A genome-wide association study identified loci for yield component traits in sugarcane (Saccharum spp.)

Autor(es)

Barreto, Fernanda Zatti ^[1] ; Bachega Feijo Rosa, Joao Ricardo ^{[2, 3]} ; Almeida Balsalobre, Thiago Willian ^[1] ; Pastina, Maria Marta ^{[2, 4]} ; Silva, Renato Rodrigues ^[5] ; Hoffmann, Hermann Paulo ^[1] ; de Souza, Anete Pereira ^{[6, 7]} ; Franco Garcia, Antonio Augusto ; Carneiro, Monalisa Sampaio ^[1]

Afiliação do(s) autor(es)

^[1] Univ Fed Sao Carlos, Ctr Ciencias Agr, Dept Biotecnol & Prod Vegetal & Anim, Sao Paulo - Brazil

^[2] Univ Sao Paulo, Escola Super Agr Luiz de Queiroz, Dept Genet, Sao Paulo - Brazil

^[3] FTS Sementes SA, Ctr Pesquisa & Desenvolvimento Cultivares Soja, Setor Pesquisa & Desenvolvimento, Ponta Grossa, Parana - Brazil

^[4] Embrapa Milho & Sorgo, Ctr Pesquisa & Desenvolvimento, Sete Lagoas, MG - Brazil

^[5] Univ Fed Goias, Inst Matemat & Estat, Campus Samambaia, Goiania, Go - Brazil

^[6] Univ Estadual Campinas, Inst Biol, Dept Biol Vegetal, Campinas, SP - Brazil

^[7] Univ Estadual Campinas, Ctr Biol Mol & Engn Genet, Campinas, SP - Brazil

• Tipo de documento: Artigo Científico
• Fonte: PLoS One; v. 14, n. 7 JUL 18 2019.
• Citações Web of Science: 1

Resumo

Sugarcane (Saccharum spp.) has a complex genome with variable ploidy and frequent aneuploidy, which hampers the understanding of phenotype and genotype relations. Despite this complexity, genome-wide association studies (GWAS) may be used to identify favorable alleles for target traits in core collections and then assist breeders in better managing crosses and selecting superior genotypes in breeding populations. Therefore, in the present study, we used a diversity panel of sugarcane, called the Brazilian Panel of Sugarcane Genotypes (BPSG), with the following objectives: (i) estimate, through a mixed model, the adjusted means and genetic parameters of the five yield traits evaluated over two harvest years; (ii) detect population structure, linkage disequilibrium (LD) and genetic diversity using simple sequence repeat (SSR) markers; (iii) perform GWAS analysis to identify marker-trait associations (MTAs); and iv) annotate the sequences giving rise to SSR markers that had fragments associated with target traits to search for putative candidate genes. The phenotypic data analysis showed that the broad-sense heritability values were above 0.48 and 0.49 for the first and second harvests, respectively. The set of 100 SSR markers produced 1,483 fragments, of which 99.5% were polymorphic. These SSR fragments were useful to estimate the most likely number of subpopulations, found to be four, and the LD in BPSG, which was stronger in the first 15 cM and present to a large extension (65 cM). Genetic diversity analysis showed that, in general, the clustering of accessions within the subpopulations was in accordance with the pedigree information. GWAS performed through a multilocus mixed model revealed 23 MTAs, six, three, seven, four and three for soluble solid content, stalk height, stalk number, stalk weight and cane yield traits, respectively. These MTAs may be validated in other populations to support sugarcane breeding programs with introgression of favorable alleles and marker-assisted selection. (AU)

• Processo FAPESP: 10/50091-4 - Mapeamento de QTLs em população derivada de cruzamento comercial bi-parental em cana-de-açúcar
• Beneficiário: Thiago Willian Almeida Balsalobre
• Linha de fomento: Bolsas no Brasil - Doutorado Direto
• Processo FAPESP: 08/52197-4 - Genomic-assisted breeding of sugarcane: using molecular markers for understanding the genetic architecture of quantitative traits and to implement marker assisted selection
• Beneficiário: Anete Pereira de Souza
• Linha de fomento: Auxílio à Pesquisa - Programa BIOEN - Temático
• Processo FAPESP: 10/06702-9 - Análise do desequilíbrio de ligação em cana-de-açúcar
• Beneficiário: João Ricardo Bachega Feijó Rosa
• Linha de fomento: Bolsas no Brasil - Mestrado
• Processo FAPESP: 08/57908-6 - Instituto Nacional de Biotecnologia para o Bioetanol
• Beneficiário: Marcos Silveira Buckeridge
• Linha de fomento: Auxílio à Pesquisa - Programa BIOEN - Temático