Whole-genome resequencing-based QTL-seq identified AhTc1 gene encoding a R2R3-MYB transcription factor controlling peanut purple testa colour

Authors: ZHAO, YUHAN - Shandong Academy Of Agricultural Sciences; MA, JUNJIE - Shandong Academy Of Agricultural Sciences; LI, MING - Shandong Academy Of Agricultural Sciences; DENG, LI - Shandong Academy Of Agricultural Sciences; LI, GUANGHUI - Shandong Academy Of Agricultural Sciences; XIA, HAN - Shandong Academy Of Agricultural Sciences; ZHAO, SHUZHEN - Shandong Academy Of Agricultural Sciences; HOU, LEI - Shandong Academy Of Agricultural Sciences; LI, PENGCHENG - Shandong Academy Of Agricultural Sciences; MA, CHANGLE - Shandong Agricultural University; YUAN, MEI - Shandong Academy Of Agricultural Sciences; REN, LI - Shandong Academy Of Agricultural Sciences; GU, JIANZHONG - Shandong Academy Of Agricultural Sciences; Guo, Baozhu; ZHAO, CHUANZHI - University Of Georgia; WANG, XINGJUN - Shandong Academy Of Agricultural Sciences

Submitted to: Plant Biotechnology Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/20/2019
Publication Date: 5/26/2019
Citation: Zhao, Y., Ma, J., Li, M., Deng, L., Li, G., Xia, H., Zhao, S., Hou, L., Li, P., Ma, C., Yuan, M., Ren, L., Gu, J., Guo, B., Zhao, C., Wang, X. 2019. Whole-genome resequencing-based QTL-seq identified AhTc1 gene encoding a R2R3-MYB transcription factor controlling peanut purple testa colour. Plant Biotechnology Journal. https://doi.org/10.1111/pbi.13175.
DOI: https://doi.org/10.1111/pbi.13175

Interpretive Summary: Peanut is widely cultivated in more than 100 countries. The testa colors of most peanut varieties are pink or red, but purple testa may have increased nutraceutical value due to higher anthocyanin content. In this study, the inheritance of purple testa of peanut was analyzed using F2 and F2:3 segregation populations. A major chromosome location was mapped using QTL-seq method. Furthermore, a candidate gene, AhTc1, encoding a R2R3-MYB transcription factor, was identified using map-based cloning method. Functional studies indicated that AhTc1 played important roles in regulating anthocynian biosynthesis. This study identified a candidate gene AhTc1 what is possible to be used in molecular breeding selection for peanut cultivars with purple testa color with potential added nutritional values.

Technical Abstract: Peanut (Arachis hypogaea L.) is an important oil crop worldwide. The common testa colors of peanut varieties are pink or red. But the peanut varieties with purple testa color have been focused in recent years due to the potential high levels of anthocyanin, an added nutritional value of antioxidant. Our objective was to study the genetic mechanisms that regulate peanut testa color. In this study, we found that the purple testa was decided by the female parent and controlled by a single major gene named AhTc1. We applied whole-genome resequencing-based approach (QTL-seq), Bulked Segregant RNA sequencing (BSR), and RNA-seq in order to identify the candidate genes controlling peanut purple testa. A total of 260.9 Gb data was generated from the parental and bulked lines. SNP index analysis indicated that AhTc1 was located in a 4.7 Mb region in chromosome A10, which was confirmed by BSR analysis in three segregation populations derived from the crosses between pink and purple testa varieties. Allele-specific markers were developed and demonstrated that the marker pTesta1089 was closely linked with AhTc1. Further, RNA-seq study identified a gene, R2R3-MYB gene (MYB113), significantly up-regulated in the purple testa parent YH29. The function of MYB113 was confirmed in overexpressed transgenic tobacco plants which led to purple color of leaves, flowers, pods and seeds. This study leads to the identification of AhTc1 for possible molecular breeding selection for peanut cultivars with purple testa color for potential increased nutritional value to consumers.