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

Theoretical and Applied Genetics; September 2019, Volume 132, Issue 9, pp 2689–2705

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.

See https://link.springer.com/article/10.1007/s00122-019-03382-5

Fig. 2

Physical map of the candidate gene region in chromosome arm 7AL and candidate genes. a Candidate gene region based on the B×R and N×C Arrows represent high-confidence genes (5′–3′ direction, RefSeq v1.0 coordinates and RefSeq v1.1 annotation). Note the different scales in the central region and distal regions. Complete gene names are provided only for the flanking genes, and only the last four numbers are provided for the other genes. Candidate gene TraesCS7A02G481600 (= WAPO-A1) is highlighted in red. b Gene models of WAPO-A1 main alleles. Alleles WAPO-A1a (in H1 haplotype) and WAPO-A1b (H2 haplotype) unique derived polymorphisms are indicated in red. “P−” indicates a 115-bp deletion in the promoter region and P+  = absence of this deletion. Negative coordinates are upstream of ATG and positive coordinates downstream (including intron). Amino acid changes are underlined and in bold and coordinates are from initial Met