QTL mapping for grain yield, flowering time, and stay-green traits in sorghum with genotyping-by-sequencing markers

Authors: SUKUMARAN, SIVAKUMAR - Kansas State University; LI, XIN - Kansas State University; LI, XIANRAN - Kansas State University; ZHU, CHENGSONG - Kansas State University; Bai, Guihua; PERUMAL, RAMASAMY - Kansas State University; TUINSTRA, MITCHELL - Purdue University; PRASAD, VARA - Kansas State University; MITCHELL, SHARON - Cornell University; TESSO, TESFAYE - Kansas State University; YU, JIANMING - Kansas State University

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/9/2016
Publication Date: 6/15/2016
Publication URL: http://handle.nal.usda.gov/10113/63354
Citation: Sukumaran, S., Li, X., Li, X., Zhu, C., Bai, G., Perumal, R., Tuinstra, M., Prasad, V., Mitchell, S., Tesso, T., Yu, J. 2016. QTL mapping for grain yield, flowering time, and stay-green traits in sorghum with genotyping-by-sequencing markers. Crop Science. 56:1429-1442. doi:10.2135/cropsci2015.02.0097.

Interpretive Summary: Sorghum is an important crop that has drought tolerance. Stay-green is an important trait to reflect drought tolerance. We evaluated a sorghum recombinant inbred line (RIL) population of Tx436 (a non-stay-green high food quality inbred) × 00MN7645 (a stay-green high yield inbred) in a hybrid background of Tx3042 (a non-stay-green A-line) in eight environments. A total of 15 QTLs were identified. A consistent QTL for grain yield under normal and stressed conditions was located in chromosome 1 and 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. The markers linked to these QTLs could be used in breeding to improve sorghum production.

Technical Abstract: 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 [Fv/Fm] 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.