A new SNP haplotype associated with blue disease resistance gene in cotton (Gossypium hirsutum L.)

Abstract

Resistance to cotton blue disease (CBD) was evaluated in 364 F(2.3) families of three populations derived from resistant variety 'Delta Opal'. The CBD resistance in 'Delta Opal' was controlled by one single dominant gene designated Cbd. Two simple sequence repeat (SSR) markers were identified as linked to Cbd by bulked segregant analysis. Cbd resides at the telomere region of chromosome 10. SSR marker DC20027 was 0.75 cM away from Cbd. DC20027 marker fragments amplified from 3 diploid species and 13 cotton varieties whose CBD resistance was known were cloned and sequenced. One single nucleotide polymorphism (SNP) was identified at the 136 th position by sequence alignment analysis. Screening SNP markers previously mapped on chromosome 10 identified an additional 3 SNP markers that were associated with Cbd. A strong association between a haplotype based on four SNP markers and Cbd was developed. This demonstrates one of the first examples in cotton where SNP markers were used to effectively tag a trait enabling marker-assisted selection for high levels of CBD resistance in breeding programs.

Molecular mapping of bunchy top disease resistance in Gossypium hirsutum L.

“…Genetic mapping of CBT resistance confirms that the gene is near the CBD resistance gene mapped by Fang et al (2010) using three populations of 'Delta Opal' crossed to the susceptible cultivars 'DP388', 'DP5305' and 'SG747'. Our mapping suggests that Cbt is located in an adjacent region but is not likely to be the same gene conferring CBD resistance (Fig.…”

“…1). However, the genetic distance and marker order between the flanking Cbd markers NG0204310 and NG0211495 (DC20027) are different in our population compared to Fang et al (2010) possibly due a chromosomal rearrangement, making direct comparisons difficult (Fig. 1).…”

“…The SNP associated with markers NG0203481, NG0204310 and NG0211495 (DC20027) were genotyped using Taqman technology using primer sequences previously used to map CBD (Fang et al 2010). The 7-lL TaqMan assay reaction contained 10 lM each of primers, 0.2 lM each of probes, 5 ng genomic DNA, and 1X TaqMan universal PCR Master Mix (Thermo Fisher Scientific, Waltham, MA).…”

“…CL213 did not completely match any region of the draft TM-1 (G. hirsutum) genome sequence (Li et al 2015;Zhang et al 2015) but was very similar to a region located on chromosome A10 (*98,755,400). Fang et al (2010), previously mapped the CBD resistance gene to a 0.8 cM region on Chr A10 flanked by SNP markers NG0204310 (Chr A10_ 99,881,319 nt) and NG0211495 (DC20027, Chr A10_ 99,894,811 nt). Since these markers are in close proximity to the likely location of CL213, three of the SNP markers developed by Fang et al (2010) for the mapping of Cbd, (another close SNP marker NG0203671, was not polymorphic in our population) and four SNP markers (GhCSIRO_2461, GhCSIRO2551, GhCSIRO_2637 and GhCSIRO_2637, Table S3), previously identified between 'Delta Opal' and 'Sicot 70' (Zhu et al 2014) that were in the same region, were mapped onto the F 2 population (Table S4).…”

“…The majority of Gossypium hirsutum L. cultivars surveyed are susceptible to CBD, but resistant cultivars (mainly of African descent) have been identified (Royo et al 2003), including the Australian cultivar 'Delta Opal' used in this study. Resistance to CBD has been shown to be controlled by a single dominant locus (Fang et al 2010;Pupim et al 2008). …”