Genome sequencing and de novo assembly elucidate the genetic basis of grain quality and fragrance in heirloom rice cultivar Mushk Budji
5 affiliations
- 1Division of Genetics & Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir
- 2Mountain Research Centre for Field Crops, Sher-e Kashmir University of Agricultural Sciences and Technology of Kashmir
- 3Division of Biotechnology, Sher-e Kashmir University of Agricultural Sciences and Technology of Kashmir
- 4Division of Food Science and Technology, Sher-e Kashmir University of Agricultural Sciences and Technology of Kashmir
- 5Division of Agronomy, Sher-e Kashmir University of Agricultural Sciences and Technology of Kashmir
Abstract
Background: Mushk Budji is a premium, GI-tagged, heritage rice landrace of Kashmir valley, J&K, India, distinguished by its short-bold grains, strong aroma, and soft texture. While its morphological and biochemical traits have been documented, no dedicated genomic resource has previously been available. Here we report a de novo genome assembly of Mushk Budji with adequate depth.
Methods: We first-time performed reference guided whole-genome sequencing of Mushk Budji using the Illumina NovaSeq 6000 platform, generating 64.97 Gb of raw data. The genome assembly was achieved using SPAdes and scaffolded using RagTag against the Nipponbare reference. Structural and functional annotations were conducted with AUGUSTUS and curated across NCBI, UniProt, and KEGG databases. The haplotype analysis was performed for loci related to quality using a set of contrasting genotypes.
Results and discussion: The final assembly comprised 378.29 Mb with an N50 of 29.24 Mb and 97.0% BUSCO completeness. A total of 43,434 non-redundant protein-coding genes were identified, with significant enrichment in pathways related to aroma (2-acetyl-1-pyrroline) and starch biosynthesis. Allelic profiling confirmed the characteristic 8-bp deletion in Badh2 , conferring fragrance, alongside additional genes shaping quality and adaptability. Unique haplotypes at SSI and RAmy1A , resembling those of temperate japonica variety Koshihikari, were associated with distinct soft and cohesive cooked texture of Mushk Budji . Comparative analyses revealed evolutionary divergence from canonical japonica references at specific loci. Selective signature analyses revealed contrasting evolutionary patterns among major quality genes. SSI showed evidence of balancing selection, whereas GS3 and Badh2 exhibited signatures of strong human-mediated selection, reflecting the historical preference for desirable grain quality and fragrance traits. Genes controlling amylose content and cooking quality ( Wx and Alk ) were under moderate purifying selection, indicating functional optimization.
Conclusion: The genomics resource generated in the present study establishes Mushk Budji as a distinct temperate japonica landrace with unique allelic combinations underpinning its aroma, texture and adaptability. The dataset provides a foundation for conservation, breeding and functional genomics, ensuring the sustainable utilization of this heritage rice.
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BibTeX
@article{khan2026genome,
title = {{Genome sequencing and de novo assembly elucidate the genetic basis of grain quality and fragrance in heirloom rice cultivar Mushk Budji}},
author = {Raheel Shafeeq Khan and Noor-ul-Ain and V. Shasi Kiran Reddy and Ishrat Rafiq and Gazala H. Khan and Fayaz Mohiddin and Sajad M. Zargar and Syed Zameer Hussain and Bashir A. Alie and Najeeb-ul-Rehman Sofi and Asif Bashir Shikari},
journal = {Frontiers in Plant Science},
year = {2026},
month = oct,
doi = {10.3389/fpls.2026.1896265},
url = {https://www.frontiersin.org/articles/10.3389/fpls.2026.1896265/full},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Genome sequencing and de novo assembly elucidate the genetic basis of grain quality and fragrance in heirloom rice cultivar Mushk Budji
AU - Raheel Shafeeq Khan
AU - Noor-ul-Ain
AU - V. Shasi Kiran Reddy
AU - Ishrat Rafiq
AU - Gazala H. Khan
AU - Fayaz Mohiddin
AU - Sajad M. Zargar
AU - Syed Zameer Hussain
AU - Bashir A. Alie
AU - Najeeb-ul-Rehman Sofi
AU - Asif Bashir Shikari
PY - 2026
DA - 2026/10/14
JO - Frontiers in Plant Science
DO - 10.3389/fpls.2026.1896265
UR - https://www.frontiersin.org/articles/10.3389/fpls.2026.1896265/full
AB - Background: Mushk Budji is a premium, GI-tagged, heritage rice landrace of Kashmir valley, J&K, India, distinguished by its short-bold grains, strong aroma, and soft texture. While its morphological and biochemical traits have been documented, no dedicated genomic resource has previously been available. Here we report a de novo genome assembly of Mushk Budji with adequate depth. Methods: We first-time performed reference guided whole-genome sequencing of Mushk Budji using the Illumina NovaSeq 6000 platform, generating 64.97 Gb of raw data. The genome assembly was achieved using SPAdes and scaffolded using RagTag against the Nipponbare reference. Structural and functional annotations were conducted with AUGUSTUS and curated across NCBI, UniProt, and KEGG databases. The haplotype analysis was performed for loci related to quality using a set of contrasting genotypes. Results and discussion: The final assembly comprised 378.29 Mb with an N50 of 29.24 Mb and 97.0% BUSCO completeness. A total of 43,434 non-redundant protein-coding genes were identified, with significant enrichment in pathways related to aroma (2-acetyl-1-pyrroline) and starch biosynthesis. Allelic profiling confirmed the characteristic 8-bp deletion in Badh2 , conferring fragrance, alongside additional genes shaping quality and adaptability. Unique haplotypes at SSI and RAmy1A , resembling those of temperate japonica variety Koshihikari, were associated with distinct soft and cohesive cooked texture of Mushk Budji . Comparative analyses revealed evolutionary divergence from canonical japonica references at specific loci. Selective signature analyses revealed contrasting evolutionary patterns among major quality genes. SSI showed evidence of balancing selection, whereas GS3 and Badh2 exhibited signatures of strong human-mediated selection, reflecting the historical preference for desirable grain quality and fragrance traits. Genes controlling amylose content and cooking quality ( Wx and Alk ) were under moderate purifying selection, indicating functional optimization. Conclusion: The genomics resource generated in the present study establishes Mushk Budji as a distinct temperate japonica landrace with unique allelic combinations underpinning its aroma, texture and adaptability. The dataset provides a foundation for conservation, breeding and functional genomics, ensuring the sustainable utilization of this heritage rice.
SN - 1664-462X
ER -