Fine mapping of a stripe rust resistance gene YrZM175 in bread wheat

The selection and application of tiller number QTLs in modern wheat breeding

Tiller number is a key factor influencing wheat plant architecture and yield potential. This study analyzed the variation in tiller number among 323 wheat accessions across nine environmental conditions. The results revealed a significant decrease in tiller number in modern cultivars compared to traditional landraces, indicating a trend in selective breeding for fewer tillers. Genome-wide association studies (GWASs) identified four quantitative trait loci (QTLs) associated with tiller number on chromosomes 2D, 5A, and 6A. Haplotypes linked to reduced tiller number at three of these QTLs have been significantly selected and are predominantly found in various Chinese agroecological zones, positively affecting grain number and/or weight. These findings suggest that contemporary Chinese wheat breeding strategies have prioritized reducing tiller number while improving spike yield. Identifying selected haplotype combinations can further enhance breeding efforts aimed at optimizing the tiller number trait. This study provides insights into the genetic basis of tiller number QTLs and their relevance to wheat breeding practices.

Identification and validation of a novel tiller inhibition locus (tin7) on chromosome 2BL in wheat

Tiller number is a key determinant of the number of spikes per plant, significantly influencing yield. Here, we identify and characterize a novel tiller inhibition line, N2496. Using an F2 segregating population derived from crossing N2496 and CN16, we mapped this locus. The F1 line demonstrated a high number of tillers, while the F2 population exhibited segregated ratios of 3:1 in tiller number. BSR-Seq analysis indicated that only one locus controls tiller number, located on chromosome 2B (Chr. 2B). This genetic analysis confirmed the presence of a single recessive locus controlling the tiller inhibition trait within this population. Subsequently, we constructed a genetic map on Chr. 2B using a wheat 55 K single nucleotide polymorphism array. By combining recombinant analysis with the genotype and phenotype of the F2-3 family, we identified and named a major and novel locus, tiller inhibition gene (tin7), mapped within a 2.43 cM interval. The influence of tin7 was verified across six different background populations all sharing N2496 as a common parent. Using new recombinant lines from these six populations, we further narrowed down the interval of tin7 to a genetic interval of 2.08 cM. Analysis of thousand grain weight and grain-related traits suggests that by regulating tiller number, tin7 holds the potential to increase yield in wheat. Our research provides access to a novel tiller number locus and available markers for regulating tiller number, which could be used in developing new cultivars with an optimal number of tillers.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-025-01567-z.

Genetic Mapping by 55K Single-Nucleotide Polymorphism Array Reveals Candidate Genes for Tillering Trait in Wheat Mutant dmc

BACKGROUND

The tiller number is a key agronomic trait for increasing the yield potential of wheat (Triticum aestivum L.). A number of quantitative trait loci (QTLs) and key genes controlling tillering have been identified, but the regulatory mechanisms remain unclear.

METHODS

In this study, we utilized the dwarf-monoculm mutant (dmc) obtained from the ethyl methane sulfonate (EMS)-treated wheat cultivar Guomai 301. The F2 populations were constructed using the dmc mutant crossed to multiple tiller parents. The F2 populations were surveyed for tillering traits at the critical fertility stage for genetic analyses. The extreme-tillering-phenotype plants from the F2 population were used to construct mixing pools that were analyzed by a wheat 55K SNP array. The tillering genes of dmc were mapped using the wheat 55K SNP array combined with transcriptomic data.

RESULTS

The results showed that the genetic phenotype of dmc is controlled by two dominant genes. The tillering genes of dmc were mapped on the 60-100 Mb region of chromosome 5B and the 135-160 Mb region of chromosome 7A. A total of sixteen candidate genes associated with the tillering trait of dmc were identified. Two candidate genes, TraesCS5B02G058800 and TraesCS7A02G184200, were predicted to be involved in indole acetic acid (IAA) response and transport, which were considered as potential regulatory genes.

CONCLUSIONS

This study elucidated the genetic basis of the dmc mutant and provided two valuable reference genes for studying the development and regulatory mechanisms of wheat tillering.

Applications of Artificial Intelligence in Wheat Breeding for Sustainable Food Security

In agriculture, especially in crop breeding, innovative approaches are required to address the urgent issues posed by climate change and global food security. Artificial intelligence (AI) is a revolutionary technology in wheat breeding that provides new approaches to improve the ability of crops to withstand and produce higher yields in response to changing climate circumstances. This review paper examines the incorporation of artificial intelligence (AI) into conventional wheat breeding methods, with a focus on the contribution of AI in tackling the intricacies of contemporary agriculture. This review aims to assess the influence of AI technologies on enhancing the efficiency, precision, and sustainability of wheat breeding projects. We conduct a thorough analysis of recent research to evaluate several applications of artificial intelligence, such as machine learning (ML), deep learning (DL), and genomic selection (GS). These technologies expedite the swift analysis and interpretation of extensive datasets, augmenting the process of selecting and breeding wheat varieties that are well-suited to a wide range of environmental circumstances. The findings from the examined research demonstrate notable progress in wheat breeding as a result of artificial intelligence. ML algorithms have enhanced the precision of predicting phenotypic traits, whereas genomic selection has reduced the duration of breeding cycles. Utilizing artificial intelligence, high-throughput phenotyping allows for meticulous examination of plant characteristics under different stress environments, facilitating the identification of robust varieties. Furthermore, AI-driven models have exhibited superior predicted accuracies for crop productivity and disease resistance in comparison to conventional methods. AI technologies play a crucial role in the modernization of wheat breeding, providing significant enhancements in crop performance and adaptability. This integration not only facilitates the growth of wheat cultivars that provide large yields and can withstand stressful conditions but also strengthens global food security in the context of climate change. Ongoing study and collaboration across several fields are crucial to improving and optimizing these AI applications, ultimately enhancing their influence on sustainable agriculture.

Natural variant of Rht27, a dwarfing gene, enhances yield potential in wheat

KEY MESSAGE

Discovery of Rht27, a dwarf gene in wheat, showed potential in enhancing grain yield by reducing plant height. Plant height plays a crucial role in crop architecture and grain yield, and semi-dwarf Reduced Height (Rht) alleles contribute to lodging resistance and were important in "Green Revolution." However, the use of these alleles is associated with some negative side effects in some environments, such as reduced coleoptile length, low nitrogen use efficiency, and reduced yield. Therefore, novel dwarf gene resources are needed to pave an alternative route to overcome these side effects. In this study, a super-dwarf mutant rht27 was obtained by the mutagenesis of G1812 (Triticum urartu, the progenitor of the A sub-genome of common wheat). Genetic analysis revealed that the dwarf phenotype was regulated by a single recessive genetic factor. The candidate region for Rht27 was narrowed to a 1.55 Mb region on chromosome 3, within which we found two potential candidate genes that showed polymorphisms between the mutant and non-mutagenized G1812. Furthermore, the natural variants and elite haplotypes of the two candidates were investigated in a natural population of common wheat. The results showed that the natural variants affect grain yield components, and the dwarf haplotypes show the potential in improving agronomic traits and grain yield. Although the mutation in Rht27 results in severe dwarf phenotype in T. urartu, the natural variants in common wheat showed desirable phenotype, which suggests that Rht27 has the potential to improve wheat yield by utilizing its weak allelic mutation or fine-tuning its expression level.

Quantitative trait loci detection for three tiller-related traits and the effects on wheat (Triticum aestivum L.) yields

KEY MESSAGE

A total of 38 putative additive QTLs and 55 pairwise putative epistatic QTLs for tiller-related traits were reported, and the candidate genes underlying qMtn-KJ-5D, a novel major and stable QTL for maximum tiller number, were characterized. Tiller-related traits play an important role in determining the yield potential of wheat. Therefore, it is important to elucidate the genetic basis for tiller number when attempting to use genetic improvement as a tool for enhancing wheat yields. In this study, a quantitative trait locus (QTL) analysis of three tiller-related traits was performed on the recombinant inbred lines (RILs) of a mapping population, referred to as KJ-RILs, that was derived from a cross between the Kenong 9204 (KN9204) and Jing 411 (J411) lines. A total of 38 putative additive QTLs and 55 pairwise putative epistatic QTLs for spike number per plant (SNPP), maximum tiller number (MTN), and ear-bearing tiller rate (EBTR) were detected in eight different environments. Among these QTLs with additive effects, three major and stable QTLs were first documented herein. Almost all but two pairwise epistatic QTLs showed minor interaction effects accounting for no more than 3.0% of the phenotypic variance. The genetic effects of two colocated major and stable QTLs, i.e., qSnpp-KJ-5D.1 and qMtn-KJ-5D, for yield-related traits were characterized. The breeding selection effect of the beneficial allele for the two QTLs was characterized, and its genetic effects on yield-related traits were evaluated. The candidate genes underlying qMtn-KJ-5D were predicted based on multi-omics data, and TraesKN5D01HG00080 was identified as a likely candidate gene. Overall, our results will help elucidate the genetic architecture of tiller-related traits and can be used to develop novel wheat varieties with high yields.

Strigolactone and abscisic acid synthesis and signaling pathways are enhanced in the wheat oligo-tillering mutant ot1

Tiller number greatly contributes to grain yield in wheat. Using ethylmethanesulfonate mutagenesis, we previously discovered the oligo-tillering mutant ot1. The tiller number was significantly lower in ot1 than in the corresponding wild type from the early tillering stage until the heading stage. Compared to the wild type, the thousand-grain weight and grain length were increased by 15.41% and 31.44%, respectively, whereas the plant height and spike length were decreased by 26.13% and 37.25%, respectively. Transcriptomic analysis was conducted at the regreening and jointing stages to identify differential expressed genes (DEGs). Functional enrichment analysis with the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) databases showed differential expression of genes associated with ADP binding, transmembrane transport, and transcriptional regulation during tiller development. Differences in tiller number in ot1 led to the upregulation of genes in the strigolactone (SL) and abscisic acid (ABA) pathways. Specifically, the SL biosynthesis genes DWARF (D27), D17, D10, and MORE AXILLARY GROWTH 1 (MAX1) were upregulated by 3.37- to 8.23-fold; the SL signal transduction genes D14 and D53 were upregulated by 1.81- and 1.32-fold, respectively; the ABA biosynthesis genes 9-CIS-EPOXICAROTENOID DIOXIGENASE 3 (NCED3) and NCED5 were upregulated by 1.66- and 3.4-fold, respectively; and SNF1-REGULATED PROTEIN KINASE2 (SnRK2) and PROTEIN PHOSPHATASE 2C (PP2C) genes were upregulated by 1.30- to 4.79-fold. This suggested that the tiller number reduction in ot1 was due to alterations in plant hormone pathways. Genes known to promote tillering growth were upregulated, whereas those known to inhibit tillering growth were downregulated. For example, PIN-FORMED 9 (PIN9), which promotes tiller development, was upregulated by 8.23-fold in ot1; Ideal Plant Architecture 1 (IPA1), which inhibits tiller development, was downregulated by 1.74-fold. There were no significant differences in the expression levels of TILLER NUMBER 1 (TN1) or TEOSINTE BRANCHED 1 (TB1), indicating that the tiller reduction in ot1 was not controlled by known genes. Our findings provide valuable data for subsequent research into the genetic bases and regulatory mechanisms of wheat tillering.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01450-3.

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.

Identification and high-resolution mapping of a novel tiller number gene (tin6) by combining forward genetics screen and MutMap approach in bread wheat

Wheat (Triticum aestivum) is one of the most important food crops worldwide, providing up to 20% of the caloric intake per day. Developing high-yielding wheat cultivars with tolerance against abiotic and biotic stresses is important to keep up with the increasing human population. Tiller number is one of the major yield-related traits, directly affecting the number of grains produced per plant; however, only a small number of QTL and underlining genes have been identified for this important factor. Identification of novel genetic variation underlying contrasting traits and their precise genetic mapping in wheat is considered difficult due to the complexity and size of the genome; however, advancements in genomic resources have made efficient gene localization more possible. In this study, we report the characterization of a novel tillering number gene using a mutant identified in the forward genetic screen of an ethyl methane sulfonate (EMS)-treated population of cv. "Jagger." By crossing the low tillering mutant with the Jagger wild-type plant, we generated an F2 population and used the MutMap approach to identify a novel physical interval on 11 Mb on chromosome 2DS. Using an F₂ population of 442 gametes and polymorphic SNP markers, we were able to delineate the tin6 locus to a 2.1 Mb region containing 22 candidate genes.

Genome-edited TaTFL1-5 mutation decreases tiller and spikelet numbers in common wheat

Tillering is a critical agronomic trait of wheat (Triticum aestivum L.) that determines the shoot architecture and affects grain yield. TERMINAL FLOWER 1 (TFL1), encoding a phosphatidylethanolamine-binding protein, is implicated in the transition to flowering and shoot architecture in plant development. However, the roles of TFL1 homologs is little known in wheat development. CRISPR/Cas9-mediated targeted mutagenesis was used in this study to generate a set of wheat (Fielder) mutants with single, double or triple-null tatfl1-5 alleles. The wheat tatfl1-5 mutations decreased the tiller number per plant in the vegetative growth stage and the effective tiller number per plant and spikelet number per spike at maturity in the field. RNA-seq analysis showed that the expression of the auxin signaling-related and cytokinin signaling-related genes was significantly changed in the axillary buds of tatfl1-5 mutant seedlings. The results suggested that wheat TaTFL1-5s were implicated in tiller regulation by auxin and cytokinin signaling.