A major QTL associated with Fusarium oxysporum race 1 resistance identified in genetic populations derived from closely related watermelon lines using selective genotyping and genotyping-by-sequencing for SNP discovery

Abstract

A major quantitative trait locus (QTL) for Fusarium oxysporum Fr. f. sp. niveum race 1 resistance was identified by employing a "selective genotyping" approach together with genotyping-by-sequencing technology to identify QTLs and single nucleotide polymorphisms associated with the resistance among closely related watermelon genotypes. Fusarium wilt is a major disease of watermelon caused by the soil-borne fungus Fusarium oxysporum Schlechtend.:Fr. f. sp. niveum (E.F. Sm.) W.C. Snyder & H.N. Hans (Fon). In this study, a genetic population of 168 F3 families (24 plants in each family) exhibited continuous distribution for Fon race 1 response. Using a "selective genotyping" approach, DNA was isolated from 91 F2 plants whose F3 progeny exhibited the highest resistance (30 F2 plants) versus highest susceptibility (32 F2 plants), or moderate resistance to Fon race 1 (29 F2 plants). Genotyping-by-sequencing (GBS) technology was used on these 91 selected F2 samples to produce 266 single nucleotide polymorphism (SNP) markers, representing the 11 chromosomes of watermelon. A major quantitative trait locus (QTL) associated with resistance to Fon race 1 was identified with a peak logarithm of odds (LOD) of 33.31 and 1-LOD confidence interval from 2.3 to 8.4 cM on chromosome 1 of the watermelon genetic map. This QTL was designated "Fo-1.1" and is positioned in a genomic region where several putative pathogenesis-related or putative disease-resistant gene sequences were identified. Additional independent, but minor QTLs were identified on chromosome 1 (LOD 4.16), chromosome 3 (LOD 4.36), chromosome 4 (LOD 4.52), chromosome 9 (LOD 6.8), and chromosome 10 (LOD 5.03 and 4.26). Following the identification of a major QTL for resistance using the "selective genotyping" approach, all 168 plants of the F 2 population were genotyped using the SNP nearest the peak LOD, confirming the association of this SNP marker with Fon race 1 resistance. The results in this study should be useful for further elucidating the mechanism of resistance to Fusarium wilt and in the development of molecular markers for use in breeding programs of watermelon.

Genotyping by sequencing for SNP discovery and genetic mapping of resistance to race 1 of Fusarium oxysporum in watermelon

“…The number of tags (933,662) generated in this study with ApeKI restriction enzyme exceeded those generated (527,844 tags) with the same enzyme in an elite by elite F 2 watermelon population described by Lambel et al (2014). Due to the low genetic diver- sity among cultivated watermelon (Levi et al, 2001), the number of usable SNPs (1024) generated in the current study was small compared to that reported for other crops such as rice (>30,000) (Spindel et al, 2013) and wheat (>130,000) (Rutkoski et al, 2013) using GBS.…”

“…The difference in disease severity observed in the F 1 in this study and previously published work might have resulted from a variation in the inoculation method and soil type used. In the current study, a modified-tray dip method was used for inoculation in sand: peat: vermiculite medium while in most studies, the root dip method and various combinations of sand, soil, peat and vermiculite are used (Dane et al, 1998;Freeman and Rodriguez, 1993;Hawkins et al, 2001;Lambel et al, 2014;Martyn and McLaughlin, 1983;Martyn and Netzer, 1991;Yetisir et al, 2003;Everts, 2004, 2007;Zhou et al, 2010). These results show that researchers should carefully consider the time (DAI) of data collection and the method of inoculation used when drawing conclusions from genetic studies of Fon.…”

“…W.C. Snyder & H.N. Hans is a tivars resistant to Fon races 0 and 1 and a few resistant to race 2 have been developed through breeding programs (Bruton, 1998;Lambel et al, 2014;Wehner, 2008).…”

“…However, as with many other crops (Barbedo, 2014;Furbank and Tester, 2011;Montes et al, 2007), advancement in high-throughput phenotyping technologies for robust trait evaluation in watermelon lags behind that of genotyping technologies for genomic applications. Several phenotyping methods have been developed for screening of fusarium wilt resistance in watermelon including the root-dip method, which is the most common in watermelon breeding and genetic studies (Dane et al, 1998;Freeman and Rodriguez, 1993;Hawkins et al, 2001;Lambel et al, 2014;Martyn and McLaughlin, 1983;Martyn and Netzer, 1991;Ren et al, 2015;Yetisir et al, 2003;Everts, 2004, 2007;Zhou et al, 2010). In this method, seedlings are uprooted at the first true leaf stage and the roots are washed off under running water, dipped in inoculum and transplanted into pots containing a substrate.…”

“…Despite the ability of GBS to generate thousands of SNP markers, the low genetic diversity in cultivated watermelon limits the number of polymorphic markers available to study elite by elite populations. Using GBS, Lambel et al (2014) identified only 266 usable SNPs in elite by elite F 2 population [HMw017 (resistant) × HMw013 (susceptible)] segregating for resistance against Fon race 1and detected seven QTL associated with resistance, including a major QTL (R 2 = 59.9%) on chromosome 1. This major QTL was independently confirmed by Ren et al (2015) in a recombinant inbred population developed from a cross between PI 296341-FR and the cultivar 97103.…”