Genotyping-by-Sequencing Based Genetic Mapping Identified Major and Consistent Genomic Regions for Productivity and Quality Traits in Peanut

    Jadhav, M P and Gangurde, S S and Hake, A A and Yadawad, A and Mahadevaiah, S S and Pattanashetti, S K and Gowda, M V C and Shirasawa, K and Varshney, R K and Pandey, M K and Bhat, R S (2021) Genotyping-by-Sequencing Based Genetic Mapping Identified Major and Consistent Genomic Regions for Productivity and Quality Traits in Peanut. Frontiers in Plant Science (TSI), 12. pp. 1-15. ISSN 1664-462X

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    Abstract

    With an objective of identifying the genomic regions for productivity and quality traits in peanut, a recombinant inbred line (RIL) population developed from an elite variety, TMV 2 and its ethyl methane sulfonate (EMS)-derived mutant was phenotyped over six seasons and genotyped with genotyping-by-sequencing (GBS), Arachis hypogaea transposable element (AhTE) and simple sequence repeats (SSR) markers. The genetic map with 700 markers spanning 2,438.1 cM was employed for quantitative trait loci (QTL) analysis which identified a total of 47 main-effect QTLs for the productivity and oil quality traits with the phenotypic variance explained (PVE) of 10–52% over the seasons. A common QTL region (46.7–50.1 cM) on Ah02 was identified for the multiple traits, such as a number of pods per plant (NPPP), pod weight per plant (PWPP), shelling percentage (SP), and test weight (TW). Similarly, a QTL (7.1–18.0 cM) on Ah16 was identified for both SP and protein content (PC). Epistatic QTL (epiQTL) analysis revealed intra- and inter-chromosomal interactions for the main-effect QTLs and other genomic regions governing these productivity traits. The markers identified by a single marker analysis (SMA) mapped to the QTL regions for most of the traits. Among the five potential candidate genes identified for PC, SP and oil quality, two genes (Arahy.7A57YA and Arahy.CH9B83) were affected by AhMITE1 transposition, and three genes (Arahy.J5SZ1I, Arahy.MZJT69, and Arahy.X7PJ8H) involved functional single nucleotide polymorphisms (SNPs). With major and consistent effects, the genomic regions, candidate genes, and the associated markers identified in this study would provide an opportunity for gene cloning and genomics-assisted breeding for increasing the productivity and enhancing the quality of peanut.

    Item Type: Article
    Divisions: Center of Excellence in Genomics and Systems Biology
    CRP: UNSPECIFIED
    Uncontrolled Keywords: peanut, productivity and quality traits, GBS, transposable elements, SSRs, main and epistatic QTL, QTL validation
    Subjects: Mandate crops > Groundnut
    Others > Genetics and Genomics
    Depositing User: Mr Nagaraju T
    Date Deposited: 10 Jan 2025 03:47
    Last Modified: 10 Jan 2025 03:47
    URI: http://oar.icrisat.org/id/eprint/12898
    Official URL: https://www.frontiersin.org/journals/plant-science...
    Projects: UNSPECIFIED
    Funders: National Agricultural Science Fund (NASF) of Indian Council of Agricultural Research, India
    Acknowledgement: The authors are thankful to the National Agricultural Science Fund (NASF) of the Indian Council of Agricultural Research, India for the financial support provided to GBS. MJ acknowledges the Senior Research Fellowship received from the Council of Scientific and Industrial Research (CSIR), Government of India.
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