Identification of a candidate gene for a QTL for spikelet number per spike on wheat chromosome arm 7AL by high-resolution genetic mapping

Authors: KUZAY, SAARAH - University Of California; XU, YUNFENG - Kansas State University; ZHANG, JUNLI - University Of California; KATZ, ANDREW - Colorad0 State University; PEARCE, STEPHEN - Colorad0 State University; SU, ZHENQI - Kansas State University; FRASER, MAX - University Of Minnesota; ANDERSON, JAMES - University Of Minnesota; Brown-Guedira, Gina; DEWITT, NOAH - North Carolina State University; PETERS HAUGRUD, AMANDA - North Dakota State University; Faris, Justin; AKHUNOV, EDUARD - Kansas State University; Bai, Guihua; DUBCOVSKY, JORGE - University Of California

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/16/2019
Publication Date: 6/28/2019
Citation: Kuzay, S., Xu, Y., Zhang, J., Katz, A., Pearce, S., Su, Z., Fraser, M., Anderson, J.A., Brown Guedira, G.L., Dewitt, N., Peters Haugrud, A., Faris, J.D., Akhunov, E., Bai, G., Dubcovsky, J. 2019. Identification of a candidate gene for a QTL for spikelet number per spike on wheat chromosome arm 7AL by high-resolution genetic mapping. Theoretical and Applied Genetics. https://doi.org/10.1007/s00122-019-03382-5.
DOI: https://doi.org/10.1007/s00122-019-03382-5

Interpretive Summary: A better understanding of the genes controlling differences in wheat grain yield components can accelerate the improvements required to satisfy future food demands. The number of spikelets per spike can influence the number of grains harvested per unit area. In this study, we identified a candidate gene underlying a quantitative trait locus (QTL) on wheat chromosome arm 7AL regulating spikelet number per spike (SNS). We used large families (>10,000 plants) from two crosses to map the 7AL QTL to an 87 kb region containing two complete and two partial genes. In this region, we found three major haplotypes that were designated as H1, H2 and H3. The H2 haplotype contributed the high SNS allele in both H1 x H2 and H2 x H3 segregating populations. The ancestral H3 haplotype is frequent in wild emmer (48%) but rare (~1%) in cultivated wheats. By contrast, the H1 and H2 haplotypes became predominant in modern cultivated durum and common wheat, respectively. Among the four candidate genes, only TraesCS7A01G481600 showed a polymorphism in the gene that differentiated H2 from the other two haplotypes. This gene, designated here as WHEAT ORTHOLOG OF APO1 (WAPO1), is an ortholog of the rice gene ABERRANT PANICLE ORGANIZATION 1 (APO1), which affects spikelet number. Taken together, the high-resolution genetic map, the association between polymorphisms in the different mapping populations with differences in SNS, and the known role of orthologous genes in other grass species suggest that WAPO-A1 is the most likely candidate gene for the 7AL SNS QTL among the four genes identified in the candidate gene region.

Technical Abstract: A better understanding of the genes controlling differences in wheat grain yield components can accelerate the improvements required to satisfy future food demands. In this study, we identified a candidate gene underlying a quantitative trait locus (QTL) on wheat chromosome arm 7AL regulating spikelet number per spike (SNS). We used large heterogeneous inbred families (>10,000 plants) from two crosses to map the 7AL QTL to an 87 kb region (674,019,191- 674,106,327 bp, RefSeq v1.0) containing two complete and two partial genes. In this region, we found three major haplotypes that were designated as H1, H2 and H3. The H2 haplotype contributed the high SNS allele in both H1 x H2 and H2 x H3 segregating populations. The ancestral H3 haplotype is frequent in wild emmer (48%) but rare (~1%) in cultivated wheats. By contrast, the H1 and H2 haplotypes became predominant in modern cultivated durum and common wheat, respectively. Among the four candidate genes, only TraesCS7A01G481600 showed a non-synonymous polymorphism that differentiated H2 from the other two haplotypes. This gene, designated here as WHEAT ORTHOLOG OF APO1 (WAPO1), is an ortholog of the rice gene ABERRANT PANICLE ORGANIZATION 1 (APO1), which affects spikelet number. Taken together, the high-resolution genetic map, the association between polymorphisms in the different mapping populations with differences in SNS, and the known role of orthologous genes in other grass species suggest that WAPO-A1 is the most likely candidate gene for the 7AL SNS QTL among the four genes identified in the candidate gene region.