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Spikelet number per spike (SNS) is the primary factor that determines wheat yield. Common wheat breeding reduces the genetic diversity among elite germplasm resources, leading to a detrimental effect on future wheat production. It is, therefore, necessary to explore new genetic resources for SNS to increase wheat yield. A tetraploid landrace “Ailanmai” × wild emmer wheat recombinant inbred line (RIL) population was used to construct a genetic map using a wheat 55K single- nucleotide polymorphism (SNP) array. The linkage map containing 1,150 bin markers with a total genetic distance of 2,411.8 cm was obtained. Based on the phenotypic data from the eight environments and best linear unbiased prediction (BLUP) values, five quantitative trait loci (QTLs) for SNS were identified, explaining 6.71–29.40% of the phenotypic variation. Two of them, QSns.sau-AM-2B.2 and QSns.sau-AM-3B.2, were detected as a major and novel QTL. Their effects were further validated in two additional F2 populations using tightly linked kompetitive allele-specific PCR (KASP) markers. Potential candidate genes within the physical intervals of the corresponding QTLs were predicted to participate in inflorescence development and spikelet formation. Genetic associations between SNS and other agronomic traits were also detected and analyzed. This study demonstrates the feasibility of the wheat 55K SNP array developed for common wheat in the genetic mapping of tetraploid population and shows the potential application of wheat-related species in wheat improvement programs.

Increasing wheat yield is essential in solving the global food shortage. The spikelet number per spike (SNS) is a primary factor that determines the kernel number per spike which has a great effect on wheat yield. Modern wheat breeding methods reduce the genetic diversity among cultivars, leading to a detrimental effect on future wheat production. It is, therefore, necessary to explore new genetic resources for SNS to increase wheat yield. A tetraploid landrace Ailanmai wild emmer wheat recombinant inbred line (RIL) population was used to construct a high-density genetic map using the wheat 55K single nucleotide polymorphism (SNP) array. The linkage map revealed that 94.83% (6204) of the mapped markers had consistent genetic and physical chromosomal locations. Fourteen quantitative trait loci (QTL) for SNS, explaining 4.23-27.26% of the phenotypic variation, were identified. QSns.sau-AM-2B.3 and QSns.sau-AM-3B.2 were detected as the major and novel QTL with a large cumulative effect that increased SNS by 17.47%. Some development-related genes within the physical intervals of QSns.sau-AM-2B.3 and QSns.sau-AM-3B.2 were predicted to participate in spikelet growth, thereby affecting SNS. Genetic associations between SNS and other agronomic traits such as a significant and positive correlation between SNS and thousand kernel weight (TKW) were detected and analyzed. QTL analysis was also performed for other spike-related traits, including spike length (SL), kernel number per spike (KNS), kernel number per spikelet (KNL), and spike density (SD). QSns.sau-AM-2B.3 was co-located with QSl.sau-AM-2B in the interval between AX-111626925 and AX-111588559. Similarly, QKns.sau-AM-5B.1 was co-related with QKnl.sau-AM-5B.2 in the region between AX-108760512 and AX-110180251. This study demonstrates the feasibility of wheat 55K SNP array in genetic mapping of tetraploid wheat population and shows the potential application of wheat related species in wheat improvement programs.

The spikelet number per spike (SNS) is a primary factor determining wheat yield. Common wheat breeding reduces the genetic diversity among elite germplasm resources, leading to a detrimental effect on future wheat production. It is, therefore, necessary to explore new genetic resources for SNS to increase wheat yield. A tetraploid landrace ‘Ailanmai’ × wild emmer wheat recombinant inbred line (RIL) population was used to construct a genetic map using the wheat 55K single nucleotide polymorphism (SNP) array. The linkage map containing 1150 bin markers with a total genetic distance of 2411.8 cM was obtained. Based on phenotypic data from eight environments and best linear unbiased prediction (BLUP) values, five quantitative trait loci (QTL) for SNS were identified, explaining 6.71-29.40% of the phenotypic variation. Two of them, QSns.sau-AM-2B.3 and QSns.sau-AM-3B.2, were detected as the major and novel QTL. Their effects were further validated in two additional F2 populations using tightly linked Kompetitive Allele-Specific PCR (KASP) markers. Potential candidate genes within the physical intervals of corresponding QTL were predicted to participate in inflorescence development and spikelet formation. Genetic associations between SNS and other agronomic traits were also detected and analyzed. This study demonstrates the feasibility of wheat 55K SNP array developed for common wheat in genetic mapping of tetraploid population and shows the potential application of wheat related species in wheat improvement programs.