Pod Dehiscence in Soybean: Genome Wide Association Study and Genomic Prediction

Shynar Mazkirat, Kulpash Bulatova, Svetlana Didorenko, Sholpan O. Bastaubayeva, D. I. Babissekova, Sholpan Khalbayeva, Azamat Tukenov, Akzhan Yespembetova, Nurgul Saparbayeva, Yuri N. Shavrukov

2025

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DOI 10.3390/plants14223505
Data confidence 70 medium
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Abstract

Pod dehiscence is one of the main factors which play a vital role on the final yield of many crops including soybean and, therefore, it is important to elucidate genetic mechanisms associated with this trait. In this study, morphological, physiological and biochemical analysis was conducted for pod and pod-related traits on 170 soybean genotypes with diverse origins. Subsequently, a genome-wide association study (GWAS) was performed using Silico-DArT and DArT SNPs markers. In total, 48 QTLs were identified with 14 stable QTLs, mostly located on chromosomes 6, 13 and 16, corresponding to pod dehiscence and pod-related traits. From putative candidate genes, two most stable and important genes for pod dehiscence with known functions were emphasised from the QTLs: Glyma.13G184500 and Glyma.16G141100, encoding transcription factors DNA-binding bromodomain-containing protein and C2H2 zinc finger protein, respectively. Finally, a genomic prediction approach was implemented to select genotypes most resistant to pod dehiscence. GWAS-derived markers confirmed the stable prediction of pod dehiscence in studied accessions from different populations and the best non-dehiscent soybean genotypes were successfully selected.