Transcriptome-Derived Tetranucleotide Microsatellites and Their Associated Genes from the Giant Panda (Ailuropoda melanoleuca).
Recently, an increasing number of microsatellites or simple sequence repeats (SSRs) have been found and characterized from transcriptomes. Such SSRs can be employed as putative functional markers to easily tag corresponding genes, which play an important role in biomedical studies and genetic analysis. However, the transcriptome-derived SSRs for giant panda (Ailuropoda melanoleuca) are not yet available. In this work, we identified and characterized 20 tetranucleotide microsatellite loci from a transcript database generated from the blood of giant panda. Furthermore, we assigned their predicted transcriptome locations: 16 loci were assigned to untranslated regions (UTRs) and 4 loci were assigned to coding regions (CDSs). Gene identities of 14 transcripts contained corresponding microsatellites were determined, which provide useful information to study the potential contribution of SSRs to gene regulation in giant panda. The polymorphic information content (PIC) values ranged from 0.293 to 0.789 with an average of 0.603 for the 16 UTRs-derived SSRs. Interestingly, 4 CDS-derived microsatellites developed in our study were also polymorphic, and the instability of these 4 CDS-derived SSRs was further validated by re-genotyping and sequencing. The genes containing these 4 CDS-derived SSRs were embedded with various types of repeat motifs. The interaction of all the length-changing SSRs might provide a way against coding region frameshift caused by microsatellite instability. We hope these newly gene-associated biomarkers will pave the way for genetic and biomedical studies for giant panda in the future. In sum, this set of transcriptome-derived markers complements the genetic resources available for giant panda.
From the Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China (Song, Huang, Du, Fan, Yue, and Zhang); The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081, China (Shen, Wang, and Hou); and China Research and Conservation Center for the Giant Panda, Wenchuan 623006, China (Huang).
Xuhao
X
Song
From the Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China (Song, Huang, Du, Fan, Yue, and Zhang); The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081, China (Shen, Wang, and Hou); and China Research and Conservation Center for the Giant Panda, Wenchuan 623006, China (Huang).
Fujun
F
Shen
From the Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China (Song, Huang, Du, Fan, Yue, and Zhang); The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081, China (Shen, Wang, and Hou); and China Research and Conservation Center for the Giant Panda, Wenchuan 623006, China (Huang).
Jie
J
Huang
From the Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China (Song, Huang, Du, Fan, Yue, and Zhang); The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081, China (Shen, Wang, and Hou); and China Research and Conservation Center for the Giant Panda, Wenchuan 623006, China (Huang).
Yan
Y
Huang
From the Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China (Song, Huang, Du, Fan, Yue, and Zhang); The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081, China (Shen, Wang, and Hou); and China Research and Conservation Center for the Giant Panda, Wenchuan 623006, China (Huang).
Lianming
L
Du
From the Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China (Song, Huang, Du, Fan, Yue, and Zhang); The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081, China (Shen, Wang, and Hou); and China Research and Conservation Center for the Giant Panda, Wenchuan 623006, China (Huang).
Chengdong
C
Wang
From the Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China (Song, Huang, Du, Fan, Yue, and Zhang); The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081, China (Shen, Wang, and Hou); and China Research and Conservation Center for the Giant Panda, Wenchuan 623006, China (Huang).
Zhenxin
Z
Fan
From the Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China (Song, Huang, Du, Fan, Yue, and Zhang); The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081, China (Shen, Wang, and Hou); and China Research and Conservation Center for the Giant Panda, Wenchuan 623006, China (Huang).
Rong
R
Hou
From the Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China (Song, Huang, Du, Fan, Yue, and Zhang); The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081, China (Shen, Wang, and Hou); and China Research and Conservation Center for the Giant Panda, Wenchuan 623006, China (Huang).
Bisong
B
Yue
From the Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China (Song, Huang, Du, Fan, Yue, and Zhang); The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081, China (Shen, Wang, and Hou); and China Research and Conservation Center for the Giant Panda, Wenchuan 623006, China (Huang). zhangxy317@126.com.
Xiuyue
X
Zhang
D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D030561:Databases, Nucleic Acid; D005819:Genetic Markers; D018895:Microsatellite Repeats; D016366:Open Reading Frames; D040641:Quantitative Trait Loci; D014158:Transcription, Genetic; D059467:Transcriptome; D020506:Untranslated Regions; D001503:Ursidae / Q000235:genetics*
D005819:Genetic Markers; D020506:Untranslated Regions
Ailuropoda melanoleuca; CDS; frameshift; functional marker; transcriptome-derived tetranucleotide microsatellites