Molecular Genetics and Genomics

, Volume 294, Issue 1, pp 57–68 | Cite as

Development of sequence-based markers for seed protein content in pigeonpea

  • Jimmy Obala
  • Rachit K. Saxena
  • Vikas K. Singh
  • C. V. Sameer Kumar
  • K. B. Saxena
  • Pangirayi Tongoona
  • Julia Sibiya
  • Rajeev K. VarshneyEmail author
Original Article


Pigeonpea is an important source of dietary protein to over a billion people globally, but genetic enhancement of seed protein content (SPC) in the crop has received limited attention for a long time. Use of genomics-assisted breeding would facilitate accelerating genetic gain for SPC. However, neither genetic markers nor genes associated with this important trait have been identified in this crop. Therefore, the present study exploited whole genome re-sequencing (WGRS) data of four pigeonpea genotypes (~ 12X coverage) to identify sequence-based markers and associated candidate genes for SPC. By combining a common variant filtering strategy on available WGRS data with knowledge of gene functions in relation to SPC, 108 sequence variants from 57 genes were identified. These genes were assigned to 19 GO molecular function categories with 56% belonging to only two categories. Furthermore, Sanger sequencing confirmed presence of 75.4% of the variants in 37 genes. Out of 30 sequence variants converted into CAPS/dCAPS markers, 17 showed high level of polymorphism between low and high SPC genotypes. Assay of 16 of the polymorphic CAPS/dCAPS markers on an F2 population of the cross ICP 5529 (high SPC) × ICP 11605 (low SPC), resulted in four of the CAPS/dCAPS markers significantly (P < 0.05) co-segregated with SPC. In summary, four markers derived from mutations in four genes will be useful for enhancing/regulating SPC in pigeonpea crop improvement programs.


Seed protein content Cajanus cajan Whole-genome resequencing Next generation sequencing Sequence variants Common variant analysis 



Authors are thankful to the United States Agency for International Development (USAID) and ICRISAT for funding various projects related to pigeonpea genomics at ICRISAT. We also thank Mr. Aamir Khan (ICRISAT) for his help in processing the WGRS data and Ms. Anu Chitikineni (ICRISAT) for coordinating Sanger sequencing and primer ordering. This work has been undertaken as part of the CGIAR Research Program on Grain Legumes and Dryland Cereals. ICRISAT is a member of CGIAR Consortium.

Compliance with ethical standards

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Conflict of interest

Jimmy Obala declares that he has no conflict of interest. Rachit K. Saxena declares that he has no conflict of interest. Vikas K. Singh declares that he has no conflict of interest, C.V. Sameer Kumar declares that he has no conflict of interest. K.B. Saxena declares that he has no conflict of interest, Pangirayi Tongoona declares that he has no conflict of interest. Julia Sibiya declares that she has no conflict of interest. Rajeev K. Varshney declares that he has no conflict of interest.

Data availability statement

All data generated or analysed during this study are included in this published article and its supplementary information files.

Supplementary material

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Jimmy Obala
    • 1
    • 2
  • Rachit K. Saxena
    • 1
  • Vikas K. Singh
    • 1
  • C. V. Sameer Kumar
    • 1
  • K. B. Saxena
    • 1
  • Pangirayi Tongoona
    • 2
  • Julia Sibiya
    • 2
  • Rajeev K. Varshney
    • 1
    Email author
  1. 1.International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)HyderabadIndia
  2. 2.University of KwaZulu-Natal, African Center for Crop ImprovementPietermaritzburgSouth Africa

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