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ARS Home » Southeast Area » Canal Point, Florida » Sugarcane Field Station » Research » Publications at this Location » Publication #339713

Research Project: Enhancement of Sugarcane Germplasm for Development of Stress Tolerant, High Yielding Cultivars

Location: Sugarcane Field Station

Title: Constructing high-density genetic maps for polyploid sugarcane (Saccharum spp.) and identifying quantitative trait loci controlling brown rust resistance

item Sood, Sushma
item Glynn, Neil - SYNGENTA
item Islam, Md
item Wang, Jianping - UNIVERSITY OF FLORIDA

Submitted to: Molecular Breeding
Publication Type: Abstract Only
Publication Acceptance Date: 8/15/2017
Publication Date: N/A
Citation: N/A

Interpretive Summary: A total of 27,221 SNPs were called for the mapping population following the established GBS pipelines. Of the 27,221 SNPs, 3,579 were single dose (SD) markers after applications of chi-square tests (P value = 0.01). In addition, 3,311presence/absence markers were identified and characterized as SD presence/absence markers. High-density sugarcane linkage maps were constructed using markers called from GBS data. The maps contained 2,900 markers forming 166 LGs with a total map length of 5,718.2 cM for CP95-1039, and 2,595 markers forming 148 LGs with a total map length of 5,782.0 cM for CP88-1762. This set of maps had a marker density of one marker per 2.0 cM for CP95-1039, and 2.2 cM for CP88-1762 map, respectively. Two major QTL controlling brown rust resistance were identified in this bi-parental population, which can explain a total of 54% of the phenotypic variation together. The comprehensive genetic map constructed in this study provided additional insight of the sugarcane genome structure. The molecular markers linked to brown rust resistance can be developed into new selection tools for breeding resistant cultivars.

Technical Abstract: Sugarcane (Saccharum spp.) is an important economic crop for producing edible sugar and bioethanol. Brown rust had long been a major disease impacting sugarcane production world widely. Resistance resource and markers linked to the resistance are valuable tools for disease resistance improvement. An F1 segregating population derived from a cross between two hybrid sugarcane clones, brown rust susceptible CP95-1039 and brown rust resistant CP88-1762, were genotyped using genotyping by sequencing approach and also phenotyped in a replicated field trial. Single nucleotide polymorphism (SNP) and presence/absence markers were called with seven different pipelines to maximize reliable marker identification. High density maps were constructed for both parental clones with a total map length of 5,718.2 cM, and a marker density of one marker per 2.0 cM for CP95-10392, and a total map length of 5,782.0 cM, and one marker per 2.2 cM for CP88-1762. Among the seven SNP callers, Tassel and GATK performed better than other callers in single dose (SD) SNPs detection and contribution to genetic maps. Two major quantitative trait loci (QTL) controlling brown rust resistance were identified, which can explain 24 and 30% of the phenotypic variation, respectively. The genetic maps generated here will improve our understanding of sugarcane complex genome structure and discovery of underlying sequence variations controlling agronomic traits. The putative QTL controlling brown rust resistance can effectively be utilized in sugarcane breeding programs to expedite the selection process of brown rust resistance after validation.