Yasin Topcu, Manoj Sapkota, Eudald Illa-Berenguer, Savithri U. Nambeesan & Esther van der Knaap

Theoretical and Applied Genetics September 2021; vol. 134: 2931–2945

Key message

Blossom-End Rot is Quantitatively Inherited and Maps to Four Loci in Tomato.

Abstract

Blossom-end rot (BER) is a devastating physiological disorder that affects tomato and other vegetables, resulting in significant crop losses. To date, most studies on BER have focused on the environmental factors that affect calcium translocation to the fruit; however, the genetic basis of this disorder remains unknown. To investigate the genetic basis of BER, two F₂ and F_3:4 populations along with a BC₁ population that segregated for BER occurrence were evaluated in the greenhouse. Using the QTL-seq approach, quantitative trait loci (QTL) associated with BER Incidence were identified at the bottom of chromosome (ch) 3 and ch11. Additionally, linkage-based QTL mapping detected another QTL, BER3.1, on ch3 and BER4.1 on ch4. To fine map the QTLs identified by QTL-seq, recombinant screening was performed. BER3.2, the major BER QTL on ch3, was narrowed down from 5.68 to 1.58 Mbp with a 1.5-LOD support interval (SI) corresponding to 209 candidate genes. BER3.2 colocalizes with the fruit weight gene FW3.2/SlKLUH, an ortholog of cytochrome P450 KLUH in Arabidopsis. Further, BER11.1, the major BER QTL on ch11, was narrowed down from 3.99 to 1.13 Mbp with a 1.5-LOD SI interval comprising of 141 candidate genes. Taken together, our results identified and fine mapped the first loci for BER resistance in tomato that will facilitate marker-assistant breeding not only in tomato but also in many other vegetables suffering for BER.

See: https://link.springer.com/article/10.1007/s00122-021-03869-0

Fig. 7: Fine mapping of the BER3.2 and BER11.1. a−c Recombinant screening and fine mapping of BER3.2 d−f Recombinant screening and fine mapping of BER11.1 Frequency distribution of recombinant F_3:4 plants for a BER3.2 in 20S74 and d BER11.1 in 19S499 F₄ populations. White, gray, and black arrowheads on each histogram show the average of BGV007900, F₁ and BGV007936 plants, respectively, for the trait of interest. b, e Linkage-based QTL mapping. b BER3.2 was further delineated to approximately 1.58-Mb region flanked by 20EP1033 (SL4.0ch3 58,308,917) and 18EP730 (SL4.0ch3 59,8912,10) markers. e BER11.1 was further fine mapped to 1.13-Mb region flanked by 18EP1043 (SL4.0ch11 52,123,165) and 18EP1114 (SL4.0ch11 53,258,120) markers. The numbers between genetic markers represent the number of recombinant plants. Bars show 1.0-LOD SI, and the whiskers represent 1.5-LOD SIs for each QTL c,f) Box plots of allelic effects of the most significant markers identified in the 1.5-LOD SI. The allelic effects of the most significant markers c 19EP2161 in BER3.1 region and f 20EP385 in BER11.1 region. “RR” indicates plants homozygous for the resistant BGV007900 allele, “RS” shows plants heterozygous at this locus, and “SS” plants homozygous for the susceptible BGV007936 allele.