Low molecular weight gluten subunits (LMW-GS) are crucial components in determining the end-use quality of common wheat. Elucidating the diversity and impact on flour quality of LMW-GS is essential for genetic improvement in wheat.

A collection of 421 Shanxi wheat accessions was utilized to identify allelic variations in the Glu-A3 and Glu-B3 using 18 specific markers. The polymorphism, genetic diversity, and cluster analysis of these alleles in Shanxi wheat was then conducted. Additionally, the effects of these alleles on the physicochemical quality, farinograph and extensograph properties, as well as dough viscosity characteristics of flour were investigated.

The allelic variations in the Glu-A3, by frequency, are Glu-A3b, Glu-A3c, Glu-A3g, Glu-A3d, Glu-A3f, Glu-A3a, and Glu-A3e. At the Glu-B3, the identified allelic variations are Glu-B3g, Glu-B3a, Glu-B3d, Glu-B3i, Glu-B3b, Glu-B3h, Glu-B3e, Glu-B3c, and Glu-B3f. The genetic distance range for Shanxi wheat is 0.000 to 0.667, with a mean value of 0.253. It was observed that cultivars exhibited a greater genetic distance than landraces. Geographical distribution and irrigation/dryland types also influenced the genetic diversity of LMW-GS. Correlation analysis revealed that six LMW-GS allelic variations significantly correlated with five physicochemical quality traits. Glu-A3b, Glu-A3d, and Glu-B3i had negative effects on protein content, while Glu-A3b and Glu-B3i had positive effects on starch content. Glu-A3d and Glu-B3i showed positive effects on fiber content, and Glu-B3i increased the whiteness value of flour by 2.10%. Fifteen LMW-GS allelic variations were identified as significantly correlated with 12 processing quality traits, with Glu-A3e and Glu-B3d increasing extensibility by 36.71 and 19.91 mm, respectively. Glu-A3a, Glu-B3b, and Glu-B3e had positive effects on improving development time, stability time, stretch area, extension resistance, stretch ratio, and farinograph quality. Five LMW-GS subunits were significantly correlated with dough viscosity characteristics, with Glu-A3a increasing peak viscosity by 183.19 cp and the pad abort value by 67.79 cp.

LMW-GS alleles in Shanxi wheat exhibited high polymorphism. Geographical distribution and accession types affected the genetic diversity at the Glu-A3 and Glu-B3 loci. Six, fifteen, and five LMW-GS allelic variations were identified as showing significant correlations with flour physicochemical, processing quality, and dough viscosity traits, respectively.

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.

In arid and semi-arid regions, the water and nutrients are scarce in the soil. The phosphorus use efficiency between different wheat genotypes varies greatly. Therefore, identification of low phosphorus-tolerant germplasm and mapping of related loci is helpful for genetic improvement of wheat.

Using 282 Shanxi wheat varieties as materials, twelve seedling morphological indicators were investigated under three phosphorus concentrations, including SDW, RDW, DW, SFW, RFW, FW, MRL, TRL, RS, RV, RD, and RN. Principal component analysis, membership function analysis, and cluster analysis were used to comprehensively evaluate the low phosphorus tolerance characteristics of different varieties at the seedling stage. On this basis, the trait evolution trend and biomass allocation at seedling stage were analyzed. At the same time, GWAS was used to identify significant loci related to the low phosphorus-related traits.

The response of different traits to low phosphorus at the seedling stage was different. Lower phosphorus concentrations led to changes in biomass allocation strategy, and shoot growth was less affected by change in phosphorus concentrations than root growth. The decrease in phosphorus concentration inhibited the growth of shoot, and SDW and SFW were significantly reduced. In contrast, low phosphorus promoted root growth, and the indicators of RDW, RFW, MRL, TRL, RV and RN increased significantly. According to the correlation analysis between D-value and morphological indicators, it was found that MRL and RD could be used as selection indicators for low phosphorus tolerance at seedling stage. Based on D-value clustering analysis, 9 low phosphorus tolerant varieties were selected, including Jinmai 46, Jinmai 61, Youmangdahongjing, Hongtumai, Hongheshang, Baikehong, Baixianmai, Huoshaotou, Baishanmai. Analysing trends in trait evolution showed that cultivars were not directly selected for their ability to tolerate low phosphorus. The ability to tolerate low phosphorus decreased first and then increased over time. Before 2010, there was a decreasing trend in the ability of varieties to tolerate low phosphorus, and after 2010, there was an increase in the ability of varieties to tolerate low phosphorus. GWAS stably detected eight loci with R²>10% in three environments, in which 1A_545074550, 2B_489279799, 6A_166899658 and 6A_273060644 were not reported previously.

The MRL and RD can be used as selection indicators for low phosphorus tolerance at seedling stage. A total of nine varieties were selected through comprehensive evaluation of ability in Shanxi wheat to tolerate low phosphorus during seedling stage. Association analysis detected four novel loci associated with low phosphorus tolerance on chromosomes 1A, 2B and 6A, and the results provide germplasm resources and QTL for future low phosphorus tolerance wheat breeding.