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One-sentence summary: Map-based cloning of a gene underlying grain shape in 22 wheat suggests that modest genetic changes induce dramatic phenotypic variations 23 associated with a new wheat subspecies during evolution. ABSTRACT 29 Six subspecies of hexaploid wheat (Triticum spp.) have been identified, but the origin 30 of Indian dwarf wheat (Triticum sphaerococcum Perc.), the only subspecies with 31 round grains, is currently unknown. Here, we isolated the grain-shape gene Tasg-D1 32 in T. sphaerococcum Perc. via positional cloning. Tasg-D1 encodes a serine/threonine 33 protein kinase glycogen synthase kinase 3 (STKc_GSK3) that negatively regulates 34 brassinosteroid signaling. Expression of TaSG-D1 and the mutant form Tasg-D1 in 35 Arabidopsis thaliana suggested that a single amino acid substitution in the TREE 36 domain of TaSG-D1 enhances protein stability in response to brassinosteroids, likely 37 leading to formation of round grains in wheat. This gain-of-function mutation has 38 pleiotropic effects on plant architecture and exhibits incomplete dominance. 39 Haplotype analysis of 898 wheat accessions indicated that the origin of T. 40 sphaerococcum Perc. in ancient India involved at least two independent mutations of 41 TaSG-D1. Our results demonstrate that modest genetic changes in a single gene can 42 induced dramatic phenotypic changes. 43 44 108 glycogen synthase kinase 3 (STKc_GSK3), the wheat orthologue of BIN2. In T. 109 sphaerococcum, a single amino acid substitution of STKc_GSK3 enhances protein 110 5 stability in response to BR, leading to round grain formation. Evolutionary analysis 111 provided evidence that the origin of T. sphaerococcum wheat involved at least two 112 independent mutations of TaSG-D1.

Major crops are all survivors of domestication bottlenecks. Studies have focused on the genetic loci related to the domestication syndrome, while the contribution of ancient haplotypes remains largely unknown. Here, an ancestral genomic haploblock dissection method is developed and applied to a resequencing dataset of 386 tetraploid/hexaploid wheat accessions, generating a pan-ancestry haploblock map. Together with cytoplastic evidences, we reveal that domesticated polyploid wheat emerged from the admixture of six founder wild emmer lineages, which contributed the foundation of ancestral mosaics. The key domestication-related loci, originated over a wide geographical range, were gradually pyramided through a protracted process. Diverse stable-inheritance ancestral haplotype groups of the chromosome central zone are identified, revealing the expanding routes of wheat and the trends of modern wheat breeding. Finally, an evolution model of polyploid wheat is proposed, highlighting the key role of wild-to-crop and interploidy introgression, that increased genomic diversity following bottlenecks introduced by domestication and polyploidization.

Grain yield in bread wheat (Triticum aestivum L.) is largely determined by inflorescence architecture. Zang734 is an endemic Tibetan wheat variety that exhibits a rare triple spikelet (TRS) phenotype with significantly increased spikelet/floret number per spike. However, the molecular basis underlying this specific spike morphology is completely unknown.Through map-based cloning, the causal genes for TRS trait in Zang734 were isolated. Furthermore, using CRISPR/Cas9-based gene mutation, transcriptome sequencing and proteinprotein interaction, the downstream signalling networks related to spikelet formation and awn elongation were defined.Results showed that the null mutation in WFZP-A together with deletion of WFZP-D led to the TRS trait in Zang734. More interestingly, WFZP plays a dual role in simultaneously repressing spikelet formation gene TaBA1 and activating awn development genes, basically through the recruitments of chromatin remodelling elements and the Mediator complex.Our findings provide insights into the molecular bases by which WFZP suppresses spikelet formation but promotes awn elongation and, more importantly, define WFZP-D as a favourable gene for high-yield crop breeding.

Along with increasing demands for high yield, elite processing quality and improved nutrient value in wheat, concerns have emerged around the effects of gluten in wheat-based foods on human health. However, knowledge of the mechanisms regulating gluten accumulation remains largely unexplored.Here we report the identification and characterization of a wheat low gluten protein 1 (lgp1) mutant that shows extremely low levels of gliadins and glutenins.The lgp1 mutation in a single c-gliadin gene causes defective signal peptide cleavage, resulting in the accumulation of an excessive amount of unprocessed c-gliadin and a reduced level of gluten, which alters the endoplasmic reticulum (ER) structure, forms the autophagosome-like structures, leads to the delivery of seed storage proteins to the extracellular space and causes a reduction in starch biosynthesis. Physiologically, these effects trigger ER stress and cell death.This study unravels a unique mechanism that unprocessed c-gliadin reduces gluten accumulation associated with ER stress and elevated cell death in wheat. Moreover, the reduced gluten level in the lgp1 mutant makes it a good candidate for specific diets for patients with diabetes or kidney diease.