A promising QTLQSns.sau-MC-3D.1likely superior toWAPO1for wheat spikelet number per spike shows no adverse effects on yield-related traits

Abstract

Spikelet number per spike (SNS) is one of the crucial factors determining wheat yield. Thus, improving our understanding of the genes that regulate SNS could help develop higher-yielding wheat varieties. A genetic linkage map constructed using the GenoBaits Wheat 16K Panel and the 660K SNP array contained 5991 polymorphic SNP markers spanning 2813.26 cM. A total of twelve QTL for SNS were detected in the recombinant inbred line (RIL) populationmsf× Chuannong 16 (MC), and two of them, i.e.,QSns.sau-MC-3D.1andQSns.sau-MC-7A, were stably expressed.QSns.sau-MC-3D.1had high LOD values ranging from 4.99 to 11.06 and explained 9.71-16.75% of the phenotypic variation. Comparison ofQSns.sau-MC-3D.1with previously reported SNS QTL suggested that it is likely a novel one. A kompetitive allele-specific PCR (KASP) marker, KASP-10, tightly linked toQSns.sau-MC-3D.1was developed to successfully validate its effect in three segregated populations and a natural population. Genetic analysis indicated thatWHEAT ORTHOLOG OFAPO1(WAPO1) was a candidate gene forQSns.sau-MC-7A. The combined additive effect ofQSns.sau-MC-3D.1andWAP01had a great additive effect increasing SNS by 7.10%. In addition, our results suggested that SNS is not affected by 1BL/1RS translocations in the MC RIL population. Correlation analysis between two major QTL and other agronomic traits showed thatQSns.sau-MC-3D.1was likely independent of these agronomic traits. However, the H2 haplotype ofWAPO1may affect effective tiller number and plant height. This indicated that the breeding potential ofQSns.sau-MC-3D.1is better than that ofWAPO1. The geographical distribution ofQSns.nsau-MC-3D.1showed thatQSns.sau-MC-3D.1positive allele frequency was dominant in most wheat-producing regions of China and it has been positively selected among modern cultivars released in China since the 1940s. Two genes,TraesCS3D03G0222600andTraesCS3D03G0216800, associated with SNS development were predicted in the physical interval ofQSns.sau-MC-3D.1. qRT-PCR results of the two genes showed that only the expression level ofTraesCS3D03G0216800was significantly different between msf and CN16. These results enrich our understanding of the genetic basis of wheat SNS and will be useful for fine mapping and cloning of genes underlyingQSns.sau-MC-3D.1, and provide a basis for marker-assisted selection breeding.Author summaryIn this study, we identified two major QTL (QSns.sau-MC-3D.1andQSns.sau-MC-7A) in a RIL population.WAPO1was demonstrated to be the candidate gene forQSns.sau-MC-7A. QSns.sau-MC-3D.1was a novel and stably expressed QTL, and further confirmed in different genetic backgrounds. Our results further demonstrate thatQSns.sau-MC-3D.1has better breeding potential because of its no adverse effect on other agronomic traits thanWAPO1, and it has been positively selected during Chinese breeding programs since the 1940s. Taken together, the identification ofQSns.sau-MC-3D.1offers a promising resource to further increase wheat yields.