Identification of a major QTL and genome-wide epistatic interactions for single vs. paired spikelets in a maize-teosinte F2 population

Maize ear carries paired spikelets, whereas the ear of its wild ancestor, teosinte, bears single spikelets. However, little is known about the genetic basis of the processes of transformation of single spikelets in teosinte ear to paired spikelets in maize ear. In this study, a two-ranked, paired-spikelets primitive maize and a two-ranked, single-spikelet teosinte were utilized to develop an F2 population, and quantitative trait locus (loci) (QTL) mapping for single vs. paired spikelets (PEDS) was performed. One major QTL (qPEDS3.1) for PEDS located on chromosome 3S was identified in the 162 F2 plants using the inclusive composite interval mapping of additive (ICIM-ADD) module, explaining 23.79% of the phenotypic variance. Out of the 409 F2 plants, 43 plants with PEDS = 0% and 43 plants with PEDS > 20% were selected for selective genotyping, and the QTL (qPEDS3.1) was detected again. Moreover, the QTL (qPEDS3.1) was validated in three environments, which explained 31.05%, 38.94%, and 23.16% of the phenotypic variance, respectively. In addition, 50 epistatic QTLs were detected in the 162 F2 plants using the two-locus epistatic QTL (ICIM-EPI) module; they were distributed on all 10 chromosomes and explained 94.40% of the total phenotypic variance. The results contribute to a better understanding of the genetic basis of domestication of paired spikelets and provide a genetic resource for future map-based cloning; in addition, the systematic dissection of epistatic interactions underlies a theoretical framework for overcoming epistatic effects on QTL fine mapping.