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Unique genetic architecture of prolificacy in ‘Sikkim Primitive’ maize unraveled through whole-genome resequencing-based DNA polymorphism

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Abstract

Key message

‘Sikkim Primitive’ maize landrace, unique for prolificacy (7–9 ears per plant) possesses unique genomic architecture in branching and inflorescence-related gene(s), and locus Zm00001eb365210 encoding glycosyltransferases was identified as the putative candidate gene underlying QTL (qProl-SP-8.05) for prolificacy. The genotype possesses immense usage in breeding high-yielding baby-corn genotypes.

Abstract

‘Sikkim Primitive’ is a native landrace of North Eastern Himalayas, and is characterized by having 7–9 ears per plant compared to 1–2 ears in normal maize. Though ‘Sikkim Primitive’ was identified in the 1960s, it has not been characterized at a whole-genome scale. Here, we sequenced the entire genome of an inbred (MGUSP101) derived from ‘Sikkim Primitive’ along with three non-prolific (HKI1128, UMI1200, and HKI1105) and three prolific (CM150Q, CM151Q and HKI323) inbreds. A total of 942,417 SNPs, 24,160 insertions, and 27,600 deletions were identified in ‘Sikkim Primitive’. The gene-specific functional mutations in ‘Sikkim Primitive’ were classified as 10,847 missense (54.36%), 402 non-sense (2.015%), and 8,705 silent (43.625%) mutations. The number of transitions and transversions specific to ‘Sikkim Primitive’ were 666,021 and 279,950, respectively. Among all base changes, (G to A) was the most frequent (215,772), while (C to G) was the rarest (22,520). Polygalacturonate 4-α-galacturonosyltransferase enzyme involved in pectin biosynthesis, cell-wall organization, nucleotide sugar, and amino-sugar metabolism was found to have unique alleles in ‘Sikkim Primitive’. The analysis further revealed the Zm00001eb365210 gene encoding glycosyltransferases as the putative candidate underlying QTL (qProl-SP-8.05) for prolificacy in ‘Sikkim Primitive’. High-impact nucleotide variations were found in ramosa3 (Zm00001eb327910) and zeaxanthin epoxidase1 (Zm00001eb081460) genes having a role in branching and inflorescence development in ‘Sikkim Primitive’. The information generated unraveled the genetic architecture and identified key genes/alleles unique to the ‘Sikkim Primitive’ genome. This is the first report of whole-genome characterization of the ‘Sikkim Primitive’ landrace unique for its high prolificacy.

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Data availability

The datasets generated during and/or analyzed during the current study are available in the NCBI Sequence Read Archives (SRA) repository with BioProject number PRJNA1078761.

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Acknowledgements

We acknowledge the financial support received from the World Bank-Indian Council of Agricultural Research funded National Agricultural Higher Education Project (NAHEP) through its Centre for Advanced Agricultural Science and Technology (CAAST) on Genomics Assisted Breeding for Crop Improvement to ICAR-IARI, New Delhi (NAHEP-CAAST 71-01). The first author grateful to Council of Scientific and Industrial Research (CSIR-India) for a fellowship (09/083(0368)/2016-EMR-I) offered during the Ph.D. programme. We also acknowledge the breeders of AICRP-Maize for sharing their inbred for analysis. Our sincere thanks to Dr. B.M. Prasanna for the collection of Sikkim Primitive (landrace) from Sikkim.

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  1. Nitish Ranjan Prakash

    Present address: ICAR-Central Soil Salinity Research Institute, Karnal, Haryana, 132001, India

Authors and Affiliations

  1. ICAR-Indian Agricultural Research Institute, New Delhi, Delhi, 110012, India

    Nitish Ranjan Prakash, Vignesh Muthusamy, Rajkumar Uttamrao Zunjare & Firoz Hossain

  2. ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, Delhi, 110012, India

    Kuldeep Kumar

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Contributions

Conduct of the experiment: NRP, data handling and analysis: KK, candidate gene analysis: VM and RUZ, drafting of manuscript: NRP and FH, designing of experiment: FH.

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Correspondence to Firoz Hossain.

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Prakash, N.R., Kumar, K., Muthusamy, V. et al. Unique genetic architecture of prolificacy in ‘Sikkim Primitive’ maize unraveled through whole-genome resequencing-based DNA polymorphism. Plant Cell Rep 43, 134 (2024). https://doi.org/10.1007/s00299-024-03176-0

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