Genome‐wide expression quantitative trait locus analysis in a recombinant inbred line population for trait dissection in peanut
The transcriptome connects genome to the gene function and ultimate phenome in biology. Sofar, transcriptomic approach was not used in peanut for performing trait mapping in bi-parentalpopulations. In this research, we sequenced the whole transcriptome in immature seeds in apeanut recombinant inbred line (RIL) population and explored thoroughly the landscape oftranscriptomic variations and its genetic basis. The comprehensive analysis identified total49 691 genes in RIL population, of which 92 genes followed a paramutation-like expressionpattern. Expression quantitative trait locus (eQTL) analysis identified 1207 local eQTLs and15 837 distant eQTLs contributing to the whole-genome transcriptomic variation in peanut.There were 94 eQTL hot spot regions detected across the genome with the dominance of distanteQTL. By integrating transcriptomic profile and annotation analyses, we unveiled a putativecandidate gene and developed a linked marker InDel02 underlying a major QTL responsible forpurple testa colour in peanut. Our result provided a first understanding of genetic basis of whole-genome transcriptomic variation in peanut and illustrates the potential of the transcriptome-aidapproach in dissecting important traits in non-model plants.