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ORIGINAL RESEARCH article

Front. Plant Sci.
Sec. Functional and Applied Plant Genomics
Volume 15 - 2024 | doi: 10.3389/fpls.2024.1395938
This article is part of the Research Topic Genetics and Genomics of Emerging and Multifactorial Stresses Affecting Plant Survival and Associated Plant Microbiomes View all 8 articles

Genome Wide Association Mapping Identifies Novel SNPs for Root Nodulation and Agronomic Traits in Chickpea

Provisionally accepted
Chandana B S Chandana B S 1ROHIT MAHTO ROHIT MAHTO 1Rajesh K. Singh Rajesh K. Singh 1Aditi Bhandari Aditi Bhandari 2Gitanjali TANDON Gitanjali TANDON 3Kumar K. Singh Kumar K. Singh 4Sunita Kushwah Sunita Kushwah 5Gera R. Lavanya Gera R. Lavanya 6Mir A. Iquebal Mir A. Iquebal 3Neelu Jain Neelu Jain 1Himabindu Kudapa Himabindu Kudapa 2Hari D. Upadhyaya Hari D. Upadhyaya 7Aladdin Hamwieh Aladdin Hamwieh 8*Rajendra Kumar Rajendra Kumar 1*
  • 1 Indian Agricultural Research Institute (ICAR), New Delhi, National Capital Territory of Delhi, India
  • 2 International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India
  • 3 Indian Agricultural Statistics Research Institute, Indian Council of Agricultural Research (ICAR), New Delhi, National Capital Territory of Delhi, India
  • 4 Other, Samstipur, India
  • 5 Dr. Rajendra Prasad Central Agricultural University, Samastipur, India
  • 6 Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad, Uttar Pradesh, India
  • 7 Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia, United States
  • 8 The International Center for Agricultural Research in the Dry Areas (ICARDA), Cairo, Beni Suef, Egypt

The final, formatted version of the article will be published soon.

    The chickpea (Cicer arietinum L.) is well-known for having climate resilience and atmospheric nitrogen fixation ability. Global demand for nitrogenous fertilizer is predicted to increase by 1.4% annually and the loss of billions of dollars in farm profit has drawn attention to the need for alternative sources of nitrogen. The ability of chickpea to obtain sufficient nitrogen via its symbiotic relationship with Mesorhizozbium ciceri is of critical importance in determining the growth and production of chickpea. In order to support findings on nodule formation in chickpea and to map the genomic regions for nodulation, we evaluated an association panel consisting of 271 genotypes, selected from the global chickpea germplasm including 4 checks (BG 372, BG 3022, BG 547 and BG 1105) selected from theglobal chickpea germplasmat four locations (IARI, New Delhi; SHUATS, Naini, Prayagraj, UP; KVK Vaishali campus, RPCAU, Samastipur, Bihar and IARI regional station, Pusa, Bihar)and data was recorded for nodulation and yield related twelve traits.namely;days to 50 % flowering, plant height, number of pods per plant, number of seeds per plant, yield per plant, number of nodules per plant, nodules per plant, nodule fresh weight, root fresh weight, root dry weight, stem fresh weight, and stem dry weight.The Genome wide Wide Association Study (GWAS) was conducted using phenotypic data and genotypic data extracted e marker datafrom whole genome resequencing data of chickpea , withby creating a hap map file consisting of 602344 SNPs in the working set was used as a genotypic datawith best fit 2 models of association mapping. The GWAS panel was found to be structured with sufficient diversity among the linesgenotypes. Linkage disequilibrium (LD) analysis has shown LD decay value of 37.3 MB indicating SNPs within this distance to behave as inheritance block. A total of 450 and 632 stringent marker trait associations (MTAs) were identified from the BLINK and FarmCPU models, respectively, for all the traits under studyand among them,. The 75 novel MTAs identified for nodulation traits were found to be stableand all the identified nodulation traits MTAs were novel.

    Keywords: Association mapping, chickpea, GWAS, Nitrogen Fixation, nodulation, PVE

    Received: 04 Mar 2024; Accepted: 09 Sep 2024.

    Copyright: © 2024 B S, MAHTO, Singh, Bhandari, TANDON, Singh, Kushwah, Lavanya, Iquebal, Jain, Kudapa, Upadhyaya, Hamwieh and Kumar. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence:
    Aladdin Hamwieh, The International Center for Agricultural Research in the Dry Areas (ICARDA), Cairo, Beni Suef, Egypt
    Rajendra Kumar, Indian Agricultural Research Institute (ICAR), New Delhi, 110 012, National Capital Territory of Delhi, India

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