Dwarf genes play a crucial role in wheat genetics and breeding. Different ecological zones and wheat varieties have varying requirements for plant height. Therefore, understanding the distribution pattern and characteristics of dwarf genes in Shanxi wheat, as well as identifying novel genetic loci related to plant height will contribute to wheat genetic improvement.

Based on the accurate identification of plant height and component traits, a total of 11 known dwarfing gene types were genotyped in 306 Shanxi wheat samples and integrated with a 16K SNP chip to conduct genome-wide association analysis aimed at identifying new loci controlling plant height.

With the exception of spike length, both of the plant height and component traits of Shanxi wheat exhibited a gradual decline over the years of breeding and the various compositional traits associated with plant height were influenced by distinct selection pressures. The distribution frequency of 11 dwarfing genes in Shanxi wheat from high to low was Rht12, Rht24, Rht8, Rht26, Rht13, Rht25, Rht2, Rht5, Rht4, Rht1, and Rht9, among which Rht1, Rht2, and Rht25 have not been found in landraces. Except for Rht2 and Rht25 is more widely distributed in irrigated cultivars than in dryland cultivars, the distribution of other dwarfing genes is relatively similar in dryland cultivars and irrigated cultivars. A total of 125 different dwarf genes combination were identified, of which the combination with the highest distribution frequency was Rht8+Rht12+Rht24. Combined with association analysis, a total of 26 stable genetic loci were identified to be distributed on 14 chromosomes including 1A, 2A, and 2B. Notably, eight loci such as QPH-6D, QPH-7A, and Q3rd IL-1D have not been reported yet. Among these, QPH-6D mainly reduced plant height by shortening the length of the third and fourth internodes by approximately 13.68%, while QPH-7A reduced the plant height by 16.87% via shortening the length of the second and third internodes.

The main dwarf genes in Shanxi wheat were mainly Rht12, Rht24, and Rht8. 26 stable genetic loci were located on chromosomes 1A, 2A, and 2B, among which eight loci such as QPH-6D, QPH-7A, and Q3rd IL-1D may be novel loci related to plant height.