Mixed Modeling of Yield Components and Brown Rust Resistance in Sugarcane Families

Balsalobre, Thiago Willian Almeida; Mancini, Melina Cristina; Pereira, Guilherme da Silva; Anoni, C. O.; Barreto, Fernando; Hoffmann, Hermann Paulo; Souza, Anete Pereira de; Garcia, Antônio Augusto Franco; Carneiro, Monalisa Sampaio

doi:10.2134/agronj2015.0430

Cited by 29 publications

(44 citation statements)

References 81 publications

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“…These cultivars have chromosome numbers ranging from 100 to 130, are vegetatively propagated, and result from the selection of populations derived from outcrossing heterozygous parents [1, 9]. Sugarcane has a very high photosynthetic efficiency and is a crop with major economic importance in many tropical and subtropical countries primarily because of its use in the production of sugar and bioethanol [10–12]. …”

Section: Introductionmentioning

confidence: 99%

GBS-based single dosage markers for linkage and QTL mapping allow gene mining for yield-related traits in sugarcane

et al. 2017

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BackgroundSugarcane (Saccharum spp.) is predominantly an autopolyploid plant with a variable ploidy level, frequent aneuploidy and a large genome that hampers investigation of its organization. Genetic architecture studies are important for identifying genomic regions associated with traits of interest. However, due to the genetic complexity of sugarcane, the practical applications of genomic tools have been notably delayed in this crop, in contrast to other crops that have already advanced to marker-assisted selection (MAS) and genomic selection. High-throughput next-generation sequencing (NGS) technologies have opened new opportunities for discovering molecular markers, especially single nucleotide polymorphisms (SNPs) and insertion-deletion (indels), at the genome-wide level. The objectives of this study were to (i) establish a pipeline for identifying variants from genotyping-by-sequencing (GBS) data in sugarcane, (ii) construct an integrated genetic map with GBS-based markers plus target region amplification polymorphisms and microsatellites, (iii) detect QTLs related to yield component traits, and (iv) perform annotation of the sequences that originated the associated markers with mapped QTLs to search putative candidate genes.ResultsWe used four pseudo-references to align the GBS reads. Depending on the reference, from 3,433 to 15,906 high-quality markers were discovered, and half of them segregated as single-dose markers (SDMs) on average. In addition to 7,049 non-redundant SDMs from GBS, 629 gel-based markers were used in a subsequent linkage analysis. Of 7,678 SDMs, 993 were mapped. These markers were distributed throughout 223 linkage groups, which were clustered in 18 homo(eo)logous groups (HGs), with a cumulative map length of 3,682.04 cM and an average marker density of 3.70 cM. We performed QTL mapping of four traits and found seven QTLs. Our results suggest the presence of a stable QTL across locations. Furthermore, QTLs to soluble solid content (BRIX) and fiber content (FIB) traits had markers linked to putative candidate genes.ConclusionsThis study is the first to report the use of GBS for large-scale variant discovery and genotyping of a mapping population in sugarcane, providing several insights regarding the use of NGS data in a polyploid, non-model species. The use of GBS generated a large number of markers and still enabled ploidy and allelic dosage estimation. Moreover, we were able to identify seven QTLs, two of which had great potential for validation and future use for molecular breeding in sugarcane.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3383-x) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

GBS-based single dosage markers for linkage and QTL mapping allow gene mining for yield-related traits in sugarcane

et al. 2017

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“…In the studies of sugarcane families of Moraes et al (2010), the results of CVg for TCH and TSH were very similar (19.51 and 19.56%), and lower for FIB, BRIX, and PC (1.46 to 5.08%). Balsalobre et al (2016) reported very close values for BRIX, PC, and FIB, and lower values for the traits TCH and TSH.…”

Section: Resultsmentioning

confidence: 87%

Research Article RESEARCH-ARTILE Agricultural performance and genetic parameters for yield-related traits of sugar- and energy cane families derived from planned crosses.

Júnior¹,

Azeredo²,

Oliveira³

et al. 2017

Genet. Mol. Res.

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ABSTRACT. The forecast of a growing energy demand in the coming years has aroused particular interest in biomass for energy cogeneration, to diversify the energy matrix by using clean and renewable sources. To meet the new demands of the sugarcane industry, this study evaluated the agronomic performance and estimated genetic parameters for yield traits in sugar-and energy cane families derived from planned crosses. The cane families were assessed in the northwest of the State of Paraná, county of Paranavaí, in a randomized complete block design, with three replications. The evaluations were carried out 12 months after the first cut, in the ratoon cane cycle, in December 2014, under very unfavorable conditions for the crop, due to the low fertility and waterholding capacity of the soil. Besides, the crop was evaluated at the end of the harvest, when the agricultural and industrial quality of the crop is reduced. The following traits were evaluated at the plot level: soluble solids content, apparent sucrose content (PC), fiber content, tons of cane per hectare, tons of sucrose per hectare (TSH), and tons of fiber per hectare (TFH). High genetic variability was observed for all evaluated traits, with accuracy estimates from 0.69 (TSH) to 0.92 (PC), and high heritability (up to 0.84), indicating the possibility of genetic progress. The sugarcane families derived from crosses of Saccharum spontaneum and Saccharum robustum species with sugarcane hybrids had the highest fiber contents. Highest sugar contents were found in sugarcane families resulting from crosses of sugarcane clones and conventional cultivars. The TSH means were highest in the families F160 x MEX68-200 and RB855156 x RB987935. The highest genotypic mean for TFH was observed in the special polycross involving cultivar RB036066 with S. spontaneum accessions as pollen donors.

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“…Os dois marcadores moleculares de diagnóstico, R12H16 e 9O20-F4-RsaI, fortemente associados ao gene Bru1 (25), foram utilizados para avaliar a presença do gene. A análise dos resultados foi feita comparando-se as respostas dos haplótipos dos marcadores com a avaliação a campo usando modelo misto linear generalizado, conforme proposto por Balsalobre et al (14).…”

Section: Análises Molecularesunclassified

“…A complexidade do genoma da cana-de-açúcar é devido ao seu elevado número de cromossomos, variando de 100 a 130 (8, 9); ao tamanho do genoma, com aproximadamente 10 Gb (10,11,12); e à ocorrência de aneuploidia, com um número variável de cromossomos em cada grupo de homeologia (13). Desta forma, a obtenção de variedades com alta performance agrícola torna-se um grande desafio (14,15,16,17).…”

Section: Introductionunclassified

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Validação de marcadores moleculares associados à resistência à ferrugem marrom em cana-de-açúcar

et al. 2017

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A ferrugem marrom causada pelo fungo Puccinia melanocephala é uma importante doença em cana-de-açúcar (Saccharum spp.) e está presente em praticamente todas as áreas de cultivo. Um gene de efeito maior, Bru1, foi descrito como fonte de resistência durável da cana-de-açúcar contra isolados de P. melanocephala. O objetivo deste estudo foi avaliar a eficiência de dois marcadores moleculares fortemente associados ao gene Bru1, R12H16 e 9O20-F4-RsaI, para predição da resistência genética à ferrugem marrom em variedades de cana-de-açúcar. ABSTRACTBrown rust caused by the fungus Puccinia melanocephala is an important disease affecting sugarcane (Saccharum spp.) and is present in almost all growing areas. A major effect gene, Bru1, was described as a durable resistance source in sugarcane against isolates of P. melanocephala. The aim of this study was to evaluate the efficiency of two molecular markers strongly associated with Bru1 gene, R12H16 and 9O20-F4-RsaI, for prediction of genetic resistance to brown rust in sugarcane varieties. Thus, this study included 14 RB varieties, developed by RIDESA (Interuniversity Network for the Development of the Sugarcane Industry), which were among the 10 most cultivated varieties in the central-south region of Brazil in the period of 1974-2015. To evaluate the disease in the field an experiment was conducted in randomized blocks with four replicates. The severity of Barreto, F.Z.; Balsalobre, T.W.A. Chapola, R.G.; Hoffmann, H.P.; Carneiro, M.S. Validation of molecular markers associated with brown rust resistance in sugarcane. Summa Phytopathologica, v.43, n.1, p.36-40, 2017. brown rust was quantified according to a diagrammatic scale ranging from 1 (most resistant) to 9 (most susceptible), and the obtained data were analyzed by using a generalized linear mixed model (GLMM). Concomitantly, total DNA was extracted from the 14 varieties, followed by amplification of the molecular markers, which were classified into haplotypes. Out of the total varieties, 12 had no symptoms of the disease and showed 99.35% probability of being resistant according to analysis via GLMM; among them, 91.66% were haplotype 1, i.e., had the presence of both markers associated with Bru1 gene. Therefore, we can conclude that the molecular markers R12H16 and 9O20-F4-RsaI were highly efficient in predicting resistant phenotypes and that Bru1 gene is probably the main source of sugarcane resistance to brown rust in commercial fields in Brazil.Keywords: Saccharum spp., breeding, Puccinia melanocephala, Bru1, disease resistance.A cana-de-açúcar (Saccharum spp.) está entre as mais importantes espécies cultivadas, principalmente para produção de açúcar e bioetanol (1). O Brasil é atualmente o país com a maior produção de cana-deaçúcar com mais de nove milhões de hectares cultivados e produtividade estimada em 76.909 kg ha -1 na safra 2015/16 (1, 2). A cana-de-açúcar é uma gramínea semi-perene com propagação vegetativa, sendo que os programas de melhoramento genético têm concentrado esforços para o desenvolviment...

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Mixed Modeling of Yield Components and Brown Rust Resistance in Sugarcane Families

Cited by 29 publications

References 81 publications

GBS-based single dosage markers for linkage and QTL mapping allow gene mining for yield-related traits in sugarcane

GBS-based single dosage markers for linkage and QTL mapping allow gene mining for yield-related traits in sugarcane

Research Article RESEARCH-ARTILE Agricultural performance and genetic parameters for yield-related traits of sugar- and energy cane families derived from planned crosses.

Validação de marcadores moleculares associados à resistência à ferrugem marrom em cana-de-açúcar

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