Table S1

Classificaition and distribution of haplotype for 769 Chinese wheat landraces"

Table S2

Genotyping and geographical distribution of 223 world wheat accessions"

Table S3

Genotyping and geographical distribution of 144 Chinese wheat varieties/lines"

Table S4

Genotyping results of 119 Sichuan wheat varieties"

Fig. 1

Gene structures (a), chromosomal locations (b), and protein structures (c) analysis of WAPO1 Ta: Triticum aestivum; Tt: Triticum turgidum; Ae: Aegilops tauschii; Hv: Hordeum vulgare; Os: O. sativa; At: Arabidopsis thaliana; c: F-box is the protein domain. Purple boxes represent low complexity regions."

Table S5

Cis-acting elements of promoters of three homeologs of WAPO1 in wheat"

Table 1

Common cis-acting elements of promoters in wheat"

Fig. S1

Expression analysis of WAPO1 in wheat Z10, Z13, Z23, Z30, Z32, Z39, Z65, Z71, Z75 and Z85 were the stages of Zadoks[49], indicating seedling stage, three leaves stage, three tillers stage, spike at 1cm stage, two nodes stage, reproductive stage, anthesis stage, filling stage, milk-ripe stage and dough stage, respectively."

Fig. 2

Genotyping of WAPO1 gene in different populations Kompetitive Allele Specific PCR (KASP) genotyping results of WAPO1 in Chinese wheat landraces (a), Sichuan wheat varieties (c), world wheat varieties and Chinese wheat varieties/lines (d); blue box represents lines carrying the allele of 140G (HEX fluorescence); orange frame represents lines carrying the allele of 140T (FAM fluorescence); black dots are blank controls; promoter genotyping results of WAPO1 in Chinese wheat landraces (b); M represents markers for DNA Ladder; 1-7 represent 115insertion lines and 8 and 9 represent 115deletion lines."

Fig. 3

Cloning and sequencing of WAPO1 and promoter in Chinese wheat landraces lines (a) and (b) are WAPO1 and promoter clones of D778 and D91, respectively; 1-3 were three replicates of D778; 4-6 were three replicates of D91; M represents markers for DNA ladder; (c) is WAPO1 sequencing results of D778, D627, D91, and D235, and red box is the F-box 140G/T; (d) is promoter sequencing results of D778, D627, D91, and D235, and red box is the 115 insertion/deletion; the reference sequence is the Chinese Spring reference genome."

Fig. 4

SNS significance analysis of four haplotypes in Chinese wheat landraces SNS represents spikelet number per spike; H1, H2, H3, and H4 represent haplotype 1, haplotype 2, haplotype 3, and haplotype 4, respectively. *: P < 0.05; **: P < 0.01. Values above the boxplot represent the difference between the two groups of materials."

Fig. S2

Sequence analysis of WAPO1 and promoter in various species (a) and (b) are sequence analysis of promoter 115 insertion/deletion and F-box 140G/T in hexaploid wheat, respectively; (c) and (d) are sequence analysis of promoter 115 insertion/deletion and F-box 140G/T in tetraploid wheat, respectively; (c) and (d) are sequence analysis of F-box 140G/T in diploid wheat and other Triticeae species, respectively; Red box is the F-box 140G/T and promoter 115 insertion/deletion; the reference sequence was the Chinese Spring reference genome, and species names were on the left side of sequence."

Fig. 5

Significance analysis of agronomic traits in Chinese wheat landraces TN, SNS, GL, GW, TGW, PH, and FP represent tiller number, spikelet number per spike, grain length, grain width, thousand-grain weight, plant height, and flowering period, respectively; Group A represents superior haplotypes H2 and H4 and Group B represents haplotypes H1 and H3; *: P < 0.05; **: P < 0.01. Values above the boxplot represent the difference between the two groups of materials."

Fig. 6

Significance analysis of agronomic traits in Sichuan wheat varieties SL, SNS and TGW represent spike length, spikelet number per spike, and thousand-grain weight, respectively; Group A represents superior haplotypes H2 and H4 and Group B represents haplotypes H1 and H3. *: P < 0.05; **: P < 0.01. Values above the boxplot represent the difference between the two groups of materials. 2017CZ and 2018CZ represent the phenotypic data of Chongzhou in 2017 and 2018, respectively."

Fig. S3

Identification of geographical distribution of four haplotypes of WAPO1 in Chinese wheat landraces H1, H2, H3 and H4 represent haplotype 1, haplotype 2, haplotype 3 and haplotype 4; Ⅰ represents Northern winter (autumn sowing) wheat area; Ⅱ represents Huang-Huai winter (autumn sowing) wheat area; Ⅲ represents Yangtze River winter (autumn sowing) wheat area; Ⅳ represents South China winter (late autumn sowing) wheat area; Ⅴ represents Southwest winter (autumn sowing) wheat area; Ⅵ represents Northeast spring wheat area; Ⅶ represents Northern spring wheat area; Ⅷ represents Northwest spring wheat area; Ⅸ represents Qinghai-Tibet spring-winter wheat area; Ⅹ represents Xinjiang winter-spring wheat area."

Table S6

Comparative analysis of agronomic traits between haplotype H2 + H4 and haplotype H1 + H3"