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Genome-Wide Association Analysis of Yield-Related Traits of Soybean Using Haplotype-Based Framework
* 1 , * 2 , 3 , 4, 5 , 2
1  Department of Agricultural Technology, Ekiti State College of Agriculture and Technology, Isan, Nigeria.
2  Soybean Research Institution, National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural Universi
3  Plant Molecular Science and Centre of Systems and Synthetic Biology, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
4  Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
5  State Agricultural Biotechnology Centre, Crop Research Innovation Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
Academic Editor: Carmen Arena


Haplotype-based breeding involving multi-marker association analysis is a promising approach to developing custom-designed high-yielding crop varieties. Here, we reported multi-marker association analysis for the number of pods per plant (PNP), the number of seeds per plant (SNP), 100-seed weight (HSW), and seed yield per plant (SYP) using 211 cultivated soybean accessions. The field experiment was conducted across six environments following a randomized complete block design with three replications. Genome-wide association study (GWAS) using 12,617 single-nucleotide polymorphism (SNP) markers from NJAU 355K SoySNP Array identified 57 significant marker associations with the studied traits across the six environments. Out of these, six markers that were consistently associated with the yield traits in two or more environments were considered stable and selected as the reference markers for building haplotype block/loci. The multi-marker association analysis within the haplotype-based framework revealed various allelic combinations regulating the phenotypic variations for the studied yield-related traits in soybean. These haplotype alleles may serve as genomic resources in breeding programmes aimed at improving the yield potential of soybean.

Keywords: GWAS; Haplotype analysis; SNP; Soybean; Yield-related traits