Plant height (PH) and spike number per plant (SN) are essential wheat yield-related traits, and identifying genes affecting PH and SN is important to improve wheat yield. In a previous study, a quantitative trait locus (QTL) on 1B, qSN1B.1, was detected controlling spike number per plant (SN) by genome-wide association study (GWAS).

In this study, a gene encoding a protein sharing high homology with carotenoid isomerase (CRTISO) (TaCRTISO-1B) was identified as the causal gene underlying the QTL, and the function of TaCRTISO in controlling wheat PH and SN was validated by genome editing and EMS mutant.

Single (aaBBDD and AAbbDD), double (AAbbdd) and triple (aabbdd) loci mutants in all three TaCRTISO homoeologous genes were obtained by gene editing. The four types of mutants were all significantly shorter than the wild-type with more loci knocked-out, the more decrease of PH. In greenhouse, aaBBDD and AAbbDD mutants had an increased SN, whereas the AAbbdd and aabbdd mutants had a reduced SN.

In growth chamber, the SN was higher in all mutants relative to the wild-type. Four types of natural allelic variations of TaCRTISO-1B in wheat germplasm lines were identified, accessions with Type Ⅲ alleles are 1BL/1RS translocation lines harboring the rye (Secale cereale) CRTISO locus.

Phenotypic evaluation indicated that the introgression of 1RS into the wheat genome affecting PH and SN. This study provided a targeting gene and high valuable information that can be used to modify PH in wheat breeding by gene editing and marker assisted breeding.