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Background  Improvement of wheat gerc Triticum aestivum  L.) yield could relieve global food shortages. Kernel size, as an important component of 1000-kernel weight (TKW), is always a significant consideration to improve yield for wheat breeders. Wheat related species possesses numerous elite genes that can be introduced into wheat breeding. It is thus vital to explore, identify, and introduce new genetic resources for kernel size from wheat wild relatives to increase wheat yield.    Results  In the present study, quantitative trait loci (QTL) for kernel length (KL) and width (KW) were detected in a recombinant inbred line (RIL) population derived from a cross between a wild emmer accession ‘LM001’ and a Sichuan endemic tetraploid wheat ‘Ailanmai’ using the Wheat 55 K single nucleotide polymorphism (SNP) array-based constructed linkage map and phenotype from six different environments. We identified eleven QTL for KL and KW including two major ones  QKL.sicau-AM-3B  and  QKW.sicau-AM-4B , the positive alleles of which were from LM001 and Ailanmai, respectively. They explained 17.57 to 44.28% and 13.91 to 39.01% of the phenotypic variance, respectively. For these two major QTL, Kompetitive allele-specific PCR (KASP) markers were developed and used to successfully validate their effects in three F 3  populations and two natural populations containing a panel of 272 Chinese wheat landraces and that of 300 Chinese wheat cultivars, respectively.  QKL.sicau-AM-3B  was located at 675.6–695.4 Mb on chromosome arm 3BL.  QKW.sicau-AM-4B  was located at 444.2–474.0 Mb on chromosome arm 4BL. Comparison with previous studies suggested that these two major QTL were likely new loci. Further analysis indicated that the positive alleles of  QKL.sicau-AM-3B  and  QKW.sicau-AM-4B  had a great additive effect increasing TKW by 6.01%. Correlation analysis between KL and other agronomic traits showed that KL was significantly correlated to spike length, length of uppermost internode, TKW, and flag leaf length. KW was also significantly correlated with TKW. Four genes,  TRIDC3BG062390 ,  TRIDC3BG062400 ,  TRIDC4BG037810 , and  TRIDC4BG037830 , associated with kernel development were predicted in physical intervals harboring these two major QTL on wild emmer and Chinese Spring reference genomes.    Conclusions  Two stable and major QTL for KL and KW across six environments were detected and verified in three biparental populations and two natural populations. Significant relationships between kernel size and yield-related traits were identified. KASP markers tightly linked the two major QTL could contribute greatly to subsequent fine mapping. These results suggested the application potential of wheat related species in wheat genetic improvement.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-08024-z.

Genetic identification and characterization of chromosomal regions for kernel length and width increase from tetraploid wheat