A single nucleotide deletion in the third exon of FT-D1 increases the spikelet number and delays heading date in wheat (Triticum aestivum L.)

Genetic variation in a tandemly duplicated TPS gene cluster contributes to the diversity of aroma in lychee fruit

Fruits undergo a similar ripening process, yet they exhibit a range of differences in color, taste, and shape, both across different species and within the same species. How does this diversity arise? We uncovered a conserved fruit ripening process in lychee fruit in which a NAC transcription factor, LcNAC1, acts as a master regulator. LcNAC1 regulates the expression of two terpene synthase genes, LcTPSa1 and LcTPSa2, which belong to a gene cluster consisting of four TPS genes. LcTPSa1-LcTPSa3 are responsible for catalyzing the production of farnesol, which in turn dictates the aromatic diversity in fruit of different lychee varieties. Through comparative, transcriptomic, and genomic analyses across various lychee varieties, we found these four TPS genes exhibit distinct expression levels due to natural genetic variation. These include copy number variations, presence/absence variations, insertions and deletions, and single nucleotide polymorphisms, many of which affect the binding affinity of LcNAC1. A single nucleotide mutation in LcTPSa1 caused a premature translational termination, resulting in a truncated version of the TPS protein, which surprisingly remains functional. All these genomic changes in the LcNAC1-regulated TPS genes are likely to contribute to the great aromatic diversity observed in lychee fruit. This diversification of fruit aroma in lychee varieties offers a compelling example of how species- or variety-specific traits evolve - the phenotypic diversity is primarily derived from natural genetic variation accumulated in downstream structural genes within an evolutionarily conserved regulatory circuit.

TaFT-D1 positively regulates grain weight by acting as a coactivator of TaFDL2 in wheat

FLOWERING LOCUS T (FT), a multifunctional regulator in crops, modulates multiple key agronomic traits such as flowering time or heading date and plant height; however, its role in grain development regulation is unclear. Herein, through genome-wide association studies (GWAS), we identified TaFT-D1, which encodes a phosphatidylethanolamine-binding protein (PEBP), as a candidate gene for grain weight in wheat. A one-bp insertion/deletion (InDel) (G/-) in the third exon of TaFT-D1, resulting in different protein lengths, was significantly associated with grain weight. TaFT-D1 knockout via the CRISPR-Cas9 system reduced grain size and weight, and TaFT-D1 increased grain size by promoting cell proliferation and starch synthesis. Transcriptome analysis revealed a significant decrease in the expression of cell cycle- and starch synthesis-related genes, including TaNAC019-3A, TaSWEET15-like-7B, TaCYCD4;1 and TaCYCD3;2, in the taft-d1 knockout line. TaFT-D1 interacted with the bZIP transcription factor TaFDL2, and the tafdl2 mutant presented relatively small grains, suggesting that TaFDL2 is a positive regulator of grain size. Moreover, TaFDL2 bound to the promoters of downstream cell cycle- and starch synthesis-related genes, activating their expression, whereas TaFT-D1 increased this activation via TaFDL2. Interaction assays demonstrated that TaFT-D1, Ta14-3-3A and TaFDL2 formed a regulatory complex. Furthermore, the TaFT-D1(G) allele was significantly correlated with greater thousand-grain weight and earlier heading. This favourable allele has undergone strong positive selection during wheat breeding in China. Our findings provide novel insights into how TaFT-D1 regulates grain weight and highlight its potential application for yield improvement in wheat.

Genome-wide association study to identify the genomic loci associated with wheat heading date variation under autumn-sowing conditions

The present study aimed to identify genetic loci associated with days to heading (DTH) in wheat under autumn-sowing conditions in Korea, where early heading is critical owing to the overlap between the wheat harvest and the rainy season. We evaluated 530 wheat core collections over five years, focusing on known heading date genes VRN-1 and PPD-1, and conducted a genome-wide association study (GWAS) to identify new genetic loci related to DTH. The results revealed that Korean accessions exhibited the earliest DTH, with modern Korean varieties heading even earlier, reflecting a strong breeding focus on early heading. Among the existing heading date genes, VRN-1 and PPD-D1 were significantly associated with DTH in the wheat core collection. However, all Korean varieties carried the same alleles for each of VRN-A1, PPD-A1, and PPD-D1, resulting in low genetic diversity, which rendered the existing heading date genes insufficient to fully account for the variation in DTH within the Korean varieties. GWAS identified nine single nucleotide polymorphisms (SNPs) associated with DTH in Group A (entire collection filtered, n=518) and six in Group B (accessions with genotypes identical to Korean varieties filtered, n=231). Four key SNPs (AX-95222044 and AX-94685526 in Group A, and AX-94550996 and AX-94970315 in Group B) were selected based on their effect sizes on DTH. In both groups, accessions with alleles for early heading at both of the selected SNPs exhibited the earliest DTH, advancing by 7.7 to 8.9 days. These findings suggest that the selected SNPs, particularly those reflecting the genotypes of Korean varieties, effectively explain the variations in DTH among Korean varieties and could enhance wheat breeding efficiency in Korea. Further research is needed to validate the four selected SNPs and identify the underlying genes, which could serve as valuable markers for developing early-heading wheat varieties suited to Korean autumn-sowing conditions.

The Q-interacted protein QIP3 recruits TaTPL to regulate spike architecture in wheat

Spike architecture is a critical determinant of grain yield in wheat; yet the regulatory mechanisms remain poorly understood. Here, we demonstrate that the AP2 transcription factor Q directly represses the expression of TaMYB30-6A, a gene associated with spike length in wheat. We further identify QIP3 as a Q-interacting protein harboring an N-terminal EAR motif. Simultaneously, we reveal that QIP3 exhibits transcriptional repression activity, dependent on the EAR motif, and physically interacts with the transcriptional corepressor TaTPL. Importantly, the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-generated qip3-aabbdd mutants exhibit reduced plant height and increased spike length phenotypes. Furthermore, RNA-seq and RT-qPCR assays show that QIP3 negatively regulates the expression of the Q target gene TaMYB30-6A in wheat. Collectively, we propose that the EAR motif-containing QIP3 interacts with Q to regulate spike architecture by recruiting the transcriptional corepressor TaTPL in wheat.

Genetic Variations and Haplotype Diversity of the Wheat FRIZZY PANICLE (WFZP) Gene in 98 Aegilops tauschii Accessions

BACKGROUND

The wheat FRIZZY PANICLE (WFZP) gene is a regulatory hub that controls spikelet formation in bread wheat, WFZP-D, as a favorable gene for wheat yield improvement. The sequences of WFZP-D in bread wheat accessions are known to be highly conserved.

METHODS

In this study, re-sequencing of WFZP homoeologous genes from 98 widely distributed Aegilops tauschii (the donor of the wheat D genome) germplasms was carried out to identify natural variations at both the nucleotide and polypeptide levels.

CONCLUSIONS

WFZP homeolog exhibited high conservation with no functional variants in the key AP2/ERF domain. Haplotype characterization identified five haplotypes (Hap-D1 to Hap-D5) based on nine single-nucleotide polymorphisms, five of which induced single amino acid residue substitutions downstream of the AP2/ERF domain. Hap-D1 (identical to Triticum aestivum WFZP-D) and Hap-D2 are two most common. Hap-D1 is concentrated in Iran and Azerbaijan, primarily associated with ssp. strangulata, while Hap-D2 displays broad distribution across the range and primarily belongs to ssp. tauschii. The remaining haplotypes (Hap-D3/4/5) are identified in ssp. tauschii accessions. These findings suggest that strategic integration of ssp. tauschii into wheat-breeding programs could enhance genetic diversity. The identified natural variations provide potential haplotype resources for improving wheat yield potential.

CRISPR/Cas9: a sustainable technology to enhance climate resilience in major Staple Crops

Climate change is a global concern for agriculture, food security, and human health. It affects several crops and causes drastic losses in yield, leading to severe disturbances in the global economy, environment, and community. The consequences on important staple crops, such as rice, maize, and wheat, will worsen and create food insecurity across the globe. Although various methods of trait improvements in crops are available and are being used, clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9 (CRISPR/Cas9) mediated genome manipulation have opened a new avenue for functional genomics and crop improvement. This review will discuss the progression in crop improvement from conventional breeding methods to advanced genome editing techniques and how the CRISPR/Cas9 technology can be applied to enhance the tolerance of the main cereal crops (wheat, rice, and maize) against any harsh climates. CRISPR/Cas endonucleases and their derived genetic engineering tools possess high accuracy, versatile, more specific, and easy to design, leading to climate-smart or resilient crops to combat food insecurity and survive harsh environments. The CRISPR/Cas9-mediated genome editing approach has been applied to various crops to make them climate resilient. This review, supported by a bibliometric analysis of recent literature, highlights the potential target genes/traits and addresses the significance of gene editing technologies in tackling the vulnerable effects of climate change on major staple crops staple such as wheat, rice, and maize.

A comprehensive map of DNA-segment copy number variation in 491 genomes of common wheat uncovers genes associated with multiple agronomic traits

DNA-segment copy number variations (DSCNVs), such as deletions and duplications, are important sources of genomic structural variation. However, the types and sizes of DSCNVs, as well as their genome-wide distribution and potential functions, are poorly understood in wheat. Here, we identified 198 985 DSCNVs by investigating 491 genomes of common wheat and found that they account for 20% of the entire genome. Interestingly, approximately 38% of genes are linked to DSCNVs. The number of DSCNVs within each accession ranges from 47 366 to 96 342, and their total sizes vary from 421.3 to 1267.9 Mb. We found that 957 and 1304 DSCNVs have been favored by breeders in China and the United States, respectively. By conducting DSCNV-based genome-wide association studies for the principal components of plant developmental and yield-component traits, we identified 34 loci as directly or indirectly involved in controlling the formation of multiple traits. Notably, a newly discovered DSCNV covering TaFT-D1 is significantly associated with flowering time and other agronomic traits. Overall, our findings highlight the potential of DSCNVs to drive fundamental discoveries in plant science. The comprehensive DSCNV map and the DSCNV-associated genes will also facilitate future research efforts to improve wheat yield, quality, and adaptation.

Optimization of tissue culture and Cas9 transgene expression in tomato: A step towards CRISPR/Cas9-based genetic improvement

Tomato (Solanum lycopersicum L.) is an essential source of antioxidants and a prime candidate for bioengineering experiments. Many studies have aimed to improve tomatoes using CRISPR/Cas9 technology; however, the success rate is limited due to the lack of efficient regeneration and genetic modification techniques. Here, we report an efficient regeneration and transformation procedure focused on developing efficient Cas9 gene transgenic tomato plants using the Agrobacterium tumefaciens strain LBA4404 harbouring pCRISPR/Cas9TK2-NIC binary vector. We optimized the concentrations and combinations of growth hormones to promote direct shoot and root regeneration via hypocotyl explants. We found that MS medium 2.0 mg/l Zeatin (Zn) + 1.5 mg/l Indole -3- acetic acid (IAA) + 0.3 mg/l Benzyl amino purine (BAP) was preeminent for shoot regeneration medium, and 0.5 mg/l BAP+ 0.1 mg/l IAA was appropriate for root regeneration. Cas9 transgenes in the tomato genome of putative tomato plants were validated using various methods, including polymerase chain reaction (PCR), and confirmed via Southern blotting. The developed protocol showed improved regeneration and transformation efficiencies in tomatoes of 88 % and 54 %, respectively. In this study, we successfully established a gene delivery platform for tomatoes using the CRISPR/Cas9 system.

Plant Productivity and Leaf Starch During Grain Fill Is Linked to QTL Containing Flowering Locus T1 (FT1) in Wheat (Triticum aestivum L.)

Shifts in the environment due to climate change necessitate breeding efforts aimed at adapting wheat to longer, warmer growing seasons. In this study, 21 modern wheat (Triticum aestivum L.) cultivars and 29 landraces were screened for flag leaf starch levels, with the goal of identifying a genetic marker for targeted breeding. The landrace PI 61693 was identified as having exceptionally high flag leaf starch values. Yield trials were carried out in a Berkut × PI 61693 recombinant inbred line (RIL) population and a negative correlation was observed between leaf starch, flowering time, and yield. Genetic mapping identified a Quantitative Trait Loci (QTL) explaining 22-34% variation for leaf starch, flowering time, biomass, and seed yield. The starch synthase TraesCS7D02G117800 (wSsI-1) is located in this region, which possibly accounts for leaf starch variation in this population; also within this QTL is TraesCS7D02G111600 (FT-D1). Sequencing of FT-D1 identified a single base pair deletion in the 3rd exon of the Berkut allele. This indel has recently been shown to significantly impact flowering time and productivity, and likely led to significant variation in flowering date and yield in this population. Here, we illustrate how allelic selection of FT-D1 within breeding programs may aid in adapting wheat to changing environments.

Wheat2035: Integrating pan-omics and advanced biotechnology for future wheat design

Wheat (Triticum aestivum) production is vital for global food security, providing energy and protein to millions of people worldwide. Recent advancements in wheat research have led to significant increases in production, fueled by technological and scientific innovation. Here, we summarize the major advancements in wheat research, particularly the integration of biotechnologies and a deeper understanding of wheat biology. The shift from multi-omics to pan-omics approaches in wheat research has greatly enhanced our understanding of the complex genome, genomic variations, and regulatory networks to decode complex traits. We also outline key scientific questions, potential research directions, and technological strategies for improving wheat over the next decade. Since global wheat production is expected to increase by 60% in 2050, continued innovation and collaboration are crucial. Integrating biotechnologies and a deeper understanding of wheat biology will be essential for addressing future challenges in wheat production, ensuring sustainable practices and improved productivity.

TaDL interacts with TaB3 and TaNF-YB1 to synergistically regulate the starch synthesis and grain quality in bread wheat

Starch biosynthesis is a critical factor in wheat (Triticum aestivum L.) quality and yield. However, the full scope of its regulation is not fully understood. Here we report that TaDL interacts with TaB3 and TaNF-YB1 to synergistically regulate starch biosynthesis and quality in wheat. Genome-edited tadl mutant lines had smaller and lighter grains with lower total starch and amylose contents compared to wild type (WT). Correspondingly, the transcript levels of starch biosynthesis-related genes, including TaSUS1, TaSUS2, TaAGPL2, TaSBEIIa, TaGBSSII, and TaSWEET2a, were markedly lower at 15 d after flowering (DAF) in tadl mutants. TaDL physically interacted with TaB3 and TaNF-YB1 and activated the transcription of TaSUS2 and TaAGPL2 through direct binding to their promoter regions. A null mutant of TaB3 also affected grain filling, with phenotypes similar to those of tadl mutants, whereas overexpression of TaNF-YB1 promoted grain filling. Our study demonstrated that TaDL plays an essential role in starch biosynthesis and identified an elite allele (TaDL-BI) associated with starch content, providing insights into the underlying molecular mechanism of wheat grain filling, which may be useful in breeding of high-yielding wheat and quality improvement.

A gain-of-function mutation at the C-terminus of FT-D1 promotes heading by interacting with 14-3-3A and FDL6 in wheat

Vernalization and photoperiod pathways converging at FT1 control the transition to flowering in wheat. Here, we identified a gain-of-function mutation in FT-D1 that results in earlier heading date (HD), and shorter plant height and spike length in the gamma ray-induced eh1 wheat mutant. Knockout of the wild-type and overexpression of the mutated FT-D1 indicate that both alleles are functional to affect HD and plant height. Protein interaction assays demonstrated that the frameshift mutation in FT-D1eh1 exon 3 led to gain-of-function interactions with 14-3-3A and FDL6, thereby enabling the formation of florigen activation complex (FAC) and consequently activating a flowering-related transcriptomic programme. This mutation did not affect FT-D1eh1 interactions with TaNaKR5 or TaFTIP7, both of which could modulate HD, potentially via mediating FT-D1 translocation to the shoot apical meristem. Furthermore, the 'Segment B' external loop is essential for FT-D1 interaction with FDL6, while residue Y85 is required for interactions with TaNaKR5 and TaFTIP7. Finally, the flowering regulatory hub gene, ELF5, was identified as the FT-D1 regulatory target. This study illustrates FT-D1 function in determining wheat HD with a suite of interaction partners and provides genetic resources for tuning HD in elite wheat lines.

The Tetratricopeptide repeat protein TaTPR-B1 regulates spike compactness in bread wheat

Spike compactness (SC) is strongly associated with wheat (Triticum aestivum L.) grain yield. In this study, we conducted a quantitative trait locus (QTL) analysis using a doubled haploid (DH) population derived from a cross between two common wheat varieties with contrasting spike morphology, revealing 16 stable QTLs associated with SC. The effect of a major QTL, QSc.cau-6B.1, was validated in 231 F7 recombinant inbred lines (RILs) derived from the same cross as the DH population. Using two residual heterozygous lines (RHLs), we delimited QSc.cau-6B.1 to an approximately 0.5-Mbp physical interval containing four high-confidence genes. The tetratricopeptide repeat-TraesCS6B03G1214400 (TaTPR-B1) was the priority candidate gene according to sequence and expression variations between near-isogenic lines. Accordingly, TaTPR-B1 knockout in the common wheat variety 'CB037' significantly increased SC compared to the wild type (WT). Conversely, TaTPR-B1 overexpression in the common wheat variety 'Fielder' significantly decreased SC compared to the WT. Moreover, we developed a PCR-based marker targeting the 32-bp insertion/deletion (InDel) between the two TaTPR-B1 alleles, which could be practical and valuable in modern wheat breeding programs for diagnostic purposes. Collectively, these findings provide insight into the genetic basis of SC in common wheat and present a valuable target with a breeder-friendly diagnostic marker for gene pyramid breeding.

Single- and multi-locus genome-wide association study reveals genomic regions of thirteen yield-related traits in common wheat

Genetic dissection of yield-related traits can be used to improve wheat yield through molecular design breeding. In this study, we genotyped 245 wheat varieties and measured 13 yield-related plant height-, grain-, and spike-related traits, in seven environments, and identified 778 loci for these traits by genome-wide association study (GWAS) using single- and multi-locus models. Among these loci, nine were major, of which seven were novel, including Qph/lph.ahau-7A for plant height (PH) and leaf pillow height (LPH), Qngps/sps.ahau-1A for number of grains per spike (NGPS) and spikelet number per spike (SPS), Qsd.ahau-2B.1 and Qsd.ahau-5A.2 for spikelet density (SD), Qlph.ahau-7B.2 for LPH, Qgl.ahau-7B.3 for grain length (GL), and Qsl.ahau-3A.3 for spike length (SL). Through marker development, re-GWAS, gene annotation and cloning, and sequence variation, haplotype, and expression analyses, we confirmed two novel major loci and identified potential candidate genes, TraesCS7A02G118000 (named TaF-box-7A) and TraesCS1A02G190200 (named TaBSK2-1A) underlying Qph/lph.ahau-7A for PH-related traits and Qngps/sps.ahau-1A for spike-related traits. We also reported two favorable haplotypes, including TaF-box-Hap1 associated with low PH and LPH and TaBSK2-Hap3 associated with high NGPS and SPS. In summary, these findings can be applied to improve wheat yield and enrich our understanding of the complex genetic mechanisms of yield-related traits.

Natural alleles of LEAFY and WAPO1 interact to regulate spikelet number per spike in wheat

KEY MESSAGE

Specific combinations of LFY and WAPO1 natural alleles maximize spikelet number per spike in wheat. Spikelet number per spike (SNS) is an important yield component in wheat that determines the maximum number of grains that can be formed in a wheat spike. In wheat, loss-of-function mutations in LEAFY (LFY) or its interacting protein WHEAT ORTHOLOG OF APO1 (WAPO1) significantly reduce SNS by reducing the rate of formation of spikelet meristems. In previous studies, we identified a natural amino acid change in WAPO1 (C47F) that significantly increases SNS in hexaploid wheat. In this study, we searched for natural variants in LFY that were associated with differences in SNS and detected significant effects in the LFY-B region in a nested association mapping population. We generated a large mapping population and confirmed that the LFY-B polymorphism R80S is linked with the differences in SNS, suggesting that LFY-B is the likely causal gene. A haplotype analysis revealed two amino acid changes P34L and R80S, which were both enriched during wheat domestication and breeding suggesting positive selection. We also explored the interactions between the LFY and WAPO1 natural variants for SNS using biparental populations and identified significant interaction, in which the positive effect of the 80S and 34L alleles from LFY-B was only detected in the WAPO-A1 47F background but not in the 47C background. Based on these results, we propose that the allele combination WAPO-A1-47F/LFY-B 34L 80S can be used in wheat breeding programs to maximize SNS and increase grain yield potential in wheat.

Genome-editing of a circadian clock gene TaPRR95 facilitates wheat peduncle growth and heading date

Plant height and heading date are important agronomic traits in wheat (Triticum aestivum L.) that affect final grain yield. In wheat, knowledge of pseudo-response regulator (PRR) genes on agronomic traits is limited. Here, we identify a wheat TaPRR95 gene by genome-wide association studies to be associated with plant height. Triple allele mutant plants produced by CRISPR/Cas9 show increased plant height, particularly the peduncle, with an earlier heading date. The longer peduncle is mainly caused by the increased cell elongation at its upper section, whilst the early heading date is accompanied by elevated expression of flowering genes, such as TaFT and TaCO1. A peduncle-specific transcriptome analysis reveals up-regulated photosynthesis genes and down-regulated IAA/Aux genes for auxin signaling in prr95aabbdd plants that may act as a regulatory mechanism to promote robust plant growth. A haplotype analysis identifies a TaPRR95-B haplotype (Hap2) to be closely associated with reduced plant height and increased thousand-grain weight. Moreover, the Hap2 frequency is higher in cultivars than that in landraces, suggesting the artificial selection on the allele during wheat breeding. These findings suggest that TaPRR95 is a regulator for plant height and heading date, thereby providing an important target for wheat yield improvement.

Pleiotropic phenotypic effects of the TaCYP78A family on multiple yield-related traits in wheat

Increasing crop yield depends on selecting and utilizing pleiotropic genes/alleles to improve multiple yield-related traits (YRTs) during crop breeding. However, synergistic improvement of YRTs is challenging due to the trade-offs between YRTs in breeding practices. Here, the favourable haplotypes of the TaCYP78A family are identified by analysing allelic variations in 1571 wheat accessions worldwide, demonstrating the selection and utilization of pleiotropic genes to improve yield and related traits during wheat breeding. The TaCYP78A family members, including TaCYP78A3, TaCYP78A5, TaCYP78A16, and TaCYP78A17, are organ size regulators expressed in multiple organs, and their allelic variations associated with various YRTs. However, due to the trade-offs between YRTs, knockdown or overexpression of TaCYP78A family members does not directly increase yield. Favourable haplotypes of the TaCYP78A family, namely A3/5/16/17Ap-Hap II, optimize the expression levels of TaCYP78A3/5/16/17-A across different wheat organs to overcome trade-offs and improve multiple YRTs. Different favourable haplotypes have both complementary and specific functions in improving YRTs, and their aggregation in cultivars under strong artificial selection greatly increase yield, even under various planting environments and densities. These findings provide new support and valuable genetic resources for molecular breeding of wheat and other crops in the era of Breeding 4.0.

Integrated meta-QTL and in silico transcriptome assessment pinpoint major genomic regions responsible for spike length in wheat (Triticum aestivum L.)

Spike length (SL) is one of the major contributors to wheat yield. Uncovering major genetic regions affecting SL is an integral part of elucidating the genetic basis of wheat yield traits and goes further pivotal for marker-assisted selection breeding. A genome-wide meta-quantitative trait locus (MQTL) analysis of wheat SL resulted in the refinement of 48 MQTLs using 227 initial QTLs retrieved from previous studies published over the past decades. The average confidence interval (CI) of these MQTLs amounted to a 5.16-fold reduction compared to the mean CI of the initial QTLs. As many as 2240 putative candidate genes (CGs) were identified from the MQTL intervals using transcriptomics data in silico of wheat, of which 58 CGs were identified based on wheat-rice homology analysis. For the key CG affecting SL, a functional kompetitive allele-specific PCR (KASP) marker, TaPP2C-3B-KASP, was developed to distinguish TaPP2C-3B-Hap I and TaPP2C-3B-Hap II based on the single nucleotide polymorphism at the 272 bp (A/G). The frequency of the elite allelic variation TaPP2C-3B-Hap II with high SL remained relatively stable at about 49.62% from the 1960s to 1990s. Integration of MQTL analysis and in silico transcriptome data led to a significant increase in the reliability of CGs for the genetic regulation of wheat SL, and the haplotype analysis for key CGs TaPP2C-3B of SL provided insights into the biological function of the TaPP2C-3B gene.

TaMYB72 directly activates the expression of TaFT to promote heading and enhance grain yield traits in wheat (Triticum aestivum L.)

Heading date, grain number per spike, and grain weight are crucial traits affecting yield and adaptability in wheat. The transcription factor TaMYB72 is an important regulator of wheat grain yield and its knock-out mutants can be used as germplasm resources for wheat improvement.

Dissecting the molecular basis of spike traits by integrating gene regulatory networks and genetic variation in wheat

Spike architecture influences both grain weight and grain number per spike, which are the two major components of grain yield in bread wheat (Triticum aestivum L.). However, the complex wheat genome and the influence of various environmental factors pose challenges in mapping the causal genes that affect spike traits. Here, we systematically identified genes involved in spike trait formation by integrating information on genomic variation and gene regulatory networks controlling young spike development in wheat. We identified 170 loci that are responsible for variations in spike length, spikelet number per spike, and grain number per spike through genome-wide association study and meta-QTL analyses. We constructed gene regulatory networks for young inflorescences at the double ridge stage and the floret primordium stage, in which the spikelet meristem and the floret meristem are predominant, respectively, by integrating transcriptome, histone modification, chromatin accessibility, eQTL, and protein-protein interactome data. From these networks, we identified 169 hub genes located in 76 of the 170 QTL regions whose polymorphisms are significantly associated with variation in spike traits. The functions of TaZF-B1, VRT-B2, and TaSPL15-A/D in establishment of wheat spike architecture were verified. This study provides valuable molecular resources for understanding spike traits and demonstrates that combining genetic analysis and developmental regulatory networks is a robust approach for dissection of complex traits.

Natural variations of HvSRN1 modulate the spike rachis node number in barley

Grain number, one of the major determinants of yield in Triticeae crops, is largely determined by spikelet number and spike rachis node number (SRN). Here, we identified three quantitative trait loci (QTLs) for SRN using 145 recombinant inbred lines derived from a barley R90/1815D cross. qSRN1, the major-effect QTL, was mapped to chromosome 2H and explained up to 38.77% of SRN variation. Map-based cloning revealed that qSRN1 encodes the RAWUL domain-containing protein HvSRN1. Further analysis revealed that two key SNPs in the HvSRN1 promoter region (∼2 kb upstream of the transcription start site) affect the transcript level of HvSRN1 and contribute to variation in SRN. Similar to its orthologous proteins OsLAX2 and ZmBA2, HvSRN1 showed protein-protein interactions with HvLAX1, suggesting that the LAX2-LAX1 model for spike morphology regulation may be conserved in Poaceae crops. CRISPR-Cas9-induced HvSRN1 mutants showed reduced SRN but increased grain size and weight, demonstrating a trade-off effect. Our results shed light on the role of HvSRN1 variation in regulating the balance between grain number and weight in barley.

Boosting Triticeae crop grain yield by manipulating molecular modules to regulate inflorescence architecture: insights and knowledge from other cereal crops

One of the challenges for global food security is to reliably and sustainably improve the grain yield of cereal crops. One solution is to modify the architecture of the grain-bearing inflorescence to optimize for grain number and size. Cereal inflorescences are complex structures, with determinacy, branching patterns, and spikelet/floret growth patterns that vary by species. Recent decades have witnessed rapid advancements in our understanding of the genetic regulation of inflorescence architecture in rice, maize, wheat, and barley. Here, we summarize current knowledge on key genetic factors underlying the different inflorescence morphologies of these crops and model plants (Arabidopsis and tomato), focusing particularly on the regulation of inflorescence meristem determinacy and spikelet meristem identity and determinacy. We also discuss strategies to identify and utilize these superior alleles to optimize inflorescence architecture and, ultimately, improve crop grain yield.

Genome resources for the elite bread wheat cultivar Aikang 58 and mining of elite homeologous haplotypes for accelerating wheat improvement

Despite recent progress in crop genomics studies, the genomic changes brought about by modern breeding selection are still poorly understood, thus hampering genomics-assisted breeding, especially in polyploid crops with compound genomes such as common wheat (Triticum aestivum). In this work, we constructed genome resources for the modern elite common wheat variety Aikang 58 (AK58). Comparative genomics between AK58 and the landrace cultivar Chinese Spring (CS) shed light on genomic changes that occurred through recent varietal improvement. We also explored subgenome diploidization and divergence in common wheat and developed a homoeologous locus-based genome-wide association study (HGWAS) approach, which was more effective than single homoeolog-based GWAS in unraveling agronomic trait-associated loci. A total of 123 major HGWAS loci were detected using a genetic population derived from AK58 and CS. Elite homoeologous haplotypes (HHs), formed by combinations of subgenomic homoeologs of the associated loci, were found in both parents and progeny, and many could substantially improve wheat yield and related traits. We built a website where users can download genome assembly sequence and annotation data for AK58, perform blast analysis, and run JBrowse. Our work enriches genome resources for wheat, provides new insights into genomic changes during modern wheat improvement, and suggests that efficient mining of elite HHs can make a substantial contribution to genomics-assisted breeding in common wheat and other polyploid crops.

CRISPR/Cas9-mediated genome editing techniques and new breeding strategies in cereals - current status, improvements, and perspectives

Cereal crops, including triticeae species (barley, wheat, rye), as well as edible cereals (wheat, corn, rice, oat, rye, sorghum), are significant suppliers for human consumption, livestock feed, and breweries. Over the past half-century, modern varieties of cereal crops with increased yields have contributed to global food security. However, presently cultivated elite crop varieties were developed mainly for optimal environmental conditions. Thus, it has become evident that taking into account the ongoing climate changes, currently a priority should be given to developing new stress-tolerant cereal cultivars. It is necessary to enhance the accuracy of methods and time required to generate new cereal cultivars with the desired features to adapt to climate change and keep up with the world population expansion. The CRISPR/Cas9 system has been developed as a powerful and versatile genome editing tool to achieve desirable traits, such as developing high-yielding, stress-tolerant, and disease-resistant transgene-free lines in major cereals. Despite recent advances, the CRISPR/Cas9 application in cereals faces several challenges, including a significant amount of time required to develop transgene-free lines, laboriousness, and a limited number of genotypes that may be used for the transformation and in vitro regeneration. Additionally, developing elite lines through genome editing has been restricted in many countries, especially Europe and New Zealand, due to a lack of flexibility in GMO regulations. This review provides a comprehensive update to researchers interested in improving cereals using gene-editing technologies, such as CRISPR/Cas9. We will review some critical and recent studies on crop improvements and their contributing factors to superior cereals through gene-editing technologies.

Unlocking Nature's Clock: CRISPR Technology in Flowering Time Engineering

Flowering is a crucial process in the life cycle of most plants as it is essential for the reproductive success and genetic diversity of the species. There are situations in which breeders want to expedite, delay, or prevent flowering, for example, to shorten or prolong vegetative growth, to prevent unwanted pollination, to reduce the risk of diseases or pests, or to modify the plant's phenotypes. This review aims to provide an overview of the current state of knowledge to use CRISPR/Cas9, a powerful genome-editing technology to modify specific DNA sequences related to flowering induction. We discuss the underlying molecular mechanisms governing the regulation of the photoperiod, autonomous, vernalization, hormonal, sugar, aging, and temperature signal pathways regulating the flowering time. In addition, we are investigating the most effective strategies for nominating target genes. Furthermore, we have collected a dataset showing successful applications of CRISPR technology to accelerate flowering in several plant species from 2015 up to date. Finally, we explore the opportunities and challenges of using the potential of CRISPR technology in flowering time engineering.

Dissection and validation of a promising QTL controlling spikelet number on 5B in bread wheat

KEY MESSAGE

Five environmentally stable QTLs for spikelet number per spike and days to heading were identified using a high-genetic map containing 95,444 SNPs, among which QSns.ucas-5B was validated using residual heterozygous line at multiple environments. Spikelet number per spike (SNS) and days to heading (DTH) play pivotal roles in the improvement of wheat yield. In this study, a high-density genetic map for a recombinant inbred lines (RILs) population derived from Zhengnong 17 (ZN17) and Yangbaimai (YBM) was constructed using 95,444 single-nucleotide polymorphism (SNP) markers from the Wheat660K SNP array. Our study identified a total of five environmentally stable QTLs for SNS and DTH, one of which was named QSns.ucas-5B, with a physical interval of approximately 545.4-552.1 Mb on the 5BL chromosome arm. Importantly, the elite haplotype within QSns.ucas-5B showed a consistent and positive effect on SNS, grain number and weight per spike, without extending the days to heading. These findings provide a foundation for future efforts to map and clone the gene(s) responsible for QSns.ucas-5B and further indicate the potential application of the developed and validated InDel marker of QSns.ucas-5B for molecular breeding purposes, aimed at improving wheat grain yield.

Deciphering spike architecture formation towards yield improvement in wheat

Wheat is the most widely grown crop globally, providing 20% of the daily consumed calories and protein content around the world. With the growing global population and frequent occurrence of extreme weather caused by climate change, ensuring adequate wheat production is essential for food security. The architecture of the inflorescence plays a crucial role in determining the grain number and size, which is a key trait for improving yield. Recent advances in wheat genomics and gene cloning techniques have improved our understanding of wheat spike development and its applications in breeding practices. Here, we summarize the genetic regulation network governing wheat spike formation, the strategies used for identifying and studying the key factors affecting spike architecture, and the progress made in breeding applications. Additionally, we highlight future directions that will aid in the regulatory mechanistic study of wheat spike determination and targeted breeding for grain yield improvement.

CRISPR-mediated acceleration of wheat improvement: advances and perspectives

Common wheat (Triticum aestivum) is one of the most widely cultivated and consumed crops globally. In the face of limited arable land and climate changes, it is a great challenge to maintain current and increase future wheat production. Enhancing agronomic traits in wheat by introducing mutations across all three homoeologous copies of each gene has proven to be a difficult task due to its large genome with high repetition. However, clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease (Cas) genome editing technologies offer a powerful means of precisely manipulating the genomes of crop species, thereby opening up new possibilities for biotechnology and breeding. In this review, we first focus on the development and optimization of the current CRISPR-based genome editing tools in wheat, emphasizing recent breakthroughs in precise and multiplex genome editing. We then describe the general procedure of wheat genome editing and highlight different methods to deliver the genome editing reagents into wheat cells. Furthermore, we summarize the recent applications and advancements of CRISPR/Cas technologies for wheat improvement. Lastly, we discuss the remaining challenges specific to wheat genome editing and its future prospects.

A major QTL simultaneously increases the number of spikelets per spike and thousand-kernel weight in a wheat line

KEY MESSAGE

A novel and stably expressed QTL QSNS.sicau-SSY-7A for spikelet number per spike in wheat without negative effects on thousand-kernel weight was identified and validated in different genetic backgrounds. Spikelet number per spike (SNS) is an important determinant of yield in wheat. In the present study, we combined bulked segregant analysis (BSA) and the wheat 660 K single-nucleotide polymorphism (SNP) array to rapidly identify genomic regions associated with SNS from a recombinant inbred line (RIL) population derived from a cross between the wheat lines S849-8 and SY95-71. A genetic map was constructed using Kompetitive Allele Specific PCR markers in the SNP-enriched region on the long arm of chromosome 7A. A major and stably expressed QTL, QSNS.sicau-SSY-7A, was detected in multiple environments. It was located in a 1.6 cM interval on chromosome arm 7AL flanked by the markers AX-109983514 and AX-109820548. This QTL explained 6.86-15.72% of the phenotypic variance, with LOD values ranging from 3.66 to 8.66. Several genes associated with plant growth and development were identified in the interval where QSNS.sicau-SSY-7A was located on the 'Chinese Spring' wheat and wild emmer reference genomes. Furthermore, the effects of QSNS.sicau-SSY-7A and WHEAT ORTHOLOG OFAPO1(WAPO1) on SNS were analyzed. Interestingly, QSNS.sicau-SSY-7A significantly increased SNS without negative effects on thousand-kernel weight, anthesis date and plant height, demonstrating its great potential for breeding aimed at improving grain yield. Taken together, these results indicate that QSNS.sicau-SSY-7A is a promising locus for yield improvement, and its linkage markers are helpful for fine mapping and molecular breeding.

Characterization and fine mapping analysis of a major stable QTL qKnps-4A for kernel number per spike in wheat

KEY MESSAGE

A major stable QTL for kernel number per spike was narrowed down to a 2.19-Mb region containing two potential candidate genes, and its effects on yield-related traits were characterized. Kernel number per spike (KNPS) in wheat is a key yield component. Dissection and characterization of major stable quantitative trait loci (QTLs) for KNPS would be of considerable value for the genetic improvement of yield potential using molecular breeding technology. We had previously reported a major stable QTL controlling KNPS, qKnps-4A. In the current study, primary fine-mapping analysis, based on the primary mapping population, located qKnps-4A to an interval of approximately 6.8-Mb from 649.0 to 655.8 Mb on chromosome 4A refering to 'Kenong 9204' genome. Further fine-mapping analysis based on a secondary mapping population narrowed qKnps-4A to an approximately 2.19-Mb interval from 653.72 to 655.91 Mb. Transcriptome sequencing, gene function annotation analysis and homologous gene related reports showed that TraesKN4A01HG38570 and TraesKN4A01HG38590 were most likely to be candidate genes of qKnps-4A. Phenotypic analysis based on paired near-isogenic lines in the target region showed that qKnps-4A increased KNPS mainly by increasing the number of central florets per spike. We also evaluated the effects of qKnps-4A on other yield-related traits. Moreover, we dissected the QTL cluster of qKnps-4A and qTkw-4A and proved that the phenotypic effects were probably due to close linkage of two or more genes rather than pleiotropic effects of a single gene. This study provides molecular marker resource for wheat molecular breeding designed to improve yield potential, and lay the foundation for gene functional analysis of qKnps-4A.

Fine mapping of qAHPS07 and functional studies of AhRUVBL2 controlling pod size in peanut (Arachis hypogaea L.)

Cultivated peanut (Arachis hypogaea L.) is an important oil and cash crop. Pod size is one of the major traits determining yield and commodity characteristic of peanut. Fine mapping of quantitative trait locus (QTL) and identification of candidate genes associated with pod size are essential for genetic improvement and molecular breeding of peanut varieties. In this study, a major QTL related to pod size, qAHPS07, was fine mapped to a 36.46 kb interval on chromosome A07 using F2 , recombinant inbred line (RIL) and secondary F2 populations. qAHPS07 explained 38.6%, 23.35%, 37.48%, 25.94% of the phenotypic variation for single pod weight (SPW), pod length (PL), pod width (PW) and pod shell thickness (PST), respectively. Whole genome resequencing and gene expression analysis revealed that a RuvB-like 2 protein coding gene AhRUVBL2 was the most likely candidate for qAHPS07. Overexpression of AhRUVBL2 in Arabidopsis led to larger seeds and plants than the wild type. AhRUVBL2-silenced peanut seedlings represented small leaves and shorter main stems. Three haplotypes were identified according to three SNPs in the promoter of AhRUVBL2 among 119 peanut accessions. Among them, SPW, PW and PST of accessions carrying Hap_ATT represent 17.6%, 11.2% and 26.3% higher than those carrying Hap_GAC，respectively. In addition, a functional marker of AhRUVBL2 was developed. Taken together, our study identified a key functional gene of peanut pod size, which provides new insights into peanut pod size regulation mechanism and offers practicable markers for the genetic improvement of pod size-related traits in peanut breeding.

CRISPR/Cas Technology Revolutionizes Crop Breeding

Crop breeding is an important global strategy to meet sustainable food demand. CRISPR/Cas is a most promising gene-editing technology for rapid and precise generation of novel germplasm and promoting the development of a series of new breeding techniques, which will certainly lead to the transformation of agricultural innovation. In this review, we summarize recent advances of CRISPR/Cas technology in gene function analyses and the generation of new germplasms with increased yield, improved product quality, and enhanced resistance to biotic and abiotic stress. We highlight their applications and breakthroughs in agriculture, including crop de novo domestication, decoupling the gene pleiotropy tradeoff, crop hybrid seed conventional production, hybrid rice asexual reproduction, and double haploid breeding; the continuous development and application of these technologies will undoubtedly usher in a new era for crop breeding. Moreover, the challenges and development of CRISPR/Cas technology in crops are also discussed.

A high-resolution genotype-phenotype map identifies the TaSPL17 controlling grain number and size in wheat

BACKGROUND

Large-scale genotype-phenotype association studies of crop germplasm are important for identifying alleles associated with favorable traits. The limited number of single-nucleotide polymorphisms (SNPs) in most wheat genome-wide association studies (GWASs) restricts their power to detect marker-trait associations. Additionally, only a few genes regulating grain number per spikelet have been reported due to sensitivity of this trait to variable environments.

RESULTS

We perform a large-scale GWAS using approximately 40 million filtered SNPs for 27 spike morphology traits. We detect 132,086 significant marker-trait associations and the associated SNP markers are located within 590 associated peaks. We detect additional and stronger peaks by dividing spike morphology into sub-traits relative to GWAS results of spike morphology traits. We propose that the genetic dissection of spike morphology is a powerful strategy to detect signals for grain yield traits in wheat. The GWAS results reveal that TaSPL17 positively controls grain size and number by regulating spikelet and floret meristem development, which in turn leads to enhanced grain yield per plant. The haplotypes at TaSPL17 indicate geographical differentiation, domestication effects, and breeding selection.

CONCLUSION

Our study provides valuable resources for genetic improvement of spike morphology and a fast-forward genetic solution for candidate gene detection and cloning in wheat.

Advances in bread wheat production through CRISPR/Cas9 technology: a comprehensive review of quality and other aspects

MAIN CONCLUSION

This review provides a comprehensive overview of the CRISPR/Cas9 technique and the research areas of this gene editing tool in improving wheat quality. Wheat (Triticum aestivum L.), the basic nutrition for most of the human population, contributes 20% of the daily energy needed because of its, carbohydrate, essential amino acids, minerals, protein, and vitamin content. Wheat varieties that produce high yields and have enhanced nutritional quality will be required to fulfill future demands. Hexaploid wheat has A, B, and D genomes and includes three like but not identical copies of genes that influence important yield and quality. CRISPR/Cas9, which allows multiplex genome editing provides major opportunities in genome editing studies of plants, especially complicated genomes such as wheat. In this overview, we discuss the CRISPR/Cas9 technique, which is credited with bringing about a paradigm shift in genome editing studies. We also provide a summary of recent research utilizing CRISPR/Cas9 to investigate yield, quality, resistance to biotic/abiotic stress, and hybrid seed production. In addition, we provide a synopsis of the laboratory experience-based solution alternatives as well as the potential obstacles for wheat CRISPR studies. Although wheat's extensive genome and complicated polyploid structure previously slowed wheat genetic engineering and breeding progress, effective CRISPR/Cas9 systems are now successfully used to boost wheat development.

Fine mapping and genetic analysis identified a C2H2-type zinc finger as a candidate gene for heading date regulation in wheat

KEY MESSAGE

A minor-effect QTL, Qhd.2AS, that affects heading date in wheat was mapped to a genomic interval of 1.70-Mb on 2AS, and gene analysis indicated that the C2H2-type zinc finger protein gene TraesCS2A02G181200 is the best candidate for Qhd.2AS. Heading date (HD) is a complex quantitative trait that determines the regional adaptability of cereal crops, and identifying the underlying genetic elements with minor effects on HD is important for improving wheat production in diverse environments. In this study, a minor QTL for HD that we named Qhd.2AS was detected on the short arm of chromosome 2A by Bulked Segregant Analysis and validated in a recombinant inbred population. Using a segregating population of 4894 individuals, Qhd.2AS was further delimited to an interval of 0.41 cM, corresponding to a genomic region spanning 1.70 Mb (from 138.87 to 140.57 Mb) that contains 16 high-confidence genes based on IWGSC RefSeq v1.0. Analyses of sequence variations and gene transcription indicated that TraesCS2A02G181200, which encodes a C2H2-type zinc finger protein, is the best candidate gene for Qhd.2AS that influences HD. Screening a TILLING mutant library identified two mutants with premature stop codons in TraesCS2A02G181200, both of which exhibited a delay in HD of 2-4 days. Additionally, variations in its putative regulatory sites were widely present in natural accession, and we also identified the allele which was positively selected during wheat breeding. Epistatic analyses indicated that Qhd.2AS-mediated HD variation is independent of VRN-B1 and environmental factors. Phenotypic investigation of homozygous recombinant inbred lines (RILs) and F2:3 families showed that Qhd.2AS has no negative effect on yield-related traits. These results provide important cues for refining HD and therefore improving yield in wheat breeding programs and will deepen our understanding of the genetic regulation of HD in cereal plants.

Natural variations of wheat EARLY FLOWERING 3 highlight their contributions to local adaptation through fine-tuning of heading time

KEY MESSAGE

We identified a large chromosomal deletion containing TaELF-B3 that confers early flowering in wheat. This allele has been preferred in recent wheat breeding in Japan to adapt to the environment. Heading at the appropriate time in each cultivation region can greatly contribute to stabilizing and maximizing yield. Vrn-1 and Ppd-1 are known as the major genes for vernalization requirement and photoperiod sensitivity in wheat. Genotype combinations of Vrn-1 and Ppd-1 can explain the variation in heading time. However, the genes that can explain the remaining variations in heading time are largely unknown. In this study, we aimed to identify the genes conferring early heading using doubled haploid lines derived from Japanese wheat varieties. Quantitative trait locus (QTL) analysis revealed a significant QTL on the long arm of chromosome 1B in multiple growing seasons. Genome sequencing using Illumina short reads and Pacbio HiFi reads revealed a large deletion of a ~ 500 kb region containing TaELF-B3, an orthologue of Arabidopsis clock gene EARLY FLOWERING 3 (ELF3). Plants with the deleted allele of TaELF-B3 (ΔTaELF-B3 allele) headed earlier only under short-day vernalization conditions. Higher expression levels of clock- and clock-output genes, such as Ppd-1 and TaGI, were observed in plants with the ΔTaELF-B3 allele. These results suggest that the deletion of TaELF-B3 causes early heading. Of the TaELF-3 homoeoalleles conferring early heading, the ΔTaELF-B3 allele showed the greatest effect on the early heading phenotype in Japan. The higher allele frequency of the ΔTaELF-B3 allele in western Japan suggests that the ΔTaELF-B3 allele was preferred during recent breeding to adapt to the environment. TaELF-3 homoeologs will help to expand the cultivated area by fine-tuning the optimal timing of heading in each environment.

CRISPR-Based Genome Editing Tools: An Accelerator in Crop Breeding for a Changing Future

Genome editing is an important strategy to maintain global food security and achieve sustainable agricultural development. Among all genome editing tools, CRISPR-Cas is currently the most prevalent and offers the most promise. In this review, we summarize the development of CRISPR-Cas systems, outline their classification and distinctive features, delineate their natural mechanisms in plant genome editing and exemplify the applications in plant research. Both classical and recently discovered CRISPR-Cas systems are included, detailing the class, type, structures and functions of each. We conclude by highlighting the challenges that come with CRISPR-Cas and offer suggestions on how to tackle them. We believe the gene editing toolbox will be greatly enriched, providing new avenues for a more efficient and precise breeding of climate-resilient crops.

Amand P, Bai G, Baker J, Baker S, Liu S. QTL mapping of yield components and kernel traits in wheat cultivars TAM 112 and Duster

In the Southern Great Plains, wheat cultivars have been selected for a combination of outstanding yield and drought tolerance as a long-term breeding goal. To understand the underlying genetic mechanisms, this study aimed to dissect the quantitative trait loci (QTL) associated with yield components and kernel traits in two wheat cultivars `TAM 112' and `Duster' under both irrigated and dryland environments. A set of 182 recombined inbred lines (RIL) derived from the cross of TAM 112/Duster were planted in 13 diverse environments for evaluation of 18 yield and kernel related traits. High-density genetic linkage map was constructed using 5,081 single nucleotide polymorphisms (SNPs) from genotyping-by-sequencing (GBS). QTL mapping analysis detected 134 QTL regions on all 21 wheat chromosomes, including 30 pleiotropic QTL regions and 21 consistent QTL regions, with 10 QTL regions in common. Three major pleiotropic QTL on the short arms of chromosomes 2B (57.5 - 61.6 Mbps), 2D (37.1 - 38.7 Mbps), and 7D (66.0 - 69.2 Mbps) colocalized with genes Ppd-B1, Ppd-D1, and FT-D1, respectively. And four consistent QTL associated with kernel length (KLEN), thousand kernel weight (TKW), plot grain yield (YLD), and kernel spike^-1 (KPS) (Qklen.tamu.1A.325, Qtkw.tamu.2B.137, Qyld.tamu.2D.3, and Qkps.tamu.6A.113) explained more than 5% of the phenotypic variation. QTL Qklen.tamu.1A.325 is a novel QTL with consistent effects under all tested environments. Marker haplotype analysis indicated the QTL combinations significantly increased yield and kernel traits. QTL and the linked markers identified in this study will facilitate future marker-assisted selection (MAS) for pyramiding the favorable alleles and QTL map-based cloning.

CRISPR/Cas9-induced modification of the conservative promoter region of VRN-A1 alters the heading time of hexaploid bread wheat

In cereals, the vernalization-related gene network plays an important role in regulating the transition from the vegetative to the reproductive phase to ensure optimal reproduction in a temperate climate. In hexaploid bread wheat (Triticum aestivum L.), the spring growth habit is associated with the presence of at least one dominant locus of VERNALIZATION 1 gene (VRN-1), which usually differs from recessive alleles due to mutations in the regulatory sequences of the promoter or/and the first intron. VRN-1 gene is a key regulator of floral initiation; various combinations of dominant and recessive alleles, especially VRN-A1 homeologs, determine the differences in the timing of wheat heading/flowering. In the present study, we attempt to expand the types of VRN-A1 alleles using CRISPR/Cas9 targeted modification of the promoter sequence. Several mono- and biallelic changes were achieved within the 125-117 bp upstream sequence of the start codon of the recessive vrn-A1 gene in plants of semi-winter cv. 'Chinese Spring'. New mutations stably inherited in subsequent progenies and transgene-free homozygous plants carrying novel VRN-A1 variants were generated. Minor changes in the promoter sequence, such as 1-4 nucleotide insertions/deletions, had no effect on the heading time of plants, whereas the CRISPR/Cas9-mediated 8 bp deletion between -125 and -117 bp of the vrn-A1 promoter shortened the time of head emergence by up to 2-3 days. Such a growth habit was consistently observed in homozygous mutant plants under nonvernalized cultivation using different long day regimes (16, 18, or 22 h), whereas the cold treatment (from two weeks and more) completely leveled the effect of the 8 bp deletion. Importantly, comparison with wild-type plants showed that the implemented alteration has no negative effects on main yield characteristics. Our results demonstrate the potential to manipulate the heading time of wheat through targeted editing of the VRN-A1 gene promoter sequence on an otherwise unchanged genetic background.

Genome-wide identification and characterization profile of phosphatidy ethanolamine-binding protein family genes in carrot

Members of the family of Phosphatidy Ethanolamine-Binding Protein (PEBP) have been shown to be key regulators of the transition of plants from vegetative to reproductive phases. Here, a total of 12 PEBP proteins were identified in the carrot (Daucus carota L.) genome and classified into FT-like (4), TFL1-like (6), and MFT-like 2) subfamilies, that had different lengths (110-267 aa) and were distributed unevenly across seven chromosomes. Moreover, 13 and 31 PEBP proteins were identified in other two Apiaceae species, celery (Apium graveolens L.) and coriander (Coriandrum sativum L.). The phylogenetic and evolutionary results of these PEBP family proteins were obtained based on the protein sequences. In the three Apiaceae species, purifying selection was the main evolutionary force, and WGD, segmental duplication, and dispersed duplication have played key roles in the PEBP family expansion. The expression analysis showed that carrot PEBP genes exhibited relatively broad expression patterns across various tissues. In the period of bolting to flowering, the carrot FT-like subfamily genes were upregulated as positive regulators, and TFL1-like subfamily genes remained at lower expression levels as inhibitors. More interestingly, the members of carrot FT-like genes had different temporal-spatial expression characteristics, suggesting that they have different regulatory functions in the carrot reproductive phase. In summary, this study contributes to our understanding of the PEBP family proteins and provides a foundation for exploring the mechanism of carrot bolting and flowering for the breeding of cultivars with bolting resistance.

Wheat genomic study for genetic improvement of traits in China

Bread wheat (Triticum aestivum L.) is a major crop that feeds 40% of the world's population. Over the past several decades, advances in genomics have led to tremendous achievements in understanding the origin and domestication of wheat, and the genetic basis of agronomically important traits, which promote the breeding of elite varieties. In this review, we focus on progress that has been made in genomic research and genetic improvement of traits such as grain yield, end-use traits, flowering regulation, nutrient use efficiency, and biotic and abiotic stress responses, and various breeding strategies that contributed mainly by Chinese scientists. Functional genomic research in wheat is entering a new era with the availability of multiple reference wheat genome assemblies and the development of cutting-edge technologies such as precise genome editing tools, high-throughput phenotyping platforms, sequencing-based cloning strategies, high-efficiency genetic transformation systems, and speed-breeding facilities. These insights will further extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process, ultimately contributing to more sustainable agriculture in China and throughout the world.

Quantitative trait loci identification and breeding value estimation of grain weight-related traits based on a new wheat 50K single nucleotide polymorphism array-derived genetic map

Mining novel and less utilized thousand grain weight (TGW) related genes are useful for improving wheat yield. In this study, a recombinant inbred line population from a cross between Zhongkemai 138 (ZKM138, high TGW) and Chuanmai 44 (CM44, low TGW) was used to construct a new Wheat 50K SNP array-derived genetic map that spanned 1,936.59 cM and contained 4, 139 markers. Based on this map, ninety-one quantitative trait loci (QTL) were detected for eight grain-related traits in six environments. Among 58 QTLs, whose superior alleles were contributed by ZKM138, QTgw.cib-6A was a noticeable major stable QTL and was also highlighted by bulked segregant analysis with RNA sequencing (BSR-Seq). It had a pyramiding effect on TGW enhancement but no significant trade-off effect on grain number per spike or tiller number, with two other QTLs (QTgw.cib-2A.2 and QTgw.cib-6D), possibly explaining the excellent grain performance of ZKM138. After comparison with known loci, QTgw.cib-6A was deduced to be a novel locus that differed from nearby TaGW2 and TaBT1. Seven simple sequence repeat (SSR) and thirty-nine kompetitive allele-specific PCR (KASP) markers were finally developed to narrow the candidate interval of QTgw.cib-6A to 4.1 Mb. Only six genes in this interval were regarded as the most likely candidate genes. QTgw.cib-6A was further validated in different genetic backgrounds and presented 88.6% transmissibility of the ZKM138-genotype and a 16.4% increase of TGW in ZKM138 derivatives. And the geographic pattern of this locus revealed that its superior allele is present in only 6.47% of 433 Chinese modern wheat varieties, indicating its potential contribution to further high-yield breeding.

Genome edited wheat- current advances for the second green revolution

Common wheat is a major source of nutrition around the globe, but unlike maize and rice hybrids, no breakthrough has been made to enhance wheat yield since Green Revolution. With the availability of reference genome sequence of wheat and advancement of allied genomics technologies, understanding of genes involved in grain yield components and disease resistance/susceptibility has opened new avenues for crop improvement. Wheat has a huge hexaploidy genome of approximately 17 GB with 85% repetition, and it is a daunting task to induce any mutation across three homeologues that can be helpful for the enhancement of agronomic traits. The CRISPR-Cas9 system provides a promising platform for genome editing in a site-specific manner. In wheat, CRISPR-Cas9 is being used in the improvement of yield, grain quality, biofortification, resistance against diseases, and tolerance against abiotic factors. The promising outcomes of the CRISPR-based multiplexing approach circumvent the constraint of targeting merely one gene at a time. Deployment of clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) 9 endonuclease (CRISPR-Cas9) and Cas9 variant systems such as cytidine base editing, adenosine base editing, and prime editing in wheat has been used to induce point mutations more precisely. Scientists have acquired major events such as induction of male sterility, fertility restoration, and alteration of seed dormancy through Cas9 in wheat that can facilitate breeding programs for elite variety development. Furthermore, a recent discovery in tissue culturing enables scientists to significantly enhance regeneration efficiency in wheat by transforming the GRF4-GIF1 cassette. Rapid generation advancement by speed breeding technology provides the opportunity for the generation advancement of the desired plants to segregate out unwanted transgenes and allows rapid integration of gene-edited wheat into the breeding pipeline. The combination of these novel technologies addresses some of the most important limiting factors for sustainable and climate-smart wheat that should lead to the second "Green Revolution" for global food security.