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

Rebecca Caroline Ulbricht Ferreira,Lucimara Chiari,Sanzio Carvalho Lima Barrios,Antonio Augusto Franco Garcia,Anete Pereira De Souza,Fabrícia Zimermann Vilela Torres,José Raul Valério,Cacilda Borges Do Valle,Letícia Aparecida De Castro Lara

doi:10.3389/fpls.2019.00092

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.

Highlights

Brazilian cultivated pastures are the basis for the production of beef cattle, and they cover extensive areas, most of which are populated by grasses of the genus Urochloa
The output of the Tassel-GBS pipeline was used as the input for the SuperMASSA software, and 9,345 SNP markers with allele dosage were selected with a minimum overall depth of 25 reads
The markers were named with the allele dosage configuration, the homology group number, and the chromosomal position of the SNP in the S. viridis genome

Summary

Introduction

Brazilian cultivated pastures are the basis for the production of beef cattle, and they cover extensive areas, most of which are populated by grasses of the genus Urochloa Brachiaria) (Jank et al, 2011; Associação Brasileira das Indústrias Exportadoras de Carne [ABIEC], 2016). This genus belongs to the Poaceae family and comprises species of plants distributed in tropical and subtropical regions, mainly in the African continent (Renvoize et al, 1996; Valle et al, 2009). This forage grass has relevant agronomic attributes, including exceptional adaptation to poor and acidic soils that are typical of the tropics, leading to good animal performance (Valle et al, 2010). The species is susceptible to several types of spittlebug, including Notozulia entreriana Berg (Hemiptera: Cercopidae), which is the most damaging pest for tropical pastures (Gusmão et al, 2016)

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