Whole-genome meta-analysis coupled with haplotype analysis reveal new genes and functional haplotypes conferring pre-harvest sprouting in rice.

Semiu Folaniyi Bello, Xiaohai Tian, Xianjin Qiu, Danielle Ama Essandoh, Juliet Nkiruku Anyanwu, Patrick Maada Ngegba, Abdul Razak Ahmed, Akwasi Yeboah, Selorm Akaba, Guoli Wang, Daniel Bimpong, Mawuli Korsi Amenyogbe, Benjamin Karikari, Hong Guo, Tianyue An, Kelvin Dodzi Aloryi, Nabieu Kamara, Nnaemeka Emmanuel Okpala

Journal: BMC plant biology 2025;25(1):527

PMID: 40275165

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Abstract

BACKGROUND

Pre-harvest sprouting (PHS), which adversely impacts grain yield and quality, is controlled by seed dormancy genes. However, only a few dormancy-related genes have been characterized, and the effects of allelic variation in genes and the genetic basis of seed dormancy in rice remain largely unknown. Here, we performed a whole-genome meta-quantitative trait loci study to elucidate the genetic basis of seed dormancy in rice.

RESULT

One hundred and sixty-seven QTL were identified for PHS from which 134 were successfully projected onto the reference map yielding 20 consensus regions, meta-QTL (mQTL). The mean confidence interval of the mQTL was narrower (9.56-fold reduction) than that of the initial QTL. Six of the 20 identified mQTL were designated as breeders' mQTL based on their small confidence intervals, large phenotypic variance explained, and the involvement of high number of QTL. Further, we retrieved 559 high-confidence genes from breeders' mQTL regions conferring resistance to PHS. Comparative analysis of genes found in breeders' mQTL loci and an RNA-seq-based transcriptomic dataset discovered 34 common genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed a significant enrichment of the common genes in amino sugar and nucleotide sugar metabolism, carbon metabolism, and carbon fixation in photosynthetic organs. Combined in silico expression profiling and qRT-PCR validation showed that LOC_Os10g18364, LOC_Os10g21940, LOC_Os10g22590, and LOC_Os10g25140 exhibited high fold-change expression in PHS resistant cultivar (23xS-261) than PHS susceptible cultivar (23xS-262). Association analysis of these genes with germination rate index demonstrated that LOC_Os10g18364, LOC_Os10g21940, LOC_Os10g22590, and LOC_Os10g25140 exhibited low germination rate (GR) in cultivars carrying these haplotypes.

CONCLUSION

In summary, this study delineates the genetic basis of PHS and provides a new set of target genes for improving PHS resistance. The natural variants identified in these genes and markers associated with breeders' mQTL serve as potential resources for incorporating PHS resistance in rice.

Address: Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Binzhou Medical University, Yantai, 264003, China.; Horticultural Science Department, University of Florida, Gainesville, FL, 32611, USA.; Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Binzhou Medical University, Yantai, 264003, China.; Hubei Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China.; Département de phytologie, Université Laval, Québec, QC, Canada.; Department of Agricultural Biotechnology, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, Tamale, Ghana.; Zhejiang Industry Polytechnic College, Shaoxing, China.; Agriculture Research Group, Organization of African Academic Doctors (OAAD), P. O. Box 25305-00100, Langata, Nairobi, Kenya.; School of Agriculture, University of Cape Coast, Cape Coast, Ghana.; Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32603, USA.; Department of Plant Protection, Akdeniz University Dumlupinar Bulvari, Antalya, 07058, Türkiye.; Sierra Leone Agricultural Research Institute, P.M.B 1313, Tower Hill, Freetown, 47235, Sierra Leone.; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.; Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, 30602, USA.; Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Binzhou Medical University, Yantai, 264003, China. [email protected].

DOI: 10.1186/s12870-025-06551-5

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MeSH Terms: Oryza, Quantitative Trait Loci, Haplotypes, Genome, Plant, Genes, Plant, Plant Dormancy, Germination