Genetic Mapping With Allele Dosage Information in Tetraploid Urochloa decumbens (Stapf) R. D. Webster Reveals Insights Into Spittlebug (Notozulia entreriana Berg) Resistance

Abstract

Urochloa decumbens (Stapf) R. D. Webster is one of the most important African forage grasses in Brazilian beef production. Currently available genetic-genomic resources for this species are restricted mainly due to polyploidy and apomixis. Therefore, crucial genomic-molecular studies such as the construction of genetic maps and the mapping of quantitative trait loci (QTLs) are very challenging and consequently affect the advancement of molecular breeding. The objectives of this work were to (i) construct an integrated U. decumbens genetic map for a full-sibling progeny using GBS-based markers with allele dosage information, (ii) detect QTLs for spittlebug (Notozulia entreriana) resistance, and (iii) seek putative candidate genes involved in defense against biotic stresses. We used the Setaria viridis genome a reference to align GBS reads and selected 4,240 high-quality SNP markers with allele dosage information. Of these markers, 1,000 were distributed throughout nine homologous groups with a cumulative map length of 1,335.09 cM and an average marker density of 1.33 cM. We detected QTLs for resistance to spittlebug, an important pasture insect pest, that explained between 4.66 and 6.24% of the phenotypic variation. These QTLs are in regions containing putative candidate genes related to defense against biotic stresses. Because this is the first genetic map with SNP autotetraploid dosage data and QTL detection in U. decumbens, it will be useful for future evolutionary studies, genome assembly, and other QTL analyses in Urochloa spp. Moreover, the results might facilitate the isolation of spittlebug-related candidate genes and help clarify the mechanism of spittlebug resistance. These approaches will improve selection efficiency and accuracy in U. decumbens molecular breeding and shorten the breeding cycle.

Keywords: Brachiaria; SNP; allele dosage; linkage map; polyploidy; quantitative traits; signalgrass.

FIGURE 1

Allele dosage in the parents and progeny, and the frequency histograms. (A) Marker S.5_20487325. Red squares represent the Aaaa parent and offspring, and blue circles represent the aaaa parent and offspring. (B) Marker D.2_28922605. Red squares represent the AAaa parent and offspring, blue circles represent the aaaa parent and the Aaaa offspring, and green triangles represent the aaaa offspring. (C) Marker XSS.1_23891474. Red squares represent AAAa parent and offspring, blue circles represent the Aaaa parent and the AAaa offspring, and green triangles represent the Aaaa offspring.

FIGURE 2

Linkage map for U. decumbens: homologous groups from 1 to 4. The genotype configuration of each marker is indicated by the marker name prefix and color. Simplex markers are represented in black; duplex markers are represented in green; double-simplex markers are represented in purple; X-double-simplex markers are represented in light blue; duplex-simplex markers are represented in dark blue and double-duplex markers are represented in orange. QTLs are identified in HG1 and HG2.

FIGURE 3

Linkage map for U. decumbens: homologous groups from 5 to 9. The genotype configuration of each marker is indicated by the marker name prefix and color. Simplex markers are represented in black; duplex markers are represented in green; double-simplex markers are represented in purple; X-double-simplex markers are represented in light blue; duplex-simplex markers are represented in dark blue and double-duplex markers are represented in orange. A QTL is identified in HG6.

FIGURE 4

Distribution of the distance between adjacent markers on the U. decumbens consensus genetic map.