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Abstract <p>Prolificacy (multiple ears per plant) is crucial to improve the yield of baby corn and understanding its genetics would help in effectively implementing the breeding program. Here, we conducted Meta-QTL (M-QTL) analysis for prolificacy using 93 known QTL from 17 previous studies. A set of 32 M-QTL located on nine chromosomes were identified with a maximum of eight M-QTL on chromosome-1. Reduction in the confidence interval of these M-QTL (mean − 17.39&#xa0;cM; range − 2.83 to 51&#xa0;cM) over the original QTL (mean − 38.06&#xa0;cM, range 1.6 to 149&#xa0;cM) was observed. Further, these 32 M-QTLs were also analyzed for genomic variants specific to ‘Sikkim Primitive’—a prolific landrace from North-Eastern Himalayan region of India for functional prediction. A total of 358 high-impact mutations within M-QTL were identified among 200 genes. Gene ontology (GO) of all these 200 genes predicted their presence in the nuclear lumen (GO: 0031981) and chloroplast stroma (GO: 0009570). We also identified 14 candidate genes having high-impact mutations and differential expression among shoot and root tissues. These candidates were specific to SPX domain-containing membrane protein8 (<i>Zm00001eb073510</i>), ATP-Binding Cassette (ABC) domain-containing transporter proteins (<i>Zm00001eb065150</i> and <i>Zm00001eb230180</i>), terpene synthase protein (<i>Zm00001eb230440</i>), protein kinase (<i>Zm00001eb086660</i>), NADB Rossmann super family dehydrogenase (<i>Zm00001eb090210</i>) and Jacalin-like lectin domain containing sugar-binding protein (<i>Zm00001eb362900</i>). Identifying consensus genomic regions and candidate genes assume great significance for their utilization in molecular breeding for prolificacy. This is the first report on M-QTL analysis for the identification of candidate genes governing prolificacy in maize.</p> Key Message <p> Meta-QTL analysis identified novel genes such as SPX membrane protein, ABC transporter, terpene synthase, protein kinase, dehydrogenase, and sugar-binding protein governing prolificacy in Sikkim Primitive maize.</p>

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Meta-QTL Analysis Explores Key Candidate Gene(s) for Ear Prolificacy in ‘Sikkim Primitive’: A Unique Maize Landrace of North Eastern Himalaya

  • 期刊论文

  • 发表日期：

    2025年9月23日

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  • Nitish Ranjan Prakash,
  • Rajkumar Uttamrao Zunjare,
  • Kuldeep Kumar,
  • Sanchika Snehi,
  • Vignesh Muthusamy,
  • Firoz Hossain

摘要

Abstract

Prolificacy (multiple ears per plant) is crucial to improve the yield of baby corn and understanding its genetics would help in effectively implementing the breeding program. Here, we conducted Meta-QTL (M-QTL) analysis for prolificacy using 93 known QTL from 17 previous studies. A set of 32 M-QTL located on nine chromosomes were identified with a maximum of eight M-QTL on chromosome-1. Reduction in the confidence interval of these M-QTL (mean − 17.39 cM; range − 2.83 to 51 cM) over the original QTL (mean − 38.06 cM, range 1.6 to 149 cM) was observed. Further, these 32 M-QTLs were also analyzed for genomic variants specific to ‘Sikkim Primitive’—a prolific landrace from North-Eastern Himalayan region of India for functional prediction. A total of 358 high-impact mutations within M-QTL were identified among 200 genes. Gene ontology (GO) of all these 200 genes predicted their presence in the nuclear lumen (GO: 0031981) and chloroplast stroma (GO: 0009570). We also identified 14 candidate genes having high-impact mutations and differential expression among shoot and root tissues. These candidates were specific to SPX domain-containing membrane protein8 (Zm00001eb073510), ATP-Binding Cassette (ABC) domain-containing transporter proteins (Zm00001eb065150 and Zm00001eb230180), terpene synthase protein (Zm00001eb230440), protein kinase (Zm00001eb086660), NADB Rossmann super family dehydrogenase (Zm00001eb090210) and Jacalin-like lectin domain containing sugar-binding protein (Zm00001eb362900). Identifying consensus genomic regions and candidate genes assume great significance for their utilization in molecular breeding for prolificacy. This is the first report on M-QTL analysis for the identification of candidate genes governing prolificacy in maize.

Key Message

Meta-QTL analysis identified novel genes such as SPX membrane protein, ABC transporter, terpene synthase, protein kinase, dehydrogenase, and sugar-binding protein governing prolificacy in Sikkim Primitive maize.