Construction of a single nucleotide polymorphism marker based QTL map and validation of resistance loci to bacterial wilt caused by Ralstonia solanacearum species complex in tomato

Abstract

Bacterial wilt (BW), caused by Ralstonia solanacearum species complex is one of the major biotic factors limiting tomato production in the humid tropics. Pyramiding of resistance genes through marker-assisted selection is an efficient way to develop durable BW resistant cultivars. Tomato line 'Hawaii 7996' (H7996) is a stable and robust resistance source against various strains of the species complex. Major BW resistance quantitative trait loci (QTLs) Bwr-12 and Bwr-6, and several minor or strain specific QTLs have been coarse-mapped in this line, but none has been fine-mapped and validated. The objective of the current study was to construct a high density genetic map using single-nucleotide polymorphism (SNP) markers derived from genotyping-bysequencing, fine-map Bwr-12 and Bwr-6 and determine the effects of these QTLs using a near isogenic line (NIL) population. A high density genetic map using 1604 SNP markers with an average distance of 0.82 cM was developed for 188 F 9 recombinant inbred lines derived from the cross H7996 9 WVa700. A total of seven QTLs associated with BW resistance to race 1-phylotype I (R. pseudosolanacearum) or/and race 3-phylotype II (R. solanacearum) strains were located on chromosomes 6 (Bwr-6.1, 6.2, 6.3 and 6.4) and 12 (Bwr-12.1, Bwr-12.2 and Bwr-12.3) with logarithm of odds (LOD) scores of 6.2-15.6 and 6.2-31.1, explaining 14.2-33.4% and 15.9-53.9% of the total phenotypic variation contributed from H7996, respectively. To validate the genetic effects of the two QTL regions, a set of 80 BC 3 F 3 NILs containing different sections of Bwr-6 with or without Bwr-12 was phenotyped for disease severity after challenge with either race 1-phylotype I Pss4 or race 3-phylotype II Pss1632 BW strains over two seasons. Bwr-6.1 specific to Pss4 and Bwr-6.3 specific to Pss1632 were mapped to an interval of 5.0 cM (P \ 0.05) between 6_33,444,000_SLM6-47 and 6_33,868,000_SLM6-124 SNP marker, and to 2.7 cM (P \ 0.01) between positions 6_35,949,000 _SLM6-107 to 6_36,750,000_SLM6-82 marker, respectively. In addition, the specific effect of Bwr-12 for resistance to Pss4 (LOD score of 5.8-16.1, P \ 0.01) was confirmed.

Image-based assessment of plant disease progression identifies new genetic loci for resistance

“…We also identified a QTL on chromosome 6, using visual assessment in both 2016 and 2019. In our study, Bwr6.1 confers 8 -11% of the variation, compared to 11.5 -33% for Bwr6a -Bwr6d 26,27 . The genes within the left and right intervals of Bwr6.1 are particularly interesting because there are two groups of NBS-LRRs located between the left and right markers for Bwr6.1 (solcap_snp_sl_14458 and the GBS-identified SNP at 39435402).…”

“…Two such clusters, detected on chromosome 12, identified QTL for CM height (Bwr12.1) and Y mass (Bwr12.2), and were located near previous QTL detected against other strains of Ralstonia (Figure 4 and Figure 5c) . These previous studies 24,26,27 detected QTL using visual wilt assessment of adult plants in the field.…”

“…In crops, resistance to Ralstonia is quantitative, but the quantitative trait loci (QTL) underlying resistance to US strains of Ralstonia are largely unknown. QTL for other strains have been mapped [20][21][22][23][24][25][26][27] but have not been cloned, and the host determinants necessary for resistance remain mostly unspecified.…”

“…Most previously identified QTL have focused on resistance to R. pseudosolanacearum, and none of them used the strain of R. solanacearum as in this work [20][21][22][23][24][25][26][27] . Using visual assessment of wilting and the same RIL population of tomato (H7996 x WV700) used here, one broadspectrum QTL for resistance to multiple strains of R. pseudosolanacearum, and one strain of R. solanacearum (JT-516) had been previously identified on chromosome 6 [20][21][22][23][24][25][26][27] . We also identified a QTL on chromosome 6, using visual assessment in both 2016 and 2019.…”

“…Each Bwr QTL explained approximately 6 to 11% of the variation in response to R. solanacearum strain K60. 27 are also displayed.…”