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Einkorn wheat (Triticum monococcum) is one of the oldest cereal crops to be domesticated by human beings, playing essential role in early agriculture development. Today, it is considered an important genomic resource for modern wheat improvement, especially for resistance against pests and diseases. However, the exploration and utilization of useful genes fromT. monococcumis limited due to the lack of a reference genome and annotation for this species. Here, we report a near-complete genome assembly forT. monococcumwith a total length of 5.11 Gb with a contig N50 of 131.2Mb and scaffold N50 of 728.66Mb, representing a genome assembly of highest quality for any wheat genome reported. Phylogenomic analysis confirmedT. monococcumis closely-related toT. urartu, the progenitor of wheat A subgenomes. A 4AL/5AL terminal translocation is present in the diploid speciesT. urartuandT. monococcum, taking place before wheat polyploidization.T. monococcumhas significantly expanded and unique gene families involved in DNA damage repair and heat stress tolerance, reflecting its adaptive evolution to cope with historical harsh climate in its natural habitat, South East Turkey. The genome sequence confirmed the introgression ofT. monococcumrust resistance genes at 5AmL into modern bread wheat varieties. This near-complete reference genome ofT. monococcumwill be an essential resource for wheat functional and evolutionary genomic studies and expedite the cloning of useful genes inT. monococcumfor future wheat improvement.

Invertase (INV) irreversibly catalyzes the conversion of sucrose into glucose and fructose, playing important role in plant development and stress tolerance. However, the functions of INV genes in wheat have been less studied. In this study, a total of 126 TaINV genes were identified using a genome-wide search method, which could be classified into five classes (TaCWI-α, TaCWI-β, TaCI-α, TaCI-β, and TaVI) based on phylogenetic relationship. A total of 101 TaINVs were collinear with their ancestors in the synteny analysis, and we speculated that polyploidy events were the main force in the expansion of the TaINV gene family. Compared with TaCI, TaCWI and TaVI are more similar in gene structure and protein properties. Transcriptome sequencing analysis showed that TaINVs expressed in multiple tissues with different expression levels. Among 19 tissue-specific expressed TaINVs, 12 TaINVs showed grain-specific expression pattern and might play an important role in wheat grain development. In addition, qRT-PCR results further confirmed that TaCWI50 and TaVI27 show different expression in grain weight NILs. Our results demonstrated that the high expression of TaCWI50 and TaVI27 may be associated with a larger TGW phenotype. This work provides the foundations for understanding the grain development mechanism.

Psathyrostachys huashanica Keng f. ex P.C.Kuo (2n = 2x = 14, NsNs) harbor numerous useful genes and exhibit application prospects as a breeding resource via distant hybridization. Here, a Wheat-P. huashanica alien substitution line, derived from common wheat 7182 and P. huashanica, was characterized by Multiple experimental evidences. The cytological results showed the chromosome number of the line was 42. Genomic in situ hybridization and fluorescence in situ hybridization (GISH-FISH) analysis indicated the line had a pair of chromosomes Ns from P. huashanica, and 40 chromosomes from common wheat. Verification using expressed sequence tag–sequence tagged site (EST-STS) (BE497584, BE443796, BG313767), polymerase chain reaction (PCR)-based landmark unique gene (PLUG) (TNAC1026-HaeIII, TNAC1043-TaqI, TNAC1091-HaeIII) and high molecular weight glutenin subunit (HMW-GS) markers confirmed that a pair of wheat chromosomes 1D in the line were substituted by a pair of P. huashanica chromosomes 1Ns. Therefore, we can conclude that the alien chromosome line was a wheat- P. huashanica 1Ns(1D) disomic substitution line and named as wheat-Ph1D. In comparison to the common wheat parent 7182, agronomic trait evaluations showed that wheat-Ph1D exhibited significant improvements, including plant height, grain length, thousand-grain weight, the contents of crude protein and gluten protein, starch content, dough stability time and resistant to stripe rust at the adult stage. Consequently, wheat-Ph1D could be a potential bridge material in wheat breeding with specific agronomic traits.

BackgroundThe degradation of sucrose plays an important role in the process of crop biomass allocation and yield formation. Invertase (INV) irreversibly catalyzes the conversion of sucrose into glucose and fructose, which doomed its’ important role in plant development and stress tolerance. However, the functions of INV genes in wheat, one of the most important crops, were less studied due to the polyploidy.ResultsHere, we systematically analyzed the INV gene family based on the latest published wheat reference genomic information. A total of 126 TaINV genes were identified and classified into three classes based on the phylogenetic relationship and their gene structure. Of which, 11 and 83 gene pairs were identified as tandem and segmental duplication genes respectively, while the Ka/Ks ratios of tandem and segmental duplication TaINV genes were less than 1. Expression profile analysis shows that 18 TaINV genes have tissue-specific expression, and 54 TaINV genes were involved in stress response. Furthermore, RNA-seq showed that 35 genes are differentially expressed in grain weight NILs N0910-81L/N0910-81S, in which 9 TaINVs were stably detected by qRT-PCR at three time-points, 4, 7 and 10 DPA. Four of them (TaCWI47, TaCWI48, TaCWI50 and TaVI27) different expressed between the NILs resided in 4 QTL segments (QTGW.nwafu-5DL.1, QTGW.nwafu-5DL.2, QTGW.nwafu-7AS.1 and QTGW.nwafu-7AS.2). These findings facilitate function investigations of the wheat INV gene family and provide new insights into the grain development mechanism in wheat.ConclusionsOur results showed that allopolyploid events were the main reason for the expansion of the TaINV gene family in hexaploid wheat, and duplication genes might undergo purifying selection. The expression profiling of TaINV genes implied that they are likely to play an important role in wheat growth and development and adaption to stressful environments. And TaCWI47, TaCWI48, TaCWI50 and TaVI27 may have more important roles in grain developments. Our study lay a base for further dissecting the functional characterization of TaINV family members.

A wheat RPP13-like isoform interacting with WPP1 contributes to quantitative and/or basal resistance to powdery mildew (Blumeria graminis f. sp. tritici) by restricting the development of Bgt conidia. Plant disease resistance (R) genes confer an ability to resist infection by pathogens expressing specific avirulence genes. Recognition of Peronospora parasitica 13-like (RPP13-like) genes belong to the nucleotide-binding site and leucine-rich repeat (NBS-LRR) superfamily and play important roles in resistance to various plant diseases. Previously, we detected a TaRPP13-like gene located on chromosome 3D (TaRPP13L1-3D) in the TaSpl1 resided region, which is strongly induced by the cell death phenotype (Zhang et al. 2021). Here, we investigated the expression and functional role of TaRPP13L1-3D in wheat responding to fungal stress. TaRPP13L1-3D encoded a typical NB-ARC structure characterized by Rx-N and P-loop NTPase domains. TaRPP13L1-3D transcripts were strongly upregulated in wheat by powdery mildew (Blumeria graminis f. sp. tritici; Bgt) and stripe rust (Puccinia striiformis f. sp. tritici; Pst) infection although opposing expression patterns were observed in response to wheat-Bgt in incompatible and compatible backgrounds. Overexpression of TaRPP13L1-3D enhanced disease resistance to Bgt, accompanied by upregulation of the defense-related marker genes encoding phytoalexin-deficient4 (PAD4), thaumatin-like protein (TLP) and chitinase 8-like protein (Chi8L), while silencing of TaRPP13L1-3D disrupted the resistance to Bgt infection. Subcellular localization studies showed that TaRPP13L1-3D is located in both the plasma membrane and nucleus, while yeast-two-hybrid (Y2H) assays indicated that TaRPP13L1-3D interacts with WPP domain-containing protein 1 (TaWPP1). This indicates that TaRPP13L1-3D shuttles between the nucleus and cytoplasm membrane via a mechanism that is mediated by the RanGAP-WPP complex in nuclear pores. This insight into TaRPP13L1-3D will be useful in dissecting the mechanism of fungal resistance in wheat, and understanding the interaction between R gene expression and pathogen defense.

Investigating the biogeographical disjunction of East Asian and North American flora is key to understanding the formation and dynamics of biodiversity in the Northern Hemisphere. The small Cupressaceae genus Thuja, comprising five species, exhibits a typical disjunct distribution in East Asia and North America. Owing to obscure relationships, the biogeographical history of the genus remains controversial. Here, complete plastomes were employed to investigate the plastome evolution, phylogenetic relationships, and biogeographic history of Thuja. All plastomes of Thuja share the same gene content arranged in the same order. The loss of an IR was evident in all Thuja plastomes, and the B-arrangement as previously recognized was detected. Phylogenomic analyses resolved two sister pairs, T. standishii-T. koraiensis and T. occidentalis-T. sutchuenensis, with T. plicata sister to T. occidentalis-T. sutchuenensis. Molecular dating and biogeographic results suggest the diversification of Thuja occurred in the Middle Miocene, and the ancestral area of extant species was located in northern East Asia. Incorporating the fossil record, we inferred that Thuja likely originated from the high-latitude areas of North America in the Paleocene with a second diversification center in northern East Asia. The current geographical distribution of Thuja was likely shaped by dispersal events attributed to the Bering Land Bridge in the Miocene and subsequent vicariance events accompanying climate cooling. The potential effect of extinction may have profound influence on the biogeographical history of Thuja.

Investigating the biogeographical disjunction of East Asian and North American flora is key to understanding the formation and dynamics of biodiversity in the Northern Hemisphere. The small Cupressaceae genus Thuja, comprising five species, exhibits a typical disjunct distribution in East Asia and North America. Owing to obscure relationships, the biogeographical history of the genus remains controversial. Here, complete plastomes were employed to investigate the plastome evolution, phylogenetic relationships, and biogeographic history of Thuja. All plastomes of Thuja share the same gene content arranged in the same order. The loss of an IR was evident in all Thuja plastomes, and the B-arrangement as previously recognized was detected. Phylogenomic analyses resolved two sister pairs, T. standishii-T. koraiensis and T. occidentalis-T. sutchuenensis, with T. plicata sister to T. occidentalis-T. sutchuenensis. Molecular dating and biogeographic results suggest the diversification of Thuja occurred in the Middle Miocene, and the ancestral area of extant species was located in northern East Asia. Incorporating the fossil record, we inferred that Thuja likely originated from the high-latitude areas of North America in the Paleocene with a second diversification center in northern East Asia. The current geographical distribution of Thuja was likely shaped by dispersal events attributed to the Bering Land Bridge in the Miocene and subsequent vicariance events accompanying climate cooling. The potential effect of extinction may have profound influence on the biogeographical history of Thuja.