Genome-Wide Association Study and Candidate Gene Mining for First Pod Height in Soybean

First pod height (FPH) is a critical agronomic trait in soybean because it directly affects mechanized harvesting efficiency and harvestable yield. Pods below the cutter-bar height are left uncollected, leading to direct seed loss. However, the genetic architecture underlying FPH remains largely underexplored. Here, we conducted a genome-wide association study (GWAS) on FPH data using 386 soybean accessions evaluated across three environments, together with best linear unbiased prediction (BLUP) values. Phenotypic analysis showed that cultivated soybean exhibited significantly greater FPH than wild accessions, consistent with selection for improved harvestability during domestication. Using two GWAS methods, RTM-GWAS and EMMAX, we identified seven stable (detected by the same method at least three times) quantitative trait nucleotides/loci (QTNs/QTLs) significantly associated with FPH. By integrating sequence variation, gene expression, and functional description, we identified GmAIR9 (corresponding to Glyma.09G084300/SoyZH13_09G078900), which encodes a microtubule-associated protein preferentially expressed in stems, as a candidate gene for further investigation. Haplotype analysis of GmAIR9 revealed that haplotype H3 was associated with low FPH and was detected exclusively in wild soybean accessions, whereas haplotype H1 was associated with increased FPH. Moreover, the frequency of H1 increased from 50.00% in wild soybeans to 71.03% in landraces and 83.47% in improved cultivars. These findings provide valuable genetic resources and promising candidate loci for future validation and breeding applications to optimize FPH and improve the suitability of soybean cultivars for mechanized harvesting.