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Genetic Resources and Crop Evolution

, Volume 61, Issue 5, pp 965–977 | Cite as

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

  • Yogesh Kumar
  • Soon Jae Kwon
  • Clarice J. Coyne
  • Jinguo Hu
  • Michael A. Grusak
  • Theodore J. Kisha
  • Rebecca J. McGee
  • Ashutosh Sarker
Research Article

Abstract

The effective utilization of crop diversity held in genebanks depends on our knowledge of useful traits and available markers associated with the target traits. Target region amplification polymorphism (TRAP) was used to evaluate the genetic diversity and underlying relationships among 263 accessions of chickpea landraces maintained by the USDA-ARS Western Regional Plant Introduction Station in Pullman, WA, USA. Two-hundred sixty-two TRAP markers were amplified by eight primer combinations. Altogether, 110 (42 %) markers were polymorphic, the other 152 (58 %) displayed no variation. These polymorphic markers revealed important differences among the accessions, with an estimated, mean pair-wise genetic distance 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 geographic 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 the concentrations of protein and nine mineral elements in the seeds. Two MTAs were significant (p < 0.01) for concentrations of Ca and K, and three MTAs were significant for Cu and Ni concentrations. The results indicate that this population is useful for genome-wide association studies on other economic traits given the level of genetic diversity uncovered and the marker-trait associations in seed minerals discovered.

Keywords

Cicerarietinum Population structure Seed minerals Seed protein 

Notes

Acknowledgments

The research leading to these results has received funding from the National Agriculture Innovative Programme, Indian Council of Agricultural Research, New Delhi (India) and from the USDA, Agricultural Research Service through a Cool Season Food Legume Germplasm Evaluation Grant to MAG and CJC. Authors express their sincere thanks to the Western Regional Plant Introduction Station, United State Department of Agriculture-Agricultural Research Service, Washington State University, Pullman 99164, WA (USA) for providing all facilities for the research experiments we conducted and to Birsa Agricultural University, Ranchi, Jharkhand (India). The contents of this publication do not necessarily reflect the views or policies of the US Department of Agriculture, nor does mention of trade names, commercial products, or organizations imply endorsement by the US Government. The authors thank the anonymous reviewers for helpful suggestions for revising the manuscript.

Supplementary material

10722_2014_89_MOESM1_ESM.tif (5.7 mb)
Fig. S1 TRAP profile of selected germplasm with primer combination MIR156A + Sa12-700. Accessions were amplified from the bulked DNA of four random plants from 263 lines; M: IR Dye®700 Sizing Standard 50-700 bp from LI-COR Biosciences (Lincoln, NE, USA) (TIFF 5827 kb)
10722_2014_89_MOESM2_ESM.tif (8.5 mb)
Fig. S2 Dendogram and model-based population structure of 110 accessions based on TRAP marker polymorphisms where the populations presented are K = 3 and K = 6. Each accession is represented by a horizontal bar partitioned by color, with each color representing the estimated membership fraction (TIFF 8729 kb)
10722_2014_89_MOESM3_ESM.tif (121 kb)
Fig. S3 The results of the population genetic sub-structure analysis generated from eight pairs of TRAP primers and 110 accessions of the USDA single-plant core collection with seed nutrient concentrations data based on the Evanno method (Evanno et al. 2005). A) The average estimated log probability of the data for K = 1 to 10. B) Delta K, the rate of change of the log probability of the data with respect to the number of clusters. C) The absolute values of the rate of change of the likelihood distribution. D) The absolute value of the rate of change divided by the standard deviation of the original 20 simulations (TIFF 121 kb)
10722_2014_89_MOESM4_ESM.docx (64 kb)
Table S1 USDA chickpea single-plant derived accessions with other plant identifier and origin used in TRAP marker genetic diversity study (DOCX 65 kb)

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Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Yogesh Kumar
    • 1
  • Soon Jae Kwon
    • 6
  • Clarice J. Coyne
    • 2
  • Jinguo Hu
    • 2
  • Michael A. Grusak
    • 3
  • Theodore J. Kisha
    • 2
  • Rebecca J. McGee
    • 4
  • Ashutosh Sarker
    • 5
  1. 1.Central Rainfed Upland Research Station (Central Rice Research Institute, Cuttack)HazaribagIndia
  2. 2.USDA-ARS Western Regional Plant Introduction Station, Johnson HallWashington State UniversityPullmanUSA
  3. 3.USDA-ARS, Children’s Nutrition Research Center, Department of PediatricsBaylor College of MedicineHoustonUSA
  4. 4.USDA-ARS, Grain Legume Genetics and Physiology Research Unit, 305 Johnson HallWashington State UniversityPullmanUSA
  5. 5.South Asia Program (ICARDA)New DelhiIndia
  6. 6.Advanced Radiation Technology InstituteKorea Atomic Energy Research InstituteJeongeup, JeonbukKorea

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