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Orphan genes are involved in drought adaptations and ecoclimatic-oriented selections in domesticated cowpea

文献类型： 外文期刊

作者： Li, Guojing 1 ; Wu, Xinyi 1 ; Hu, Yaowen 1 ; Munoz-Amatriain, Maria 3 ; Luo, Jie 4 ; Zhou, Wen 1 ; Wang, Baogen 1 ; Wang, 1 ;

作者机构： 1.Zhejiang Acad Agr Sci, Inst Vegetables, Hangzhou, Zhejiang, Peoples R China

2.Zhejiang Acad Agr Sci, State Key Lab Breeding Base Sustainable Control P, Hangzhou, Zhejiang, Peoples R China

3.Univ Calif Riverside, Dept Bot & Plant Sci, Riverside, CA 92521 USA

4.Zhejiang Acad Agr Sci, Cent Lab, Hangzhou, Zhejiang, Peoples R China

5.Northwest Agr & Forestry Univ, Coll Hort, Yangling, Shaanxi, Peoples R China

6.Colorado State Univ, Dept Soil & Crop Sci, Ft Collins, CO 80523 USA

关键词： Capture-sequencing; cowpea; drought adaptation; hairy-root transformation; lineage-specific gene; orphan gene; Tajima's D

期刊名称：JOURNAL OF EXPERIMENTAL BOTANY （ 影响因子：6.992； 五年影响因子：7.86 ）

ISSN： 0022-0957

年卷期： 2019 年 70 卷 12 期

页码：

收录情况： SCI

摘要： Orphan genes (OGs) are genes that are restricted to a single species or a particular taxonomic group. To date, little is known about the functions of OGs in domesticated crops. Here, we report our findings on the relationships between OGs and environmental adaptation in cowpea (Vigna unguiculata). We identified 578 expressed OGs, of which 73.2% were predicted to be non-coding. Transcriptomic analyses revealed a high rate of OGs that were drought inducible in roots when compared with conserved genes. Co-expression analysis further revealed the possible involvement of OGs in stress response pathways. Overexpression 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 single nucleotide polymorphisms (SNPs) on OGs across a 223 accession cowpea germplasm collection. Population genomic parameters, including polymorphism information content (PIC), expected heterozygosity (H-e), nucleotide diversity (pi), and Tajima's D statistics, that were calculated based on these SNPs, showed distinct signatures between the grain- and vegetable-type subpopulations of cowpea. This study reinforces the idea that OGs are a valuable resource for identifying new genes related to species-specific environmental adaptations and fosters new insights that artificial selection on OGs might have contributed to balancing the adaptive and agronomic traits in domesticated crops in various ecoclimatic conditions.

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