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United States Department of Agriculture

Agricultural Research Service

Research Project: DEVELOPMENT AND CHARACTERIZATION OF GENETIC RESOURCES FOR AGRONOMIC AND QUALITY TRAITS USING GENOMIC TOOLS Title: Genotypic and phenotypic characterization of genetic differentiation and diversity in the USDA rice mini-core collection

Authors
item Li, Xiaobai -
item Yan, Wengui
item Agrama, Hesham -
item Hu, Biaolin -
item Jia, Limeng -
item Jia, Melissa
item Jackson, Aaron
item Moldenhauer, Karen -
item McClung, Anna
item McClung, Anna
item Wu, Dianxing -

Submitted to: Genetica
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: November 1, 2010
Publication Date: November 16, 2010
Citation: Li, X., Yan, W., Agrama, H., Hu, B., Jia, L., Jia, M.H., Jackson, A.K., Moldenhauer, K., McClung, A.M., Wu, D. 2010. Genotypic and phenotypic characterization of genetic differentiation and diversity in the USDA rice mini-core collection. Genetica. 138(11):1221-1230.

Interpretive Summary: Genetic differentiation and diversity in a germplasm collection are usually studied using molecular markers. The present study characterized the USDA rice mini-core collection consisting of 217 accessions using both genotypic (128 molecular markers) and phenotypic (14 numerical traits) data. This mini-core was the most diversified among the reported germplasm collections of rice. The high genetic diversity in the mini-core suggests that there is a good possibility of mining genes of interest and selecting parents which will improve food production and quality. The correlation coefficient of genetic distance resulting from genotypic marker data with phenotypic traits was 0.85, which is much higher than it is in cassava, the only other crop in which differentiation has been studied by both genotypic and phenotypic characterization. Genetic differentiation could be helpful for conducting association mapping of genes of interest. Pre-cautions for determining genetic differentiation using phenotypic characteristics were discussed.

Technical Abstract: A rice mini-core collection consisting of 217 accessions has been developed to represent the USDA core and whole collections that include 1,794 and 18,709 accessions, respectively. To improve the efficiency of mining valuable genes and broadening the genetic diversity in breeding, genetic structure and diversity were analyzed using both genotypic (128 molecular markers) and phenotypic (14 numerical traits) data. This mini-core had 13.5 alleles per locus, which is the most among the reported germplasm collections of rice. Similarly, polymorphic information content (PIC) value was 0.71 in the mini-core which is the highest with one exception. The high genetic diversity in the mini-core suggests there is a good possibility of mining genes of interest and selecting parents which will improve food production and quality. A model-based clustering analysis resulted in lowland rice including three groups, aus (39 accessions), indica (71) and their admixtures (5), upland rice including temperate japonica (32), tropical japonica (40), aromatic (6) and their admixtures (12) and wild rice (12) including glaberrima and four other species of Oryza. Group differentiation was analyzed using both genotypic distance Fst from 128 molecular markers and phenotypic (Mahalanobis) distance D2 from 14 traits. Both dendrograms built by Fst and D2 reached similar-differentiative relationship among these genetic groups. The correlation coefficient of genotypic distance with phenotypic distance among the groups was 0.85, which is much higher than it in cassava (Manihot esculenta Crantz), the only another crop in which differentiation has been studied by both genotypic and phenotypic characterization. Genetic differentiation could be helpful for the association mapping of genes of interest. Precautions for genetic differentiation using phenotypic characteristics were discussed.

Last Modified: 10/26/2014