Identification and map-based cloning a new gene TaSP1 related to spike shape by EMS-induced wheat mutant

Abstract Spike shape, an important factor for wheat grain yield, is mainly defined by spike length (SPL), spikelet number (SPN) and compactness. ZM1160, a mutant obtained from ethyl methane sulfonate (EMS) treatment of hexaploid wheat variety Zhoumai32, was used to identify and clone the candidate gene conditioned the spike shape. Genetic analysis of an F₂ population derived from a cross of ZM1160 and Bainong207 suggested that the compact spike shape in ZM1160 was controlled by a single recessive gene, and therefore the mutated gene was designated as Tasp1. With polymorphic markers identified through bulked segregant analysis (BSA), the gene was mapped to a 2.65 cM interval flanked by markers YZU0852 and MIS46239 on chromosome 7D, corresponding to a 0.42 Mb physical interval of Chinese spring (CS) reference sequences (RefSeq v1.0). To fine map TaSP1, 15 and 7 recombinants were respectively screened from 1599 and 1903 F₃ plants derived from the heterozygous F₂plants. Finally, TaSP1 was delimited to a 21.9 Kb (4,870,562 to 4,892,493 bp) Xmis48123-Xmis48104 interval. Only one high-confidence gene TraesCS7D02G010200 was annotated in this region, which encodes an unknown protein with a putative vWA domain. The quantitative reverse transcription PCR (qRT-PCR) analysis showed that TraesCS7D02G010200 was mainly expressed in the spike. Haplotype analysis of 655 wheat cultivars using the candidate gene-specific marker G010200P2 identified a superior haplotype TaSP1b with longer spike. TaSP1 is beneficial to the improvement of wheat spike shape.