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United States Department of Agriculture

Agricultural Research Service

Research Project: CHARACTERIZATION AND ENHANCEMENT OF PLANT RESISTANCE TO WATER-DEFICIT AND THERMAL STRESSES

Location: Plant Stress and Germplasm Development Research

Title: Assessing genetic diversity in Valencia peanut germplasm using SSR markers

Authors
item Kottapalli, Pratibha -
item Upadhyaya, Hari -
item Kottapalli, Kameswara -
item Payton, Paxton
item Dwivedi, Sangam -
item Burow, Mark -
item Puppala, Naveen -

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: September 27, 2010
Publication Date: May 1, 2011
Citation: Kottapalli, P., Upadhyaya, H., Kottapalli, K.R., Payton, P.R., Dwivedi, S., Burow, M., Puppala, N. 2011. Assessing genetic diversity in Valencia peanut germplasm using SSR markers. Crop Science. 51:1089-1100.

Interpretive Summary: Cultivated peanut (Arachis hypogaea L.) also known as groundnut, is an important food and oil producing legume, grown annually on 23.10 M ha in tropical and subtropical regions of the world. Peanut is rich in oil and protein content and has a high mineral and vitamin content making it a valued crop for direct human consumption, while its fodder is highly nutritious and palatable animal feed. Peanut production in the US is geared primarily toward the confectionary industry and the manufacturing of peanut butter, rather than oil production. The four market types (i.e., Virginia, Runner, Spanish, and Valencia) grown in US are characterized by distinct growth habit, pod/seed size, and flavor attributes. While Valencia (ssp. fastigiata var. fastigaita) peanuts constitute only 1 - 2% of the total US market and are almost exclusively cultivated in New Mexico and Texas, they possess a sweet flavor desired by the confectionary industry, have a very high in-shell market value, and remain a viable niche crop. The key to the success of any crop improvement depends on the researcher's ability to detect and exploit genetic diversity locked in germplasm, including wild relatives, that are conserved in various gene banks worldwide. Core collections have been suggested as a gateway to enhance use of germplasm in crop improvement programs. In peanut, both core and mini-core collections have been developed which have been used to identify new sources of genetic variation and diversity for a variety of traits including oil content, pathogen response, and abiotic stress tolerance. The aims of this study were to characterize the Valencia core collection using SSR markers, estimate the genetic diversity within this germplasm and analyze the population structure. Here we report our findings regarding the genetic diversity and population structure of the Valencia core collection as a means to enhance our ability to select diverse accessions for breeding and crop improvement. The molecular diversity that we observed in the Valencia germplasm provides useful information to aid selection of genetically diverse accessions which have subsequently been introduced into our breeding programs. Our future efforts will focus on evaluation of the Valencia germplasm for important agronomic and see quality traits and for resistance to biotic and abiotic stresses to identify trait-specific, genetically diverse germplasm to broaden the genetic base of Valencia peanut cultivars.

Technical Abstract: Valencia peanuts (Arachis hypogaea L.ssp. fastigiata var. fastigiata) are well known for their in-shell market value. Assessment of genetic diversity of the available Valencia germplasm is key to the success of developing improved cultivars with desirable agronomic and quality traits. In the present study,we report the molecular characterization and diversity analysis among 114 Valencia germplasm accessions including 78 US Valencia core collection accessions and 36 Valencia accessions from the global mini-core collection developed at ICRISAT. Fifty two SSRs amplified a total of 683 alleles with an average of 13 alleles per primer pair and a mean gene diversity of 0.335. Genetic similarities among accessions were estimated and an average genetic distance of 0.631 was detected. UPGMA clustering, PCA, and STRUCTURE analysis consistently separated the Valencia germplasm into five clusters with two distinct major groups. The first major cluster consisted of genotypes from S. America (59.6%) with very few genotypes from African, N. American, Caribbean, or European regions. The second cluster consisted of accessions mostly from diverse regions of Africa, N. America, Asia, the Caribbean, and S. America. However, the structuration was not related to the geographic origin and several admixtures were observed. The information generated in this study and phenotyping of this material for biotic and abiotic stress responses and yield quality traits will facilitate selection of trait-specific, genetically diverse parents for developing Valencia cultivars with a broad genetic base.

Last Modified: 9/10/2014
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