R China
6.Liaoning Acad Agr Sci, Inst Vegetable, Shenyang 110161, Liaoning, Peoples R China
关键词： Persea americana; ecological races; SLAF-seq; transcriptomics; phylogenetic relationships
期刊名称：GENES （ 影响因子：4.096； 五年影响因子：4.339 ）
ISSN： 2073-4425
年卷期： 2019 年 10 卷 3 期
页码：
收录情况： SCI
摘要： Genomic data is a powerful tool. However, the phylogenetic relationships among different ecological races of avocado remain unclear. Here, we used the results from specific length amplified fragment sequencing (SLAF-seq) and transcriptome data to infer the population structure and genetic diversity of 21 avocado cultivars and reconstructed the phylogeny of three ecological races and two interracial hybrids. The results of the three analyses performed (unweighted pair-group methods with arithmetic means (UPGMA) cluster, Principal coordinate analysis (PCoA), and STRUCTURE) based on single nucleotide polymorphisms (SNPs) from SLAF-seq all indicated the existence of two populations based on botanical race: Mexican-Guatemalan and West Indian genotype populations. Our results based on SNPs from SLAF-seq indicated that the Mexican and Guatemalan races were more closely related to each other than either was to the West Indian race, which also was confirmed in the UPGMA cluster results based on SNPs from transcriptomic data. SNPs from SLAF-seq provided strong evidence that the Guatemalan, Mexican, and Guatemalan x Mexican hybrid accession possessed higher genetic diversity than the West Indian races and Guatemalan x West Indian hybrid accessions. Six race-specific Kompetitive allele specific PCR (KASP) markers based on SNPs from SLAF-seq were then developed and validated.
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