Development of EST-SSR markers in Larix principis-rupprechtii Mayr and evaluation of their polymorphism and cross-species amplification

被引:26
|
作者
Dong, Mingliang [1 ,2 ,3 ]
Wang, Zewei [1 ,2 ,3 ]
He, Qingwei [1 ,2 ,3 ]
Zhao, Jian [1 ,2 ,3 ]
Fan, Zhirong [4 ]
Zhang, Jinfeng [1 ,2 ,3 ]
机构
[1] Beijing Forestry Univ, Key Lab Genet & Breeding Forest Trees & Ornamenta, Beijing Adv Innovat Ctr Tree Breeding Mol Design, Minist Educ,Natl Engn Lab Tree Breeding, Campus Box 118, Beijing 100083, Peoples R China
[2] Beijing Forestry Univ, Biol Engn State Forestry Adm, Key Lab Forest Trees & Ornamental Plants, Campus Box 118, Beijing 100083, Peoples R China
[3] Beijing Forestry Univ, Coll Biol Sci & Biotechnol, Campus Box 118, Beijing 100083, Peoples R China
[4] Jingle Cty Forestry Bur, Jingle 035100, Shanxi, Peoples R China
来源
TREES-STRUCTURE AND FUNCTION | 2018年 / 32卷 / 06期
基金
中国国家自然科学基金; 国家重点研发计划;
关键词
EST-SSR markers; Genetic diversity; Larix principis-rupprechtii; Transcriptome; Transferability; GENIC MICROSATELLITE MARKERS; GENETIC DIVERSITY; SEED ORCHARD; TRANSCRIPTOME; LOCI; SELECTION; LARCH;
D O I
10.1007/s00468-018-1733-9
中图分类号
S7 [林业];
学科分类号
0829 ; 0907 ;
摘要
Key messageWe developed and validated a new set of polymorphic EST-SSR markers across Larix species and evaluated genetic diversity in a clonal seed orchard of Larix principis-rupprechtii Mayr.AbstractPrince Rupprecht's larch (Larix principis-rupprechtii Mayr) is an important deciduous conifer species that has been widely planted in North China due to its major ecological and commercial value. However, the paucity of genomic data and robust molecular markers has hampered genetic and genomic studies. Here, transcriptome sequencing of L. principis-rupprechtii callus was performed using the Illumina platform. By mining 43,753 assembled unigenes, 1418 expressed sequence tag-simple sequence repeats (EST-SSRs) derived from 1300 unigenes were identified. A total of 1065 primer pairs were designed and 240 of these selected at random for validation among 24L. principis-rupprechtii individuals. Of these, 52 primer pairs were scored as polymorphic, and 20 polymorphic EST-SSR markers were further selected to genotype 66 clones deployed in a clonal seed orchard of L. principis-rupprechtii; these exhibited a moderate level of genetic diversity, as reflected by the mean values of the number of alleles (Na=3.85) and polymorphism information content (PIC=0.424). Additionally, all of the 20 EST-SSR markers could amplify clear and stable bands across three related Larix species. A neighbor-joining (NJ) clustering tree uniquely distinguished 66 clones and distributed these into three main clusters, which was further validated by principal coordinate analysis (PCoA). The developed EST-SSR markers will serve as valuable tools for future genetics and breeding research in larch species. The evaluation of genetic diversity among 66 clones will provide important information for efficient management and utilization of genetic material in L. principis-rupprechtii breeding programs.
引用
收藏
页码:1559 / 1571
页数:13
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