The difference in TGW between the haplotypes TaFlo2-A1a and TaFlo2-A1b was statistically significant in both populations (P < 0.05, Table 2). In the MCC, the mean difference in TGW between the groups of accessions having TaFlo2-A1a and TaFlo2-A1b was significant (P ≤ 0.05) across the 3 years of data. The mean differences in TGW between the two haplotypes in 2002, 2005 and 2006 were 7.00 ± 1.12 g, 7.80 ± 1.11 g and 8.40 ± 0.94 g, respectively. Consistent with the results of the MCC, the mean difference in TGW between groups of accessions having TaFlo2-A1a and TaFlo2-A1b was also significant (P ≤ 0.05) across both years of data in the Pakistani wheat collection. The values of the mean difference between the two haplotypes (TaFlo2-A1a and TaFlo2-A1b) in the Pakistani wheat population were 4.50 ± 0.71 g and 5.20 ± 0.72 g for 2009 and 2010, respectively. The phenotypic variance for TGW explained by TaFlo2-A1 haplotypes was 6.19% in 2002, 7.76% in 2005 and 8.37% in 2006 in the MCC. In the Pakistani collection, the phenotypic variance for TGW explained by TaFlo2-A1 haplotypes was 4.42% in 2009 and 5.11% in 2010 (Table 2). Moreover, to determine whether TaFlo2-A1 also affects grain number per spike (GpS), an association analysis was performed for GpS in both populations. However, the differences in GpS between the haplotypes TaFlo2-A1a and TaFlo2-A1b were not significant in either population (P < 0.05, Table 2).Table 2Association of TGW and GpS with TaFlo2-A1 in the Chinese Micro Core Collection and Pakistani wheat collectionsNatural populationsYear (number of accessions) TaFlo2-A1a Mean ± SEa (number of accessions) TaFlo2-A1b Mean ± SE (number of accessions)Mean difference ± SEPVE (%)b TGWTGWGpSTGWGpSTGWGpSChinese Micro Core Collection2002 (137)33.6 ± 0.54(98)50.8 ± 1.2(98)40.6 ± 1.2(39)49.7 ± 1.5(39)7.0 ± 1.1**1.06 ± 2.1ns 6.192005 (169)30.7 ± 0.52(128)43.1 ± 0.8(128)38.5 ± 1.1(41)40.5 ± 1.1(41)7.8 ± 1.1**2.6 ± 1.5 ns 7.762006 (185)32.8 ± 0.43(141)51.4 ± 0.7(141)41.2 ± 0.9(44)48.6 ± 1.2(43)8.4 ± 0.9**2.7 ± 1.5 ns 8.37Pakistani collection2009 (130)40.6 ± 0.43(85)46.6 ± 1.1(85)45.1 ± 0.55(45)44.4–1.8(45)4.5 + 0.71**2.2 ± 1.9 ns 4.422010 (130)40.5 ± 0.47(85)47.8 ± 1.2(85)45.7 ± 0.46(45)44.9 + 1.6(45)5.2 ± 0.72**2.9 ± 2.0 ns 5.11 **indicates significant differences, and ns indicates non-significant differences (P < 0.01; Student’s t-test) among groups carrying different haplotypes aStandard error bPercentage of phenotypic variance explained by association analysis