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Article|10 Feb 2022|OPEN
Construction of a high-density genetic map based on specific-locus amplified fragment sequencing and identification of loci controlling anthocyanin pigmentation in Yunnan red radish
Jing Tao1,2 ,† , Shikai Li2 ,† , Qian Wang2 , Yi Yuan2 , Jiqiong Ma3 , Minghui Xu3 , Yi Yang3 , Cui Zhang4 and Lijuan Chen1 , , Yiding Sun,3 ,
1College of Agronomy and Biotechnology, Yunnan Agriculture University, 452 Fengyuan Road, Kunming, 650201, China
2Engineering Research Center of Vegetable Germplasm Innovation and Support Production Technology, Horticultural Research Institute, Yunnan Academy of Agricultural Sciences; 2238 Beijing Road, Kunming, 650205, China
3Key Lab of Agricultural Biotechnology of Yunnan Province, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation of Ministry of Agriculture, Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, 2238 Beijing Road, Kunming, 650205, China
4College of Plant Protection, Yunnan Agricultural University, 452 Fengyuan Road, Kunming, 650201, China
*Corresponding author. E-mail:,
Both authors contributed equally to the study.

Horticulture Research 9,
Article number: uhab031 (2022)
Views: 651

Received: 07 Jan 2021
Revised: 23 Oct 2021
Accepted: 19 Jan 2022
Published online: 10 Feb 2022


Radish (Raphanus sativus L.) belongs to the family Brassicaceae. The Yunnan red radish variety contains relatively large amounts of anthocyanins, making them important raw materials for producing edible red pigment. However, the genetic mechanism underlying this pigmentation has not been fully characterized. Here, the radish inbred line YAAS-WR1 (white root skin and white root flesh) was crossed with the inbred line YAAS-RR1 (red root skin and red root flesh) to produce F1, F2, BC1P1, and BC1P2 populations. Genetic analyses revealed that the pigmented/non-pigmented and purple/red traits were controlled by two genetic loci. The F2 population and the specific-locus amplified fragment sequencing (SLAF-seq) technique were used to construct a high-density genetic map (1230.16 cM), which contained 4032 markers distributed in nine linkage groups, with a mean distance between markers of 0.31 cM. Additionally, two quantitative trait loci (QAC1 and QAC2) considerably affecting radish pigmentation were detected. A bioinformatics analysis of the QAC1 region identified 58 predicted protein-coding genes. Of these, RsF3′H, which is related to anthocyanin biosynthesis, was revealed as a likely candidate gene responsible for the purple/red trait. The results were further verified by analyzing gene structure and expression. Regarding QAC2, RsMYB1.3 was determined to be a likely candidate gene important for the pigmented/non-pigmented trait, with a 4-bp insertion in the first exon that introduced a premature termination codon in the YAAS-WR1 sequence. Assays demonstrated that RsMYB1.3 interacted with RsTT8 and activated RsTT8 and RsUFGT expression. These findings may help clarify the complex regulatory mechanism underlying radish anthocyanin synthesis. Furthermore, this study’s results may be relevant for the molecular breeding of radish to improve the anthocyanin content and appearance of the taproots.