Nuclear and chloroplast genome diversity revealed by low-coverage whole-genome shotgun sequence in 44 Brassica oleracea breeding lines

作     者：Sampath Perumal Nomar Espinosa Waminal Jonghoon Lee Hyun-Jin Koo Boem-soon Choi Jee Young Park Kyounggu Ahn Tae-Jin Yang Sampath Perumal;Nomar Espinosa Waminal;Jonghoon Lee;Hyun-Jin Koo;Boem-soon Choi;Jee Young Park;Kyounggu Ahn;Tae-Jin Yang

作者机构：Department of AgricultureForestry and BioresourcesPlant Genomics and Breeding Instituteand Research Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoul 08826Republic of Korea Global Institute for Food SecurityUniversity of Saskatchewan421 Downey RoadSaskatoonSK S7N 4L8Canada Agriculture and Agri-Food Canada107 Science PlaceSaskatoon S7N 0X2Canada Chromosome Research InstituteDepartment of Life ScienceSahmyook UniversitySeoul 01795Republic of Korea Joeun Seeds.Co.LtdGoesan-GunChungcheongbuk-Do 367-833Republic of Korea Phyzen Genomics Institute13Seongnam-daero 331beon-gilBundang-guSeongnam-siGyeonggi-do 13558Republic of Korea 

出 版 物：《Horticultural Plant Journal》 (园艺学报（英文版）)

年 卷 期：2021年第7卷第6期

页      面：539-551页

核心收录：

学科分类：09[农学] 0902[农学-园艺学] 090202[农学-蔬菜学] 

基　　金：Golden Seed Project(Center for Horticultural Seed Development,Grant No.213003-04-1-SB430) Ministry of Agriculture,Food and Rural Affairs(MAFRA) Ministry of Oceans and Fisheries(MOF) “Cooperative Research Program for Agriculture Science&Technology Development(Grant No.PJ013238)”Rural Development Administration,Republic of Korea 

主　　题：Brassica oleracea subspecies Chloroplast genome Nuclear ribosomal DNA Genetic diversity Phylogeny 

摘      要：Whole-genome shogun sequence(WGS)data generated by next-generation sequencing(NGS)platforms are a valuable resource for crop *** produced 5–6×WGS coverage of 44 Brassica oleracea breeding lines representing seven subspecies/morphotypes:cabbage,broccoli,cauliflower,kailan,kale,Brussels sprout,and kohlrabi to systematically evaluate the nuclear and chloroplast(Cp)diversity in the 44 *** breeding *** then exploited the impact of low-coverage NGS by evaluating nuclear genome diversity and assembly,annotation of complete chloroplast(Cp)genomes and 45 S nuclear ribosomal DNA(45S nrDNA)sequences,and copy number variation for major *** genome diversity analysis has revealed a total of 496463 SNPs and 37493 indels in the nuclear genome across the 44 ***,some SNPs showed subspecies enrichment at certain chromosomal *** assembly of complete Cp genomes contained 153361–153372 bp with 37 variants including SNPs and *** 45S nrDNA transcription unit was 5802 bp long with a total of 31 SNPs from the 44 *** phylogenetic tree inferred from the nuclear and Cp genomes coincided and clustered broccoli,cauliflower,and kailan in one group and cabbage,Brussels sprout,kale,and kohlrabi in another *** morphotypes diverged during the last 0.17 million *** Cp genome diversity reflected the unique cytoplasm of each subspecies,and revealed that the cytoplasm of many breeding lines was replaced and intermingled via inter-subspecies crosses during the breeding process *** polymorphic Cp markers provide a classification system for the cytoplasm types in ***,copy numbers of major transposable elements(TEs)showed high diversity among the 44 accessions,indicating that many TEs have become active ***,we demonstrated a comprehensive utilization of low-coverage NGS data and might shed light on the genetic diversity and evolution of diverse *** morphotypes.