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

Saarah Kuzay, Yunfeng Xu, Junli Zhang, Andrew Katz, Stephen Pearce, Zhenqi Su, Max Fraser, James A Anderson, Gina Brown-Guedira, Noah DeWitt, Amanda Peters Haugrud, Justin D. Faris, Eduard Akhunov, Guihua Bai, Jorge Dubcovsky

Research output: Contribution to journalArticlepeer-review

21 Scopus citations


Key message: A high-resolution genetic map combined with haplotype analyses identified a wheat ortholog of rice gene APO1 as the best candidate gene for a 7AL locus affecting spikelet number per spike. 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 promising 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 × H2 and H2 × 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 TraesCS7A02G481600 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.

Original languageEnglish (US)
Pages (from-to)2689-2705
Number of pages17
JournalTheoretical and Applied Genetics
Issue number9
StatePublished - Sep 1 2019

Bibliographical note

Funding Information:
Acknowledgements This project was supported by the Agriculture and Food Research Initiative Competitive Grants 2017–67007-25939 (WheatCAP) from the USDA National Institute of Food and Agriculture, by the International Wheat Yield Partnership (IWYP), by the Bill and Melinda Gates Foundation and by the Howard Hughes Medical Institute. We thank Yana Olifir for excellent technical assistance and Juan Debernardi and Huiqiong Lin for cDNA samples of spike development. We thank Rudi Appels, Chengxia Li, Juan Debernardi and Daniel Woods for valuable advice. We thank Patrick Byrne and Scott Haley from Colorado State University for providing the CO-940610 × Platte RIL population.

Publisher Copyright:
© 2019, The Author(s).

Copyright 2019 Elsevier B.V., All rights reserved.

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