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QTL Mapping for Grain Yield, Flowering Time, and Stay-Green Traits in Sorghum with Genotyping-by-Sequencing Markers

Sukumaran, Sivakumar, Li, Xin, Li, Xianran, Zhu, Chengsong, Bai, Guihua, Perumal, Ramasamy, Tuinstra, Mitchell R., Prasad, P.V. Vara, Mitchell, Sharon E., Tesso, Tesfaye T., Yu, Jianming
Crop science 2016 v.56 no.4 pp. 1429-1442
Sorghum (Poaceae), agronomic traits, breeding, chlorophyll, chromosome mapping, chromosomes, flowering, fluorescence, food quality, genetic distance, genetic improvement, genetic markers, genotype-phenotype correlation, genotyping, grain yield, hybrids, inbred lines, leaf area, leaves, phenotype, phenotypic variation, quantitative trait loci, single nucleotide polymorphism
Molecular breeding can complement traditional breeding approaches to achieve genetic gains in a more efficient way. In the present study, genetic mapping was conducted in a sorghum recombinant inbred line (RIL) population developed from Tx436 (a non-stay-green high food quality inbred) × 00MN7645 (a stay-green high yield inbred) and evaluated in eight environments (location and year combination) in a hybrid background of Tx3042 (a non-stay-green A-line). Phenotyping was conducted for agronomic traits (grain yield and flowering time), physiological traits of stay-green (chlorophyll content [SPAD] and chlorophyll fluorescence [F/F] measured on the leaves), and green leaf area visual score (GLAVS). This population was genotyped with genotyping-by-sequencing (GBS) technology. Data processing resulted in 7144 high quality single nucleotide polymorphisms (SNPs) that were used in a genome-wide single marker scan with physical distance. A selected subset of 1414 SNPs was used for composite interval mapping (CIM) with genetic distance. These complementary methods revealed fifteen QTLs for the traits studied. In addition, QTL mapping for individual environments and year-wise combinations revealed 42 QTLs. A consistent QTL for grain yield under normal and stressed conditions was identified in chromosome 1 that explained 8 to 16% of the phenotypic variation. QTLs for flowering time were identified in chromosomes 2, 6, and 9 that explained 6 to 11% of the phenotypic variation. Stay-green QTLs in chromosomes 3 and 4 explained 8 to 24% of the phenotypic variation. These identified QTLs with flanking SNPs of known genomic positions could be used to improve grain yield, flowering time, and stay-green in sorghum molecular breeding programs.