QTL mapping including codominant SNP markers with ploidy level information in a sugarcane progeny

Quantitative trait locus (QTL) mapping contributes to sugarcane (Saccharum spp.) breeding programs by providing information about the genetic effects, positioning and number of QTLs. Combined with marker-assisted selection, it can help breeders reduce the time required to develop new sugarcane varieties. We performed a QTL mapping study for important agronomic traits in sugarcane using the composite interval mapping method for outcrossed species. A new approach allowing the 1:2:1 segregation ratio and different ploidy levels for SNP markers was used to construct an integrated genetic linkage map that also includes AFLP and SSR markers. Were used 688 molecular markers with 1:1, 3:1 and 1:2:1 segregation ratios. A total of 187 individuals from a bi-parental cross (IACSP95-3018 and IACSP93-3046) were assayed across multiple harvests from two locations. The evaluated yield components included stalk diameter (SD), stalk weight (SW), stalk height (SH), fiber percentage (Fiber), sucrose content (Pol) and soluble solid content (Brix). The genetic linkage map covered 4512.6 cM and had 118 linkage groups corresponding to 16 putative homology groups. A total of 25 QTL were detected for SD (six QTL), SW (five QTL), SH (four QTL), Fiber (five QTL), Pol (two QTL) and Brix (three QTL). The percentage of phenotypic variation explained by each QTL ranged from 0.069 to 3.87 %, with a low individual effect because of the high ploidy level. The mapping model provided estimates of the segregation ratio of each mapped QTL (1:2:1, 3:1 or 1:1). Our results provide information about the genetic organization of the sugarcane genome and constitute the first step toward a better dissection of complex traits.Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq) from Brazil [145478/2012-2]Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP) from Brazil [2005/55258-6, 2008/52197-4, 2010/50031-1, 2010/06715-3, 2010/50549-0]Instituto Nacional de Ciencia e Tecnologia do Bioetanol [574002/2008-1, 2008/57908-6]Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES, Computacional Biology Program)CeProBio ProjectCNPqUniv Estadual Campinas UNICAMP, CBMEG, Dept Genet & Evolucao, Cidade Univ ZeferinoVaz,CP 6010, BR-13083875 Campinas, SP, BrazilUniv Sao Paulo, Dept Genet, ESALQ, CP 83, BR-13400970 Piracicaba, SP, BrazilCtr Avancado Pesquisa Tecnol Agronegocio Cana, IAC Apta, CP 206, BR-14001970 Ribeirao Preto, SP, BrazilUniv Fed Sao Paulo, Ctr Cincias Agr, Rodovia Anhanguera,Km 174, BR-14001970 Araras, SP, BrazilEmbrapa Milho & Sorgo, Nucleo Biol Aplicada, Rodovia MG 424,Km 65, BR-35701970 Sete Lagoas, MG, BrazilUniv Estadual Paulista UNESP, Dept Ciencias Exatas, Jaboticabal, SP, BrazilUniv Estadual Campinas, Inst Biol, Dept Biol Vegetal, BR-13083892 Campinas, SP, BrazilFed Sao Paulo UNIFESP, Unidade Parque Tecnol, Ave Cesare Mansueto Giulio Lattes 1201, BR-12247014 Sao Jose Dos Campos, SP, BrazilTexas A&M Univ Syst, Agrilife Res & Extens Ctr, 2415 E Hwy 83, Weslaco, TX 78596 USANorth Carolina State Univ, Bioinformat Res Ctr, 332 Ricks Hall, Raleigh, NC 27607 USAFed Sao Paulo UNIFESP, Unidade Parque Tecnol, Ave Cesare Mansueto Giulio Lattes 1201, BR-12247014 Sao Jose Dos Campos, SP, BrazilCNPq:145478/2012-2FAPESP:2005/55258-62008/52197-42010/50032-12010/06715-32010/50549-0INCT:574002/2008-12008/57908-6Web of Scienc

Geno_Data

Additive and dominance genomic relationship matrices

Pheno_Data

Field data of 312 single-cross maize hybrids evaluated in 8 trials