XB-ART-43050Dev Biol. June 1, 2011; 354 (1): 1-8.
A genetic map of Xenopus tropicalis.
We present a genetic map for Xenopus tropicalis, consisting of 2886 Simple Sequence Length Polymorphism (SSLP) markers. Using a bioinformatics-based strategy, we identified unique SSLPs within the X. tropicalis genome. Scaffolds from X. tropicalis genome assembly 2.0 (JGI) were scanned for Simple Sequence Repeats (SSRs); unique SSRs were then tested for amplification and polymorphisms using DNA from inbred Nigerian and Ivory Coast individuals. Thus identified, the SSLPs were genotyped against a mapping cross panel of DNA samples from 190 F2 individuals. Nearly 4000 SSLPs were genotyped, yielding a 2886-marker genetic map consisting of 10 major linkage groups between 73 and 132cM in length, and 4 smaller linkage groups between 7 and 40cM. The total effective size of the map is 1658cM, and the average intermarker distance for each linkage group ranged from 0.27 to 0.75cM. Fluorescence In Situ Hybridization (FISH) was carried out using probes for genes located on mapped scaffolds to assign linkage groups to chromosomes. Comparisons of this map with the X. tropicalis genome Assembly 4.1 (JGI) indicate that the map provides representation of a minimum of 66% of the X. tropicalis genome, incorporating 758 of the approximately 1300 scaffolds over 100,000bp. The genetic map and SSLP marker database constitute an essential resource for genetic and genomic analyses in X. tropicalis.
PubMed ID: 21458440
PMC ID: PMC3098391
Article link: Dev Biol.
Grant support: R01 HD046661 NICHD NIH HHS , R01 HD046661 NICHD NIH HHS
Genes referenced: acp2 adamts18 adgra1 adh1b agmat ap2m1 atp6v1h b4galt6 babam2 cabin1 camk2d cbl cdc40 chd3 crim1 csrnp1 cyp1b1 dao dmap1 dusp9 e2f4 exoc1 ext2 fgfr4 fignl1 fut1 glipr2 got1 hoxb3 kdm7a map2k4 mast2 mef2d mfn2 mgc145260 mpp7 myo6 nmt1 nop2 nr6a1 pan3 pcsk9 pias2 ppp4r2 prepl ptprg rasgrp2 rhbg rps6ka6 rybp smarcal1 smc1a sox6 sp2 taf4 tbcel tbr1 tram2 trit1 ttc27 ubqln4 uspl1 zfp36l2.1 znf142
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