Genotyping-by-sequencing of Brassica oleracea vegetables reveals unique phylogenetic patterns, population structure and domestication footprints  

作　　者：Zachary Stansell Katie Hyma Jonathan Fresnedo-Ramírez Qi Sun Sharon Mitchell Thomas Björkman Jian Hua 

机构地区：[1]School of Integrative Plant Science,Horticulture Section,Cornell University,Geneva,NY,14456,USA [2]Genomic Diversity Facility,Institute of Biotechnology,Cornell University,Ithaca,NY,14853,USA [3]Bioinformatics Facility,Institute of Biotechnology,Cornell University,Ithaca,NY,14853,USA [4]School of Integrative Plant Science,Plant Biology Section,Cornell University,Ithaca,NY,14853,USA [5]Syracuse University,Syracuse,NY,USA [6]Department of Horticulture and Crop Science,The Ohio State University/OARDC,Wooster,OH,44691,USA

出　　处：《Horticulture Research》2018年第1期460-469,共10页园艺研究（英文）

基　　金：This work is supported by Specialty Crop Research Initiative grant no.2016-51181-25402 from the USDA National Institute of Food and Agriculture.

摘　　要：Brassica oleracea forms a diverse and economically significant crop group.Improvement efforts are often hindered by limited knowledge of diversity contained within available germplasm.Here,we employ genotyping-by-sequencing to investigate a diverse panel of 85 landrace and improved B.oleracea broccoli,cauliflower,and Chinese kale entries.Ultimately,21,680 high-quality SNPs were used to reveal a complex and admixed population structure and clarify phylogenetic relationships among B.oleracea groups.Each broccoli landrace contained,on average,8.4 times as many unique alleles as an improved broccoli and landraces collectively represented 81%of all broccoli-specific alleles.Commercial broccoli hybrids were largely represented by a single subpopulation identified within a complex population structure.Greater allelic diversity in landrace broccoli and 96.1%of SNPs differentiating improved cauliflower from landrace cauliflower were common to the larger pool of broccoli germplasm,supporting a parallel or later development of cauliflower due to introgression events from broccoli.Chinese kale was readily distinguished by principal coordinate analysis.Genotyping was accomplished with and without reliance upon a reference genome producing 141,317 and 20,815 filtered SNPs,respectively,supporting robust SNP discovery methods in neglected or unimproved crop groups that lack a reference genome.This work clarifies the population structure,phylogeny,and domestication footprints of landrace and improved B.oleracea broccoli using many genotyping-by-sequencing markers.Additionally,a large pool of genetic diversity contained in broccoli landraces is described which may enhance future breeding efforts.

关 键 词：breeding structure supporting 

分 类 号：S63[农业科学—蔬菜学]