Integrating QTL mapping and transcriptome analysis to provide molecular insights into gynophore-pod strength in cultivated peanut (Arachis hypogaea L.)

Both genotypic factor and environments affected gynophore-pod strength significantly, and its broad sense heritability (<i>h²</i> ) was estimated as 0.77. Two QTLs that were stable in at least two environments were detected. <i>qGPS.A05-1</i> was mapped 4cM (about 1.09Mb) on chromosome A05, and <i>qGPS.B02-1</i> was mapped 3cM (about 1.71Mb) on chromosome B02. Anatomical analysis showed higher lignin content in lines with extreme high gynophore-pod strength compared to those with extreme low gynophore-pod strength. Additionally, comparative transcriptome analysis unveiled that phenylpropanoid biosynthesis was the main pathway associated with high gynophore-pod strength. Further, we predicted <i>VJ8B3Q</i> and <i>H82QG0</i> as the candidate genes for <i>qGPS.A05-1</i> and <i>qGPS.B02-1</i>, respectively. The two stable QTLs and their associated markers could help modify gynophore-pod strength. Our findings may offer genetic resources for the molecular-assisted breeding of new peanut varieties with improved mechanized harvesting quality.