Genotype; Polymorphism, Single Nucleotide; Phenotype; Chromosome Mapping; Quantitative Trait Loci; Polyploidy; Genome-Wide Association Study/methods; Saccharum/genetics; Genome, Plant/genetics; Genome, Plant; Genome-Wide Association Study; Saccharum; Genetics
Abstract :
[en] Genome-wide association studies in complex polyploids are hindered by genotyping ambiguity and allele dosage complexity. Here we present KMERIA, a k-mer-based framework specifically designed to address these challenges, enabling efficient genotyping and robust association mapping in complex polyploid genomes. Rigorous benchmarking with simulated and empirical datasets demonstrates that KMERIA surpasses existing methods in accuracy and statistical power. By applying KMERIA to 290 wild sugarcane (Saccharum spontaneum) accessions and integrating a 15-accession graph pangenome to capture structural variations, we identified new genes regulating sucrose biosynthesis (SsMGT) and tillering (for example, SsERF14, SsNGA5, SsNAC, SsARF8, SsLOG and SsSCR). These findings elucidate the genetic architecture of yield-related traits and provide actionable targets for sugarcane breeding. Collectively, KMERIA bridges a critical methodological gap in polyploid genomics, while our graph-pangenome integration provides a powerful framework for deciphering genotype-phenotype relationships in crops with complex architectures.
Disciplines :
Genetics & genetic processes
Author, co-author :
Chen, Shuai ; State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
Liu, Xinlong; State Key Laboratory for Tropical Crop Breeding, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, China
Qu, Shenyang; State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
Song, Yuhan ; Université de Liège - ULiège > TERRA Research Centre > Plant Sciences ; State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
Chai, Kun; State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
Liu, Hongbo; State Key Laboratory for Tropical Crop Breeding, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, China
Zhang, Yuebin; State Key Laboratory for Tropical Crop Breeding, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, China
Xia, Zhongqiang ; State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
Li, Xiaofeng ; State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
Wang, Jungang; State Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Sanya, China
Zhang, Muqing ; Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, China
Li, Hongbo; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
Chen, Guo-Bo ; Center for Laboratory Medicine, Department of Genetic and Genomic Medicine, and Clinical Research Institute, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
Maliepaard, Chris ; Plant Breeding, Wageningen University and Research, Wageningen, the Netherlands
Zhang, Xingtan ; State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China. zhangxingtan@caas.cn
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