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园艺学报 ›› 2020, Vol. 47 ›› Issue (1): 98-110.doi: 10.16420/j.issn.0513-353x.2019-0062

• 研究报告 • 上一篇    下一篇

中国樱桃InDel标记开发及其在蔷薇科果树中通用性评价

王 珏1,*,王 燕1,2,*,张 静2,陈 涛1,3,王 磊2,陈 清1,汤浩茹1,2,王小蓉1,2,**   

  1. 1四川农业大学园艺学院,成都 611130;2四川农业大学果蔬研究所,成都 611130;3四川农业大学生命科学学院,雅安 625014
  • 出版日期:2020-01-25 发布日期:2020-01-25
  • 基金资助:
    国家自然科学基金项目(31672114,31801826);四川省青年科技创新研究团队项目(2019JDTD0010)

Development of Insertion-Deletion(InDel)Markers Based on Whole- genome Sequencing Data in Chinese Cherry and Their Transferability in Rosaceae Fruit Trees

WANG Jue1,*,WANG Yan1,2,*,ZHANG Jing2,CHEN Tao1,3,WANG Lei2,CHEN Qing1,TANG Haoru1,2,and WANG Xiaorong1,2,**   

  1. 1College of Horticulture,Sichuan Agricultural University,Chengdu 611130,China;2Institute of Pomology and Olericulture,Sichuan Agricultural University,Chengdu 611130,China;3College of Life Science,Sichuan Agricultural University,Ya’an,Sichuan 625014,China
  • Online:2020-01-25 Published:2020-01-25

摘要:

对栽培和野生中国樱桃进行De novo基因组测序和比对,在全基因组范围内检测筛选出50 617InDel位点,并挑选均匀分布的200个标记进行验证,其中,27个标记在中国樱桃种内表现出多态性。利用多态性标记,对不同来源的192份中国樱桃(168份栽培和24份野生)种质进行基因型分型,共检测到60个等位基因(Na),平均每个标记2.2个;基因多样性指数(Hs)为0.010 ~ 0.500,平均0.239;多态性信息含量(PIC)为0.010 ~ 0.375,平均0.198,表明中国樱桃遗传基础相对狭窄。根据聚类结果和地理分布将192份中国樱桃种质大致划分为5个群体。筛选出在蔷薇科李亚科樱属、李属、桃属、杏属、苹果亚科梨属、苹果属和蔷薇亚科草莓属、悬钩子属等重要果树共8个属156个个体中表现出较好通用性标记34个。物种与中国樱桃亲缘关系越近,InDel标记的多态性越高。

关键词: 中国樱桃, 全基因组, InDel标记, 蔷薇科果树, 通用性

Abstract: The De novo whole-genome sequencing data of cultivated and wild Chinese cherry [Cerasus pseudocerasus(Lindl.)G. Don]were applied to identify 50 617 InDel markers,and 200 markers with uniform distribution across the genome were selected to be evaluated. Twenty-seven polymorphic markers were identified,which accounted for 13.5% of screened markers. Among 192(168 cultivated and 24 wild)Chinese cherry accessions,a total of 60 allelic loci were detected using the 27 polymorphic markers,which meant that per marker corresponded to 2.2 allelic loci on average,with an average gene diversity(Hs)of 0.239(ranging from 0.010 to 0.500)and mean polymorphic information content(PIC)of 0.198(ranging from 0.010 to 0.375),indicating a relatively low genetic diversity. Population structure analysis and geographical location revealed five groups within Chinese cherry,which consisted of cultivated Chinese cherry in East and North China Plain,Qinling Mountains,Sichuan Basin,and Yun-Gui Plateau,and wild ones. Thirty-four of 200 InDel markers showed moderate transferability rate among 156 individuals from eight genera including Cerasus,Prunus,Amygdalus,Armeniaca,Pyrus,Malus,Fragaria,and Rubus of the subfamilies Prunoideae,Maloideae,and Rosoideae in the family Rosaceae with important economic values. The polymorphism of InDel markers were higher with the increasing relationships between species and Chinese cherry.

Key words: Cerasus pseudocerasus, whole-genome, Insertion-Deletion(InDel)marker, Rosaceae fruit trees, transferability

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