In this research, we sequenced the whole transcriptome in immature seeds in a peanut recombinant inbred line (RIL) population and explored thoroughly the landscape of transcriptomic variations and its genetic basis. The comprehensive analysis identified total 49 691 genes in RIL population, of which 92 genes followed a paramutation-like expression pattern. Expression quantitative trait locus (eQTL) analysis identified 1207 local eQTLs and 15 837 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 distant eQTL. By integrating transcriptomic profile and annotation analyses, we unveiled a putative candidate gene and developed a linked marker InDel02 underlying a major QTL responsible for purple testa colour in peanut. Our result provided a first understanding of genetic basis of wholegenome transcriptomic variation in peanut and illustrates the potential of the transcriptome-aid approach in dissecting important traits in non-model plants.
Integrating transcriptomic data empowered rapid gene exploration for purple testa. (a) Phenotype of testa colour in peanut seed. The left panel indicates the Zhonghua 10 (pink) and ICG 12625 (purple), while right panel shows the colour variability in the population. (b) Identification of a major QTL underlying testa colour on chromosome A10. The red rectangle indicates the 99% support interval of the QTL, while the red dash lines mean the closest markers flanking the QTL interval in the map. (c) The relationship between gene expression and testa colour in the population. A total of 196 genes were tested at the candidate region (97.0~102.3 Mb). The genes with P < 0.001 were highlighted as red dots. (d) Integrative analyses help determine putative genes responsible for purple colour. The top layer indicates the extent of expression difference (DE) between parents. The circle size is proportional to the DE level, while the red filled ones mean the significantly different expression based on t test (P < 0.01). The middle layer indicates whether the gene expression can be regulated itself, as local eQTL and filled in blue, otherwise in grey. The bottom layer indicates whether the gene may be involved in anthocyanidin biological synthesis pathway according to the peanut and Arabidopsis annotation, as filled in green, otherwise in gray.