SummaryCommon wheat is a hexaploid species with most of the genes present as triplicate homoeologs. Expression divergences of homoeologs are frequently observed in wheat, as well as in other polyploid plants. However, the mechanisms underlying this phenomenon are poorly understood.Expansin genes play important roles in the regulation of cell size, as well as organ size. We found that all three TaEXPA1 homoeologs were silenced in seedling roots. In seedling leaves, TaEXPA1-A and TaEXPA1-D were expressed, but TaEXPA1-B was silenced. Further analysis revealed that silencing of TaEXPA1-B in leaves occurred after the formation of the hexaploid.Chromatin immunoprecipitation assays revealed that the transcriptional silencing of three TaEXPA1 homoeologs in roots was correlated with an increased level of H3K9 dimethylation and decreased levels of H3K4 trimethylation and H3K9 acetylation. Reactivation of TaEXPA1-A and TaEXPA1-D expression in leaves was correlated with increased levels of H3K4 trimethylation and H3K9 acetylation, and decreased levels of H3K9 dimethylation in their promoters, respectively. Moreover, a higher level of cytosine methylation was detected in the promoter region of TaEXPA1-B, which may contribute to its silencing in leaves.We demonstrated that epigenetic modifications contribute to the expression divergence of three TaEXPA1 homoeologs during wheat development.

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.

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Key message Two QTL with pleiotropic effects on plant height and spike length linked in coupling phase on chromosome 2DS were dissected, and diagnostic marker for each QTL was developed. Abstract Plant height (PHT) is a crucial trait related to plant architecture and yield potential, and dissection of its underlying genetic basis would help to improve the efficiency of designed breeding in wheat. Here, two quantitative trait loci (QTL) linked in coupling phase on the short arm of chromosome 2D with pleiotropic effects on PHT and spike length, QPht/Sl.cau - 2D.1 and QPht/Sl.cau - 2D.2, were separated and characterized. QPht/Sl.cau - 2D.1 is a novel QTL located between SNP makers BS00022234_51 and BobWhite_rep_c63957_1472. QPht/Sl.cau - 2D.2 is mapped between two SSR markers, SSR - 2062 and Xgwm484 , which are located on the same genomic interval as Rht8 . Moreover, the diagnostic marker tightly linked with each QTL was developed for the haplotype analysis using diverse panels of wheat accessions. The frequency of the height-reduced allele of QPht/Sl.cau - 2D.1 is much lower than that of QPht/Sl.cau - 2D.2 , suggesting that this novel QTL may be an attractive target for genetic improvement. Consistent with a previous study of Rht8 , a significant difference in cell length was observed between the NILs of QPht/Sl.cau - 2D.2 . By contrast, there was no difference in cell length between NILs of QPht/Sl.cau - 2D.1 , indicating that the underlying molecular mechanism for these two QTL may be different. Collectively, these data provide a new example of QTL dissection, and the developed diagnostic markers will be useful in marker-assisted pyramiding of QPht/Sl.cau - 2D.1 and/or QPht/Sl.cau - 2D.2 with the other genes in wheat breeding. Electronic supplementary material The online version of this article (10.1007/s00122-019-03318-z) contains supplementary material, which is available to authorized users.

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.