Geographic description of genetic diversity and relationships in the USDA rice world collection

WenGui Yan, Hesham Agrama, Melissa Jia, Robert Fjellstrom, Anna McClung

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

Knowledge of genetic diversity and relationships among global germplasms of rice collected by the USDA since 1866 is critical for utilization, conservation, and management of the collection. A core subset developed from this collection, including 1794 accessions obtained from 112 countries in 14 geographic regions, was genotyped with one indel and 71 simple sequence repeat (SSR) markers. Total alleles were 1005, averaging 14 alleles per locus. A great majority of genetic variance was due to within instead of among geographic regions and within instead of among countries. The regions and countries were highly and significantly differentiated using these markers. Germplasm accessions obtained from the southern Asia, Southeast Asia, and Africa were highly diversified, while those from North America and western and eastern Europe had the lowest diversity. Different measurements of genetic diversity, including average number of alleles per locus, polymorphism information content (PIC), Nei index, and average number of private alleles per locus uniformly reached this conclusion. Three main clusters were revealed by both analyses of principal coordinates and Nei genetic similarities for the 14 regions. Seventy-eight countries, from which five or more accessions were collected in the core subset, were differentiated into five main clusters. Germplasm accessions obtained from Myanmar, Indonesia, Cambodia, Malaysia, and Nepal were highly diversified, while those from France, Spain, Romania, Italy, and the United States were poorly diversified. This study proves that the USDA global collection effectively supports the U.S. rice industry with vast genetic diversity responsive to biotic and abiotic stresses.

Original languageEnglish
Pages (from-to)2406-2417
Number of pages12
JournalCrop Science
Volume50
Issue number6
DOIs
Publication statusPublished - Nov 2010

Fingerprint

USDA
genetic relationships
alleles
rice
genetic variation
germplasm
loci
Cambodia
Myanmar
Eastern European region
Romania
Nepal
Western European region
biotic stress
genetic variance
South East Asia
Malaysia
abiotic stress
Indonesia
France

ASJC Scopus subject areas

  • Agronomy and Crop Science

Cite this

Geographic description of genetic diversity and relationships in the USDA rice world collection. / Yan, WenGui; Agrama, Hesham; Jia, Melissa; Fjellstrom, Robert; McClung, Anna.

In: Crop Science, Vol. 50, No. 6, 11.2010, p. 2406-2417.

Research output: Contribution to journalArticle

Yan, WenGui ; Agrama, Hesham ; Jia, Melissa ; Fjellstrom, Robert ; McClung, Anna. / Geographic description of genetic diversity and relationships in the USDA rice world collection. In: Crop Science. 2010 ; Vol. 50, No. 6. pp. 2406-2417.
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