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Title: High-throughput development of SSR markers from pea (Pisum sativum L.) based on next generation sequencing of a purified Chinese commercial variety

Author
item YANG, TAO - Chinese Academy Of Agricultural Sciences
item FANG, LI - Chinese Academy Of Agricultural Sciences
item ZHANG, XIAOYAN - Chinese Academy Of Agricultural Sciences
item Hu, Jinguo
item BAO, SHIYING - Yunnan Academy Of Agriculture Sciences
item HAO, JUNJIE - Chinese Academy Of Agricultural Sciences
item LI, LING - Chinese Academy Of Agricultural Sciences
item HE, YUHUA - Yunnan Academy Of Agriculture Sciences
item JIANG, JUNYE - Chinese Academy Of Agricultural Sciences
item WANG, FANG - Chinese Academy Of Agricultural Sciences
item TIAN, SHUFANG - Chinese Academy Of Agricultural Sciences
item ZONG, XUXIAO - Chinese Academy Of Agricultural Sciences

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/17/2015
Publication Date: 10/6/2015
Publication URL: http://handle.nal.usda.gov/10113/63040
Citation: Yang, T., Fang, L., Zhang, X., Hu, J., Bao, S., Hao, J., Li, L., He, Y., Jiang, J., Wang, F., Tian, S., Zong, X. 2015. High-throughput development of SSR markers from pea (Pisum sativum L.) based on next generation sequencing of a purified Chinese commercial variety. PLoS One. 10:e0139775.

Interpretive Summary: Pea (Pisum sativum L.) is one of the most important and popular legume crops in many countries. The global harvested area was approximately 6.4 million hectares and production was almost 11 million metric tons of dry peas in 2013. Like other legume crops, pea has the capacity of fixing atmospheric nitrogen via symbiosis and plays an indispensable role in the sustainable cropping system. SSR (simple sequence repeat) markers are the markers of choice in marker-assisted selection to expedite crop genetic improvement. The available SSR markers for pea, especially of that developed from Chinese pea varieties, are not abundant as for other crop plants. This paper reports the results of the development of large number of SSR markers from a purified Chinese commercial pea varietyusing the next generation sequencing platform and bioinformatics. The reported marker information is useful for the global pea research community.

Technical Abstract: Pea (Pisum sativum L.) is an important food legume globally, and is the plant species that J.G. Mendel used to lay the foundation of modern genetics. However, genomics resources of pea are limited comparing to other crop species. Application of marker assisted selection (MAS) in pea breeding has lagged behind many other crops. Development of a large number of novel and reliable SSR (simple sequence repeat) or microsatellite markers will help both basic and applied genomics research of this crop. The Illumina HiSeq 2500 System was used to uncover 8,899 putative SSR containing sequences, and 3,275 non-redundant primers were designed to amplify these SSRs. Among the 1,644 SSRs that were randomly selected for primer validation, 841 yielded reliable amplifications of detectable polymorphisms among 24 genotypes of cultivated pea (Pisum sativum L.) and wild relatives (P. fulvum Sm.) originated from diverse geographical locations. The dataset indicated that the allele number per locus ranged from 2 to 10, and that the polymorphism information content (PIC) ranged from 0.08 to 0.82 with an average of 0.38. These 1,644 novel SSR markers were also tested for polymorphism between genotypes G0003973 and G0005527. Finally, 33 polymorphic SSR markers were anchored on the genetic linkage map of G0003973 × G0005527 F2 population.