The wheat 55K SNP-based exploration of loci for spikelet number per spike from a tetraploid wheat (Triticum turgidum L.) recombinant inbred line population derived from a Chinese landrace Ailanmai and a wild emmer accession

Spikelet number per spike (SNS) is a key factor in determining kernel number per spike which has a great effect on wheat grain yield. Modern wheat breeding narrows genetic diversity among cultivars leading to a detrimental effect on future wheat improvement. It is thus of great significance to explore new genetic resources for SNS to increase wheat yield. Here, a tetraploid landrace Ailanmai x 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. Our results showed that the genetic and physical locations of 94.83% (6204) of the mapped markers were consistent. Subsequently, 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 considered as major and novel QTL and their combination had the largest effect and increased SNS by 17.47%. In the physical intervals of QSns.sau-AM-2B.3 and QSns.sau-AM-3B.2, some development-related genes were predicted to participate in the spikelet growth and affect SNS. Additionally, significant correlations between SNS and other agronomic traits like significant and positive correlation between SNS and thousand kernel weight were detected and analyzed. Our findings demonstrated the feasibility of wheat 55K SNP array in genetic mapping of tetraploid wheat and provided an example of exploring outstanding genetic resources from wheat related species for further utilization in common wheat improvement. Key messageThe wheat 55K SNP array was firstly and successfully applied to construct a genetic map and explore two major and novel QTL for SNS in a tetraploid wheat RIL population.