Transcriptome sequencing of field pea and faba bean for discovery and validation of SSR genetic markers

BMC Genomics

Research Article

Tony Leonforte¹  Michael Materne¹  Noel OI Cogan²  Luke W Pembleton²  Sukhjiwan Kaur²  Keith W Savin²  John W Forster³  Jeffrey Paull⁴ 

[1] Department of Primary Industries, Biosciences Research Division, Grains Innovation Park, 3401, Horsham, Victoria, Australia;Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, 1 Park Drive, La Trobe University Research and Development Park, 3083, Bundoora, Victoria, Australia;Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, 1 Park Drive, La Trobe University Research and Development Park, 3083, Bundoora, Victoria, Australia;La Trobe University, 3086, Bundoora, Victoria, Australia;School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, 5064, Glen Osmond, South Australia, Australia;

关键词: Faba Bean;    Simple Sequence Repeat Locus;    Simple Sequence Repeat Prime Pair;    Rare Transcript;    Unique Match;   

DOI  :  10.1186/1471-2164-13-104

 received in 2011-10-07, accepted in 2012-03-20,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundField pea (Pisum sativum L.) and faba bean (Vicia faba L.) are cool-season grain legume species that provide rich sources of food for humans and fodder for livestock. To date, both species have been relative 'genomic orphans' due to limited availability of genetic and genomic information. A significant enrichment of genomic resources is consequently required in order to understand the genetic architecture of important agronomic traits, and to support germplasm enhancement, genetic diversity, population structure and demographic studies.ResultscDNA samples obtained from various tissue types of specific field pea and faba bean genotypes were sequenced using 454 Roche GS FLX Titanium technology. A total of 720,324 and 304,680 reads for field pea and faba bean, respectively, were de novo assembled to generate sets of 70,682 and 60,440 unigenes. Consensus sequences were compared against the genome of the model legume species Medicago truncatula Gaertn., as well as that of the more distantly related, but better-characterised genome of Arabidopsis thaliana L.. In comparison to M. truncatula coding sequences, 11,737 and 10,179 unique hits were obtained from field pea and faba bean. Totals of 22,057 field pea and 18,052 faba bean unigenes were subsequently annotated from GenBank. Comparison to the genome of soybean (Glycine max L.) resulted in 19,451 unique hits for field pea and 16,497 unique hits for faba bean, corresponding to c. 35% and 30% of the known gene space, respectively. Simple sequence repeat (SSR)-containing expressed sequence tags (ESTs) were identified from consensus sequences, and totals of 2,397 and 802 primer pairs were designed for field pea and faba bean. Subsets of 96 EST-SSR markers were screened for validation across modest panels of field pea and faba bean cultivars, as well as related non-domesticated species. For field pea, 86 primer pairs successfully obtained amplification products from one or more template genotypes, of which 59% revealed polymorphism between 6 genotypes. In the case of faba bean, 81 primer pairs displayed successful amplification, of which 48% detected polymorphism.ConclusionsThe generation of EST datasets for field pea and faba bean has permitted effective unigene identification and functional sequence annotation. EST-SSR loci were detected at incidences of 14-17%, permitting design of comprehensive sets of primer pairs. The subsets from these primer pairs proved highly useful for polymorphism detection within Pisum and Vicia germplasm.

【 授权许可】

Unknown   
© Kaur et al; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.