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

Abstract

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.

Parallel selection of loss‐of‐function alleles of Pdh1 orthologous genes in warm‐season legumes for pod indehiscence and plasticity is related to precipitation

“…Similar results have been observed in the common bean (Parker et al ., 2020), another warm‐season legume. In addition, Pdh1 is significantly highly expressed in pods of the domesticated accessions of lima bean ( Phaseolus lunatus ) compared with wild accessions (Garcia et al ., 2021), and Pdh1 transcript is significantly increased during pod development in cowpea (Marsh et al ., 2023), implying a general role in the evolution of the Pdh1 orthologous genes in leguminous crops.…”

“…A glimpse on this presumption is from the work of Marsh et al . (2023), who used 12 legume species and found that the typical genomic background surrounding Pdh1 is only relatively recent in Vigna , Phaseolus , and Glycine . In our work, genome‐wide characterization, phylogenetic, microsynteny, and ancestral reconstruction analyses using 39 legume species revealed the unique occurrences of orthologous genes of Pdh1 in warm‐season legume crops, including in genera Glycine , Phaseolus , Vigna , Amphicarpaea , Macrotyloma , and Lablab .…”

Approaches to increase the validity of gene family identification using manual homology search tools

“…The BLAST tblastn tool can be used to search all frame translations of the genome sequence for regions of sequence identity using protein query sequences. This method was used in Fernandez-Pozo et al ( 2021 ) and in Marsh et al ( 2023 ) to extract gene hits within over 1 kbp flanking regions and predict ORFs using Augustus (Stanke et al 2006 ). Similar methods to predict ORFs were followed in Chen et al ( 2021 ) using the BLAST-Like Alignment Tool (BLAT) (Ward and Moreno-Hagelsieb 2014 ) to detect potential homologs, and in Ji et al ( 2021 ) using GeneWise (Birney et al 2004 ).…”

The Exceptionally Large Genomes of the Fabeae Tribe: Comparative Genomics and Applications in Abiotic and Biotic Stress Studies

“…Fundamental knowledge and molecular tools for breeding have been boosted on the legume tolerance against abiotic stresses after peas entered the genomic era with the pea Caméor genome sequenced. Diverse studies have been performed to better understand the legume tolerance mainly to drought [64][65][66][67][68] and heat [19,68,70] stresses but also to frost [73,74], cold [75], and salinity [78]. For drought, the pea cv.…”