Title: “Orphan genes are involved in drought adaptations and ecoclimatic-oriented selections in domesticated cowpea”




Dr Xu Pei



Research Fellow,
Institute of Vegetables
Zhejiang Academy of Agricultural Sciences

Dr. Pei Xu, a professor and cowpea/bottle gourd breeder at Zhejiang Academy of Agricultural Sciences in Hangzhou, received his PhD from Nanjing Agricultural University, China, in 2008. In 2010 and 2012, he worked as a visiting scientist at the Hebrew University of Jerusalem and UC-Riverside, respectively. He is currently an executive council member of the Young Section of the Chinese Society for Horticultural Sciences and a member of the Chinese Society for Molecular Horticultural Breeding. He has also served as an academic editor for the Indian-based international journal “Legume Research” since 2013.Prof. Xu was elected to the prestigious “National Program for the Support of Top-Notch Young Professionals” in 2015.


Orphan genes (OGs) are genes that are restricted to a single species or a particular taxonomic group. So far, little is known about functions of OGs in domesticated crops. Here, we report our findings on OG-environmental adaptation relationships in cowpea (Vignaunguiculata). We identified 578 expressed cowpea OGs, of which 73.2% were predicted to be non-coding. Transcriptomic analyses revealed a strikingly high rate of OGs that were drought-inducible in roots only, as compared with conserved genes. Co-expression analysis further revealed the possible involvement of OGs in known stress response pathways. Over-expression of UP12_8740, a drought-inducible OG, conferred enhanced tolerance to osmotic stresses and soil drought. By combining Capture-Seq and fluorescence-based Kompetitive allele specific PCR (KASP), we efficiently genotyped SNPs on OGs across a 223-line cowpea germplasm collection. Population genomic parameters including PIC, He, Pi and Tajima’s D statistics, calculated based on these SNPs, showed distinct signatures between the grain- and vegetable-type subpopulations of cowpea. This work reinforces that OGs are a valuable resource for identifying new genes related to species-characteristic environmental adaptations, and fosters a new insight that artificial selections on OGs might have contributed to balancing the adaptive and agronomical traits in domesticated crops in various eco-climatic conditions.