Legume-wide comparative analysis of pod shatter locus PDH1 reveals phaseoloid specificity, high cowpea expression, and stress responsive genomic context

Pod dehiscence is a major source of yield loss in legumes, which is exacerbated by aridity. Disruptive mutations in Pod indehiscent 1 (PDH1), a pod sclerenchyma-specific lignin biosynthesis gene, has been linked to significant reductions in dehiscence in several legume species. We compared syntenic PDH1 regions across 12 legumes and two outgroups to uncover key historical evolutionary trends at this important locus. Our results clarified the extent to which PDH1 orthologs are present in legumes, showing the typical genomic context surrounding PDH1 has only arisen relatively recently in certain phaseoloid species (Vigna, Phaseolus, Glycine). The notable absence of PDH1 in Cajanus cajan may be a major contributor to its indehiscent phenotype compared with other phaseoloids. In addition, we identified a novel PDH1 ortholog in Vigna angularis and detected remarkable increases in PDH1 transcript abundance during Vigna unguiculata pod development. Investigation of the shared genomic context of PDH1 revealed it lies in a hotspot of transcription factors and signaling gene families that respond to abscisic acid and drought stress, which we hypothesize may be an additional factor influencing expression of PDH1 under specific environmental conditions. Our findings provide key insights into the evolutionary history of PDH1 and lay the foundation for optimizing the pod dehiscence role of PDH1 in major and understudied legume species.

Automated summary

Pod dehiscence is a major cause of yield loss in legumes, especially under arid conditions. This study investigates the evolution of the Pod indehiscent 1 (PDH1) gene in legumes and its role in controlling pod dehiscence. The results reveal the presence of PDH1 orthologs in certain legume species and the absence of PDH1 in Cajanus cajan, suggesting its contribution to indehiscence in this species. Additionally, the study identifies a novel PDH1 ortholog in Vigna angularis and highlights the potential influence of transcription factors and signaling gene families in regulating PDH1 expression under specific environmental conditions. These findings provide valuable insights into the evolutionary history of PDH1 and its potential application in optimizing pod dehiscence in legume crops.