qSL2B/TaeEF1A regulates spike development and grain number in wheat

Spike length (SL) is an important factor affecting yield in wheat ( Triticum aestivum L.). Here, a recombinant inbred line (RIL) population derived from a cross between Shannong 4155 (SN4155) and Shimai 12 (SM12) was used to map quantitative trait loci (QTL) controlling SL. A QTL, qSL2B , on chromosome 2B was identified in all experiments and explained 9.92%–12.71% of the phenotypic variation. Through transcriptome and gene expression analysis, we identified a gene encoding Elongation Factor 1-alpha ( TaeEF1A ) as the candidate gene for qSL2B . Genome editing of TaeEF1A demonstrated that TaeEF1A positively regulates SL, spikelet number per spike (SNS), and grain number per spike (GN). Transcriptome analysis showed that TaeEF1A may affect the protein translation process and photosynthesis to regulate spike development. We used haplotype analysis of wheat germplasm to identify seven types of genetic variations in TaeEF1A , with Type I, Type II, and Type III being the major haplotypes. Screening of 428 cultivars and breeding lines identified 225 and 203 accessions as Type I and Type II haplotypes, respectively, with Type III not detected. Comparison of SL, SNS, and GN between the Type I and Type II haplotypes revealed that the Type I allele can increase SL, SNS, and GN simultaneously, and is thus preferred for use in wheat molecular breeding efforts to increase SL, SNS, and GN.