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

doi:10.1007/s00122-019-03382-5

Abstract

Key messageA 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.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.

Highlights

Common wheat (Triticum aestivum L.) and durum wheat (T. turgidum subsp. durum (Desf.) Husn.) provide more than 20% of the calories and protein consumed by the human population (FAOSTAT 2017)
Using spikelet number per spike (SNS) data previously collected from four field experiments (Zhang et al 2018), we identified three significant quantitative trait locus (QTL) for SNS on chromosome arms 2BS, 7AS and 7AL that were consistent across environments (Fig. 1a)
In the screening of the Berkut × RAC875 recombinant inbred lines (RILs), we found that RIL23 ( F5) and RIL42 ( F6) were heterozygous for flanking markers IWB53096 and IWB713 and selected them to generate heterogeneous inbred families (HIFs) populations

Summary

Introduction

Common wheat (Triticum aestivum L.) and durum wheat (T. turgidum subsp. durum (Desf.) Husn.) provide more than 20% of the calories and protein consumed by the human population (FAOSTAT 2017). GNS can be further divided into grain number per spikelet and spikelet number per spike (SNS), which is the focus of this study. SNS is determined by the number of lateral spikelet meristems generated by the spike meristem before it transitions to a terminal spikelet. This number is determined at an early stage of wheat reproductive development and is less affected by growing conditions than other yield components (Zhang et al 2018). In a recent genome-wide association study (GWAS) including 262 common wheat photoperiod-insensitive spring lines, heritability values for SNS (average H2 = 0.84) were ~ 30% higher than those for GNS (average H2 = 0.64) (Zhang et al 2018)

Methods

Results

Conclusion