Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Genome Based Meta-QTL Analysis of Grain Weight in Tetraploid Wheat Identifies Rare Alleles of GRF4 Associated with Larger Grains

Raz Avni
ORCID logo ,
Leah Oren
,
Gai Shabtai
,
Siwar Assili
,
Curtis Pozniak
,
Iago Hale
,
Roi Ben-David
,
Zvi Peleg
ORCID logo ,
Assaf Distelfeld
*
Version 1 : Received: 1 November 2018 / Approved: 2 November 2018 / Online: 2 November 2018 (15:16:48 CET)

A peer-reviewed article of this Preprint also exists.

Avni, R.; Oren, L.; Shabtay, G.; Assili, S.; Pozniak, C.; Hale, I.; Ben-David, R.; Peleg, Z.; Distelfeld, A. Genome Based Meta-QTL Analysis of Grain Weight in Tetraploid Wheat Identifies Rare Alleles of GRF4 Associated with Larger Grains. Genes 2018, 9, 636. Avni, R.; Oren, L.; Shabtay, G.; Assili, S.; Pozniak, C.; Hale, I.; Ben-David, R.; Peleg, Z.; Distelfeld, A. Genome Based Meta-QTL Analysis of Grain Weight in Tetraploid Wheat Identifies Rare Alleles of GRF4 Associated with Larger Grains. Genes 2018, 9, 636.

Abstract

The domestication and subsequent genetic improvement of wheat led to the development of large-seeded cultivated wheat species relative to their smaller-seeded wild progenitors. While increased grain weight (GW) continues to be an important goal of many wheat breeding programs, few genes underlying this trait have been identified despite an abundance of studies reporting quantitative trait loci (QTLs) for GW. Here we perform a QTL analysis for GW using a population of recombinant inbred lines (RILs) derived from the cross between wild emmer wheat accession ‘Zavitan’ and durum wheat variety ‘Svevo’. Identified QTLs in this population were anchored to the recent Zavitan reference genome, along with previously published QTLs for GW in tetraploid wheat. This genome-based, meta-QTL analysis enabled the identification of a locus on chromosome 6A whose introgression from wild wheat positively affects GW. The locus was validated using an introgression line carrying the 6A GW QTL region from Zavitan in a Svevo background, resulting in >8% increase in GW compared to Svevo. Using the reference sequence for the 6A QTL region, we identified a wheat ortholog to OsGRF4, a rice gene previously associated with GW. The coding sequence of this gene (TtGRF4-A) contains four SNPs between Zavitan and Svevo, one of which reveals the Zavitan allele to be rare in a core collection of wild emmer and completely absent from the domesticated emmer genepool. Similarly, another wild emmer accession (G18-16) was found to carry a rare allele of TtGRF4-A that also positively affects GW and is characterized by a unique SNP absent from the entire core collection. These results exemplify the rich genetic diversity of wild wheat, posit TtGRF4-A as a candidate gene underlying the 6A GW QTL, and suggest that the natural Zavitan and G18-16 alleles of TtGRF4-A have potential to increase wheat yields in breeding programs.

Keywords

Wheat, emmer; domestication; genome assembly; QTL, meta-QTL; grain weight; GRF4

Subject

Biology and Life Sciences, Plant Sciences

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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