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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: Target region amplification polymorphism (TRAP) for assessing genetic diversity and marker-trait associations in chickpea (Cicer arietinum l.) germplasm

Authors
item Kumar, Yogesh -
item Kwon, Soon
item Coyne, Clarice
item Hu, Jinguo
item Grusak, Michael
item Kisha, Theodore
item McGee, Rebecca
item Sarker, Ashutosh -

Submitted to: Genetic Resources and Crop Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 13, 2014
Publication Date: March 20, 2014
Citation: Kumar, Y., Kwon, S.J., Coyne, C.J., Hu, J., Grusak, M.A., Kisha, T.J., Mcgee, R.J., Sarker, A. 2014. Target region amplification polymorphism (TRAP) for assessing genetic diversity and marker-trait associations in chickpea (Cicer arietinum l.) germplasm. Genetic Resources and Crop Evolution. DOI: 10.1007/s10722-014-0089-2.

Interpretive Summary: Chickpea (garbonzo bean) is an economically important crop as it is the third most important pulse crop in the world after common bean and pea. Chickpea provides a protein-rich supplement to cereal-based diets - its seeds contain 23% protein, 64% carbohydrates, 47% starch, 5% fat, 6% crude fiber, 6% soluble sugar and 3% ash. Chickpea crops restore and maintain soil fertility by biological nitrogen fixation and are an integral part of many cereal-based cropping systems. Information on the genetic diversity of the crop and its wild relatives can provide information regarding sources of useful alleles for plant reeders. Knowledge of the genetic diversity and the relationships among conserved germplasm collections of a crop is essential for establishing, managing and ensuring the long-term success of crop improvement programs. We report here on the genetic diversity of the USDA chickpea core collection and the discovery of DNA marker to economic trait associations.

Technical Abstract: Utilization of crop diversity held in genebanks is dependent on knowledge of useful traits including those identified genotypically. Target region amplification polymorphism (TRAP) markers were used to evaluate the genetic diversity and relationship among a sample of 263 chickpea landrace germplasm accessions maintained at USDA-ARS, Pullman, WA. Two-hundred sixty-two TRAP markers were amplified by eight primer combinations. Altogether, 110 (42%) markers were polymorphic, while 152 (58%) presented as monomorphic. The high level of polymorphism was revealed among the accessions with an estimated pair-wise genetic similarity of 25.82%, ranging from 2.8 to 50.0%. Genetic distance analysis divided the accessions into two major groups with 113 and 150 accessions each and substantial association between molecular diversity and origin was evident. Bayesian analysis of population structure revealed two groups (K = 2) with evidence for six sub-groups. Additionally, the population structure of a subset of 110 lines was determined (K = 3) for testing marker-trait associations (MTAs). Phenotypic traits included seed concentrations for protein and nine mineral elements. Two MTAs were significant (p <0.01) for seed concentrations of the macrominerals Ca and K and three MTAs were significant for the microminerals Cu and Ni seed concentrations using three statistical models. The results indicate that this will be a useful population for genome-wide association studies.

Last Modified: 12/22/2014
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