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United States Department of Agriculture

Agricultural Research Service

Research Project: Management of Plant Genetic Resources and Associated Information

Location: Plant Germplasm Introduction and Testing

Title: Large-scale microsatellite development in grasspea (Lathyrus sativus L.), an orphan legume of the arid areas

Authors
item Yang, Tao -
item Jiang, Junye -
item Burlyaeva, Marina -
item Hu, Jinguo
item Coyne, Clarice
item Kumar, Shiv -
item Redden, Robert -
item Sun, Xuelian -
item Wang, Fang -
item Chang, Jianwu -
item Hao, Xiaopeng -
item Guan, Jianping -
item Zong, Xuxiao -

Submitted to: Biomed Central (BMC) Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: March 12, 2014
Publication Date: March 17, 2014
Citation: Yang, T., Jiang, J., Burlyaeva, M., Hu, J., Coyne, C.J., Kumar, S., Redden, R., Sun, X., Wang, F., Chang, J., Hao, X., Guan, J., Zong, X. 2014. Large-scale microsatellite development in grasspea (Lathyrus sativus L.), an orphan legume of the arid areas. Biomed Central (BMC) Plant Biology. 14:65.

Interpretive Summary: The grass pea is a legume crop cultivated as food and feed in southern parts of Europe, North Africa and across Asia. It has been reported that grass pea possesses the ability to survive in extreme environments, such as drought, flood and salinity in which all other crops fail. Facing the challenge of climate change, researchers started recently to pay increased attention to grass pea which could be an important 'insurance crop' in areas that are prone to abiotic stresses. This paper reports the result of an international collaborative project of developing reliable microsatellite or SSR (simple sequence repeat) markers for this orphan legume crop. We generated almost half a million reads using the next generation sequencing 454 GS FLX Titanium platform from the SSR-enriched libraries constructed with grass pea genomic DNA. We identified 651,827 SSR sequences in the data and designed 50,144 non-redundant primer pairs to amplify these SSRs using available bioinformatics tools. To validate the newly identified SSR markers, we randomly picked 288 primer pairs and run PCR amplification on DNA samples extracted from 24 accessions including 23 grass pea and one related the species. Seventy-four primer pairs amplified polymorphic fragments on the 24 samples and the resulting marker data could discriminate each of the 24 genotypes and construct a meaningful dendrogram reflecting the genetic relationship among the genotypes. These newly discovered markers are useful for both basic and applied research in grass pea.

Technical Abstract: Grasspea (Lathyrus sativus L., 2n = 14), a member of the family Leguminosae, holds great agronomic potential as grain and forage legume crop in the arid areas for its superb resilience to abiotic stresses such as drought, flood and salinity. The crop could not make much progress through conventional breeding in the past, and there are hardly any detailed molecular biology studies due to paucity of reliable molecular markers representative of the entire genome. Using the 454 FLX Titanium pyrosequencing technique, 651,827 simple sequence repeat (SSR) loci were identified and 50,144 nonredundant primer pairs were successfully designed, of which 288 were randomly selected for validation among 23?L. sativus and one L. cicera accessions of diverse provenance. 74 were polymorphic, 70 monomorphic, and 144 with no PCR product. The number of observed alleles ranged from two to five, the observed heterozygosity from 0 to 0.9545, and Shannon?s information index ranged from 0.1013 to 1.0980, respectively. The dendrogram constructed by using unweighted pair group method with arithmetic mean (UPGMA) based on Nei's genetic distance, showed obvious distinctions and understandable relationships among the 24 accessions. The large number of SSR primer pairs developed in this study would make a significant contribution to genomics enabled improvement of grasspea.leaves. Further investigation is needed to elucidate the genetic basis of this useful trait, which can be addressed by further evaluation of the extensive collection of faba bean lines in the USDA collection.

Last Modified: 10/22/2014
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